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Sample records for passive molecular transport

  1. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    Science.gov (United States)

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  2. Passive water and ion transport by cotransporters

    DEFF Research Database (Denmark)

    Loo, D D; Hirayama, B A; Meinild, A K

    1999-01-01

    the Lp of control oocytes. Passive Na+ transport (Na+ leak) was obtained from the blocker-sensitive Na+ currents in the absence of substrates (glucose and GABA). 2. Passive Na+ and water transport through SGLT1 were blocked by phlorizin with the same sensitivity (inhibitory constant (Ki), 3-5 micro......1. The rabbit Na+-glucose (SGLT1) and the human Na+-Cl--GABA (GAT1) cotransporters were expressed in Xenopus laevis oocytes, and passive Na+ and water transport were studied using electrical and optical techniques. Passive water permeabilities (Lp) of the cotransporters were determined from......M). When Na+ was replaced with Li+, phlorizin also inhibited Li+ and water transport, but with a lower affinity (Ki, 100 microM). When Na+ was replaced by choline, which is not transported, the SGLT1 Lp was indistinguishable from that in Na+ or Li+, but in this case water transport was less sensitive...

  3. 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...

  4. Charge transport through molecular switches

    International Nuclear Information System (INIS)

    Jan van der Molen, Sense; Liljeroth, Peter

    2010-01-01

    We review the fascinating research on charge transport through switchable molecules. In the past decade, detailed investigations have been performed on a great variety of molecular switches, including mechanically interlocked switches (rotaxanes and catenanes), redox-active molecules and photochromic switches (e.g. azobenzenes and diarylethenes). To probe these molecules, both individually and in self-assembled monolayers (SAMs), a broad set of methods have been developed. These range from low temperature scanning tunneling microscopy (STM) via two-terminal break junctions to larger scale SAM-based devices. It is generally found that the electronic coupling between molecules and electrodes has a profound influence on the properties of such molecular junctions. For example, an intrinsically switchable molecule may lose its functionality after it is contacted. Vice versa, switchable two-terminal devices may be created using passive molecules ('extrinsic switching'). Developing a detailed understanding of the relation between coupling and switchability will be of key importance for both future research and technology. (topical review)

  5. Charge transport through molecular switches

    Energy Technology Data Exchange (ETDEWEB)

    Jan van der Molen, Sense [Kamerlingh Onnes Laboratorium, Leiden University, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Liljeroth, Peter, E-mail: molen@physics.leidenuniv.n [Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, University of Utrecht, PO Box 80000, 3508 TA Utrecht (Netherlands)

    2010-04-07

    We review the fascinating research on charge transport through switchable molecules. In the past decade, detailed investigations have been performed on a great variety of molecular switches, including mechanically interlocked switches (rotaxanes and catenanes), redox-active molecules and photochromic switches (e.g. azobenzenes and diarylethenes). To probe these molecules, both individually and in self-assembled monolayers (SAMs), a broad set of methods have been developed. These range from low temperature scanning tunneling microscopy (STM) via two-terminal break junctions to larger scale SAM-based devices. It is generally found that the electronic coupling between molecules and electrodes has a profound influence on the properties of such molecular junctions. For example, an intrinsically switchable molecule may lose its functionality after it is contacted. Vice versa, switchable two-terminal devices may be created using passive molecules ('extrinsic switching'). Developing a detailed understanding of the relation between coupling and switchability will be of key importance for both future research and technology. (topical review)

  6. Passive scalar transport in peripheral regions of random flows

    International Nuclear Information System (INIS)

    Chernykh, A.; Lebedev, V.

    2011-01-01

    We investigate statistical properties of the passive scalar mixing in random (turbulent) flows assuming its diffusion to be weak. Then at advanced stages of the passive scalar decay, its unmixed residue is primarily concentrated in a narrow diffusive layer near the wall and its transport to the bulk goes through the peripheral region (laminar sublayer of the flow). We conducted Lagrangian numerical simulations of the process for different space dimensions d and revealed structures responsible for the transport, which are passive scalar tongues pulled from the diffusive boundary layer to the bulk. We investigated statistical properties of the passive scalar and of the passive scalar integrated along the wall. Moments of both objects demonstrate scaling behavior outside the diffusive boundary layer. We propose an analytic scheme for the passive scalar statistics, explaining the features observed numerically.

  7. Role of molecular charge in nucleocytoplasmic transport.

    Directory of Open Access Journals (Sweden)

    Alexander Goryaynov

    Full Text Available Transport of genetic materials and proteins between the nucleus and cytoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs. A selective barrier formed by phenylalanine-glycine (FG nucleoporins (Nups with net positive charges in the NPC allows for passive diffusion of signal-independent small molecules and transport-receptor facilitated translocation of signal-dependent cargo molecules. Recently, negative surface charge was postulated to be another essential criterion for selective passage through the NPC. However, the charge-driven mechanism in determining the transport kinetics and spatial transport route for either passive diffusion or facilitated translocation remains obscure. Here we employed high-speed single-molecule fluorescence microscopy with an unprecedented spatiotemporal resolution of 9 nm and 400 µs to uncover these mechanistic fundamentals for nuclear transport of charged substrates through native NPCs. We found that electrostatic interaction between negative surface charges on transiting molecules and the positively charged FG Nups, although enhancing their probability of binding to the NPC, never plays a dominant role in determining their nuclear transport mode or spatial transport route. A 3D reconstruction of transport routes revealed that small signal-dependent endogenous cargo protein constructs with high positive surface charges that are destined to the nucleus, rather than repelled from the NPC as suggested in previous models, passively diffused through an axial central channel of the NPC in the absence of transport receptors. Finally, we postulated a comprehensive map of interactions between transiting molecules and FG Nups during nucleocytoplasmic transport by combining the effects of molecular size, signal and surface charge.

  8. Photoinduced diffusion molecular transport

    Energy Technology Data Exchange (ETDEWEB)

    Rozenbaum, Viktor M., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, Generala Naumova St. 17, Kiev 03164 (Ukraine); Dekhtyar, Marina L. [Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya St. 5, Kiev 02094 (Ukraine); Lin, Sheng Hsien [Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu 300, Taiwan (China); Trakhtenberg, Leonid I., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, Moscow 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudnyi, Moscow Region 141700 (Russian Federation)

    2016-08-14

    We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).

  9. Transport properties of molecular junctions

    CERN Document Server

    Zimbovskaya, Natalya A

    2013-01-01

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

  10. Passive cooling during transport of asphyxiated term newborns

    Science.gov (United States)

    O’Reilly, Deirdre; Labrecque, Michelle; O’Melia, Michael; Bacic, Janine; Hansen, Anne; Soul, Janet S

    2014-01-01

    Objective To evaluate the efficacy and safety of passive cooling during transport of asphyxiated newborns. Study Design Retrospective medical record review of newborns with perinatal asphyxia transported for hypothermia between July 2007 and June 2010. Results Forty-three newborns were transported, 27 of whom were passively cooled. Twenty (74%) passively cooled newborns arrived with axillary temperature between 32.5 and 34.5 °C. One newborn (4%) arrived with a subtherapeutic temperature, and 6 (22%) had temperatures >34.5 °C. Time from birth to hypothermia was significantly shorter among passively cooled newborns compared with newborns not cooled (215 vs. 327 minutes, pencephalopathy results in significantly earlier achievement of effective therapeutic hypothermia without significant adverse events. PMID:23154670

  11. Passive heat transport in advanced CANDU containment

    International Nuclear Information System (INIS)

    Krause, M.; Mathew, P.M.

    1994-01-01

    A passive CANDU containment design has been proposed to provide the necessary heat removal following a postulated accident to maintain containment integrity. To study its feasibility and to optimize the design, multi-dimensional containment modelling may be required. This paper presents a comparison of two CFD codes, GOTHIC and PHOENICS, for multi-dimensional containment analysis and gives pressure transient predictions from a lumped-parameter and a three-dimensional GOTHIC model for a modified CANDU-3 containment. GOTHIC proved suitable for multidimensional post-accident containment analysis, as shown by the good agreement with pressure transient predictions from PHOENICS. GOTHIC is, therefore, recommended for passive CANDU containment modelling. (author)

  12. Passive, wireless corrosion sensors for transportation infrastructure.

    Science.gov (United States)

    2011-07-01

    Many industrial segments including utilities, manufacturing, government and infrastructure have an urgent need for a means to detect corrosion before significant damage occurs. Transportation infrastructure, such as bridges and roads, rely on reinfor...

  13. Lagrangian Transport Calculations Using UARS Data. Part I: Passive Tracers

    Science.gov (United States)

    Manney, G. L.; Lahoz, W. A.; Harwood, R. S.; Zurek, R. W.; Kumer, J. B.; Mergenthaler, J. L.; Roche, A. E.; O'Neill, A; Swinbank, R.; Waters, J. W.

    1994-01-01

    The transport of passive tracers observed by UARS has been simulated using computed trajectories of thousands of air parcels initialized on a three-dimensional stratospheric grid. These trajectories are calculated in isentropic coordinates using horizontal winds provided by the United Kingdom Meteorological Office data assimilation system and vertical (cross-isentropic) velocities computed using a fast radiation code.

  14. Passivation Using Molecular Halides Increases Quantum Dot Solar Cell Performance

    KAUST Repository

    Lan, Xinzheng; Voznyy, Oleksandr; Kiani, Amirreza; Garcí a de Arquer, F. Pelayo; Abbas, Abdullah Saud; Kim, Gi-Hwan; Liu, Mengxia; Yang, Zhenyu; Walters, Grant; Xu, Jixian; Yuan, Mingjian; Ning, Zhijun; Fan, Fengjia; Kanjanaboos, Pongsakorn; Kramer, Illan; Zhitomirsky, David; Lee, Philip; Perelgut, Alexander; Hoogland, Sjoerd; Sargent, Edward H.

    2015-01-01

    © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Here we report a solution-based passivation scheme is developed featuring the use of molecular iodine and PbS colloidal quantum dots (CQDs). The improved passivation translates into a longer carrier diffusion length in the solid film. This allows thicker solar-cell devices to be built while preserving efficient charge collection, leading to a certified power conversion efficiency of 9.9%, which is a new record in CQD solar cells.

  15. Passivation Using Molecular Halides Increases Quantum Dot Solar Cell Performance.

    Science.gov (United States)

    Lan, Xinzheng; Voznyy, Oleksandr; Kiani, Amirreza; García de Arquer, F Pelayo; Abbas, Abdullah Saud; Kim, Gi-Hwan; Liu, Mengxia; Yang, Zhenyu; Walters, Grant; Xu, Jixian; Yuan, Mingjian; Ning, Zhijun; Fan, Fengjia; Kanjanaboos, Pongsakorn; Kramer, Illan; Zhitomirsky, David; Lee, Philip; Perelgut, Alexander; Hoogland, Sjoerd; Sargent, Edward H

    2016-01-13

    A solution-based passivation scheme is developed featuring the use of molecular iodine and PbS colloidal quantum dots (CQDs). The improved passivation translates into a longer carrier diffusion length in the solid film. This allows thicker solar-cell devices to be built while preserving efficient charge collection, leading to a certified power conversion efficiency of 9.9%, which is a new record in CQD solar cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Passivation Using Molecular Halides Increases Quantum Dot Solar Cell Performance

    KAUST Repository

    Lan, Xinzheng

    2015-11-18

    © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Here we report a solution-based passivation scheme is developed featuring the use of molecular iodine and PbS colloidal quantum dots (CQDs). The improved passivation translates into a longer carrier diffusion length in the solid film. This allows thicker solar-cell devices to be built while preserving efficient charge collection, leading to a certified power conversion efficiency of 9.9%, which is a new record in CQD solar cells.

  17. Passive scalar transport mediated by laminar vortex rings

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, R H; Rodríguez, G, E-mail: rohernan@ing.uchile.cl [LEAF-NL, Depto. Ingeniería Civil Mecánica, Universidad de Chile, Casilla 2777, Santiago (Chile)

    2017-04-15

    Numerical simulations were used to study the dynamics of a passive conserved scalar quantity entrained by a self-propelling viscous vortex ring. The transport and mixing process of the passive scalar variable were studied considering two initial scalar distributions: (i) The scalar substance was introduced into the ring during its formation, further focusing in the shedding into the wake of the ring; (ii) A disk-like scalar layer was placed in the ring’s path where the entrainment of the scalar substance into the ring bubble was studied as a function of the ring strength. In both cases, the scalar concentration inside the vortex bubble exhibits a steady decay with time. In the second case, it was shown that the entrained scalar mass grows with both the Reynolds number of the ring and the thickness of the scalar layer in the propagation direction. The ring can be viewed as a mechanism for scalar transportation along important distances. (paper)

  18. Connecting Ellipses to Rectangles in Passive Scalar Transport

    Science.gov (United States)

    Aminian, Manuchehr; Bernardi, Francesca; Camassa, Roberto; Harris, Daniel; McLaughlin, Richard

    2017-11-01

    We study how passive scalar transport in Poiseuille flow is affected by the shape of the pipe cross section. Our previous results have established nontrivial dependence of the skewness of the tracer distribution upon the pipe shape. Previously, we have studied the families of rectangles and ellipses, with the behavior past diffusive timescales primarily depending on aspect ratio, and the type of geometry being secondary. However, at timescales well before the diffusion timescale, the family of ellipses is distinct compared to rectangles. We investigate this phenomenon by studying a collection of exotic cross sections connecting the ellipses and rectangles, using a combination of theoretical and computational tools.

  19. Active and passive transport of cargo in a corrugated channel: A lattice model study

    Science.gov (United States)

    Dey, Supravat; Ching, Kevin; Das, Moumita

    2018-04-01

    Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.

  20. Charge Transport Processes in Molecular Junctions

    Science.gov (United States)

    Smith, Christopher Eugene

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

  1. Molecular motor transport through hollow nanowires

    DEFF Research Database (Denmark)

    Lard, Mercy; Ten Siethoff, Lasse; Generosi, Johanna

    2014-01-01

    -driven motion of fluorescent probes (actin filaments) through 80 nm wide, Al2O 3 hollow nanowires of micrometer length. The motor-driven transport is orders of magnitude faster than would be possible by passive diffusion. The system represents a necessary element for advanced devices based on gliding assays...

  2. Spin transport in dangling-bond wires on doped H-passivated Si(100)

    International Nuclear Information System (INIS)

    Kepenekian, Mikaël; Robles, Roberto; Lorente, Nicolás; Rurali, Riccardo

    2014-01-01

    New advances in single-atom manipulation are leading to the creation of atomic structures on H-passivated Si surfaces with functionalities important for the development of atomic and molecular based technologies. We perform total-energy and electron-transport calculations to reveal the properties and understand the features of atomic wires crafted by H removal from the surface. The presence of dopants radically change the wire properties. Our calculations show that dopants have a tendency to approach the dangling-bond wires, and in these conditions, transport is enhanced and spin selective. These results have important implications in the development of atomic-scale spintronics showing that boron, and to a lesser extent phosphorous, convert the wires in high-quality spin filters. (paper)

  3. Understanding charge transport in molecular electronics.

    Science.gov (United States)

    Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

    2003-12-01

    For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

  4. The Sodium Glucose Cotransporter SGLT1 Is an Extremely Efficient Facilitator of Passive Water Transport.

    Science.gov (United States)

    Erokhova, Liudmila; Horner, Andreas; Ollinger, Nicole; Siligan, Christine; Pohl, Peter

    2016-04-29

    The small intestine is void of aquaporins adept at facilitating vectorial water transport, and yet it reabsorbs ∼8 liters of fluid daily. Implications of the sodium glucose cotransporter SGLT1 in either pumping water or passively channeling water contrast with its reported water transporting capacity, which lags behind that of aquaporin-1 by 3 orders of magnitude. Here we overexpressed SGLT1 in MDCK cell monolayers and reconstituted the purified transporter into proteoliposomes. We observed the rate of osmotic proteoliposome deflation by light scattering. Fluorescence correlation spectroscopy served to assess (i) SGLT1 abundance in both vesicles and plasma membranes and (ii) flow-mediated dilution of an aqueous dye adjacent to the cell monolayer. Calculation of the unitary water channel permeability, pf, yielded similar values for cell and proteoliposome experiments. Neither the absence of glucose or Na(+), nor the lack of membrane voltage in vesicles, nor the directionality of water flow grossly altered pf Such weak dependence on protein conformation indicates that a water-impermeable occluded state (glucose and Na(+) in their binding pockets) lasts for only a minor fraction of the transport cycle or, alternatively, that occlusion of the substrate does not render the transporter water-impermeable as was suggested by computational studies of the bacterial homologue vSGLT. Although the similarity between the pf values of SGLT1 and aquaporin-1 makes a transcellular pathway plausible, it renders water pumping physiologically negligible because the passive flux would be orders of magnitude larger. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Quantum Transport Through Tunable Molecular Diodes

    KAUST Repository

    Obodo, Tobechukwu Joshua

    2017-07-31

    Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.

  6. Electron and Phonon Transport in Molecular Junctions

    DEFF Research Database (Denmark)

    Li, Qian

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

  7. Molecular monolayers for electrical passivation and functionalization of silicon-based solar energy devices

    NARCIS (Netherlands)

    Veerbeek, Janneke; Firet, Nienke J.; Vijselaar, Wouter; Elbersen, R.; Gardeniers, Han; Huskens, Jurriaan

    2017-01-01

    Silicon-based solar fuel devices require passivation for optimal performance yet at the same time need functionalization with (photo)catalysts for efficient solar fuel production. Here, we use molecular monolayers to enable electrical passivation and simultaneous functionalization of silicon-based

  8. Rigorous upper bounds for fluid and plasma transport due to passive advection

    International Nuclear Information System (INIS)

    Krommes, J.A.; Smith, R.A.; Kim, C.B.

    1987-07-01

    The formulation of variational principles for transport due to passive advection is described. A detailed account of the work has been published elsewhere. In the present paper, the motivations, philosophy, and implications of the method are briefly discussed. 15 refs

  9. Psychosocial and Environmental Correlates of Walking, Cycling, Public Transport and Passive Transport to Various Destinations in Flemish Older Adolescents.

    Directory of Open Access Journals (Sweden)

    Hannah Verhoeven

    Full Text Available Active transport is a convenient way to incorporate physical activity in adolescents' daily life. The present study aimed to investigate which psychosocial and environmental factors are associated with walking, cycling, public transport (train, tram, bus, metro and passive transport (car, motorcycle, moped over short distances (maximum eight kilometres among older adolescents (17-18 years, to school and to other destinations.562 older adolescents completed an online questionnaire assessing socio-demographic variables, psychosocial variables, environmental variables and transport to school/other destinations. Zero-inflated negative binomial regression models were performed.More social modelling and a higher residential density were positively associated with walking to school and walking to other destinations, respectively. Regarding cycling, higher self-efficacy and a higher social norm were positively associated with cycling to school and to other destinations. Regarding public transport, a higher social norm, more social modelling of siblings and/or friends, more social support and a higher land use mix access were positively related to public transport to school and to other destinations, whereas a greater distance to school only related positively to public transport to school. Regarding passive transport, more social support and more perceived benefits were positively associated with passive transport to school and to other destinations. Perceiving less walking and cycling facilities at school was positively related to passive transport to school only, and more social modelling was positively related to passive transport to other destinations.Overall, psychosocial variables seemed to be more important than environmental variables across the four transport modes. Social norm, social modelling and social support were the most consistent psychosocial factors which indicates that it is important to target both older adolescents and their social

  10. Molecular Monolayers for Electrical Passivation and Functionalization of Silicon-Based Solar Energy Devices.

    Science.gov (United States)

    Veerbeek, Janneke; Firet, Nienke J; Vijselaar, Wouter; Elbersen, Rick; Gardeniers, Han; Huskens, Jurriaan

    2017-01-11

    Silicon-based solar fuel devices require passivation for optimal performance yet at the same time need functionalization with (photo)catalysts for efficient solar fuel production. Here, we use molecular monolayers to enable electrical passivation and simultaneous functionalization of silicon-based solar cells. Organic monolayers were coupled to silicon surfaces by hydrosilylation in order to avoid an insulating silicon oxide layer at the surface. Monolayers of 1-tetradecyne were shown to passivate silicon micropillar-based solar cells with radial junctions, by which the efficiency increased from 8.7% to 9.9% for n + /p junctions and from 7.8% to 8.8% for p + /n junctions. This electrical passivation of the surface, most likely by removal of dangling bonds, is reflected in a higher shunt resistance in the J-V measurements. Monolayers of 1,8-nonadiyne were still reactive for click chemistry with a model catalyst, thus enabling simultaneous passivation and future catalyst coupling.

  11. Charge Transport Phenomena in Peptide Molecular Junctions

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  12. The role of large scale motions on passive scalar transport

    Science.gov (United States)

    Dharmarathne, Suranga; Araya, Guillermo; Tutkun, Murat; Leonardi, Stefano; Castillo, Luciano

    2014-11-01

    We study direct numerical simulation (DNS) of turbulent channel flow at Reτ = 394 to investigate effect of large scale motions on fluctuating temperature field which forms a passive scalar field. Statistical description of the large scale features of the turbulent channel flow is obtained using two-point correlations of velocity components. Two-point correlations of fluctuating temperature field is also examined in order to identify possible similarities between velocity and temperature fields. The two-point cross-correlations betwen the velocity and temperature fluctuations are further analyzed to establish connections between these two fields. In addition, we use proper orhtogonal decompotion (POD) to extract most dominant modes of the fields and discuss the coupling of large scale features of turbulence and the temperature field.

  13. Modulation of electronic transport properties in armchair phosphorene nanoribbons by doping and edge passivation.

    Science.gov (United States)

    Guo, Caixia; Wang, Tianxing; Xia, Congxin; Liu, Yufang

    2017-10-09

    The electronic structures and transport properties of group IV atoms (C, Si, Ge)-doped armchair phosphorene nanoribbons (APNRs) are investigated using first-principles calculations, considering different edge passivation. The results show that the C, Si, Ge dopants can induce the transition occur from semiconductor to metal in the APNRs. The negative differential resistance (NDR) behavior in the doped APNR system is robust with respect to the doping concentration and edge passivation type. However, their current peak positions and peak-to-valley ratio (PVR) values are correlated with doping concentration and edge passivation type. In particular, for the C, Si-doped APNRs, the low bias NDR behavior with the PVR (10 5 -10 8 ) can be observed when doping concentration is low in the APNRs with the F and H edge passivation. These results may play an important role for the fabrication of future low power consumption nano-electronic devices.

  14. 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

  15. Risk reduction in road and rail LPG transportation bij passive fire protection

    NARCIS (Netherlands)

    Molag e.a., M. (Menso)

    2009-01-01

    The potential reduction of risk in LPG (Liquified Petroleum Gas) road transport due to the adoption of passive fire protectionswas investigated. Experimental data available for small scale vessels fully engulfed by a fire were extended to real scale road and rail tankers through a finite elements

  16. Risk reduction in road and rail LPG transportation by passive fire protection

    NARCIS (Netherlands)

    Paltrinieri, N.; Landucci, G.; Molag, M.; Bonvicini, S.; Spadoni, G.; Cozzani, V.

    2009-01-01

    The potential reduction of risk in LPG (Liquefied Petroleum Gas) road transport due to the adoption of passive fire protections was investigated. Experimental data available for small scale vessels fully engulfed by a fire were extended to real scale road and rail tankers through a finite elements

  17. Rethinking passive transport: bus fare exemptions and young people's wellbeing.

    Science.gov (United States)

    Jones, Alasdair; Steinbach, Rebecca; Roberts, Helen; Goodman, Anna; Green, Judith

    2012-05-01

    Much recent public health research has emphasised the health impacts for young people of 'active travel' modes, typically defined as walking and cycling. Less research has focused on public transport modes. Drawing on qualitative data, we examine the links between bus travel and wellbeing in London, where young people currently have free bus travel. Our findings indicate that bus travel can be both a physically and socially active experience for young people. We suggest a more nuanced understanding of 'active travel' is now needed, alongside greater attention to urban public transport networks as key sites that impact on important determinants of wellbeing such as independent mobility and social inclusion. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. DNS of a spatially developing turbulent boundary layer with passive scalar transport

    Energy Technology Data Exchange (ETDEWEB)

    Li Qiang [Linne Flow Centre, KTH Mechanics, Osquars Backe 18, SE-100 44 Stockholm (Sweden)], E-mail: qiang@mech.kth.se; Schlatter, Philipp; Brandt, Luca; Henningson, Dan S. [Linne Flow Centre, KTH Mechanics, Osquars Backe 18, SE-100 44 Stockholm (Sweden)

    2009-10-15

    A direct numerical simulation (DNS) of a spatially developing turbulent boundary layer over a flat plate under zero pressure gradient (ZPG) has been carried out. The evolution of several passive scalars with both isoscalar and isoflux wall boundary condition are computed during the simulation. The Navier-Stokes equations as well as the scalar transport equation are solved using a fully spectral method. The highest Reynolds number based on the free-stream velocity U{sub {infinity}} and momentum thickness {theta} is Re{sub {theta}}=830, and the molecular Prandtl numbers are 0.2, 0.71 and 2. To the authors' knowledge, this Reynolds number is to date the highest with such a variety of scalars. A large number of turbulence statistics for both flow and scalar fields are obtained and compared when possible to existing experimental and numerical simulations at comparable Reynolds number. The main focus of the present paper is on the statistical behaviour of the scalars in the outer region of the boundary layer, distinctly different from the channel-flow simulations. Agreements as well as discrepancies are discussed while the influence of the molecular Prandtl number and wall boundary conditions is also highlighted. A Pr scaling for various quantities is proposed in outer scalings. In addition, spanwise two-point correlation and instantaneous fields are employed to investigate the near-wall streak spacing and the coherence between the velocity and the scalar fields. Probability density functions (PDF) and joint probability density functions (JPDF) are shown to identify the intermittency both near the wall and in the outer region of the boundary layer. The present simulation data will be available online for the research community.

  19. DNS of a spatially developing turbulent boundary layer with passive scalar transport

    International Nuclear Information System (INIS)

    Li Qiang; Schlatter, Philipp; Brandt, Luca; Henningson, Dan S.

    2009-01-01

    A direct numerical simulation (DNS) of a spatially developing turbulent boundary layer over a flat plate under zero pressure gradient (ZPG) has been carried out. The evolution of several passive scalars with both isoscalar and isoflux wall boundary condition are computed during the simulation. The Navier-Stokes equations as well as the scalar transport equation are solved using a fully spectral method. The highest Reynolds number based on the free-stream velocity U ∞ and momentum thickness θ is Re θ =830, and the molecular Prandtl numbers are 0.2, 0.71 and 2. To the authors' knowledge, this Reynolds number is to date the highest with such a variety of scalars. A large number of turbulence statistics for both flow and scalar fields are obtained and compared when possible to existing experimental and numerical simulations at comparable Reynolds number. The main focus of the present paper is on the statistical behaviour of the scalars in the outer region of the boundary layer, distinctly different from the channel-flow simulations. Agreements as well as discrepancies are discussed while the influence of the molecular Prandtl number and wall boundary conditions is also highlighted. A Pr scaling for various quantities is proposed in outer scalings. In addition, spanwise two-point correlation and instantaneous fields are employed to investigate the near-wall streak spacing and the coherence between the velocity and the scalar fields. Probability density functions (PDF) and joint probability density functions (JPDF) are shown to identify the intermittency both near the wall and in the outer region of the boundary layer. The present simulation data will be available online for the research community.

  20. 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.

  1. Electronic transport properties of phenylacetylene molecular junctions

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  2. Molecular modeling of auxin transport inhibitors

    International Nuclear Information System (INIS)

    Gardner, G.; Black-Schaefer, C.; Bures, M.G.

    1990-01-01

    Molecular modeling techniques have been used to study the chemical and steric properties of auxin transport inhibitors. These bind to a specific site on the plant plasma membrane characterized by its affinity for N-1-naphthylphthalamic acid (NPA). A three-dimensional model was derived from critical features of ligands for the NPA receptor, and a suggested binding conformation is proposed. This model, along with three-dimensional structural searching techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the search criteria, 77 representative molecules were evaluated for their ability to compete for [ 3 H]NPA binding to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, from chemical classes not included in the original compound set, also inhibited polar auxin transport through corn coleoptile sections

  3. Theory of transport through molecular magnets

    Science.gov (United States)

    Schoeller, Herbert

    2007-03-01

    Quantum transport through single molecular magnets (SMM) is starting to become a new exciting field in molecular spin electronics. Recent experiments [1,2] have shown that magnetic excitations can be identified in transport measurements and that NDC effects and complete current suppression can be explained by charge dependent anisotropies. Recent theoretical investigations [3,4,5] are presented which demonstrate fingerprints of quantum tunneling of magnetization (QTM). For weak tunneling, the violation of spin-selection rules leads to the occurence of fake resonances with temperature-dependent position [3]. For strongtunneling, it is show that a pseudo spin-1/2 Kondo effect is induced by QTM. If the Kondo temperature TK is smaller than the distance to excited magnetic states, selection rules depending on spin and symmetry of the SMM are derived for the Kondo effect to occur [4]. If TK exceeds the anisotropy barrier, it is shown that a reentrant Kondo effect can be induced by application of a longitudinal magnetic field for SMM with half-integer or integer spin [5]. This effect can be used for transport spectroscopy of the various anisotropies characterizing a SMM. [1] H.B. Heersche et al., Phys. Rev. Lett. 96, 206801 (2006). [2] Moon-Ho Jo et al., Nano Lett. 6, 2014 (2006). [3] C. Romeike, M.R. Wegewijs, H. Schoeller, Phys. Rev. Lett. 96, 196805 (2006). [4] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, Phys. Rev. Lett. 96, 196601 (2006). [5] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, to be published in Phys. Rev. Lett., cond-mat/0605514.

  4. Molecular Tools for Facilitative Carbohydrate Transporters (Gluts).

    Science.gov (United States)

    Tanasova, Marina; Fedie, Joseph R

    2017-09-19

    Facilitative carbohydrate transporters-Gluts-have received wide attention over decades due to their essential role in nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors directed towards understanding the mechanisms of Glut-mediated nutrient uptake have resulted in a multidisciplinary research field spanning protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics. In this review, the current state of knowledge of the molecular interactions behind Glut-mediated sugar uptake, Glut-targeting probes, therapeutics, and inhibitors are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Molecular dynamics study of solid-liquid heat transfer and passive liquid flow

    Science.gov (United States)

    Yesudasan Daisy, Sumith

    High heat flux removal is a challenging problem in boilers, electronics cooling, concentrated photovoltaic and other power conversion devices. Heat transfer by phase change is one of the most efficient mechanisms for removing heat from a solid surface. Futuristic electronic devices are expected to generate more than 1000 W/cm2 of heat. Despite the advancements in microscale and nanoscale manufacturing, the maximum passive heat flux removal has been 300 W/cm2 in pool boiling. Such limitations can be overcome by developing nanoscale thin-film evaporation based devices, which however require a better understanding of surface interactions and liquid vapor phase change process. Evaporation based passive flow is an inspiration from the transpiration process that happens in trees. If we can mimic this process and develop heat removal devices, then we can develop efficient cooling devices. The existing passive flow based cooling devices still needs improvement to meet the future demands. To improve the efficiency and capacity of these devices, we need to explore and quantify the passive flow happening at nanoscales. Experimental techniques have not advanced enough to study these fundamental phenomena at the nanoscale, an alternative method is to perform theoretical study at nanoscales. Molecular dynamics (MD) simulation is a widely accepted powerful tool for studying a range of fundamental and engineering problems. MD simulations can be utilized to study the passive flow mechanism and heat transfer due to it. To study passive flow using MD, apart from the conventional methods available in MD, we need to have methods to simulate the heat transfer between solid and liquid, local pressure, surface tension, density, temperature calculation methods, realistic boundary conditions, etc. Heat transfer between solid and fluids has been a challenging area in MD simulations, and has only been minimally explored (especially for a practical fluid like water). Conventionally, an

  6. Adsorption of molecular additive onto lead halide perovskite surfaces: A computational study on Lewis base thiophene additive passivation

    Science.gov (United States)

    Zhang, Lei; Yu, Fengxi; Chen, Lihong; Li, Jingfa

    2018-06-01

    Organic additives, such as the Lewis base thiophene, have been successfully applied to passivate halide perovskite surfaces, improving the stability and properties of perovskite devices based on CH3NH3PbI3. Yet, the detailed nanostructure of the perovskite surface passivated by additives and the mechanisms of such passivation are not well understood. This study presents a nanoscopic view on the interfacial structure of an additive/perovskite interface, consisting of a Lewis base thiophene molecular additive and a lead halide perovskite surface substrate, providing insights on the mechanisms that molecular additives can passivate the halide perovskite surfaces and enhance the perovskite-based device performance. Molecular dynamics study on the interactions between water molecules and the perovskite surfaces passivated by the investigated additive reveal the effectiveness of employing the molecular additives to improve the stability of the halide perovskite materials. The additive/perovskite surface system is further probed via molecular engineering the perovskite surfaces. This study reveals the nanoscopic structure-property relationships of the halide perovskite surface passivated by molecular additives, which helps the fundamental understanding of the surface/interface engineering strategies for the development of halide perovskite based devices.

  7. A structure-based model for the transport of passive scalars in homogeneous turbulent flows

    International Nuclear Information System (INIS)

    Panagiotou, C.F.; Kassinos, S.C.

    2016-01-01

    Highlights: • The Interacting Particle Representation Model (IPRM) is extended for passive scalar transport. • We develop a structure-based set of scale equations for the scalar field and couple them to the IPRM. • The complete model is evaluated for several cases of homogeneous deformation with good results. • We outline steps for coupling the new scalar scales to the Algebraic Structure-Based Model (ASBM). - Abstract: A structure-based model has been constructed, for the first time, for the study of passive scalar transport in turbulent flows. The scalar variance and the large-scale scalar gradient variance are proposed as the two turbulence scales needed for closure of the scalar equations in the framework of the Interacting Particle Representation Model (IPRM). The scalar dissipation rate is modeled in terms of the scalar variance and the large-scale enstrophy of the velocity field. Model parameters are defined by matching the decay rates in freely isotropic turbulence. The model is validated for a large number of cases of deformation in both fixed and rotating frames, showing encouraging results. The model shows good agreement with DNS results for the case of pure shear flow in the presence of either transverse or streamwise mean scalar gradient, while it correctly predicts the presence of direct cascade for the passive scalar variance in two dimensional isotropic turbulence.

  8. Turbulence and transport of passive scalar in magnetohydrodynamic channel flows with different orientations of magnetic field

    International Nuclear Information System (INIS)

    Dey, Prasanta K.; Zikanov, Oleg

    2012-01-01

    Highlights: ► Turbulent passive scalar transport in an MHD flow in a channel is studied using DNS. ► Magnetic fields of wall-normal, spanwise, and streamwise orientations are considered. ► Magnetic fields suppress turbulent transport and modifies scalar distribution. ► The effect is particularly strong at wall-normal and spanwise magnetic fields. ► Decrease of Nusselt number is approximated by a linear function of magnetic interaction parameter. - Abstract: DNS of turbulent flow and passive scalar transport in a channel are conducted for the situation when the fluid is electrically conducting (for example, a liquid metal) and the flow is affected by an imposed magnetic field. The cases of wall-normal, spanwise, and streamwise orientation of the magnetic field are considered. As main results, we find that the magnetic fields, especially those in the wall-normal and spanwise directions, significantly reduce the turbulent scalar transport and modify the properties of the scalar distribution.

  9. Charge transport in single photochromic molecular junctions

    Science.gov (United States)

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

    2012-02-01

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

  10. Molecular Transport Studies Through Unsupported Lipid Membranes

    Science.gov (United States)

    Rock, William; Parekh, Sapun; Bonn, Mischa

    2014-03-01

    Dendrimers, spherical polymeric nanoparticles made from branched monomers around a central core, show great promise as drug delivery vehicles. Dendrimer size, core contents, and surface functionality can be synthetically tuned, providing unprecedented versatility. Polyamidoamine (PAMAM) dendrimers have been shown to enter cells; however, questions remain about their biophysical interactions with the cell membrane, specifically about the presence and size of transient pores. We monitor dendrimer-lipid bilayer interactions using unsupported black lipid membranes (BLMs) as model cell membranes. Custom bilayer slides contain two vertically stacked aqueous chambers separated by a 25 μm Teflon sheet with a 120 μm aperture where the bilayer is formed. We vary the composition of model membranes (cholesterol content and lipid phase) to create biomimetic systems and study the interaction of PAMAM G6 and G3 dendrimers with these bilayers. Dendrimers, dextran cargo, and bilayers are monitored and quantified using time-lapse fluorescence imaging. Electrical capacitance measurements are simultaneously recorded to determine if the membrane is porous, and the pore size is deduced by monitoring transport of fluorescent dextrans of increasing molecular weight. These experiments shed light on the importance of cholesterol content and lipid phase on the interaction of dendrimer nanoparticles with membranes.

  11. Quantum transport through a deformable molecular transistor

    Science.gov (United States)

    Cornaglia, P. S.; Grempel, D. R.; Ness, H.

    2005-02-01

    The linear transport properties of a model molecular transistor with electron-electron and electron-phonon interactions were investigated analytically and numerically. The model takes into account phonon modulation of the electronic energy levels and of the tunneling barrier between the molecule and the electrodes. When both effects are present they lead to asymmetries in the dependence of the conductance on gate voltage. The Kondo effect is observed in the presence of electron-phonon interactions. There are important qualitative differences between the cases of weak and strong coupling. In the first case the standard Kondo effect driven by spin fluctuations occurs. In the second case, it is driven by charge fluctuations. The Fermi-liquid relation between the spectral density of the molecule and its charge is altered by electron-phonon interactions. Remarkably, the relation between the zero-temperature conductance and the charge remains unchanged. Therefore, there is perfect transmission in all regimes whenever the average number of electrons in the molecule is an odd integer.

  12. Multiscale Roughness Influencing on Transport Behavior of Passive Solute through a Single Self-affine Fracture

    Science.gov (United States)

    Dou, Z.

    2017-12-01

    In this study, the influence of multi-scale roughness on transport behavior of the passive solute through the self-affine fracture was investigated. The single self-affine fracture was constructed by the successive random additions (SRA) and the fracture roughness was decomposed into two different scales (i.e. large-scale primary roughness and small-scale secondary roughness) by the Wavelet analysis technique. The fluid flow in fractures, which was characterized by the Forchheimer's law, showed the non-linear flow behaviors such as eddies and tortuous streamlines. The results indicated that the small-scale secondary roughness was primarily responsible for the non-linear flow behaviors. The direct simulations of asymptotic passive solute transport represented the Non-Fickian transport characteristics (i.e. early arrivals and long tails) in breakthrough curves (BTCs) and residence time distributions (RTDs) with and without consideration of the secondary roughness. Analysis of multiscale BTCs and RTDs showed that the small-scale secondary roughness played a significant role in enhancing the Non-Fickian transport characteristics. We found that removing small-scale secondary roughness led to the lengthening arrival and shortening tail. The peak concentration in BTCs decreased as the secondary roughness was removed, implying that the secondary could also enhance the solute dilution. The estimated BTCs by the Fickian advection-dispersion equation (ADE) yielded errors which decreased with the small-scale secondary roughness being removed. The mobile-immobile model (MIM) was alternatively implemented to characterize the Non-Fickian transport. We found that the MIM was more capable of estimating Non-Fickian BTCs. The small-scale secondary roughness resulted in the decreasing mobile domain fraction and the increasing mass exchange rate between immobile and mobile domains. The estimated parameters from the MIM could provide insight into the inherent mechanism of roughness

  13. Amine treatment induced perovskite nanowire network in perovskite solar cells: efficient surface passivation and carrier transport

    Science.gov (United States)

    Xiao, Ke; Cui, Can; Wang, Peng; Lin, Ping; Qiang, Yaping; Xu, Lingbo; Xie, Jiangsheng; Yang, Zhengrui; Zhu, Xiaodong; Yu, Xuegong; Yang, Deren

    2018-02-01

    In the fabrication of high efficiency organic-inorganic metal halide perovskite solar cells (PSCs), an additional interface modifier is usually applied for enhancing the interface passivation and carrier transport. In this paper, we develop an innovative method with in-situ growth of one-dimensional perovskite nanowire (1D PNW) network triggered by Lewis amine over the perovskite films. To our knowledge, this is the first time to fabricate PSCs with shape-controlled perovskite surface morphology, which improved power conversion efficiency (PCE) from 14.32% to 16.66% with negligible hysteresis. The amine molecule can passivate the trap states on the polycrystalline perovskite surface to reduce trap-state density. Meanwhile, as a fast channel, the 1D PNWs would promote carrier transport from the bulk perovskite film to the electron transport layer. The PSCs with 1D PNW modification not only exhibit excellent photovoltaic performances, but also show good stability with only 4% PCE loss within 30 days in the ambient air without encapsulation. Our results strongly suggest that in-situ grown 1D PNW network provides a feasible and effective strategy for nanostructured optoelectronic devices such as PSCs to achieve superior performances.

  14. A consistent transported PDF model for treating differential molecular diffusion

    Science.gov (United States)

    Wang, Haifeng; Zhang, Pei

    2016-11-01

    Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.

  15. Turbulent transport of passive scalar behind line sources in an unstably stratified open channel flow

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Chun-Ho [The Hong Kong Polytechnic University, Kowloon (Hong Kong). Department of Building and Real Estate; Leung, Dennis Y.C. [The University of Hong Kong (Hong Kong). Department of Mechanical Engineering

    2006-11-15

    This study employs a direct numerical simulation (DNS) technique to study the flow, turbulence structure, and passive scalar plume transport behind line sources in an unstably stratified open channel flow. The scalar transport behaviors for five emission heights (z{sub s}=0, 0.25H, 0.5H, 0.75H, and H, where H is the channel height) at a Reynolds number of 3000, a Prandtl number and a Schmidt number of 0.72, and a Richardson number of -0.2 are investigated. The vertically meandering mean plume heights and dispersion coefficients calculated by the current DNS model agree well with laboratory results and field measurements in literature. It is found that the plume meandering is due to the movement of the positive and negative vertical turbulent scalar fluxes above and below the mean plume heights, respectively. These findings help explaining the plume meandering mechanism in the unstably stratified atmospheric boundary layer. (author)

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

    Science.gov (United States)

    Joachim, Christian; Ratner, Mark A

    2005-06-21

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

  17. Transdermal therapeutic systems for memantine delivery. Comparison of passive and iontophoretic transport.

    Science.gov (United States)

    Del Río-Sancho, S; Serna-Jiménez, C E; Sebastián-Morelló, M; Calatayud-Pascual, M A; Balaguer-Fernández, C; Femenía-Font, A; Kalia, Y N; Merino, V; López-Castellano, A

    2017-01-30

    Memantine is a non-competitive N-methyl-d-aspartate (NMDA) receptor antagonist used in the treatment of moderate to severe dementia including the symptoms of Alzheimer's disease (AD). It is administered orally but compliance, swallowing problems and the routine use of multiple medications in elderly AD patients means that an alternative route of administration would be of interest. The aim of the present study was to develop memantine hydrochloride occlusive transdermal therapeutic systems (TTS) for passive and iontophoretic delivery across the skin. Polyvinyl pyrrolidone (PVP) and a mixture with polyvinyl alcohol (PVA) were employed as polymeric matrices. The study involved the TTS characterization in addition to quantification of the memantine transport across porcine skin in vitro. The evaluation of the TTS physical properties suggested that systems were made more mechanically resistant by including PVA (6%) or high concentrations of PVP (24%). Moreover, a linear correlation was observed between the concentration of PVP and the bioadhesion of the systems. Drug delivery experiments showed that the highest transdermal flux provided by a passive TTS (PVP 24% w/w limonene) was 8.89±0.81μgcm -2 h -1 whereas the highest iontophoretic transport was 46.4±3.6μgcm -2 h -1 . These innovative TTS would enable two dosage regimens that could lead to therapeutic plasma concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Passivation of Molecular n-Doping: Exploring the Limits of Air Stability

    KAUST Repository

    Tietze, Max Lutz; Rose, Bradley Daniel; Schwarze, Martin; Fischer, Axel; Runge, Steffen; Blochwitz-Nimoth, Jan; Lü ssem, Bjö rn; Leo, Karl; Bredas, Jean-Luc

    2016-01-01

    © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Molecular doping is a key technique for flexible and low-cost organic complementary semiconductor technologies that requires both efficient and stable p- and n-type doping. However, in contrast to molecular p-dopants, highly efficient n-type dopants are commonly sensitive to rapid degradation in air due to their low ionization energies (IEs) required for electron donation, e.g., IE = 2.4 eV for tetrakis(1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinato)ditungsten(II) (W2(hpp)4). Here, the air stability of various host:W2(hpp)4 combinations is compared by conductivity measurements and photoemission spectroscopy. A partial passivation of the n-doping against degradation is found, with this effect identified to depend on the specific energy levels of the host material. Since host-W2(hpp)4 electronic wavefunction hybridization is unlikely due to confinement of the dopant highest occupied molecular orbital (HOMO) to its molecular center, this finding is explained via stabilization of the dopant by single-electron transfer to a host material whose energy levels are sufficiently low for avoiding further charge transfer to oxygen-water complexes. Our results show the feasibility of temporarily handling n-doped organic thin films in air, e.g., during structuring of organic field effect transistors (OFETs) by lithography.

  19. Passivation of Molecular n-Doping: Exploring the Limits of Air Stability

    KAUST Repository

    Tietze, Max Lutz

    2016-03-03

    © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Molecular doping is a key technique for flexible and low-cost organic complementary semiconductor technologies that requires both efficient and stable p- and n-type doping. However, in contrast to molecular p-dopants, highly efficient n-type dopants are commonly sensitive to rapid degradation in air due to their low ionization energies (IEs) required for electron donation, e.g., IE = 2.4 eV for tetrakis(1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinato)ditungsten(II) (W2(hpp)4). Here, the air stability of various host:W2(hpp)4 combinations is compared by conductivity measurements and photoemission spectroscopy. A partial passivation of the n-doping against degradation is found, with this effect identified to depend on the specific energy levels of the host material. Since host-W2(hpp)4 electronic wavefunction hybridization is unlikely due to confinement of the dopant highest occupied molecular orbital (HOMO) to its molecular center, this finding is explained via stabilization of the dopant by single-electron transfer to a host material whose energy levels are sufficiently low for avoiding further charge transfer to oxygen-water complexes. Our results show the feasibility of temporarily handling n-doped organic thin films in air, e.g., during structuring of organic field effect transistors (OFETs) by lithography.

  20. Macroscopic transport by synthetic molecular machines

    NARCIS (Netherlands)

    Berna, J; Leigh, DA; Lubomska, M; Mendoza, SM; Perez, EM; Rudolf, P; Teobaldi, G; Zerbetto, F

    Nature uses molecular motors and machines in virtually every significant biological process, but demonstrating that simpler artificial structures operating through the same gross mechanisms can be interfaced with - and perform physical tasks in - the macroscopic world represents a significant hurdle

  1. Thermal hydraulic studies for passive heat transport systems relevant to advanced reactors

    International Nuclear Information System (INIS)

    Vijayan, P.K.; Sharma, M.; Borgohain, A.; Srivastava, A.K.; Pilkhwal, D.S.; Maheshwari, N.K.

    2014-01-01

    Nuclear is the only non-green house gas generating power source that can replace fossil fuels and can be commercially deployed in large scale. However, the enormous developmental efforts and safety upgrades during the past six decades have somewhat eroded the economic competitiveness of water-cooled reactors which form the mainstay of the current nuclear power programme. Further, the introduction of the supercritical Rankine cycle and the gas turbine based advanced fuel cycles have enhanced the efficiency of fossil fired power plants (FPP) thereby reducing its greenhouse gas emissions. The ongoing development of ultra-supercritical and advanced ultra-supercritical turbines aims to further reduce the greenhouse gas emissions and economic competitiveness of FPPs. In the backdrop of these developments, the nuclear industry also initiated development of advanced nuclear power plants (NPP) with improved efficiency, sustainability and enhanced safety as the main goals. A review of the advanced reactor concepts being investigated currently reveals that excepting the SCWR, all other concepts use coolants other than water. The coolants used are lead, lead bismuth eutectic, liquid sodium, molten salts, helium and supercritical water. Besides, some of these are employing passive systems to transport heat from the core under normal operating conditions. In view of this, a study is in progress at BARC to examine the performance of simple passive systems using SC CO 2 , SCW, LBE and molten salts as the coolant. This paper deals with some of the recent results of these studies. The study focuses on the steady state, transient and stability behaviour of the passive systems with these coolants. (author)

  2. Charge Transport Along Phenylenevinylene Molecular Wires

    OpenAIRE

    2006-01-01

    Abstract A model to calculate the mobility of charges along molecular wires is presented. The model is based on the tight-binding approximation and combines a quantum mechanical description of the charge with a classical description of the structural degrees of freedom. It is demonstrated that the average mobility of charge carriers along molecular wires can be obtained by time-propagation of states which are initially localised. The model is used to calculate the mobility of charg...

  3. Quantum Transport Through Tunable Molecular Diodes

    KAUST Repository

    Obodo, Tobechukwu Joshua; Murat, Altynbek; Schwingenschlö gl, Udo

    2017-01-01

    Employing self-interaction corrected density functional theory combined with the non-equilibrium Green's function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings

  4. Observation of quantum interference in molecular charge transport

    DEFF Research Database (Denmark)

    Guedon, Constant M.; Valkenier, Hennie; Markussen, Troels

    2012-01-01

    for such behaviour has been indirect. Here, we report the observation of destructive quantum interference in charge transport through two-terminal molecular junctions at room temperature. We studied five different rigid p-conjugated molecular wires, all of which form self-assembled monolayers on a gold surface......, and find that the degree of interference can be controlled by simple chemical modifications of the molecular wire....

  5. [Assessment of therapeutic passive hypothermia in newborns with hypoxic-ischemic encephalopathy that need interhospital transport].

    Science.gov (United States)

    Fuentes-Ruiz, José A; Lagares-Franco, Carolina; Rodríguez-Molina, Óscar; Cordero-Cañas, Enrique; Benavente-Fernández, Isabel

    2015-04-01

    Induced hypothermia for the first hours of life in a newborn is an effective treatment to reduce mortality and serious effects in neonates that had suffered a hypoxia episode. This method needs an universal attendance independently of the place of birth being usually necessary a transfer to the reference hospital. To analyze the efficacy of the newborn with hypoxic-ischemic encephalopathy transfer in passive hypothermia. Descriptive study of series of cases with retrospective character of newborn from Cadiz's province that need induced hypothermia. 46 newborn were included in the study: 33 of them (71.74%) needed being transfer by the Critical Patients Transport service (CPT group), the rest (28.26%) were born into the reference hospital. Both groups are similar in age gestational at birth, sex, weight and hypoxic-ischemic encephalopathy degree. It analyzed variables related to hypothermia therapy and in addition in CPT group transfer specific variables. At discharge, it does not exist significant differences between groups in the efficiency-consequence of neuroprotection therapy with hypothermia (p = 0.159). It does not find complications derived from the interhospital move. Neonatal inter-hospital transfer in passive therapeutic hypothermia is effective, safe and necessary for the therapy compliance. It is required reach an agreement between the attendance and the reference service, setting up guides for the support and suitable range of temperature.

  6. Measuring gravel transport and dispersion in a mountain river using passive radio tracers

    Science.gov (United States)

    Bradley, D. N.; Tucker, G. E.

    2012-01-01

    Random walk models of fluvial sediment transport recognize that grains move intermittently, with short duration steps separated by rests that are comparatively long. These models are built upon the probability distributions of the step length and the resting time. Motivated by these models, tracer experiments have attempted to measure directly the steps and rests of sediment grains in natural streams. This paper describes results from a large tracer experiment designed to test stochastic transport models. We used passive integrated transponder (PIT) tags to label 893 coarse gravel clasts and placed them in Halfmoon Creek, a small alpine stream near Leadville, Colorado, USA. The PIT tags allow us to locate and identify tracers without picking them up or digging them out of the streambed. They also enable us to find a very high percentage of our rocks, 98% after three years and 96% after the fourth year. We use the annual tracer displacement to test two stochastic transport models, the Einstein–Hubbell–Sayre (EHS) model and the Yang–Sayre gamma-exponential model (GEM). We find that the GEM is a better fit to the observations, particularly for slower moving tracers and suggest that the strength of the GEM is that the gamma distribution of step lengths approximates a compound Poisson distribution. Published in 2012. This article is a US Government work and is in the public domain in the USA.

  7. Molecular and ionic mimicry and the transport of toxic metals

    Science.gov (United States)

    Bridges, Christy C.; Zalups, Rudolfs K.

    2008-01-01

    Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport of selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues. PMID:15845419

  8. Molecular and ionic mimicry and the transport of toxic metals

    International Nuclear Information System (INIS)

    Bridges, Christy C.; Zalups, Rudolfs K.

    2005-01-01

    Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport of selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues

  9. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    OpenAIRE

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferre...

  10. Molecular enzymology of carnitine transfer and transport

    NARCIS (Netherlands)

    Ramsay, RR; Gandour, RD; van der Leij, FR

    2001-01-01

    Carnitine (L-3-hydroxy-4-N-trimethylaminobutyric acid) forms esters with a wide range of acyl groups and functions to transport and excrete these groups. It is found in most cells at millimolar levels after uptake via the sodium-dependent carrier, OCTN2. The acylation state of the mobile carnitine

  11. Molecular properties of bacterial multidrug transporters

    NARCIS (Netherlands)

    Putman, M; van Veen, HW; Konings, WN

    2000-01-01

    One of the mechanisms that bacteria utilize to evade the toxic effects of antibiotics is the active extrusion of structurally unrelated drugs from the cell. Both intrinsic and acquired multidrug transporters play an important role in antibiotic resistance of several pathogens, including Neisseria

  12. Molecular transport calculations with Wannier Functions

    DEFF Research Database (Denmark)

    Thygesen, Kristian Sommer; Jacobsen, Karsten Wedel

    2005-01-01

    We present a scheme for calculating coherent electron transport in atomic-scale contacts. The method combines a formally exact Green's function formalism with a mean-field description of the electronic structure based on the Kohn-Sham scheme of density functional theory. We use an accurate plane...

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

    Science.gov (United States)

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

    2018-04-01

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

  14. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  15. Rigorous upper bounds for transport due to passive advection by inhomogeneous turbulence

    International Nuclear Information System (INIS)

    Krommes, J.A.; Smith, R.A.

    1987-05-01

    A variational procedure, due originally to Howard and explored by Busse and others for self-consistent turbulence problems, is employed to determine rigorous upper bounds for the advection of a passive scalar through an inhomogeneous turbulent slab with arbitrary generalized Reynolds number R and Kubo number K. In the basic version of the method, the steady-state energy balance is used as a constraint; the resulting bound, though rigorous, is independent of K. A pedagogical reference model (one dimension, K = ∞) is described in detail; the bound compares favorably with the exact solution. The direct-interaction approximation is also worked out for this model; it is somewhat more accurate than the bound, but requires considerably more labor to solve. For the basic bound, a general formalism is presented for several dimensions, finite correlation length, and reasonably general boundary conditions. Part of the general method, in which a Green's function technique is employed, applies to self-consistent as well as to passive problems, and thereby generalizes previous results in the fluid literature. The formalism is extended for the first time to include time-dependent constraints, and a bound is deduced which explicitly depends on K and has the correct physical scalings in all regimes of R and K. Two applications from the theory of turbulent plasmas ae described: flux in velocity space, and test particle transport in stochastic magnetic fields. For the velocity space problem the simplest bound reproduces Dupree's original scaling for the strong turbulence diffusion coefficient. For the case of stochastic magnetic fields, the scaling of the bounds is described for the magnetic diffusion coefficient as well as for the particle diffusion coefficient in the so-called collisionless, fluid, and double-streaming regimes

  16. Molecular mechanisms of water transport in the eye

    DEFF Research Database (Denmark)

    Hamann, Steffen

    2002-01-01

    The four major sites for ocular water transport, the corneal epithelium and endothelium, the ciliary epithelium, and the retinal pigment epithelium, are reviewed. The cornea has an inherent tendency to swell, which is counteracted by its two surface cell layers, the corneal epithelium...... and endothelium. The bilayered ciliary epithelium secretes the aqueous humor into the posterior chamber, and the retinal pigment epithelium transports water from the retinal to the choroidal site. For each epithelium, ion transport mechanisms are associated with fluid transport, but the exact molecular coupling...... sites between ion and water transport remain undefined. In the retinal pigment epithelium, a H+-lactate cotransporter transports water. This protein could be the site of coupling between salt and water in this epithelium. The distribution of aquaporins does not suggest a role for these proteins...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-14

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

  18. Mass transport thermodynamics in nonisothermal molecular liquid mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Semenov, Semen N [Institute for Biochemical Physics, Russian Academy of Sciences, Moscow (Russian Federation); Schimpf, M E [Department of Chemistry and Biochemistry, Boise State University, Boise, ID (United States)

    2009-10-31

    Mass transport in a nonisothermal binary molecular mixture is systematically discussed in terms of nonequilibrium thermodynamics, which for the first time allows a consistent and unambiguous description of the process. The thermodynamic and hydrodynamic approaches are compared, revealing that nonequilibrium thermodynamics and physicochemical hydrodynamics yield essentially the same results for molecular systems. The applicability limits for the proposed version of the thermodynamic approach are determined for large particles. (methodological notes)

  19. Theoretical and practical aspects of improving the durability of steel reinforcement in transport designs, using passivation and plasticizing chemical additives

    Science.gov (United States)

    Velichko, Evgenij; Talipov, Linar

    2017-10-01

    The article deals with the problem of steel reinforcement corrosion in reinforced concrete structures exposed to aggressive media, in particular in reinforced concrete construction of transport infrastructure, in snowy areas, and subject to the influence of chlorides contained in applied deicing agents. Basic schemes for preventing the reinforcement corrosion in reinforced-concrete structures have been considered and analyzed. Prospects of primary protection against corrosion of reinforcement by introducing chemical additives with plasticizing/passivating action in a concrete mixture with mixing water have been considered in detail. The physical/chemical mechanism of the protective action of a superplasticizer together with a passivator has been highlighted.

  20. Psychosocial and environmental correlates of active and passive transport behaviors in college educated and non-college educated working young adults.

    Science.gov (United States)

    Simons, Dorien; De Bourdeaudhuij, Ilse; Clarys, Peter; De Cocker, Katrien; de Geus, Bas; Vandelanotte, Corneel; Van Cauwenberg, Jelle; Deforche, Benedicte

    2017-01-01

    This study aimed to examine potential differences in walking, cycling, public transport and passive transport (car/moped/motorcycle) to work and to other destinations between college and non-college educated working young adults. Secondly, we aimed to investigate which psychosocial and environmental factors are associated with the four transport modes and whether these associations differ between college and non-college educated working young adults. In this cross-sectional study, 224 working young adults completed an online questionnaire assessing socio-demographic variables (8 items), psychosocial variables (6 items), environmental variables (10 items) and transport mode (4 types) and duration to work/other destinations. Zero-inflated negative binomial regression models were performed in R. A trend (pyoung adults participated in cycling and public transport. However, another trend indicated that cycle time and public transport trips were longer and passive transport trips were shorter in non-college compared to college educated working young adults. In all working young adults, high self-efficacy towards active transport, and high perceived benefits and low perceived barriers towards active and public transport were related to more active and public transport. High social support/norm/modeling towards active, public and passive transport was related to more active, public and passive transport. High neighborhood walkability was related to more walking and less passive transport. Only in non-college educated working young adults, feeling safe from traffic and crime in their neighborhood was related to more active and public transport and less passive transport. Educational levels should be taken into account when promoting healthy transport behaviors in working young adults. Among non-college educated working young adults, focus should be on increasing active and public transport participation and on increasing neighborhood safety to increase active and public

  1. Reaction-diffusion systems in intracellular molecular transport and control.

    Science.gov (United States)

    Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A

    2010-06-07

    Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.

  2. DNS of passive scalar transport in turbulent channel flow at high Schmidt numbers

    International Nuclear Information System (INIS)

    Schwertfirm, Florian; Manhart, Michael

    2007-01-01

    We perform DNS of passive scalar transport in low Reynolds number turbulent channel flow at Schmidt numbers up to Sc = 49. The high resolutions required to resolve the scalar concentration fields at such Schmidt numbers are achieved by a hierarchical algorithm in which only the scalar fields are solved on the grid dictated by the Batchelor scale. The velocity fields are solved on coarser grids and prolonged by a conservative interpolation to the fine-grid. The trends observed so far at lower Schmidt numbers Sc ≤ 10 are confirmed, i.e. the mean scalar gradient steepens at the wall with increasing Schmidt number, the peaks of turbulent quantities increase and move towards the wall. The instantaneous scalar fields show a dramatic change. Observable structures get longer and thinner which is connected with the occurrence of steeper gradients, but the wall concentrations penetrate less deeply into the plateau in the core of the channel. Our data shows that the thickness of the conductive sublayer, as defined by the intersection point of the linear with the logarithmic asymptote scales with Sc -0.29 . With this information it is possible to derive an expression for the dimensionless transfer coefficient K + which is only dependent on Sc and Re τ . This expression is in full accordance to previous results which demonstrates that the thickness of the conductive sublayer is the dominating quantity for the mean scalar profile

  3. DNS of passive scalar transport in turbulent channel flow at high Schmidt numbers

    Energy Technology Data Exchange (ETDEWEB)

    Schwertfirm, Florian [Fachgebiet Hydromechanik, Technische Universitaet Muenchen, Arcisstr. 21, 80337 Muenchen (Germany); Manhart, Michael [Fachgebiet Hydromechanik, Technische Universitaet Muenchen, Arcisstr. 21, 80337 Muenchen (Germany)], E-mail: m.manhart@bv.tum.de

    2007-12-15

    We perform DNS of passive scalar transport in low Reynolds number turbulent channel flow at Schmidt numbers up to Sc = 49. The high resolutions required to resolve the scalar concentration fields at such Schmidt numbers are achieved by a hierarchical algorithm in which only the scalar fields are solved on the grid dictated by the Batchelor scale. The velocity fields are solved on coarser grids and prolonged by a conservative interpolation to the fine-grid. The trends observed so far at lower Schmidt numbers Sc {<=} 10 are confirmed, i.e. the mean scalar gradient steepens at the wall with increasing Schmidt number, the peaks of turbulent quantities increase and move towards the wall. The instantaneous scalar fields show a dramatic change. Observable structures get longer and thinner which is connected with the occurrence of steeper gradients, but the wall concentrations penetrate less deeply into the plateau in the core of the channel. Our data shows that the thickness of the conductive sublayer, as defined by the intersection point of the linear with the logarithmic asymptote scales with Sc{sup -0.29}. With this information it is possible to derive an expression for the dimensionless transfer coefficient K{sup +} which is only dependent on Sc and Re{sub {tau}}. This expression is in full accordance to previous results which demonstrates that the thickness of the conductive sublayer is the dominating quantity for the mean scalar profile.

  4. Molecular Level Manipulation of Interfacial Charge Transport

    Science.gov (United States)

    Song, Charles Kiseok

    The bulk-heterojunction organic (BHJ) photovoltaics (OPVs) and lithium ion battery (LiB) have been extensively studied. Power conversion efficiency (PCE) of an OPV greater than 10% and utilizing group 4 elements as the anode to accommodate high capacity for LiBs are the goals of many studies. However, the currently ubiquitous hole-collecting layer of OPVs limit device performance and durability, and group 4 elements are unstable and brittle to be commercially produced. Thus, my thesis has focused on developing functional and durable interfacial layers (IFLs) for OPVs and characterizing flexible artificial solid-electrolyte interphase (SEI) for LiBs. In Chapter 2, a series of robust organosilane-based dipolar self-assembled monolayer (SAM) IFLs on the tin-doped indium oxide (ITO) anodes of OPVs are developed. These hydrophobic and amorphous IFLs modify anode work functions from 4.66 to 5.27 eV. Two series of Glass/ITO/SAM IFL/Active Layer/LiF/Al BHJ OPVs are fabricated, and a strong positive correlation between the electrochemically-derived heterogeneous electron transport rate constants (ks) and OPV PCEs are observed due to enhanced anode carrier extraction. In Chapter 3, a series of unusually denser organosilane-based SAM IFLs on ITO anodes of OPVs are developed. Precursor mixtures having short and long tail groups were simultaneously deposited to minimize sterical encumbrance and denser SAM IFLs are achieved. These heterogeneous supersaturated SAMs (SHSAMs), with PCE (7.62%) exceeding that of PEDOT:PSS IFL, are found to be 17% denser and enhances PCE by 54% versus comparable devices with homogeneous SAM IFLs due to enhanced charge selectivity and collection. In Chapter 4, libraries of electron affinities (EAs) of widely used conductive polymers are constructed by cyclic voltammetry (CV) in conventional and LiB media. The EAs of the conductive polymer films measured via CV in conventional (EAC) and Li+ battery (EAB) media could be linearly correlated by EAB = (1

  5. Molecular fundamentals of nitrogen uptake and transport in trees.

    Science.gov (United States)

    Castro-Rodríguez, Vanessa; Cañas, Rafael A; de la Torre, Fernando N; Pascual, Ma Belén; Avila, Concepción; Cánovas, Francisco M

    2017-05-01

    Nitrogen (N) is frequently a limiting factor for tree growth and development. Because N availability is extremely low in forest soils, trees have evolved mechanisms to acquire and transport this essential nutrient along with biotic interactions to guarantee its strict economy. Here we review recent advances in the molecular basis of tree N nutrition. The molecular characteristics, regulation, and biological significance of membrane proteins involved in the uptake and transport of N are addressed. The regulation of N uptake and transport in mycorrhized roots and transcriptome-wide studies of N nutrition are also outlined. Finally, several areas of future research are suggested. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Coupled particle–fluid transport and magnetic separation in microfluidic systems with passive magnetic functionality

    International Nuclear Information System (INIS)

    Khashan, Saud A; Furlani, Edward P

    2013-01-01

    A study is presented of coupled particle–fluid transport and field-directed particle capture in microfluidic systems with passive magnetic functionality. These systems consist of a microfluidic flow cell on a substrate that contains embedded magnetic elements. Two systems are considered that utilize soft- and hard-magnetic elements, respectively. In the former, an external field is applied to magnetize the elements, and in the latter, they are permanently magnetized. The field produced by the magnetized elements permeates into the flow cell giving rise to an attractive force on magnetic particles that flow through it. The systems are studied using a novel numerical/closed-form modelling approach that combines numerical transport analysis with closed-form field analysis. Particle–fluid transport is computed using computational fluid dynamics (CFD), while the magnetic force that governs particle capture is obtained in closed form. The CFD analysis takes into account dominant particle forces and two-way momentum transfer between the particles and the fluid. The two-way particle–fluid coupling capability is an important feature of the model that distinguishes it from more commonly used and simplified one-way coupling analysis. The model is used to quantify the impact of two-way particle–fluid coupling on both the capture efficiency and the flow pattern in the systems considered. Many effects such as particle-induced flow-enhanced capture efficiency and flow circulation are studied that cannot be predicted using one-way coupling analysis. In addition, dilute particle dispersions are shown to exhibit significant localized particle–fluid coupling near the capture regions, which contradicts the commonly held view that two-way coupling can be ignored when analysing high-gradient magnetic separation involving such particle systems. Overall, the model demonstrates that two-way coupling needs to be taken into account for rigorous predictions of capture efficiency

  7. Charge transport through molecular rods with reduced pi-conjugation.

    Science.gov (United States)

    Lörtscher, Emanuel; Elbing, Mark; Tschudy, Meinrad; von Hänisch, Carsten; Weber, Heiko B; Mayor, Marcel; Riel, Heike

    2008-10-24

    A series of oligophenylene rods of increasing lengths is synthesized to investigate the charge-transport mechanisms. Methyl groups are attached to the phenyl rings to weaken the electronic overlap of the pi-subsystems along the molecular backbones. Out-of-plane rotation of the phenyl rings is confirmed in the solid state by means of X-ray analysis and in solution by using UV/Vis spectroscopy. The influence of the reduced pi-conjugation on the resonant charge transport is studied at the single-molecule level by using the mechanically controllable break-junction technique. Experiments are performed under ultra-high-vacuum conditions at low temperature (50 K). A linear increase of the conductance gap with increasing number of phenyl rings (from 260 meV for one ring to 580 meV for four rings) is revealed. In addition, the absolute conductance of the first resonant peaks does not depend on the length of the molecular wire. Resonant transport through the first molecular orbital is found to be dominated by charge-carrier injection into the molecule, rather than by the intrinsic resistance of the molecular wire length.

  8. Elucidation of the glucose transport pathway in glucose transporter 4 via steered molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Aswathy Sheena

    Full Text Available BACKGROUND: GLUT4 is a predominant insulin regulated glucose transporter expressed in major glucose disposal tissues such as adipocytes and muscles. Under the unstimulated state, GLUT4 resides within intracellular vesicles. Various stimuli such as insulin translocate this protein to the plasma membrane for glucose transport. In the absence of a crystal structure for GLUT4, very little is known about the mechanism of glucose transport by this protein. Earlier we proposed a homology model for GLUT4 and performed a conventional molecular dynamics study revealing the conformational rearrangements during glucose and ATP binding. However, this study could not explain the transport of glucose through the permeation tunnel. METHODOLOGY/PRINCIPAL FINDINGS: To elucidate the molecular mechanism of glucose transport and its energetic, a steered molecular dynamics study (SMD was used. Glucose was pulled from the extracellular end of GLUT4 to the cytoplasm along the pathway using constant velocity pulling method. We identified several key residues within the tunnel that interact directly with either the backbone ring or the hydroxyl groups of glucose. A rotation of glucose molecule was seen near the sugar binding site facilitating the sugar recognition process at the QLS binding site. CONCLUSIONS/SIGNIFICANCE: This study proposes a possible glucose transport pathway and aids the identification of several residues that make direct interactions with glucose during glucose transport. Mutational studies are required to further validate the observation made in this study.

  9. Modeling of the Transport Phenomena in Passive Direct Methanol Fuel Cells Using a Two-Phase Anisotropic Model

    Directory of Open Access Journals (Sweden)

    Zheng Miao

    2014-04-01

    Full Text Available The transport phenomena in a passive direct methanol fuel cell (DMFC were numerically simulated by the proposed two-dimensional two-phase nonisothermal mass transport model. The anisotropic transport characteristic and deformation of the gas diffusion layer (GDL were considered in this model. The natural convection boundary conditions were adopted for the transport of methanol, oxygen, and heat at the GDL outer surface. The effect of methanol concentration in the reservoir on cell performance was examined. The distribution of multiphysical fields in the membrane electrode assembly (MEA, especially in the catalyst layers (CLs, was obtained and analyzed. The results indicated that transport resistance for the methanol mainly existed in the MEA while that for oxygen and heat was primarily due to natural convection at the GDL outer surface. Because of the relatively high methanol concentration, the local reaction rate in CLs was mainly determined by the overpotential. Methanol concentration between 3 M and 4 M was recommended for passive liquid feed DMFC in order to achieve a balance between the cell performance and the methanol crossover.

  10. Molecular transport network security using multi-wavelength optical spins.

    Science.gov (United States)

    Tunsiri, Surachai; Thammawongsa, Nopparat; Mitatha, Somsak; Yupapin, Preecha P

    2016-01-01

    Multi-wavelength generation system using an optical spin within the modified add-drop optical filter known as a PANDA ring resonator for molecular transport network security is proposed. By using the dark-bright soliton pair control, the optical capsules can be constructed and applied to securely transport the trapped molecules within the network. The advantage is that the dark and bright soliton pair (components) can securely propagate for long distance without electromagnetic interference. In operation, the optical intensity from PANDA ring resonator is fed into gold nano-antenna, where the surface plasmon oscillation between soliton pair and metallic waveguide is established.

  11. Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

    Science.gov (United States)

    Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H

    2016-01-01

    Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

  12. Molecular electronics--resonant transport through single molecules.

    Science.gov (United States)

    Lörtscher, Emanuel; Riel, Heike

    2010-01-01

    The mechanically controllable break-junction technique (MCBJ) enables us to investigate charge transport through an individually contacted and addressed molecule in ultra-high vacuum (UHV) environment at variable temperature ranging from room temperature down to 4 K. Using a statistical measurement and analysis approach, we acquire current-voltage (I-V) characteristics during the repeated formation, manipulation, and breaking of a molecular junction. At low temperatures, voltages accessing the first molecular orbitals in resonance can be applied, providing spectroscopic information about the junction's energy landscape, in particular about the molecular level alignment in respect to the Fermi energy of the electrodes. Thereby, we can investigate the non-linear transport properties of various types of functional molecules and explore their potential use as functional building blocks for future nano-electronics. An example will be given by the reversible and controllable switching between two distinct conductive states of a single molecule. As a proof-of-principle for functional molecular devices, a single-molecule memory element will be demonstrated.

  13. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    Science.gov (United States)

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry. PMID:22455919

  14. Molecular electronics: insight from first-principles transport simulations.

    Science.gov (United States)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2010-01-01

    Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

  15. A simplified tether model for molecular motor transporting cargo

    International Nuclear Information System (INIS)

    Fang-Zhen, Li; Li-Chun, Jiang

    2010-01-01

    Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor–cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity. (general)

  16. Intracellular Requirements for Passive Proton Transport through the Na+,K+-ATPase.

    Science.gov (United States)

    Stanley, Kevin S; Meyer, Dylan J; Gatto, Craig; Artigas, Pablo

    2016-12-06

    The Na + ,K + -ATPase (NKA or Na/K pump) hydrolyzes one ATP to exchange three intracellular Na+ (Na + i ) for two extracellular K+ (K + o ) across the plasma membrane by cycling through a set of reversible transitions between phosphorylated and dephosphorylated conformations, alternately opening ion-binding sites externally (E2) or internally (E1). With subsaturating [Na + ] o and [K + ] o , the phosphorylated E2P conformation passively imports protons generating an inward current (I H ), which may be exacerbated in NKA-subunit mutations associated with human disease. To elucidate the mechanisms of I H , we studied the effects of intracellular ligands (transported ions, nucleotides, and beryllium fluoride) on I H and, for comparison, on transient currents measured at normal Na + o (Q Na ). Utilizing inside-out patches from Xenopus oocytes heterologously expressing NKA, we observed that 1) in the presence of Na + i , I H and Q Na were both activated by ATP, but not ADP; 2) the [Na + ] i dependence of I H in saturating ATP showed K 0.5,Na  = 1.8 ± 0.2 mM and the [ATP] dependence at saturating [Na + ] i yielded K 0.5,ATP  = 48 ± 11 μM (in comparison, Na + i -dependent Q Na yields K 0.5,Na  = 0.8 ± 0.2 mM and K 0.5,ATP  = 0.43 ± 0.03 μM; 3) ATP activated I H in the presence of K + i (∼15% of the I H observed in Na + i ) only when Mg 2+ i was also present; and 4) beryllium fluoride induced maximal I H  even in the absence of nucleotide. These data indicate that I H occurs when NKA is in an externally open E2P state with nucleotide bound, a conformation that can be reached through forward Na/K pump phosphorylation of E1, with Na + i and ATP, or by backward binding of K + i to E1, which drives the pump to the occluded E2(2K), where free P i (at the micromolar levels found in millimolar ATP solutions) promotes external release of occluded K + by backdoor NKA phosphorylation. Maximal I H through beryllium-fluorinated NKA indicates that this complex mimics ATP

  17. Theoretical investigations of molecular wires: Electronic spectra and electron transport

    Science.gov (United States)

    Palma, Julio Leopoldo

    The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

  18. Effects of high frequency fluctuations on DNS of turbulent open-channel flow with high Pr passive scalar transport

    International Nuclear Information System (INIS)

    Yamamoto, Yoshinobu; Kunugi, Tomoaki; Serizawa, Akimi

    2002-01-01

    In this study, investigation on effects of high frequency fluctuations on DNS of turbulent open-channel flows with high Pr passive scalar transport was conducted. As the results, although significant differences of energy spectra behaviors in temperature fields, are caused at high wave number region where insignificant area for velocity components, large difference dose not caused in mean and statistic behaviors in temperature component. But, if the buoyancy were considered, this temperature high-frequency fluctuations would be greatly changed mean and statistics behaviors from the difference of the accuracy and resolution at high wave number region. (author)

  19. Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1.

    Directory of Open Access Journals (Sweden)

    Min-Sun Park

    Full Text Available Glucose transporters (GLUTs provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and cancer. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE, a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM domains and the intracellular helices (ICH domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states.

  20. Sugar transport across lactose permease probed by steered molecular dynamics

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad

    2007-01-01

    Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic...... details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of the narrowest parts of the channel during permeation, the widening being largest within the periplasmic half-channel. During permeation, the water-filled lumen of LacY only partially hydrates lactose......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly...

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  2. Passive hypothermia (≥35 - <36°C during transport of newborns with hypoxic-ischaemic encephalopathy.

    Directory of Open Access Journals (Sweden)

    Aurélie Sellam

    Full Text Available Hypothermia initiated in the first six hours of life in term infants with hypoxic ischemic encephalopathy reduces the risk of death and severe neurological sequelae. Our study's principal objective was to evaluate transport predictors potentially influencing arrival in NICU (Neonatal Intensive Care Unit at a temperature ≥35-<36°C.A multi-centric, prospective cohort study was conducted during 18 months by the three Neonatal Transport Teams and 13 NICUs. Newborns were selected for inclusion according to biological and clinical criteria before transport using passive hypothermia using a target temperature of ≥35-<36°C. Data on 120 of 126 inclusions were available for analysis. Thirty-three percent of the children arrived in NICU with the target temperature of ≥35-<36°C. The mean temperature for the whole group of infants on arrival in NICU was 35.4°C (34.3-36.5. The median age of all infants on arrival in NICU was 3h03min [2h25min-3h56min]. Three infants arrived in NICU with a temperature of <33°C and eleven with a temperature ≥37°C. Adrenaline during resuscitation was associated with a lower mean temperature on arrival in NICU.Our strategy using ≥35-<36°C passive hypothermia combined with short transport times had little effect on temperature after the arrival of Neonatal Transport Team although did reduce numbers of infants arriving in NICU in deep hypothermia. For those infants where hypothermia was discontinued in NICU our strategy facilitated re-warming. Re-adjustment to a lower target temperature to ≥34.5-<35.5°C may reduce the proportion of infants with high/normothermic temperatures.

  3. Conserving GW scheme for nonequilibrium quantum transport in molecular contacts

    DEFF Research Database (Denmark)

    Thygesen, Kristian Sommer; Rubio, Angel

    2008-01-01

    We give a detailed presentation of our recent scheme to include correlation effects in molecular transport calculations using the nonequilibrium Keldysh formalism. The scheme is general and can be used with any quasiparticle self-energy, but for practical reasons, we mainly specialize to the so......-called GW self-energy, widely used to describe the quasiparticle band structures and spectroscopic properties of extended and low-dimensional systems. We restrict the GW self-energy to a finite, central region containing the molecule, and we describe the leads by density functional theory (DFT). A minimal...

  4. Passive transport pathways for Ca2+ and Co2+ in human red blood cells

    DEFF Research Database (Denmark)

    Simonsen, Lars Ole; Harbak, Henrik; Bennekou, Poul

    2011-01-01

    The passive transport of calcium and cobalt and their interference were studied in human red cells using (45)Ca and (57)Co as tracers. In ATP-depleted cells, with the ATP concentration reduced to about 1µM, the progress curve for (45)Ca uptake at 1mM rapidly levels off with time, consistent...... with a residual Ca-pump activity building up at increasing [Ca(T)](c) to reach at [Ca(T)](c) about 5µmol(lcells)(-1) a maximal pump rate that nearly countermands the passive Ca influx, resulting in a linear net uptake at a low level. In ATP-depleted cells treated with vanadate, supposed to cause Ca-pump arrest......, a residual pump activity is still present at high [Ca(T)](c). Moreover, vanadate markedly increases the passive Ca(2+) influx. The residual Ca-pump activity in ATP-depleted cells is fuelled by breakdown of the large 2,3-DPG pool, rate-limited by the sustainable ATP-turnover at about 40-50µmol(lcells)(-1)h(-1...

  5. Molecular Imaging of Transporters with Positron Emission Tomography

    Science.gov (United States)

    Antoni, Gunnar; Sörensen, Jens; Hall, Håkan

    Positron emission tomography (PET) visualization of brain components in vivo is a rapidly growing field. Molecular imaging with PET is also increasingly used in drug development, especially for the determination of drug receptor interaction for CNS-active drugs. This gives the opportunity to relate clinical efficacy to per cent receptor occupancy of a drug on a certain targeted receptor and to relate drug pharmacokinetics in plasma to interaction with target protein. In the present review we will focus on the study of transporters, such as the monoamine transporters, the P-glycoprotein (Pgp) transporter, the vesicular monoamine transporter type 2, and the glucose transporter using PET radioligands. Neurotransmitter transporters are presynaptically located and in vivo imaging using PET can therefore be used for the determination of the density of afferent neurons. Several promising PET ligands for the noradrenaline transporter (NET) have been labeled and evaluated in vivo including in man, but a really useful PET ligand for NET still remains to be identified. The most promising tracer to date is (S,S)-[18F]FMeNER-D2. The in vivo visualization of the dopamine transporter (DAT) may give clues in the evaluation of conditions related to dopamine, such as Parkinson's disease and drug abuse. The first PET radioligands based on cocaine were not selective, but more recently several selective tracers such as [11C]PE2I have been characterized and shown to be suitable as PET radioligands. Although there are a large number of serotonin transporter inhibitors used today as SSRIs, it was not until very recently, when [11C]McN5652 was synthesized, that this transporter was studied using PET. New candidates as PET radioligands for the SERT have subsequently been developed and [11C]DASB and [11C]MADAM and their analogues are today the most promising ligands. The existing radioligands for Pgp transporters seem to be suitable tools for the study of both peripheral and central drug

  6. Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

    Science.gov (United States)

    Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

    2018-01-01

    Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.

  7. Molecular simulation of adsorption and transport in hierarchical porous materials.

    Science.gov (United States)

    Coasne, Benoit; Galarneau, Anne; Gerardin, Corine; Fajula, François; Villemot, François

    2013-06-25

    Adsorption and transport in hierarchical porous solids with micro- (~1 nm) and mesoporosities (>2 nm) are investigated by molecular simulation. Two models of hierarchical solids are considered: microporous materials in which mesopores are carved out (model A) and mesoporous materials in which microporous nanoparticles are inserted (model B). Adsorption isotherms for model A can be described as a linear combination of the adsorption isotherms for pure mesoporous and microporous solids. In contrast, adsorption in model B departs from adsorption in pure microporous and mesoporous solids; the inserted microporous particles act as defects, which help nucleate the liquid phase within the mesopore and shift capillary condensation toward lower pressures. As far as transport under a pressure gradient is concerned, the flux in hierarchical materials consisting of microporous solids in which mesopores are carved out obeys the Navier-Stokes equation so that Darcy's law is verified within the mesopore. Moreover, the flow in such materials is larger than in a single mesopore, due to the transfer between micropores and mesopores. This nonzero velocity at the mesopore surface implies that transport in such hierarchical materials involves slippage at the mesopore surface, although the adsorbate has a strong affinity for the surface. In contrast to model A, flux in model B is smaller than in a single mesopore, as the nanoparticles act as constrictions that hinder transport. By a subtle effect arising from fast transport in the mesopores, the presence of mesopores increases the number of molecules in the microporosity in hierarchical materials and, hence, decreases the flow in the micropores (due to mass conservation). As a result, we do not observe faster diffusion in the micropores of hierarchical materials upon flow but slower diffusion, which increases the contact time between the adsorbate and the surface of the microporosity.

  8. Assessing the transport of PAH in the surficial sediment layer by passive sampler approach.

    Science.gov (United States)

    Belles, Angel; Alary, Claire; Criquet, Justine; Ivanovsky, Anastasia; Billon, Gabriel

    2017-02-01

    A new method based on passive samplers has been developed to assess the diffusive flux of fluorene, fluoranthene and pyrene in the sediment bed and across the sediment-water interface. The dissolved compound concentration gradient in the sediment in the vertical direction was measured at the outlet of a storm water pond by using polyethylene strips as passive samplers. Simultaneously, the dissipation of a set of tracer compounds preloaded in the passive samplers was measured to estimate the effective diffusion coefficients of the pollutants in the sediment. Both measurements were used to evaluate the diffusive flux of the compounds according to Fick's first law. The diffusive fluxes of the 3 studied compounds have been estimated with a centimetre-scale resolution in the upper 44cm of the sediment. According to the higher compound diffusion coefficient and the steeper concentration gradient in the surficial sediment layer, the results show that the net flux of compounds near the sediment interface (1cm depth) is on average 500 times higher than in the deep sediment, with average fluxes at 1cm depth on the order of 5, 0.1 and 0.1ng/m 2 /y for fluorene, fluoranthene and pyrene, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  10. Theoretical modeling of electronic transport in molecular devices

    Science.gov (United States)

    Piccinin, Simone

    In this thesis a novel approach for simulating electronic transport in nanoscale structures is introduced. We consider an open quantum system (the electrons of structure) accelerated by an external electromotive force and dissipating energy through inelastic scattering with a heat bath (phonons) acting on the electrons. This method can be regarded as a quantum-mechanical extension of the semi-classical Boltzmann transport equation. We use periodic boundary conditions and employ Density Functional Theory to recast the many-particle problem in an effective single-particle mean-field problem. By explicitly treating the dissipation in the electrodes, the behavior of the potential is an outcome of our method, at variance with the scattering approaches based on the Landauer formalism. We study the self-consistent steady-state solution, analyzing the out-of-equilibrium electron distribution, the electrical characteristics, the behavior of the self-consistent potential and the density of states of the system. We apply the method to the study of electronic transport in several molecular devices, consisting of small organic molecules or atomic wires sandwiched between gold surfaces. For gold wires we recover the experimental evidence that transport in short wires is ballistic, independent of the length of the wire and with conductance of one quantum. In benzene-1,4-dithiol we find that the delocalization of the frontier orbitals of the molecule is responsible for the high value of conductance and that, by inserting methylene groups to decouple the sulfur atoms from the carbon ring, the current is reduced, in agreement with the experimental measurements. We study the effect a geometrical distortion in a molecular device, namely the relative rotation of the carbon rings in a biphenyl-4,4'-dithiol molecule. We find that the reduced coupling between pi orbitals of the rings induced by the rotation leads to a reduction of the conductance and that this behavior is captured by a

  11. Modelling the Molecular Transportation of Subcutaneously Injected Salubrinal

    Directory of Open Access Journals (Sweden)

    Andy Chen

    2011-01-01

    Full Text Available For the subcutaneous administration of a chemical agent (salubrinal, we constructed a mathematical model of molecule transportation and subsequently evaluated the kinetics of diffusion, convection, and molecular turnover. Salubrinal is a potential therapeutic agent that can reduce cellular damage and death. The understanding of its temporal profiles in local tissue as well as in a whole body is important to develop a proper strategy for its administration. Here, the diffusion and convection kinetics was formulated using partial and ordinary differential equations in one- and three-dimensional (semi-spherical coordinates. Several key parameters including an injection velocity, a diffusion coefficient, thickness of subcutaneous tissue, and a permeability factor at the tissue-blood boundary were estimated from experimental data in rats. With reference to analytical solutions in a simplified model without convection, numerical solutions revealed that the diffusion coefficient and thickness of subcutaneous tissue determined the timing of the peak concentration in the plasma, and its magnitude was dictated by the permeability factor. Furthermore, the initial velocity, induced by needle injection, elevated an immediate transport of salubrinal at t < 1h. The described analysis with a combination of partial and ordinary differential equations contributes to the prediction of local and systemic effects and the understanding of the transportation mechanism of salubrinal and other agents.

  12. Electrochemical dissolution of fresh and passivated chalcopyrite electrodes. Effect of pyrite on the reduction of Fe3+ ions and transport processes within the passive film

    International Nuclear Information System (INIS)

    Olvera, O.G.; Quiroz, L.; Dixon, D.G.; Asselin, E.

    2014-01-01

    Graphical abstract: - Highlights: • FeS 2 increased the dissolution rate of fresh and passivated CuFeS 2 electrodes. • Fe 3+ reduction was the rate controlling step in the dissolution of fresh CuFeS 2 . • Diffusion within the passive film controlled the dissolution rate of passivated CuFeS 2 . - Abstract: The effect of pyrite (FeS 2 ) on the electrochemical dissolution of fresh and passivated chalcopyrite (CuFeS 2 ) electrodes has been studied. Current density values for the dissolution of CuFeS 2 were calculated from EIS measurements. FeS 2 increased the dissolution rate of fresh and passivated CuFeS 2 electrodes indicating that the galvanic effect continued even after the electrode was chemically passivated. The dissolution rate of CuFeS 2 decreased by a factor of 3 after the passivation treatment. Due to the low diffusion rates of ions within the CuFeS 2 passive film and due to an increase in the resistance to the transfer of electrons at the electrode/film interface, the activity of FeS 2 for the reduction of Fe 3+ ions was also reduced by a factor of 2.3 even though FeS 2 was not exposed to any chemical treatment. The results in this work indicate that the dissolution rate of the fresh CuFeS 2 electrode was controlled by the reduction of Fe 3+ ions whereas for the passivated CuFeS 2 electrode the dissolution rate was controlled by diffusion within the passive film

  13. Do the recommended standards for in vitro biopharmaceutic classification of drug permeability meet the "passive transport" criterion for biowaivers?

    Science.gov (United States)

    Žakelj, Simon; Berginc, Katja; Roškar, Robert; Kraljič, Bor; Kristl, Albin

    2013-01-01

    BCS based biowaivers are recognized by major regulatory agencies. An application for a biowaiver can be supported by or even based on "in vitro" measurements of drug permeability. However, guidelines limit the application of biowaivers to drug substances that are transported only by passive mechanisms. Regarding published permeability data as well as measurements obtained in our institution, one can rarely observe drug substances that conform to this very strict criterion. Therefore, we measured the apparent permeability coefficients of 13 drugs recommended by FDA's Guidance to be used as standards for "in vitro" permeability classification. The asymmetry of permeability data determined for both directions (mucosal-to-serosal and serosalto- mucosal) through the rat small intestine revealed significant active transport for four out of the nine high-permeability standards and for all four low-permeability standard drugs. As could be expected, this asymmetry was abolished at 4°C on rat intestine. The permeability of all nine high-permeability, but none of the low permeability standards, was also much lower when measured with intestinal tissue, Caco-2 cell monolayers or artificial membranes at 4°C compared to standard conditions (37°C). Additionally, concurrent testing of several standard drugs revealed that membrane transport can be affected by the use of internal permeability standards. The implications of the results are discussed regarding the regulatory aspects of biopharmaceutical classification, good practice in drug permeability evaluation and regarding the general relevance of transport proteins with broad specificity in drug absorption.

  14. The Texas horned lizard as model for robust capillary structures for passive directional transport of cooling lubricants

    Science.gov (United States)

    Comanns, Philipp; Winands, Kai; Pothen, Mario; Bott, Raya A.; Wagner, Hermann; Baumgartner, Werner

    2016-04-01

    Moisture-harvesting lizards, such as the Texas horned lizard Phrynosoma cornutum, have remarkable adaptations for inhabiting arid regions. Special skin structures, in particular capillary channels in between imbricate overlapping scales, enable the lizard to collect water by capillarity and to transport it to the snout for ingestion. This fluid transport is passive and directional towards the lizard's snout. The directionality is based on geometric principles, namely on a periodic pattern of interconnected half-open capillary channels that narrow and widen. Following a biomimetic approach, these principles were transferred to technical prototype design and manufacturing. Capillary structures, 50 μm to 300 μm wide and approx. 70 μm deep, were realized by use of a pulsed picosecond laser in hot working tool steel, hardened to 52 HRC. In order to achieve highest functionality, strategies were developed to minimize potential structural inaccuracies, which can occur at the bottom of the capillary structures caused by the laser process. Such inaccuracies are in the range of 10 μm to 15 μm and form sub-capillary structures with greater capillary forces than the main channels. Hence, an Acceleration Compensation Algorithm was developed for the laser process to minimize or even avoid these inaccuracies. The capillary design was also identified to have substantial influence; by a hexagonal capillary network of non-parallel capillaries potential influences of sub-capillaries on the functionality were reduced to realize a robust passive directional capillary transport. Such smart surface structures can lead to improvements of technical systems by decreasing energy consumption and increasing the resource efficiency.

  15. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  16. Stable High-Performance Perovskite Solar Cells via Grain Boundary Passivation

    KAUST Repository

    Niu, Tianqi; Lu, Jing; Munir, Rahim; Li, Jianbo; Barrit, Dounya; Zhang, Xu; Hu, Hanlin; Yang, Zhou; Amassian, Aram; Zhao, Kui; Liu, Shengzhong Frank

    2018-01-01

    the energy offset between the semiconducting molecules and the perovskite influences trap states and intergrain carrier transport. The superior optoelectronic properties are attained by optimizing the molecular passivation treatments. These benefits

  17. Transport properties of hydrogen passivated silicon nanotubes and silicon nanotube field effect transistors

    KAUST Repository

    Montes Muñ oz, Enrique; Schwingenschlö gl, Udo

    2017-01-01

    We investigate the electronic transport properties of silicon nanotubes attached to metallic electrodes from first principles, using density functional theory and the non-equilibrium Green's function method. The influence of the surface termination

  18. Effect of Molecular Structure on Modulation of Passivation Films on Copper Chemical Mechanical Planarization

    Science.gov (United States)

    Mlynarski, Amy

    In order to optimize the chemical mechanical planarization (CMP) process, there is a need to further understand the synergistic relationship between chemical and mechanical parameters to enhance the polishing process. CMP chemistry is very complex, as it contains complexing agents, oxidizing agents, passivating agents, and abrasive particles. This variety of components ensues chaos within the system, which complicates the understanding of the direct impact each component has on the CMP process. In order for there to be efficiency in the polishing process, specifically for copper (Cu) polishing, the chemistry must create a softened passivation layer on the Cu surface that is able to be readily removed by applied mechanical abrasion. Focusing on Cu CMP, the oxidation of Cu to Cu2+ needs to be thoroughly understood in order to probe the formation of creating this ideal passivated layer, which protects recessed Cu regions. The type of film that is formed, the strength of the film, and even the efficiency of film removal will be altered depending on the chemistry of interaction at the Cu surface. This thesis focuses on understanding the working mechanism of the film formation on Cu, depending on the passivating agent added to the system. The different passivating agents used, more specifically benzotriazole (BTA), triazole (TAZ), salicylhydroxamic acid (SHA), and benzimidazole (BIA), have all been known to create a light coat of protection on the recessed metal, providing corrosion resistance. In order to study the differences in these films, many different techniques can be utilized to characterize the films, such as electrochemical scans, referred to as Tafel plots, which will be performed to compare the differences of the films. By altering the temperature within the system, the activation energy for each system can also be determined as another way to characterize the density of the passive film formed. Furthermore, the generation of *OH will be monitored since the

  19. Passivation effect on optical and electrical properties of molecular beam epitaxy-grown HgCdTe/CdTe/Si layers

    Science.gov (United States)

    Kiran, Rajni; Mallick, Shubhrangshu; Hahn, Suk-Ryong; Lee, T. S.; Sivananthan, Sivalingam; Ghosh, Siddhartha; Wijewarnasuriya, P. S.

    2006-06-01

    The effects of passivation with two different passivants, ZnS and CdTe, and two different passivation techniques, physical vapor deposition (PVD) and molecular beam epitaxy (MBE), were quantified in terms of the minority carrier lifetime and extracted surface recombination velocity on both MBE-grown medium-wavelength ir (MWIR) and long-wavelength ir HgCdTe samples. A gradual increment of the minority carrier lifetime was reported as the passivation technique was changed from PVD ZnS to PVD CdTe, and finally to MBE CdTe, especially at low temperatures. A corresponding reduction in the extracted surface recombination velocity in the same order was also reported for the first time. Initial data on the 1/ f noise values of as-grown MWIR samples showed a reduction of two orders of noise power after 1200-Å ZnS deposition.

  20. Modeled Downward Transport of a Passive Tracer over Western North America during an Asian Dust Event in April 1998.

    Science.gov (United States)

    Hacker, Joshua P.; McKendry, Ian G.; Stull, Roland B.

    2001-09-01

    An intense Gobi Desert dust storm in April 1998 loaded the midtroposphere with dust that was transported across the Pacific to western North America. The Mesoscale Compressible Community (MC2) model was used to investigate mechanisms causing downward transport of the midtropospheric dust and to explain the high concentrations of particulate matter of less than 10-m diameter measured in the coastal urban areas of Washington and southern British Columbia. The MC2 was initialized with a thin, horizontally homogeneous layer of passive tracer centered at 650 hPa for a simulation from 0000 UTC 26 April to 0000 UTC 30 April 1998. Model results were in qualitative agreement with observed spatial and temporal patterns of particulate matter, indicating that it captured the important meteorological processes responsible for the horizontal and vertical transport over the last few days of the dust event. A second simulation was performed without topography to isolate the effects of topography on downward transport.Results show that the dust was advected well east of the North American coast in southwesterly midtropospheric flow, with negligible dust concentration reaching the surface initially. Vertically propagating mountain waves formed during this stage, and differences between downward and upward velocities in these waves could account for a rapid descent of dust to terrain height, where the dust was entrained into the turbulent planetary boundary layer. A deepening outflow (easterly) layer near the surface transported the tracer westward and created a zonal-shear layer that further controlled the tracer advection. Later, the shear layer lifted, leading to a downward hydraulic acceleration along the western slopes, as waves generated in the easterly flow amplified below the shear layer that was just above mountain-crest height. Examination of 10 yr of National Centers for Environmental Prediction-National Center for Atmospheric Research reanalyses suggests that such events

  1. Modeling cytoskeletal traffic: an interplay between passive diffusion and active transport.

    Science.gov (United States)

    Neri, Izaak; Kern, Norbert; Parmeggiani, Andrea

    2013-03-01

    We introduce the totally asymmetric simple exclusion process with Langmuir kinetics on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm. We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales: we find three regimes for steady state transport, corresponding to the scale of the network, of individual segments, or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.

  2. Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip

    DEFF Research Database (Denmark)

    Comtet, Jean; Jensen, Kaare Hartvig; Turgeon, Robert

    2017-01-01

    Vascular plants rely on differences in osmotic pressure to export sugars from regions of synthesis (mature leaves) to sugar sinks (roots, fruits). In this process, known as Münch pressure flow, the loading of sugars from photosynthetic cells to the export conduit (the phloem) is crucial, as it sets...... the pressure head necessary to power long-distance transport. Whereas most herbaceous plants use active mechanisms to increase phloem sugar concentration above that of the photosynthetic cells, in most tree species, for which transport distances are largest, loading seems, counterintuitively, to occur by means......, diffusion-limited export leads to small phloem concentrations and weak scaling of flow rates with hydraulic resistance. We then show that the effective regime of convection-limited export is predominant in plants with large transport resistances and low xylem pressures. Moreover, hydrostatic pressures...

  3. Squaring the Circle: Geometric Skewness and Symmetry Breaking for Passive Scalar Transport in Ducts and Pipes.

    Science.gov (United States)

    Aminian, Manuchehr; Bernardi, Francesca; Camassa, Roberto; McLaughlin, Richard M

    2015-10-09

    We study the role geometry plays in the emergence of asymmetries in diffusing passive scalars advected by pressure-driven flows in ducts and pipes of different aspect ratios. We uncover nonintuitive, multi-time-scale behavior gauged by a new statistic, which we term "geometric skewness" S^{G}, which measures instantaneously forming asymmetries at short times due to flow geometry. This signature distinguishes elliptical pipes of any aspect ratio, for which S^{G}=0, from rectangular ducts whose S^{G} is generically nonzero, and, interestingly, shows that a special duct of aspect ratio ≈0.53335 behaves like a circular pipe as its geometric skewness vanishes. Using a combination of exact solutions, novel short-time asymptotics, and Monte Carlo simulations, we establish the relevant time scales for plateaus and extrema in the evolution of the skewness and kurtosis for our class of geometries. For ducts limiting to channel geometries, we present new exact, single-series formulas for the first four moments on slices used to benchmark Monte Carlo simulations.

  4. Reply to "Can the levels of Can f 1 in indoor environments be evaluated without considering passive transport of allergen indoors?"

    NARCIS (Netherlands)

    Krop, E.J.M.; Vredegoor, D.W.; Chapman, M.D.; Willemse, A.; Heederik, D.J.J.

    2013-01-01

    Response to Liccardi G, Salzillo A, Piccolo A, D’Amato M, D’Amato G. Can the levels of Can f 1 in indoor environments be evaluated without considering passive transport of allergen indoors? J Allergy Clin Immunol 2013;131:1258-9.

  5. Transport properties of hydrogen passivated silicon nanotubes and silicon nanotube field effect transistors

    KAUST Repository

    Montes Muñoz, Enrique

    2017-01-24

    We investigate the electronic transport properties of silicon nanotubes attached to metallic electrodes from first principles, using density functional theory and the non-equilibrium Green\\'s function method. The influence of the surface termination is studied as well as the dependence of the transport characteristics on the chirality, diameter, and length. Strong electronic coupling between nanotubes and electrodes is found to be a general feature that results in low contact resistance. The conductance in the tunneling regime is discussed in terms of the complex band structure. Silicon nanotube field effect transistors are simulated by applying a uniform potential gate. Our results demonstrate very high values of transconductance, outperforming the best commercial silicon field effect transistors, combined with low values of sub-threshold swing.

  6. Passive larval transport explains recent gene flow in a Mediterranean gorgonian

    Science.gov (United States)

    Padrón, Mariana; Costantini, Federica; Baksay, Sandra; Bramanti, Lorenzo; Guizien, Katell

    2018-06-01

    Understanding the patterns of connectivity is required by the Strategic Plan for Biodiversity 2011-2020 and will be used to guide the extension of marine protection measures. Despite the increasing accuracy of ocean circulation modelling, the capacity to model the population connectivity of sessile benthic species with dispersal larval stages can be limited due to the potential effect of filters acting before or after dispersal, which modulates offspring release or settlement, respectively. We applied an interdisciplinary approach that combined demographic surveys, genetic methods (assignment tests and coalescent-based analyses) and larval transport simulations to test the relative importance of demographics and ocean currents in shaping the recent patterns of gene flow among populations of a Mediterranean gorgonian ( Eunicella singularis) in a fragmented rocky habitat (Gulf of Lion, NW Mediterranean Sea). We show that larval transport is a dominant driver of recent gene flow among the populations, and significant correlations were found between recent gene flow and larval transport during an average single dispersal event when the pelagic larval durations (PLDs) ranged from 7 to 14 d. Our results suggest that PLDs that efficiently connect populations distributed over a fragmented habitat are filtered by the habitat layout within the species competency period. Moreover, a PLD ranging from 7 to 14 d is sufficient to connect the fragmented rocky substrate of the Gulf of Lion. The rocky areas located in the centre of the Gulf of Lion, which are currently not protected, were identified as essential hubs for the distribution of migrants in the region. We encourage the use of a range of PLDs instead of a single value when estimating larval transport with biophysical models to identify potential connectivity patterns among a network of Marine Protected Areas or even solely a seascape.

  7. Improved rigorous upper bounds for transport due to passive advection described by simple models of bounded systems

    International Nuclear Information System (INIS)

    Kim, Chang-Bae; Krommes, J.A.

    1988-08-01

    The work of Krommes and Smith on rigorous upper bounds for the turbulent transport of a passively advected scalar [/ital Ann. Phys./ 177:246 (1987)] is extended in two directions: (1) For their ''reference model,'' improved upper bounds are obtained by utilizing more sophisticated two-time constraints which include the effects of cross-correlations up to fourth order. Numerical solutions of the model stochastic differential equation are also obtained; they show that the new bounds compare quite favorably with the exact results, even at large Reynolds and Kubo numbers. (2) The theory is extended to take account of a finite spatial autocorrelation length L/sub c/. As a reasonably generic example, the problem of particle transport due to statistically specified stochastic magnetic fields in a collisionless turbulent plasma is revisited. A bound is obtained which reduces for small L/sub c/ to the quasilinear limit and for large L/sub c/ to the strong turbulence limit, and which provides a reasonable and rigorous interpolation for intermediate values of L/sub c/. 18 refs., 6 figs

  8. GLOBAL RANDOM WALK SIMULATIONS FOR SENSITIVITY AND UNCERTAINTY ANALYSIS OF PASSIVE TRANSPORT MODELS

    Directory of Open Access Journals (Sweden)

    Nicolae Suciu

    2011-07-01

    Full Text Available The Global Random Walk algorithm (GRW performs a simultaneoustracking on a fixed grid of huge numbers of particles at costscomparable to those of a single-trajectory simulation by the traditional Particle Tracking (PT approach. Statistical ensembles of GRW simulations of a typical advection-dispersion process in groundwater systems with randomly distributed spatial parameters are used to obtain reliable estimations of the input parameters for the upscaled transport model and of their correlations, input-output correlations, as well as full probability distributions of the input and output parameters.

  9. Numerical investigations of passive scalar transport in Taylor-Couette flows: Counter-rotation effect

    Science.gov (United States)

    Ouazib, Nabila; Salhi, Yacine; Si-Ahmed, El-Khider; Legrand, Jack; Degrez, G.

    2017-07-01

    Numerical methods for solving convection-diffusion-reaction (CDR) scalar transport equation in three-dimensional flow are used in the present investigation. The flow is confined between two concentric cylinders both the inner cylinder and the outer one are allowed to rotate. Direct numerical simulations (DNS) have been achieved to study the effects of the gravitational and the centrifugal potentials on the stability of incompressible Taylor-Couette flow. The Navier-Stokes equations and the uncoupled convection-diffusion-reaction equation are solved using a spectral development in one direction combined together with a finite element discretization in the two remaining directions. The complexity of the patterns is highlighted. Since, it increases as the rotation rates of the cylinders increase. In addition, the effect of the counter-rotation of the cylinders on the mass transfer is pointed out.

  10. Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

    2017-05-01

    The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  12. Assessing factors affecting the thermal properties of a passive thermal refuge using three-dimensional hydrodynamic flow and transport modeling

    Science.gov (United States)

    Decker, Jeremy D.; Swain, Eric D.; Stith, Bradley M.; Langtimm, Catherine A.

    2013-01-01

    Everglades restoration activities may cause changes to temperature and salinity stratification at the Port of the Islands (POI) marina, which could affect its suitability as a cold weather refuge for manatees. To better understand how the Picayune Strand Restoration Project (PSRP) may alter this important resource in Collier County in southwestern Florida, the USGS has developed a three-dimensional hydrodynamic model for the marina and canal system at POI. Empirical data suggest that manatees aggregate at the site during winter because of thermal inversions that provide warmer water near the bottom that appears to only occur in the presence of salinity stratification. To study these phenomena, the environmental fluid dynamics code simulator was used to represent temperature and salinity transport within POI. Boundary inputs were generated using a larger two-dimensional model constructed with the flow and transport in a linked overland-aquifer density-dependent system simulator. Model results for a representative winter period match observed trends in salinity and temperature fluctuations and produce temperature inversions similar to observed values. Modified boundary conditions, representing proposed PSRP alterations, were also tested to examine the possible effect on the salinity stratification and temperature inversion within POI. Results show that during some periods, salinity stratification is reduced resulting in a subsequent reduction in temperature inversion compared with the existing conditions simulation. This may have an effect on POI’s suitability as a passive thermal refuge for manatees and other temperature-sensitive species. Additional testing was completed to determine the important physical relationships affecting POI’s suitability as a refuge.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  14. Interfacial Passivation of the p-Doped Hole-Transporting Layer Using General Insulating Polymers for High-Performance Inverted Perovskite Solar Cells.

    Science.gov (United States)

    Zhang, Fan; Song, Jun; Hu, Rui; Xiang, Yuren; He, Junjie; Hao, Yuying; Lian, Jiarong; Zhang, Bin; Zeng, Pengju; Qu, Junle

    2018-05-01

    Organic-inorganic lead halide perovskite solar cells (PVSCs), as a competing technology with traditional inorganic solar cells, have now realized a high power conversion efficiency (PCE) of 22.1%. In PVSCs, interfacial carrier recombination is one of the dominant energy-loss mechanisms, which also results in the simultaneous loss of potential efficiency. In this work, for planar inverted PVSCs, the carrier recombination is dominated by the dopant concentration in the p-doped hole transport layers (HTLs), since the F4-TCNQ dopant induces more charge traps and electronic transmission channels, thus leading to a decrease in open-circuit voltages (V OC ). This issue is efficiently overcome by inserting a thin insulating polymer layer (poly(methyl methacrylate) or polystyrene) as a passivation layer with an appropriate thickness, which allows for increases in the V OC without significantly sacrificing the fill factor. It is believed that the passivation layer attributes to the passivation of interfacial recombination and the suppression of current leakage at the perovskite/HTL interface. By manipulating this interfacial passivation technique, a high PCE of 20.3% is achieved without hysteresis. Consequently, this versatile interfacial passivation methodology is highly useful for further improving the performance of planar inverted PVSCs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A n-vector model for charge transport in molecular semiconductors.

    Science.gov (United States)

    Jackson, Nicholas E; Kohlstedt, Kevin L; Chen, Lin X; Ratner, Mark A

    2016-11-28

    We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

  16. Molecular Mechanisms of Urea Transport in Health and Disease

    Science.gov (United States)

    Klein, Janet D.; Blount, Mitsi A.; Sands, Jeff M.

    2012-01-01

    In the late 1980s, urea permeability measurements produced values that could not be explained by paracellular transport or lipid phase diffusion. The existence of urea transport proteins were thus proposed and less than a decade later, the first urea transporter was cloned. The SLC14A family of urea transporters has two major subgroups, designated SLC14A1 (or UT-B) and Slc14A2 (or UT-A). UT-B and UT-A gene products are glycoproteins located in various extra-renal tissues however, a majority of the resulting isoforms are found in the kidney. The UT-B (Slc14A1) urea transporter was originally isolated from erythrocytes and two isoforms have been reported. In kidney, UT-B is located primarily in the descending vasa recta. The UT-A (Slc14A2) urea transporter yields 6 distinct isoforms, of which 3 are found chiefly in the kidney medulla. UT-A1 and UT-A3 are found in the inner medullary collecting duct (IMCD), while UT-A2 is located in the thin descending limb. These transporters are crucial to the kidney’s ability to concentrate urine. The regulation of urea transporter activity in the IMCD involves acute modification through phosphorylation and subsequent movement to the plasma membrane. UT-A1 and UT-A3 accumulate in the plasma membrane in response to stimulation by vasopressin or hypertonicity. Long term regulation of the urea transporters in the IMCD involves altering protein abundance in response to changes in hydration status, low protein diets, or adrenal steroids. Urea transporters have been studied using animal models of disease including diabetes mellitus, lithium intoxication, hypertension, and nephrotoxic drug responses. Exciting new genetically engineered mouse models are being developed to study these transporters. PMID:23007461

  17. Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

    Science.gov (United States)

    Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

    2017-03-01

    Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

  18. Molecular cloning and characterization of glucose transporter 1 ...

    African Journals Online (AJOL)

    Glucose transporter type-1 (glut1) and citrate synthase plays crucial role in glucose transport and regulation of tricarboxylic acid cycle (TCA) cycle in mammalian energy metabolism. The present study was aimed to clone and characterize glut1 and citrate synthase cDNA in water buffalo (Bubalus bubalis). Total of 90 ...

  19. Ionic and molecular transport in beta- and beta''-alumina

    International Nuclear Information System (INIS)

    Bates, J.B.

    1984-03-01

    Investigations of rapid transport of cations and water molecules in the β- and β''-alumina family of superionic conductors are reviewed. Particular topics that are discussed include the Haven ratio and mixed-ion effects in β-alumina, and the influence of superlattice ordering on ionic transport in β''-alumina

  20. Bistetracene Thin Film Polymorphic Control to Unravel the Effect of Molecular Packing on Charge Transport

    KAUST Repository

    Burnett, Edmund K.

    2018-02-26

    Polymorphism, the ability for a given material to adopt multiple crystalline packing states, is a powerful approach for investigating how changes in molecular packing influence charge transport within organic semiconductors. In this study, a new

  1. Hollow Nanospheres with Fluorous Interiors for Transport of Molecular Oxygen in Water

    KAUST Repository

    Vu, Khanh B.; Chen, Tianyou; Almahdali, Sarah; Bukhriakov, Konstantin; Rodionov, Valentin

    2016-01-01

    are gas-permeable and feature reactive functional groups for easy modification of the exterior. These features make the SFC-filled nanospheres promising vehicles for respiratory oxygen storage and transport. Uptake of molecular oxygen into nanosphere

  2. Bistetracene Thin Film Polymorphic Control to Unravel the Effect of Molecular Packing on Charge Transport

    KAUST Repository

    Burnett, Edmund K.; Ly, Jack; Niazi, Muhammad Rizwan; Zhang, Lei; McCuskey, Samantha R.; Amassian, Aram; Smilgies, Detlef-M.; Mannsfeld, Stefan C. B.; Briseno, Alejandro L.

    2018-01-01

    Polymorphism, the ability for a given material to adopt multiple crystalline packing states, is a powerful approach for investigating how changes in molecular packing influence charge transport within organic semiconductors. In this study, a new

  3. Which Socio-Ecological Factors Associate with a Switch to or Maintenance of Active and Passive Transport during the Transition from Primary to Secondary School?

    Science.gov (United States)

    Vanwolleghem, Griet; Van Dyck, Delfien; De Meester, Femke; De Bourdeaudhuij, Ilse; Cardon, Greet; Gheysen, Freja

    2016-01-01

    The aim was to investigate which individual, psychosocial and physical neighborhood environmental factors associate with children's switch to or maintenance of active/passive transport to school and to leisure time destinations during the transition from primary to secondary school. Children (n = 313) filled out a questionnaire in the last year of primary school and 2 years later to assess socio-demographic characteristics and self-reported transport. One of their parents completed a questionnaire to assess parental perceptions of psychosocial and physical neighborhood environmental factors. The increase of the home-school distance was significantly associated with children's switch to or maintenance of passive transport to school compared to a switch to (OR = 0.81; p = 0.03) and maintenance (OR = 0.87; p = 0.03) of active transport to school. Low SES was associated with children's switch to active transport to school compared to maintenance of active transport (OR = 3.67; p = 0.07). For transport to leisure time destinations, other factors such as parental perceived neighborhood safety from traffic and crime (OR = 2.78; p = 0.004), a positive social norm (OR = 1.49; p = 0.08), positive attitudes (OR = 1.39; p = 0.08) (i.e. more benefits, less barriers) towards their children's physical activity and poor walking/cycling facilities in the neighborhood (OR = 0.70; p = 0.06) were associated with children's maintenance of active transport to leisure time destinations compared to a switch to or maintenance of passive transport. This longitudinal study can give directions for interventions promoting children's active transport during the transition to secondary school. It is necessary to promote different possibilities at primary school for children to use active transport when going to secondary school. Walking/cycling a part of the home-school trip can be a possible solution for children who will be living at non-feasible distances from secondary school. Providing safe

  4. Dissecting the molecular mechanisms of intraflagellar transport in Chlamydomonas

    DEFF Research Database (Denmark)

    Pedersen, L. B.; Geimer, S.; Rosenbaum, J. L.

    2006-01-01

    Background The assembly and maintenance of eukaryotic cilia and flagella are mediated by intraflagellar transport (IFT), a bidirectional microtubule (MT)-based transport system. The IFT system consists of anterograde (kinesin-2) and retrograde (cDynein1b) motor complexes and IFT particles...... comprising two complexes, A and B. In the current model for IFT, kinesin-2 carries cDynein1b, IFT particles, and axonemal precursors from the flagellar base to the tip, and cDynein1b transports kinesin-2, IFT particles, and axonemal turnover products from the tip back to the base. Most of the components...... of the IFT system have been identified and characterized, but the mechanisms by which these different components are coordinated and regulated at the flagellar base and tip are unclear. Results Using a variety of Chlamydomonas mutants, we confirm that cDynein1b requires kinesin-2 for transport toward the tip...

  5. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  6. Molecular cloning, expression and characterization of a bovine serotonin transporter

    DEFF Research Database (Denmark)

    Mortensen, O V; Kristensen, A S; Rudnick, G

    1999-01-01

    The serotonin transporter (SERT) is a member of a highly homologous family of sodium/chloride dependent neurotransmitter transporters responsible for reuptake of biogenic amines from the extracellular fluid. SERT constitutes the pharmacological target of several clinically important antidepressan......-methylenedioxymethamphetamine (MDMA) was mainly unchanged. RT-PCR amplification of RNA from different tissues demonstrated expression of SERT in placenta, brain stem, bone marrow, kidney, lung, heart, adrenal gland, liver, parathyroid gland, thyroid gland, small intestine and pancreas....

  7. ChemCam Passive Sky Spectroscopy at Gale Crater, Mars: Interannual Variability in Dust Aerosol Particle Size, Missing Water Vapor, and the Molecular Oxygen Problem

    Science.gov (United States)

    McConnochie, T. H.; Smith, M. D.; Wolff, M. J.; Bender, S. C.; Lemmon, M. T.; Wiens, R. C.; Maurice, S.; Gasnault, O.; Lasue, J.; Meslin, P. Y.; Harri, A. M.; Genzer, M.; Kemppinen, O.; Martinez, G.; DeFlores, L. P.; Blaney, D. L.; Johnson, J. R.; Bell, J. F., III; Trainer, M. G.; Lefèvre, F.; Atreya, S. K.; Mahaffy, P. R.; Wong, M. H.; Franz, H. B.; Guzewich, S.; Villanueva, G. L.; Khayat, A. S.

    2017-12-01

    The Mars Science Laboratory's (MSL) ChemCam spectrometer measures atmospheric aerosol properties and gas abundances by operating in passive mode and observing scattered sky light at two different elevation angles. We have previously [e. g. 1, 2] presented the methodology and results of these ChemCam Passive Sky observations. Here we will focus on three of the more surprising results that we have obtained: (1) depletion of the column water vapor at Gale Crater relative to that of the surrounding region combined with a strong enhancement of the local column water vapor relative to pre-dawn in-situ measurements, (2) an interannual change in the effective particle size of dust aerosol during the aphelion season, and (3) apparent seasonal and interannual variability in molecular oxygen that differs significantly from the expected behavior of a non-condensable trace gas and differs significantly from global climate model expectations. The ChemCam passive sky water vapor measurements are quite robust but their interpretation depends on the details of measurements as well as on the types of water vapor vertical distributions that can be produced by climate models. We have a high degree of confidence in the dust particle size changes but since aerosol results in general are subject to a variety of potential systematic effects our particle size results would benefit from confirmation by other techniques [c.f. 3]. For the ChemCam passive sky molecular oxygen results we are still working to constrain the uncertainties well enough to confirm the observed surprising behavior, motivated by similarly surprising atmospheric molecular oxygen variability observed by MSL's Sample Analysis at Mars (SAM) instrument [4]. REFERENCES: [1] McConnochie, et al. (2017), Icarus (submitted). [2] McConnochie, et al. (2017), abstract # 3201, The 6th International Workshop on the Mars Atmosphere: Granada, Spain. [3] Vicente-Retortillo et al. (2017), GRL, 44. [4] Trainer et al. (2017), 2017 AGU Fall

  8. Electron and phonon drag in thermoelectric transport through coherent molecular conductors

    DEFF Research Database (Denmark)

    Lü, Jing-Tao; Wang, Jian-Sheng; Hedegård, Per

    2016-01-01

    We study thermoelectric transport through a coherent molecular conductor connected to two electron and two phonon baths using the nonequilibrium Green's function method. We focus on the mutual drag between electron and phonon transport as a result of ‘momentum’ transfer, which happens only when...

  9. Role of Molecular Weight Distribution on Charge Transport in Semiconducting Polymers

    KAUST Repository

    Himmelberger, Scott

    2014-10-28

    © 2014 American Chemical Society. Model semiconducting polymer blends of well-controlled molecular weight distributions are fabricated and demonstrated to be a simple method to control intermolecular disorder without affecting intramolecular order or degree of aggregation. Mobility measurements exhibit that even small amounts of low molecular weight material are detrimental to charge transport. Trends in charge carrier mobility can be reproduced by a simple analytical model which indicates that carriers have no preference for high or low molecular weight chains and that charge transport is limited by interchain hopping. These results quantify the role of long polymer tie-chains and demonstrate the need for controlled polydispersity for achieving high carrier mobilities.

  10. Nonequilibrium transport through molecular junctions in the quantum regime

    Czech Academy of Sciences Publication Activity Database

    Koch, T.; Loos, Jan; Alvermann, A.; Fehske, H.

    2011-01-01

    Roč. 84, č. 12 (2011), 125131/1-125131/16 ISSN 1098-0121 Institutional research plan: CEZ:AV0Z10100521 Keywords : the ory of electron ic transport * scattering mechanisms * polarons and electron -phonon interactions * quantum dots Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.691, year: 2011

  11. Molecular transport behaviour of organic solvents through halloysite ...

    Indian Academy of Sciences (India)

    Micro and Nano Materials Laboratory, Department of Chemistry, Institute of Technical ... The transport behaviour of three organic solvents (benzene, toluene and xylene) through halloysite nan- ... ena play important roles in different areas of engineering and ... their blends by an equilibrium swelling method has been.

  12. Radiation transport and the kinematics of molecular clouds

    International Nuclear Information System (INIS)

    Kwan, J.

    1978-01-01

    We compare line profiles calculated under either the systematic mottion interpretation or the turbulent motion interpretation of the molecular line widths, with the stipulation that both the density and temperature distributions be decreasing functions of radius. In systematic motion of the form V (r) proportional/sup -alpha/, α>0, optically thin lines observed toward the center are flat-topped or double-peaked, and optically thick lines are asymmetric. In a constant collapes or outflow velocity, optically thin lines observed toward the center are double-peaked, and optically thick lines arfe flat-topped. In systematic motion of the form V (r) proportionalr/sup α/,α>0, both optically thin and optically thick lines are centrally peaked. The distinguishing feature in this case is that the width (FWHM) of the CS 3→ 2 line is considerably smaller that that of the 13 CO 1 → 0 line. In turbulent motion, the CO 1 → 0, 2 → 1, and 3 → 2 lines are marked by progressively more pronounced self-absorptions.The observations at M17 SW and the Kleinmann-Low (KL) nebula are studied. At M17 SW, they are best accounted for by a model in which turbulence dominates the central part of the molecular region but collapse prevails at the outer part. At KL, the present observations can be equally well explained by one of two models. The first model postulates that KL is at the front face of the molecular cloud and that the temperature is highest at the surface. Turbulence gives rise to the line broadening. The second model postulates that KL is deep within the molecular cloud. Systematic motion about KL accounts for the CO and 13 CO line widths, but high-density fragments at KL are required to provide excitations in other molecular lines with considerably larger spontaneous emission rates

  13. Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses.

    Science.gov (United States)

    Smith, Kyle C; Weaver, James C

    2011-08-19

    Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. The molecular mechanism for overcoming the rate-limiting step in monoamine neurotransmitter transport

    DEFF Research Database (Denmark)

    Sinning, Steffen; Said, Saida; Malinauskaite, Lina

    The monoamine transporter family consists of dopamine (DAT), norepinephrine (NET) and serotonin transporters (SERT) that mediate the reuptake of the monoamine neurotransmitters after their release during neurotransmission. These transporters play prominent roles in psychiatric disorders and are t......The monoamine transporter family consists of dopamine (DAT), norepinephrine (NET) and serotonin transporters (SERT) that mediate the reuptake of the monoamine neurotransmitters after their release during neurotransmission. These transporters play prominent roles in psychiatric disorders...... membrane. The rate-limiting step in monoamine reuptake is the return of the empty transporter from an inward-facing to an outward-facing conformation without neurotransmitter and sodium bound. The molecular mechanism underlying this important conformational transition has not been described. Crystal...

  15. Control of Ambipolar Transport in SnO Thin-Film Transistors by Back-Channel Surface Passivation for High Performance Complementary-like Inverters.

    Science.gov (United States)

    Luo, Hao; Liang, Lingyan; Cao, Hongtao; Dai, Mingzhi; Lu, Yicheng; Wang, Mei

    2015-08-12

    For ultrathin semiconductor channels, the surface and interface nature are vital and often dominate the bulk properties to govern the field-effect behaviors. High-performance thin-film transistors (TFTs) rely on the well-defined interface between the channel and gate dielectric, featuring negligible charge trap states and high-speed carrier transport with minimum carrier scattering characters. The passivation process on the back-channel surface of the bottom-gate TFTs is indispensable for suppressing the surface states and blocking the interactions between the semiconductor channel and the surrounding atmosphere. We report a dielectric layer for passivation of the back-channel surface of 20 nm thick tin monoxide (SnO) TFTs to achieve ambipolar operation and complementary metal oxide semiconductor (CMOS) like logic devices. This chemical passivation reduces the subgap states of the ultrathin channel, which offers an opportunity to facilitate the Fermi level shifting upward upon changing the polarity of the gate voltage. With the advent of n-type inversion along with the pristine p-type conduction, it is now possible to realize ambipolar operation using only one channel layer. The CMOS-like logic inverters based on ambipolar SnO TFTs were also demonstrated. Large inverter voltage gains (>100) in combination with wide noise margins are achieved due to high and balanced electron and hole mobilities. The passivation also improves the long-term stability of the devices. The ability to simultaneously achieve field-effect inversion, electrical stability, and logic function in those devices can open up possibilities for the conventional back-channel surface passivation in the CMOS-like electronics.

  16. Passive safety; Passive Sicherheit

    Energy Technology Data Exchange (ETDEWEB)

    Rueckert, J. [Skoda Auto a.s., Mlada Boleslav (Czech Republic). Interieurentwicklung und Versuche; Hau, M. [Skoda Auto a.s., Mlada Boleslav (Czech Republic). Koordination der Fahrzeugsicherung

    2004-05-01

    The specifications for passive safety are partly based on the legal requirements for all export markets combined with the strict internal standards of Volkswagen Group. The Euro NCAP tests and their precisely defined testing methods using the new point assessment are very important. (orig.)

  17. Charge carrier transport on molecular wire controlled by dipolar species: towards light-driven molecular switch

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.

    438-439, - (2003), s. 268-278 ISSN 0040-6090. [International Conference on Nano- Molecular Electronics /5./. Kobe, 10.12.2002-12.12.2002] R&D Projects: GA AV ČR KSK4050111 Keywords : molecular electronics * polymers * quantum effects Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.598, year: 2003

  18. Salmonella infection inhibits intestinal biotin transport: cellular and molecular mechanisms.

    Science.gov (United States)

    Ghosal, Abhisek; Jellbauer, Stefan; Kapadia, Rubina; Raffatellu, Manuela; Said, Hamid M

    2015-07-15

    Infection with the nontyphoidal Salmonella is a common cause of food-borne disease that leads to acute gastroenteritis/diarrhea. Severe/prolonged cases of Salmonella infection could also impact host nutritional status, but little is known about its effect on intestinal absorption of vitamins, including biotin. We examined the effect of Salmonella enterica serovar Typhimurium (S. typhimurium) infection on intestinal biotin uptake using in vivo (streptomycin-pretreated mice) and in vitro [mouse (YAMC) and human (NCM460) colonic epithelial cells, and human intestinal epithelial Caco-2 cells] models. The results showed that infecting mice with wild-type S. typhimurium, but not with its nonpathogenic isogenic invA spiB mutant, leads to a significant inhibition in jejunal/colonic biotin uptake and in level of expression of the biotin transporter, sodium-dependent multivitamin transporter. In contrast, infecting YAMC, NCM460, and Caco-2 cells with S. typhimurium did not affect biotin uptake. These findings suggest that the effect of S. typhimurium infection is indirect and is likely mediated by proinflammatory cytokines, the levels of which were markedly induced in the intestine of S. typhimurium-infected mice. Consistent with this hypothesis, exposure of NCM460 cells to the proinflammatory cytokines TNF-α and IFN-γ led to a significant inhibition of biotin uptake, sodium-dependent multivitamin transporter expression, and activity of the SLC5A6 promoter. The latter effects appear to be mediated, at least in part, via the NF-κB signaling pathway. These results demonstrate that S. typhimurium infection inhibits intestinal biotin uptake, and that the inhibition is mediated via the action of proinflammatory cytokines.

  19. Electronic transport properties in [n]cycloparaphenylenes molecular devices

    Science.gov (United States)

    Hu, Lizhi; Guo, Yandong; Yan, Xiaohong; Zeng, Hongli; Zhou, Jie

    2017-07-01

    The electronic transport of [n]cycloparaphenylenes ([n]CPPs) is investigated based on nonequilibrium Green's function formalism in combination with the density-functional theory. Negative differential resistance (NDR) phenomenon is observed. Further analysis shows that the reduction of the transmission peak induced by the bias changing near Fermi energy results in the NDR effect. Replacing the electrode (from carbon chain to Au electrode), doping with N atom and changing the size of the nanohoop (n = 5, 6, 8, 10) have also been studied and the NDR still exists, suggesting the NDR behavior is the intrinsic feature of such [n]CPPs systems, which would be quite useful in future nanoelectronic devices.

  20. Tuning spin transport properties and molecular magnetoresistance through contact geometry

    Science.gov (United States)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-01

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ˜5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ˜400%.

  1. Tuning spin transport properties and molecular magnetoresistance through contact geometry

    International Nuclear Information System (INIS)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-01

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its “closed” and “open” conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%

  2. Tuning spin transport properties and molecular magnetoresistance through contact geometry.

    Science.gov (United States)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-28

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%.

  3. Spin-polarized transport properties of a pyridinium-based molecular spintronics device

    Science.gov (United States)

    Zhang, J.; Xu, B.; Qin, Z.

    2018-05-01

    By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

  4. A review on nanomechanical resonators and their applications in sensors and molecular transportation

    International Nuclear Information System (INIS)

    Arash, Behrouz; Rabczuk, Timon; Jiang, Jin-Wu

    2015-01-01

    Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators

  5. A review on nanomechanical resonators and their applications in sensors and molecular transportation

    Energy Technology Data Exchange (ETDEWEB)

    Arash, Behrouz; Rabczuk, Timon, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus Universität Weimar, Marienstr 15, D-99423 Weimar (Germany); Jiang, Jin-Wu [Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072 (China)

    2015-06-15

    Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators.

  6. Modeling the transport of organic chemicals between polyethylene passive samplers and water in finite and infinite bath conditions.

    Science.gov (United States)

    Tcaciuc, A Patricia; Apell, Jennifer N; Gschwend, Philip M

    2015-12-01

    Understanding the transfer of chemicals between passive samplers and water is essential for their use as monitoring devices of organic contaminants in surface waters. By applying Fick's second law to diffusion through the polymer and an aqueous boundary layer, the authors derived a mathematical model for the uptake of chemicals into a passive sampler from water, in finite and infinite bath conditions. The finite bath model performed well when applied to laboratory observations of sorption into polyethylene (PE) sheets for various chemicals (polycyclic aromatic hydrocarbons, polychlorinated biphenyls [PCBs], and dichlorodiphenyltrichloroethane [DDT]) and at varying turbulence levels. The authors used the infinite bath model to infer fractional equilibration of PCB and DDT analytes in field-deployed PE, and the results were nearly identical to those obtained using the sampling rate model. However, further comparison of the model and the sampling rate model revealed that the exchange of chemicals was inconsistent with the sampling rate model for partially or fully membrane-controlled transfer, which would be expected in turbulent conditions or when targeting compounds with small polymer diffusivities and small partition coefficients (e.g., phenols, some pesticides, and others). The model can be applied to other polymers besides PE as well as other chemicals and in any transfer regime (membrane, mixed, or water boundary layer-controlled). Lastly, the authors illustrate practical applications of this model such as improving passive sampler design and understanding the kinetics of passive dosing experiments. © 2015 SETAC.

  7. Modeling molecular effects on plasmon transport: Silver nanoparticles with tartrazine

    Science.gov (United States)

    Arntsen, Christopher; Lopata, Kenneth; Wall, Michael R.; Bartell, Lizette; Neuhauser, Daniel

    2011-02-01

    Modulation of plasmon transport between silver nanoparticles by a yellow fluorophore, tartrazine, is studied theoretically. The system is studied by combining a finite-difference time-domain Maxwell treatment of the electric field and the plasmons with a time-dependent parameterized method number 3 simulation of the tartrazine, resulting in an effective Maxwell/Schrödinger (i.e., classical/quantum) method. The modeled system has three linearly arranged small silver nanoparticles with a radius of 2 nm and a center-to-center separation of 4 nm; the molecule is centered between the second and third nanoparticles. We initiate an x-polarized current on the first nanoparticle and monitor the transmission through the system. The molecule rotates much of the x-polarized current into the y-direction and greatly reduces the overall transmission of x-polarized current.

  8. Electroporation of Skin Stratum Corneum Lipid Bilayer and Molecular Mechanism of Drug Transport: A Molecular Dynamics Study.

    Science.gov (United States)

    Gupta, Rakesh; Rai, Beena

    2018-04-30

    Skin electroporation has been used significantly to increase the drug permeation. However, molecular mechanism, which resulted in enhancement of flux through skin, is still not known. In this study, extensive atomistic molecular dynamics simulation of skin lipids (made up of ceramide (CER), cholesterol (CHOL) and free fatty acid (FFA)) have been performed at various external electric field. We show for the first time the pore formation in the skin lipid bilayer during the electroporation. We show the effect of applied external electrical field on the pore formation dynamics in lipid bilayer of different size and composition. The pore formation and resealing kinetics were different and was found to be highly dependent on the composition of skin lipid bilayer. The pore formation time decreased with increase in the bilayer size. The pore sustaining electric field was found to be in the range of 0.20-0.25 V/nm for equimolar CER, CHOL and FFA lipid bilayer. The skin lipid bilayer (1:1:1), sealed itself within 20 ns after the removal of external electric field. We also present the molecular mechanism of enhancement of drug permeation in the presence of external field as compared to the passive diffusion. The molecular level understanding obtained here could help in optimizing/designing the electroporation experiments for effective drug delivery. For a given skin composition and size of drug molecule, the combination of pore formation time and pore growth model can be used to know aproiri the desired electric field and time for application of electric field.

  9. Active versus passive transportation to school-differences in screen time, socio-economic position and perceived environmental characteristics in adolescent girls.

    Science.gov (United States)

    Mota, Jorge; Gomes, Helena; Almeida, Mariana; Ribeiro, José Carlos; Carvalho, Joana; Santos, Maria Paula

    2007-01-01

    The aims of this study were (1) to assess the relationships between transport to and from school (active vs. passive), sedentary behaviours, measures of socio-economic position and perceived environmental variables, and (2) to determine which, if any, variables were predictors of active transportation. The sample comprised 705 girls with mean age of 14.7 (SD = 1.6) years old. Questionnaires were used to describe travel mode to school and to estimate weekly television and computer use (screen time). Girls were assigned to active transportation (AT) or passive transportation (PT) groups depending on whether they walked or bicycled (AT) to and from school or travelled by car or bus (PT). Screen time was determined by the number of hours they reported watching television and using computers in the week preceding the examination, including weekends. Socio-economic position was established by parental occupation and educational level. A questionnaire assessed Perceived Neighbourhood Environments. No statistically significant differences were seen for screen time between travel groups. Occupational status of both mother (r = -0.17) and father (r = -0.15) and father's educational level (r = -0.10) were significantly and negatively associated with AT, while street connectivity (r = 0.10) was positively and significantly associated with AT. Logistic regression analysis showed that the likelihood of active commuting decreased by around 50% with increasing father's occupation (odds ratio (OR) = 0.51; p active (OR = 1.63; p active commuting to school and that street connectivity is a predictor of active transportation in adolescent girls.

  10. Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

    Science.gov (United States)

    Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

    2017-07-12

    A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

  11. Molecular evolution of a novel family of putative calcium transporters.

    Directory of Open Access Journals (Sweden)

    Didier Demaegd

    Full Text Available The UPF0016 family is a group of uncharacterized membrane proteins, well conserved through evolution and defined by the presence of one or two copies of an E-Φ-G-D-(KR-(ST consensus motif. Our previous results have shown that two members of this family, the human TMEM165 and the budding yeast Gdt1p, are functionally related and might form a new group of cation/Ca2+ exchangers. Most members of the family are made of two homologous clusters of three transmembrane spans, separated by a central loop and assembled with an opposite orientation in the membrane. However, some bacterial members of the family have only one cluster of transmembrane domains. Among these 'single-domain membrane proteins' some cyanobacterial members were found as pairs of adjacent genes within the genome, but each gene was slightly different. We performed a bioinformatic analysis to propose the molecular evolution of the UPF0016 family and the emergence of the antiparallel topology. Our hypotheses were confirmed experimentally using functional complementation in yeast. This suggests an important and conserved function for UPF0016 proteins in a fundamental cellular process. We also show that members of the UPF0016 family share striking similarities, but no primary sequence homology, with members of the cation/Ca2+ exchangers (CaCA superfamily. Such similarities could be an example of convergent evolution, supporting the previous hypothesis that members of the UPF0016 family are cation/Ca2+ exchangers.

  12. Molecular cell biology and physiology of solute transport

    Science.gov (United States)

    Caplan, Michael J.; Seo-Mayer, Patricia; Zhang, Li

    2010-01-01

    Purpose of review An enormous body of research has been focused on exploring the mechanisms through which epithelial cells establish their characteristic polarity. It is clear that under normal circumstances cell–cell contacts mediated by the calcium-dependent adhesion proteins of the intercellular adhesion junctions are required to initiate complete polarization. Furthermore, formation of the tight, or occluding, junctions that limit paracellular permeability has long been thought to help to establish polarity by preventing the diffusion of membrane proteins between the two plasmalemmal domains. This review will discuss several selected kinases and protein complexes and highlight their relevance to transporting epithelial cell polarization. Recent findings Recent work has shed new light on the roles of junctional complexes in establishing and maintaining epithelial cell polarity. In addition, work from several laboratories, suggests that the formation of these junctions is tied to processes that regulate cellular energy metabolism. Summary Junctional complexes and energy sensing kinases constitute a novel class of machinery whose capacity to generate and modulate epithelial cell polarity is likely to have wide ranging and important physiological ramifications. PMID:18695392

  13. Efficacy of passive hypothermia and adverse events during transport of asphyxiated newborns according to the severity of hypoxic-ischemic encephalopathy.

    Science.gov (United States)

    Carreras, Nuria; Alsina, Miguel; Alarcon, Ana; Arca-Díaz, Gemma; Agut, Thais; García-Alix, Alfredo

    To determine if the efficacy of passive hypothermia and adverse events during transport are related to the severity of neonatal hypoxic-ischemic encephalopathy. This was a retrospective study of 67 infants with hypoxic-ischemic encephalopathy, born between April 2009 and December 2013, who were transferred for therapeutic hypothermia and cooled during transport. Fifty-six newborns (84%) were transferred without external sources of heat and 11 (16%) needed an external heat source. The mean temperature at departure was 34.4±1.4°C and mean transfer time was 3.3±2.0h. Mean age at arrival was 5.6±2.5h. Temperature at arrival was between 33 and 35°C in 41 (61%) infants, between 35°C and 36.5°C in 15 (22%) and encephalopathy had greater risk of having an admission temperatureencephalopathy and the umbilical artery pH were independent risk factors for a low temperature on admission (pencephalopathy. The risk of overcooling during transport is greater in newborns with severe hypoxic-ischemic encephalopathy and those with more severe acidosis at birth. The most common adverse events during transport are related to physiological deterioration and bleeding from the endotracheal tube. This observation provides useful information to identify those asphyxiated infants who require closer clinical surveillance during transport. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  14. Aerosol transport and wet scavenging in deep convective clouds: a case study and model evaluation using a multiple passive tracer analysis approach

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qing; Easter, Richard C.; Campuzano-Jost, Pedro; Jimenez, Jose L.; Fast, Jerome D.; Ghan, Steven J.; Wang, Hailong; Berg, Larry K.; Barth, Mary; Liu, Ying; Shrivastava, ManishKumar B.; Singh, Balwinder; Morrison, H.; Fan, Jiwen; Ziegler, Conrad L.; Bela, Megan; Apel, Eric; Diskin, G. S.; Mikoviny, Tomas; Wisthaler, Armin

    2015-08-20

    The effect of wet scavenging on ambient aerosols in deep, continental convective clouds in the mid-latitudes is studied for a severe storm case in Oklahoma during the Deep Convective Clouds and Chemistry (DC3) field campaign. A new passive-tracer based transport analysis framework is developed to characterize the convective transport based on the vertical distribution of several slowly reacting and nearly insoluble trace gases. The passive gas concentration in the upper troposphere convective outflow results from a mixture of 47% from the lower level (0-3 km), 21% entrained from the upper troposphere, and 32% from mid-atmosphere based on observations. The transport analysis framework is applied to aerosols to estimate aerosol transport and wet-scavenging efficiency. Observations yield high overall scavenging efficiencies of 81% and 68% for aerosol mass (Dp < 1μm) and aerosol number (0.03< Dp < 2.5μm), respectively. Little chemical selectivity to wet scavenging is seen among observed submicron sulfate (84%), organic (82%), and ammonium (80%) aerosols, while nitrate has a much lower scavenging efficiency of 57% likely due to the uptake of nitric acid. Observed larger size particles (0.15 - 2.5μm) are scavenged more efficiently (84%) than smaller particles (64%; 0.03 - 0.15μm). The storm is simulated using the chemistry version of the WRF model. Compared to the observation based analysis, the standard model underestimates the wet scavenging efficiency for both mass and number concentrations with low biases of 31% and 40%, respectively. Adding a new treatment of secondary activation significantly improves simulation results, so that the bias in scavenging efficiency in mass and number concentrations is reduced to <10%. This supports the hypothesis that secondary activation is an important process for wet removal of aerosols in deep convective storms.

  15. Coupled electron-phonon transport from molecular dynamics with quantum baths

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Wang, J. S.

    2009-01-01

    Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi...

  16. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    Energy Technology Data Exchange (ETDEWEB)

    Uppulury, Karthik, E-mail: karthik.uppulury@gmail.com [Department of Chemistry, Texas Tech University, Lubbock, TX 79409 (United States); Kolomeisky, Anatoly B. [Department of Chemistry, Department of Chemical and Biomolecular Engineering, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 (United States)

    2016-12-20

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  17. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    International Nuclear Information System (INIS)

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-01-01

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

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

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

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

  19. Molecular Determinants for Substrate Interactions with the Glycine Transporter GlyT2.

    Science.gov (United States)

    Carland, Jane E; Thomas, Michael; Mostyn, Shannon N; Subramanian, Nandhitha; O'Mara, Megan L; Ryan, Renae M; Vandenberg, Robert J

    2018-03-21

    Transporters in the SLC6 family play key roles in regulating neurotransmission and are the targets for a wide range of therapeutics. Important insights into the transport mechanisms and the specificity of drug interactions of SLC6 transporters have been obtained from the crystal structures of a bacterial homologue of the family, LeuT Aa , and more recently the Drosophila dopamine transporter and the human serotonin transporter. However, there is disputed evidence that the bacterial leucine transporter, LeuT Aa , contains two substrate binding sites that work cooperatively in the mechanism of transport, with the binding of a second substrate being required for the release of the substrate from the primary site. An alternate proposal is that there may be low affinity binding sites that serve to direct the flow of substrates to the primary site. We have used a combination of molecular dynamics simulations of substrate interactions with a homology model of GlyT2, together with radiolabeled amino acid uptake assays and electrophysiological analysis of wild-type and mutant transporters, to provide evidence that substrate selectivity of GlyT2 is determined entirely by the primary substrate binding site and, furthermore, if a secondary site exists then it is a low affinity nonselective amino acid binding site.

  20. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1

    Science.gov (United States)

    Simmons, Katie J; Jackson, Scott M; Brueckner, Florian; Patching, Simon G; Beckstein, Oliver; Ivanova, Ekaterina; Geng, Tian; Weyand, Simone; Drew, David; Lanigan, Joseph; Sharples, David J; Sansom, Mark SP; Iwata, So; Fishwick, Colin WG; Johnson, A Peter; Cameron, Alexander D; Henderson, Peter JF

    2014-01-01

    The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1. PMID:24952894

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  3. Thermodynamics of competitive molecular channel transport: application to artificial nuclear pores.

    Directory of Open Access Journals (Sweden)

    Wolfgang R Bauer

    Full Text Available In an analytical model channel transport is analyzed as a function of key parameters, determining efficiency and selectivity of particle transport in a competitive molecular environment. These key parameters are the concentration of particles, solvent-channel exchange dynamics, as well as particle-in-channel- and interparticle interaction. These parameters are explicitly related to translocation dynamics and channel occupation probability. Slowing down the exchange dynamics at the channel ends, or elevating the particle concentration reduces the in-channel binding strength necessary to maintain maximum transport. Optimized in-channel interaction may even shift from binding to repulsion. A simple equation gives the interrelation of access dynamics and concentration at this transition point. The model is readily transferred to competitive transport of different species, each of them having their individual in-channel affinity. Combinations of channel affinities are determined which differentially favor selectivity of certain species on the cost of others. Selectivity for a species increases if its in-channel binding enhances the species' translocation probability when compared to that of the other species. Selectivity increases particularly for a wide binding site, long channels, and fast access dynamics. Recent experiments on competitive transport of in-channel binding and inert molecules through artificial nuclear pores serve as a paradigm for our model. It explains qualitatively and quantitatively how binding molecules are favored for transport at the cost of the transport of inert molecules.

  4. Thermodynamics of competitive molecular channel transport: application to artificial nuclear pores.

    Science.gov (United States)

    Bauer, Wolfgang R; Nadler, Walter

    2010-12-13

    In an analytical model channel transport is analyzed as a function of key parameters, determining efficiency and selectivity of particle transport in a competitive molecular environment. These key parameters are the concentration of particles, solvent-channel exchange dynamics, as well as particle-in-channel- and interparticle interaction. These parameters are explicitly related to translocation dynamics and channel occupation probability. Slowing down the exchange dynamics at the channel ends, or elevating the particle concentration reduces the in-channel binding strength necessary to maintain maximum transport. Optimized in-channel interaction may even shift from binding to repulsion. A simple equation gives the interrelation of access dynamics and concentration at this transition point. The model is readily transferred to competitive transport of different species, each of them having their individual in-channel affinity. Combinations of channel affinities are determined which differentially favor selectivity of certain species on the cost of others. Selectivity for a species increases if its in-channel binding enhances the species' translocation probability when compared to that of the other species. Selectivity increases particularly for a wide binding site, long channels, and fast access dynamics. Recent experiments on competitive transport of in-channel binding and inert molecules through artificial nuclear pores serve as a paradigm for our model. It explains qualitatively and quantitatively how binding molecules are favored for transport at the cost of the transport of inert molecules.

  5. Molecular cloning and expression analysis of turnip (Brassica rapa var. rapa sucrose transporter gene family

    Directory of Open Access Journals (Sweden)

    Yuanyuan Liu

    2017-06-01

    Full Text Available In higher plants, sugars (mainly sucrose are produced by photosynthetically assimilated carbon in mesophyll cells of leaves and translocated to heterotrophic organs to ensure plant growth and development. Sucrose transporters, or sucrose carriers (SUCs, play an important role in the long-distance transportation of sucrose from source organs to sink organs, thereby affecting crop yield and quality. The identification, characterization, and molecular function analysis of sucrose transporter genes have been reported for monocot and dicot plants. However, no relevant study has been reported on sucrose transporter genes in Brassica rapa var. rapa, a cruciferous root crop used mainly as vegetables and fodder. We identified and cloned 12 sucrose transporter genes from turnips, named BrrSUC1.1 to BrrSUC6.2 according to the SUC gene sequences of B. rapa pekinensis. We constructed a phylogenetic tree and analyzed conserved motifs for all 12 sucrose transporter genes identified. Real-time quantitative polymerase chain reaction was conducted to understand the expression levels of SUC genes in different tissues and developmental phases of the turnip. These findings add to our understanding of the genetics and physiology of sugar transport during taproot formation in turnips.

  6. First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, P., E-mail: ss_zhaop@ujn.edu.c [School of Science, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Qufu 273155 (China); Wang, P.J.; Zhang, Z. [School of Science, University of Jinan, Jinan 250022 (China); Fang, C.F.; Ji, G.M. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China)

    2011-02-15

    By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.

  7. First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

    International Nuclear Information System (INIS)

    Zhao, P.; Liu, D.S.; Wang, P.J.; Zhang, Z.; Fang, C.F.; Ji, G.M.

    2011-01-01

    By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.

  8. Optimization of charge transfer and transport processes at the CdSe quantum dots/TiO2 nanorod interface by TiO2 interlayer passivation

    International Nuclear Information System (INIS)

    Jaramillo-Quintero, O A; Rincon, M E; Triana, M A

    2017-01-01

    Surface trap states hinder charge transfer and transport properties in TiO 2 nanorods (NRs), limiting its application on optoelectronic devices. Here, we study the interfacial processes between rutile TiO 2 NR and CdSe quantum dots (QDs) using TiO 2 interlayer passivation treatments. Anatase or rutile TiO 2 thin layers were deposited on an NR surface by two wet-chemical deposition treatments. Reduced interfacial charge recombination between NRs and CdSe QDs was observed by electrochemical impedance spectroscopy with the introduction of TiO 2 thin film interlayers compared to bare TiO 2 NRs. These results can be ascribed to in-gap trap state passivation of the TiO 2 NR surface, which led to an increase in open circuit voltage. Moreover, the rutile thin layer was more efficient than anatase to promote a higher photo-excited electron transfer from CdSe QDs to TiO 2 NRs due to a large driving force for charge injection, as confirmed by surface photovoltage spectroscopy. (paper)

  9. Mechanism of molecular transport in novel reverse-selective nanocomposite membranes

    International Nuclear Information System (INIS)

    Merkel, T.C.; Freeman, B.D.; Spontak, R.J.; Meakin, P.; Hill, A.J.; Monash University, VIC

    2002-01-01

    Full text: Polymer nanocomposites continue to receive tremendous attention as organic-inorganic hybrid materials exhibiting a wide range of interesting, as well as technologically relevant, properties. This work reports a novel use of polymer nanocomposites as reverse-selective membranes. We have found that physical dispersion of nonporous fumed silica [FS] into glassy poly(4-methyl-2-pentyne) [PMP] simultaneously enhances membrane permeability (by as much as 240%) and selectivity for large organic molecules over small permanent gases. This surprising observation, in stark contrast to conventional filled polymer systems, reflects silica-induced disruption of local polymer chain packing and, as discerned by positron annihilation lifetime spectroscopy [PALS], a resulting subtle increase in the size of free volume elements through which molecular transport occurs. Such nanoscale hybridization represents an innovative means of tuning the transport properties of glassy polymeric media through control of molecular ordering

  10. Molecular Diagnostics of Copper-Transporting Protein Mutations Allows Early Onset Individual Therapy of Menkes Disease.

    Science.gov (United States)

    Králík, L; Flachsová, E; Hansíková, H; Saudek, V; Zeman, J; Martásek, P

    2017-01-01

    Menkes disease is a severe X-linked recessive disorder caused by a defect in the ATP7A gene, which encodes a membrane copper-transporting ATPase. Deficient activity of the ATP7A protein results in decreased intestinal absorption of copper, low copper level in serum and defective distribution of copper in tissues. The clinical symptoms are caused by decreased activities of copper-dependent enzymes and include neurodegeneration, connective tissue disorders, arterial changes and hair abnormalities. Without therapy, the disease is fatal in early infancy. Rapid diagnosis of Menkes disease and early start of copper therapy is critical for the effectiveness of treatment. We report a molecular biology-based strategy that allows early diagnosis of copper transport defects and implementation of individual therapies before the full development of pathological symptoms. Low serum copper and decreased activity of copperdependent mitochondrial cytochrome c oxidase in isolated platelets found in three patients indicated a possibility of functional defects in copper-transporting proteins, especially in the ATPA7 protein, a copper- transporting P-type ATPase. Rapid mutational screening of the ATP7A gene using high-resolution melting analysis of DNA indicated presence of mutations in the patients. Molecular investigation for mutations in the ATP7A gene revealed three nonsense mutations: c.2170C>T (p.Gln724Ter); c.3745G>T (p.Glu1249Ter); and c.3862C>T (p.Gln1288Ter). The mutation c.3745G>T (p.Glu1249Ter) has not been identified previously. Molecular analysis of the ATOX1 gene as a possible modulating factor of Menkes disease did not reveal presence of pathogenic mutations. Molecular diagnostics allowed early onset of individual therapies, adequate genetic counselling and prenatal diagnosis in the affected families.

  11. Hollow Nanospheres with Fluorous Interiors for Transport of Molecular Oxygen in Water

    KAUST Repository

    Vu, Khanh B.

    2016-08-11

    A dispersion system for saturated fluorocarbon (SFC) liquids based on permeable hollow nanospheres with fluorous interiors is described. The nanospheres are well dispersible in water and are capable of immediate uptake of SFCs. The nanosphere shells are gas-permeable and feature reactive functional groups for easy modification of the exterior. These features make the SFC-filled nanospheres promising vehicles for respiratory oxygen storage and transport. Uptake of molecular oxygen into nanosphere-stabilized SFC dispersions is demonstrated.

  12. Optically directed molecular transport and 3D isoelectric positioning of amphoteric biomolecules

    International Nuclear Information System (INIS)

    Hafeman, Dean G.; Harkins, James B.; Witkowski, Charles E. II; Lewis, Nathan S.; Brown, Gilbert M.; Warmack, Robert J. Bruce; Thundat, Thomas George

    2006-01-01

    We demonstrate the formation of charged molecular packets and their transport within optically created electrical force-field traps in a pH-buffered electrolyte. We call this process photoelectrophoretic localization and transport (PELT). The electrolyte is in contact with a photoconductive semiconductor electrode and a counterelectrode that are connected through an external circuit. A light beam directed to coordinates on the photoconductive electrode surface produces a photocurrent within the circuit and electrolyte. Within the electrolyte, the photocurrent creates localized force-field traps centered at the illuminated coordinates. Charged molecules, including polypeptides and proteins, electrophoretically accumulate into the traps and subsequently can be transported in the electrolyte by moving the traps over the photoconductive electrode in response to movement of the light beam. The molecules in a single trap can be divided into aliquots, and the aliquots can be directed along multiple routes simultaneously by using multiple light beams. This photoelectrophoretic transport of charged molecules by PELT resembles the electrostatic transport of electrons within force-field wells of solid-state charge-coupled devices. The molecules, however, travel in a liquid electrolyte rather than a solid. Furthermore, we have used PELT to position amphoteric biomolecules in three dimensions. A 3D pH gradient was created in an electrolyte medium by controlling the illumination position on a photoconductive anode where protons were generated electrolytically. Photoelectrophoretic transport of amphoteric molecules through the pH gradient resulted in accumulation of the molecules at their apparent 3D isoelectric coordinates in the medium.

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

    Science.gov (United States)

    Parashar, Sweta

    2018-05-01

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

  14. Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

    Science.gov (United States)

    Eu, Byung Chan

    2008-09-07

    In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel.

  15. Molecular dynamics simulation of continuous nanoflow transport through the uneven wettability channel

    Science.gov (United States)

    Zhang, Kai; Wang, Feng-hui; Lu, Yong-jun

    2018-01-01

    It is necessary to understand and predict the behavior of continuous nanoflow, especially inside the nanochannel with uneven wettability. Because the properties of fluid confined in the nanochannel are different from the macroscopic fluid, molecular level understanding is critical for future applications. In this work, a series of molecular dynamics simulations were executed to investigate the effect of the wettability gradient on the continuous nanofluid. In the simulations, different osmotic pressures were applied to make the water transport through different nanochannels. Simulation data was analyzed to obtain water flow rate, shear viscosity, capillary force, density distributions along the height directions of channel and apparent friction factor. Results show that the uneven wettability has a significant effect on the transportation of confined water only under the proper applied osmotic pressure and the height of channel. Under the appropriate conditions, the uneven wettability has a promotion on the transportation of water when it is at the exit of channel. When the uneven wettability locates in the entrance and middle of the channel, the uneven wettability will hinder the transportation of water. Especially, it is worth mentioning that there is a special phenomenon when the height of the nanochannel becomes 0.8 nm. Depending on the applied osmotic pressure, the uneven wettability has a double-sided effect on the confined fluid inside the channel with H = 0.8 nm. Our work may contribute to the design of nanochannels.

  16. Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system

    DEFF Research Database (Denmark)

    Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

    2007-01-01

    We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate S-HT or the selective serotonin reuptake inhibitor escitaloprom. We have also included a transporter homologue......, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystal logrophic B factors. Furthermore, key interactions identified in the X....... Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitaloprom complexes. Our finding5 are in good agreement with predictions from mutagenesis studies....

  17. Transport Properties of the Nuclear Pasta Phase with Quantum Molecular Dynamics

    Science.gov (United States)

    Nandi, Rana; Schramm, Stefan

    2018-01-01

    We study the transport properties of nuclear pasta for a wide range of density, temperature, and proton fractions, relevant for different astrophysical scenarios adopting a quantum molecular dynamics model. In particular, we estimate the values of shear viscosity as well as electrical and thermal conductivities by calculating the static structure factor S(q) using simulation data. In the density and temperature range where the pasta phase appears, the static structure factor shows irregular behavior. The presence of a slab phase greatly enhances the peak in S(q). However, the effect of irregularities in S(q) on the transport coefficients is not very dramatic. The values of all three transport coefficients are found to have the same orders of magnitude as found in theoretical calculations for the inner crust matter of neutron stars without the pasta phase; therefore, the values are in contrast to earlier speculations that a pasta layer might be highly resistive, both thermally and electrically.

  18. Impairment of retrograde neuronal transport in oxaliplatin-induced neuropathy demonstrated by molecular imaging.

    Directory of Open Access Journals (Sweden)

    Dawid Schellingerhout

    Full Text Available BACKGROUND AND PURPOSE: The purpose of our study was to utilize a molecular imaging technology based on the retrograde axonal transport mechanism (neurography, to determine if oxaliplatin-induced neurotoxicity affects retrograde axonal transport in an animal model. MATERIALS AND METHODS: Mice (n = 8/group were injected with a cumulative dose of 30 mg/kg oxaliplatin (sufficient to induce neurotoxicity or dextrose control injections. Intramuscular injections of Tetanus Toxin C-fragment (TTc labeled with Alexa 790 fluorescent dye were done (15 ug/20 uL in the left calf muscles, and in vivo fluorescent imaging performed (0-60 min at baseline, and then weekly for 5 weeks, followed by 2-weekly imaging out to 9 weeks. Tissues were harvested for immunohistochemical analysis. RESULTS: With sham treatment, TTc transport causes fluorescent signal intensity over the thoracic spine to increase from 0 to 60 minutes after injection. On average, fluorescence signal increased 722%+/-117% (Mean+/-SD from 0 to 60 minutes. Oxaliplatin treated animals had comparable transport at baseline (787%+/-140%, but transport rapidly decreased through the course of the study, falling to 363%+/-88%, 269%+/-96%, 191%+/-58%, 121%+/-39%, 75%+/-21% with each successive week and stabilizing around 57% (+/-15% at 7 weeks. Statistically significant divergence occurred at approximately 3 weeks (p≤0.05, linear mixed-effects regression model. Quantitative immuno-fluorescence histology with a constant cutoff threshold showed reduced TTc in the spinal cord at 7 weeks for treated animals versus controls (5.2 Arbitrary Units +/-0.52 vs 7.1 AU +/-1.38, p0.56, T-test. CONCLUSION: We show-for the first time to our knowledge-that neurographic in vivo molecular imaging can demonstrate imaging changes in a model of oxaliplatin-induced neuropathy. Impaired retrograde neural transport is suggested to be an important part of the pathophysiology of oxaliplatin-induced neuropathy.

  19. Intracellular loop 5 is important for the transport mechanism and molecular pharmacology of the human serotonin transporter

    DEFF Research Database (Denmark)

    Said, Saida; Neubauer, Henrik Amtoft; Müller, Heidi Kaastrup

    2015-01-01

    The serotonin transporter (SERT) belongs to a family of transport proteins called the neurotransmitter:sodium symporters. The specialized members of this family transport different neurotransmitters across the cell membrane, thereby regulating signaling between neurons. Most of these transporters...

  20. Passive Education

    Science.gov (United States)

    Bojesen, Emile

    2018-01-01

    This paper does not present an advocacy of a passive education as opposed to an active education nor does it propose that passive education is in any way 'better' or more important than active education. Through readings of Maurice Blanchot, Jacques Derrida and B.S. Johnson, and gentle critiques of Jacques Rancière and John Dewey, passive…

  1. Velocity-Resolved LES (VR-LES) technique for simulating turbulent transport of high Schmidt number passive scalars

    Science.gov (United States)

    Verma, Siddhartha; Blanquart, Guillaume; P. K. Yeung Collaboration

    2011-11-01

    Accurate simulation of high Schmidt number scalar transport in turbulent flows is essential to studying pollutant dispersion, weather, and several oceanic phenomena. Batchelor's theory governs scalar transport in such flows, but requires further validation at high Schmidt and high Reynolds numbers. To this end, we use a new approach with the velocity field fully resolved, but the scalar field only partially resolved. The grid used is fine enough to resolve scales up to the viscous-convective subrange where the decaying slope of the scalar spectrum becomes constant. This places the cutoff wavenumber between the Kolmogorov scale and the Batchelor scale. The subgrid scale terms, which affect transport at the supergrid scales, are modeled under the assumption that velocity fluctuations are negligible beyond this cutoff wavenumber. To ascertain the validity of this technique, we performed a-priori testing on existing DNS data. This Velocity-Resolved LES (VR-LES) technique significantly reduces the computational cost of turbulent simulations of high Schmidt number scalars, and yet provides valuable information of the scalar spectrum in the viscous-convective subrange.

  2. Surface Effect on Oil Transportation in Nanochannel: a Molecular Dynamics Study.

    Science.gov (United States)

    Zheng, Haixia; Du, Yonggang; Xue, Qingzhong; Zhu, Lei; Li, Xiaofang; Lu, Shuangfang; Jin, Yakang

    2017-12-01

    In this work, we investigate the dynamics mechanism of oil transportation in nanochannel using molecular dynamics simulations. It is demonstrated that the interaction between oil molecules and nanochannel has a great effect on the transportation properties of oil in nanochannel. Because of different interactions between oil molecules and channel, the center of mass (COM) displacement of oil in a 6-nm channel is over 30 times larger than that in a 2-nm channel, and the diffusion coefficient of oil molecules at the center of a 6-nm channel is almost two times more than that near the channel surface. Besides, it is found that polarity of oil molecules has the effect on impeding oil transportation, because the electrostatic interaction between polar oil molecules and channel is far larger than that between nonpolar oil molecules and channel. In addition, channel component is found to play an important role in oil transportation in nanochannel, for example, the COM displacement of oil in gold channel is very few due to great interaction between oil and gold substrate. It is also found that nano-sized roughness of channel surface greatly influences the speed and flow pattern of oil. Our findings would contribute to revealing the mechanism of oil transportation in nanochannels and therefore are very important for design of oil extraction in nanochannels.

  3. Molecular dynamics study on heat transport from single-walled carbon nanotubes to Si substrate

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Ya; Zhu, Jie, E-mail: zhujie@iet.cn; Tang, Da-Wei

    2015-02-06

    In this paper, non-equilibrium molecular dynamics simulations were performed to investigate the heat transport between a vertically aligned single-walled carbon nanotube (SWNT) and Si substrate, to find out the influence of temperature and system sizes, including diameter and length of SWNT and measurements of substrate. Results revealed that high temperature hindered heat transport in SWNT itself but was a beneficial stimulus for heat transport at interface of SWNT and Si. Furthermore, the system sizes strongly affected the peaks in vibrational density of states of Si, which led to interfacial thermal conductance dependent on system sizes. - Highlights: • NEMD is performed to simulate the heat transport from SWNT to Si substrate. • We analyze both interfacial thermal conductance and thermal conductivity of SWNT. • High temperature is a beneficial stimulus for heat transport at the interface. • Interfacial thermal conductance strongly depends on the sizes of SWNT and substrate. • We calculate VDOS of C and Si atoms to analyze phonon couplings between them.

  4. Power maximization method for land-transportable fully passive lead–bismuth cooled small modular reactor systems

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jaehyun, E-mail: chojh@kaeri.re.kr [Korea Atomic Energy Research Institute, 1405 Daedeok-daero, Yuseong-gu, Daejeon 305-353 (Korea, Republic of); Shin, Yong-Hoon; Hwang, Il Soon [Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742 (Korea, Republic of)

    2015-08-15

    Highlights: • The power maximization method for LBE natural circulation cooled SMRs was developed. • The two powers in view of neutronics and thermal-hydraulics were considered. • The limitations for designing of LBE natural circulation cooled SMRs were summarized. • The necessary conditions for safety shutdown in accidents were developed. • The maximized power in the case study is 206 MW thermal. - Abstract: Although current pressurized water reactors (PWRs) have significantly contributed to global energy supply, PWR technology has not been considered a trustworthy energy solution owing to its problems of spent nuclear fuels (SNFs), nuclear safety, and nuclear economy. In order to overcome these problems, a lead–bismuth eutectic (LBE) fully passive cooling small modular reactor (SMR) system is suggested. This technology can not only provide the solution for the problems of SNFs through the transmutation feature of the LBE coolant, but also strengthen safety and economy through the concept of natural circulation cooling SMRs. It is necessary to maximize the advantages, namely safety and economy, of this type of nuclear power plants for broader applications in the future. Accordingly, the objective of this study is to maximize the reactor core power while satisfying the limitations of shipping size, materials endurance, and criticality of a long-burning core as well as safety under beyond design basis events. To achieve these objectives, the design limitations of natural circulating LBE-cooling SMRs are derived. Then, the power maximization method is developed based on obtaining the design limitations. The results of this study are expected to contribute to the effectiveness of the reactor design stage by providing insights to designers, as well as by formulating methods for the power maximization of other types of SMRs.

  5. Molecular Simulation and Biochemical Studies Support an Elevator-type Transport Mechanism in EIIC.

    Science.gov (United States)

    Lee, Jumin; Ren, Zhenning; Zhou, Ming; Im, Wonpil

    2017-06-06

    Enzyme IIC (EIIC) is a membrane-embedded sugar transport protein that is part of the phosphoenolpyruvate-dependent phosphotransferases. Crystal structures of two members of the glucose EIIC superfamily, bcChbC in the inward-facing conformation and bcMalT in the outward-facing conformation, were previously solved. Comparing the two structures led us to the hypothesis that sugar translocation could be achieved by an elevator-type transport mechanism in which a transport domain binds to the substrate and, through rigid body motions, transports it across the membrane. To test this hypothesis and to obtain more accurate descriptions of alternate conformations of the two proteins, we first performed collective variable-based steered molecular dynamics (CVSMD) simulations starting with the two crystal structures embedded in model lipid bilayers, and steered their transport domain toward their own alternative conformation. Our simulations show that large rigid-body motions of the transport domain (55° in rotation and 8 Å in translation) lead to access of the substrate binding site to the alternate side of the membrane. H-bonding interactions between the sugar and the protein are intact, although the side chains of the binding-site residues were not restrained in the simulation. Pairs of residues in bcMalT that are far apart in the crystal structure become close to each other in the simulated model. Some of these pairs can be cross-linked by a mercury ion when mutated to cysteines, providing further support for the CVSMD-generated model. In addition, bcMalT binds to maltose with similar affinities before and after the cross-linking, suggesting that the binding site is preserved after the conformational change. In combination, these results support an elevator-type transport mechanism in EIIC. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Electronic structure and molecular orbital study of hole-transport material triphenylamine derivatives

    International Nuclear Information System (INIS)

    Wang, B.-C.; Liao, H.-R.; Chang, J.-C.; Chen Likey; Yeh, J.-T.

    2007-01-01

    Recently, triphenylamine (TPA), 4,4'-bis(phenyl-m-tolylamino)biphenyl (TPD), 4,4'-bis(1-naphthylphenylamino)biphenyl (NPB) and their derivatives are widely used in the organic light-emitting diode (OLED) devices as a hole-transporting material (HTM) layer. We have optimized twenty different structures of HTM materials by using density functional theory (DFT), B3LYP/6-31G method. All these different structures contain mono-amine and diamine TPA derivatives. The energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) along with molecular orbitals for these HTMs are also determined. We have found that the central amine nitrogen atom and the phenyl ring, which is next to the central amine nitrogen atom, show significant contribution to the HOMO and LUMO, respectively. The sum of the calculated bond angles (α+β+γ) of the central amine nitrogen atom has been applied to describe the bonding and the energy difference for HOMO and LUMO in these TPA derivatives. Electronic structure calculations have been performed for these TPA derivatives. Again, the LCAO-MO patterns of HOMO and LUMO levels of these derivatives are used to investigate their electron density. A series of electron-transporting steps are predicted for these compounds employing these calculated results

  7. Performance of Four Transport and Storage Systems for Molecular Detection of Multidrug-Resistant Tuberculosis

    Science.gov (United States)

    Rabodoarivelo, Marie Sylvianne; Imperiale, Bélen; andrianiavomikotroka, Rina; Brandao, Angela; Kumar, Parveen; Singh, Sarman; Ferrazoli, Lucilaine; Morcillo, Nora; Rasolofo, Voahangy; Palomino, Juan Carlos; Vandamme, Peter; Martin, Anandi

    2015-01-01

    Background Detection of drug-resistant tuberculosis is essential for the control of the disease but it is often hampered by the limitation of transport and storage of samples from remote locations to the reference laboratory. We performed a retrospective field study to evaluate the performance of four supports enabling the transport and storage of samples to be used for molecular detection of drug resistance using the GenoType MTBDRplus. Methods Two hundred Mycobacterium tuberculosis strains were selected and spotted on slides, FTA cards, GenoCards, and in ethanol. GenoType MTBDRplus was subsequently performed with the DNA extracted from these supports. Sensitivity and specificity were calculated and compared to the results obtained by drug susceptibility testing. Results For all supports, the overall sensitivity and specificity for detection of resistance to RIF was between 95% and 100%, and for INH between 95% and 98%. Conclusion The four transport and storage supports showed a good sensitivity and specificity for the detection of resistance to RIF and INH in M. tuberculosis strains using the GenoType MTBDRplus. These supports can be maintained at room temperature and could represent an important alternative cost-effective method useful for rapid molecular detection of drug-resistant TB in low-resource settings. PMID:26431352

  8. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

  9. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Directory of Open Access Journals (Sweden)

    Kuan Peng

    2010-01-01

    Full Text Available As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SPn, and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  10. Study on photon transport problem based on the platform of molecular optical simulation environment.

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  11. The role of nano-contacts in electrical transport through a molecular wire

    International Nuclear Information System (INIS)

    Shokri, Ali A.; Mardaani, M.

    2006-01-01

    Theoretical studies on electrical transport in a nano-device which consisting of two semi-infinite cubic leads with finite cross-sections separated by a typical molecular wire (MW) are carried out by including the effect of single and multiple contacts. The calculations are based on the tight-binding model and Green's function method in the coherent regime. In order to calculate the effect of contact coupling on molecular wire transport, we derive a theoretical formula based on the nearest and next nearest neighbor coupling strengths between the MW and the surface atoms in the simple cubic leads. This approach can be generalized to other leads with different lattice structure. The results show small changes in the transport properties with changing next nearest neighbor coupling strength. Some asymmetry is noted in the strong multiple contact limit. Also, we observe that with enlarging the cross-section size of leads, the current density increases and then leads to the quantum unit of conductance. Hence, our derived formalism can be used for devices attached to macroscopic surfaces. The theoretical results obtained, can be a base for developments in designing nano-electronic devices

  12. Entanglement of conjugated polymer chains influences molecular self-assembly and carrier transport

    KAUST Repository

    Zhao, Kui

    2013-06-26

    The influence of polymer entanglement on the self-assembly, molecular packing structure, and microstructure of low-Mw (lightly entangled) and high-Mw (highly entangled) poly (3-hexylthiophene) (P3HT), and the carrier transport in thin-film transistors, are investigated. The polymer chains are gradually disentangled in a marginal solvent via ultrasonication of the polymer solution, and demonstrate improved diffusivity of precursor species (coils, aggregates, and microcrystallites), enhanced nucleation and crystallization of P3HT in solution, and self-assembly of well-ordered and highly textured fibrils at the solid-liquid interface. In low-Mw P3HT, reducing chain entanglement enhances interchain and intrachain ordering, but reduces the interconnectivity of ordered domains (tie molecules) due to the presence of short chains, thus deteriorating carrier transport even in the face of improving crystallinity. Reducing chain entanglement in high-Mw P3HT solutions increases carrier mobility up to ≈20-fold, by enhancing interchain and intrachain ordering while maintaining a sufficiently large number of tie molecules between ordered domains. These results indicate that charge carrier mobility is strongly governed by the balancing of intrachain and interchain ordering, on the one hand, and interconnectivity of ordered domains, on the other hand. In high-Mw P3HT, intrachain and interchain ordering appear to be the key bottlenecks to charge transport, whereas in low-Mw P3HT, the limited interconnectivity of the ordered domains acts as the primary bottleneck to charge transport. Conjugated polymer chains of poly(3-hexylthiophene) (P3HT) are gradually disentangled in solution and trends in carrier transport mechanisms in organic thin film transistors for low- and high-molecular weight P3HT are investigated. While intrachain and interchain ordering within ordered domains are the key bottlenecks to charge transport in high-Mw P3HT films, the limited interconnectivity of ordered

  13. Entanglement of conjugated polymer chains influences molecular self-assembly and carrier transport

    KAUST Repository

    Zhao, Kui; Khan, Hadayat Ullah; Li, Ruipeng; Su, Yisong; Amassian, Aram

    2013-01-01

    The influence of polymer entanglement on the self-assembly, molecular packing structure, and microstructure of low-Mw (lightly entangled) and high-Mw (highly entangled) poly (3-hexylthiophene) (P3HT), and the carrier transport in thin-film transistors, are investigated. The polymer chains are gradually disentangled in a marginal solvent via ultrasonication of the polymer solution, and demonstrate improved diffusivity of precursor species (coils, aggregates, and microcrystallites), enhanced nucleation and crystallization of P3HT in solution, and self-assembly of well-ordered and highly textured fibrils at the solid-liquid interface. In low-Mw P3HT, reducing chain entanglement enhances interchain and intrachain ordering, but reduces the interconnectivity of ordered domains (tie molecules) due to the presence of short chains, thus deteriorating carrier transport even in the face of improving crystallinity. Reducing chain entanglement in high-Mw P3HT solutions increases carrier mobility up to ≈20-fold, by enhancing interchain and intrachain ordering while maintaining a sufficiently large number of tie molecules between ordered domains. These results indicate that charge carrier mobility is strongly governed by the balancing of intrachain and interchain ordering, on the one hand, and interconnectivity of ordered domains, on the other hand. In high-Mw P3HT, intrachain and interchain ordering appear to be the key bottlenecks to charge transport, whereas in low-Mw P3HT, the limited interconnectivity of the ordered domains acts as the primary bottleneck to charge transport. Conjugated polymer chains of poly(3-hexylthiophene) (P3HT) are gradually disentangled in solution and trends in carrier transport mechanisms in organic thin film transistors for low- and high-molecular weight P3HT are investigated. While intrachain and interchain ordering within ordered domains are the key bottlenecks to charge transport in high-Mw P3HT films, the limited interconnectivity of ordered

  14. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD

    Science.gov (United States)

    Calmettes, Charles; Ing, Christopher; Buckwalter, Carolyn M.; El Bakkouri, Majida; Chieh-Lin Lai, Christine; Pogoutse, Anastassia; Gray-Owen, Scott D.; Pomès, Régis; Moraes, Trevor F.

    2015-01-01

    Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops. PMID:26282243

  15. A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter

    DEFF Research Database (Denmark)

    Skovstrup, Soren; David, Laurent; Taboureau, Olivier

    2012-01-01

    The entire substrate translocation pathway in the human GABA transporter (GAT-1) was explored for the endogenous substrate GABA and the anti-convulsive drug tiagabine. Following a steered molecular dynamics (SMD) approach, in which a harmonic restraining potential is applied to the ligand...... to the open-to-in conformation. The simulations are validated by literature data and provide a substrate pathway fingerprint in terms of which, how, and in which sequence specific residues are interacted with. They reveal the essential functional roles of specific residues, e.g. the role of charged residues...

  16. Theoretical analysis of selectivity mechanisms in molecular transport through channels and nanopores

    International Nuclear Information System (INIS)

    Agah, Shaghayegh; Pasquali, Matteo; Kolomeisky, Anatoly B.

    2015-01-01

    Selectivity is one of the most fundamental concepts in natural sciences, and it is also critically important in various technological, industrial, and medical applications. Although there are many experimental methods that allow to separate molecules, frequently they are expensive and not efficient. Recently, a new method of separation of chemical mixtures based on utilization of channels and nanopores has been proposed and successfully tested in several systems. However, mechanisms of selectivity in the molecular transport during the translocation are still not well understood. Here, we develop a simple theoretical approach to explain the origin of selectivity in molecular fluxes through channels. Our method utilizes discrete-state stochastic models that take into account all relevant chemical transitions and can be solved analytically. More specifically, we analyze channels with one and two binding sites employed for separating mixtures of two types of molecules. The effects of the symmetry and the strength of the molecular-pore interactions are examined. It is found that for one-site binding channels, the differences in the strength of interactions for two species drive the separation. At the same time, in more realistic two-site systems, the symmetry of interaction potential becomes also important. The most efficient separation is predicted when the specific binding site is located near the entrance to the nanopore. In addition, the selectivity is higher for large entrance rates into the channel. It is also found that the molecular transport is more selective for repulsive interactions than for attractive interactions. The physical-chemical origin of the observed phenomena is discussed

  17. Pharmacogenomics of the human ABC transporter ABCG2: from functional evaluation to drug molecular design

    Science.gov (United States)

    Ishikawa, Toshihisa; Tamura, Ai; Saito, Hikaru; Wakabayashi, Kanako; Nakagawa, Hiroshi

    2005-10-01

    In the post-genome-sequencing era, emerging genomic technologies are shifting the paradigm for drug discovery and development. Nevertheless, drug discovery and development still remain high-risk and high-stakes ventures with long and costly timelines. Indeed, the attrition of drug candidates in preclinical and development stages is a major problem in drug design. For at least 30% of the candidates, this attrition is due to poor pharmacokinetics and toxicity. Thus, pharmaceutical companies have begun to seriously re-evaluate their current strategies of drug discovery and development. In that light, we propose that a transport mechanism-based design might help to create new, pharmacokinetically advantageous drugs, and as such should be considered an important component of drug design strategy. Performing enzyme- and/or cell-based drug transporter, interaction tests may greatly facilitate drug development and allow the prediction of drug-drug interactions. We recently developed methods for high-speed functional screening and quantitative structure-activity relationship analysis to study the substrate specificity of ABC transporters and to evaluate the effect of genetic polymorphisms on their function. These methods would provide a practical tool to screen synthetic and natural compounds, and these data can be applied to the molecular design of new drugs. In this review article, we present an overview on the genetic polymorphisms of human ABC transporter ABCG2 and new camptothecin analogues that can circumvent AGCG2-associated multidrug resistance of cancer.

  18. Fabrication and Molecular Transport Studies of Highly c-Oriented AFI Membranes

    KAUST Repository

    Liu, Yang

    2017-01-10

    The AFI membrane with one-dimensional straight channels is an ideal platform for various applications. In this work, we report the fabrication of a highly c-oriented, compact and stable AFI membrane by epitaxial growth from an almost close-packed and c-oriented monolayer of plate-like seeds that is manually assembled on a porous alumina support. The straight channels in the membrane are not only aligned vertically along the membrane depth, but are also continuous without disruption. The transport resistance is thus minimized and as a result, the membrane shows almost two orders of magnitude greater permeance in pervaporation of hydrocarbons compared to reported values in the literature. The selectivity of p-xylene to 1,3,5-triisopropylbenzene (TIPB) is approximately 850. In addition, through gas permeation studies on a number of gas and liquid molecules, different transport mechanisms including activated Knudsen diffusion, surface diffusion and molecular sieving were discovered for different diffusion species. The ratio of kinetic diameter to channel diameter, dm/dc, and the ratio of the Lennard-Jones length constant to channel diameter, σm/dc, are found very useful in explaining the different transport behaviors. These results should be useful not only for potential industrial applications of the AFI membranes but also for the fundamental understanding of transport in nanoporous structures.

  19. Transport in aluminized RDX under shock compression explored using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Losada, M; Chaudhuri, S

    2014-01-01

    Shock response of energetic materials is controlled by a combination of mechanical response, thermal, transport, and chemical properties. How these properties interplay in condensed-phase energetic materials is of fundamental interest for improving predictive capabilities. Due to unknown nature of chemistry during the evolution and growth of high-temperature regions within the energetic material (so called hot spots), the connection between reactive and unreactive equations of state contain a high degree of empiricism. In particular, chemistry in materials with high degree of heterogeneity such as aluminized HE is of interest. In order to identify shock compression states and transport properties in high-pressure/temperature (HP-HT) conditions, we use molecular dynamics (MD) simulations in conjunction with the multi-scale shock technique (MSST). Mean square displacement calculations enabled us to track the diffusivity of stable gas products. Among decomposition products, H 2 O and CO 2 are found to be the dominant diffusing species under compression conditions. Heat transport and diffusion rates in decomposed RDX are compared and the comparison shows that around 2000 K, transport can be a major contribution during propagation of the reaction front.

  20. Molecular dynamics study of interfacial thermal transport between silicene and substrates.

    Science.gov (United States)

    Zhang, Jingchao; Hong, Yang; Tong, Zhen; Xiao, Zhihuai; Bao, Hua; Yue, Yanan

    2015-10-07

    In this work, the interfacial thermal transport across silicene and various substrates, i.e., crystalline silicon (c-Si), amorphous silicon (a-Si), crystalline silica (c-SiO2) and amorphous silica (a-SiO2) are explored by classical molecular dynamics (MD) simulations. A transient pulsed heating technique is applied in this work to characterize the interfacial thermal resistance in all hybrid systems. It is reported that the interfacial thermal resistances between silicene and all substrates decrease nearly 40% with temperature from 100 K to 400 K, which is due to the enhanced phonon couplings from the anharmonicity effect. Analysis of phonon power spectra of all systems is performed to interpret simulation results. Contradictory to the traditional thought that amorphous structures tend to have poor thermal transport capabilities due to the disordered atomic configurations, it is calculated that amorphous silicon and silica substrates facilitate the interfacial thermal transport compared with their crystalline structures. Besides, the coupling effect from substrates can improve the interface thermal transport up to 43.5% for coupling strengths χ from 1.0 to 2.0. Our results provide fundamental knowledge and rational guidelines for the design and development of the next-generation silicene-based nanoelectronics and thermal interface materials.

  1. Positrons in gas filled traps and their transport in molecular gases

    Energy Technology Data Exchange (ETDEWEB)

    Petrovic, Z Lj; Bankovic, A; Marjanovic, S; Suvakov, M; Dujko, S; Malovic, G [Institute of Physics, University of Belgrade, Pregrevica 118, POB 68, Zemun (Serbia); White, R D [ARC Centre for Antimatter-Matter Studies, James Cook University, Townsville 4810, QLD (Australia); Buckman, S J, E-mail: zoran@ipb.ac.rs [ARC Centre for Antimatter-Matter Studies, Australian National University, Canberra, ACT, 0200 (Australia)

    2011-01-01

    In this paper we give a review of two recent developments in positron transport, calculation of transport coefficients for a relatively complete set of collision cross sections for water vapour and for application of they Monte Carlo technique to model gas filled subexcitation positron traps such as Penning Malmberg Surko (Surko) trap. Calculated transport coefficients, very much like those for argon and other molecular gases show several new kinetic phenomena. The most important is the negative differential conductivity (NDC) for the bulk drift velocity when the flux drift velocity shows no sign of NDC. These results in water vapour are similar to the results in argon or hydrogen. The same technique that has been used for positron (and previously electron) transport may be applied to model development of particles in a Surko trap. We have provided calculation of the ensemble of positrons in the trap from an initial beam like distribution to the fully thermalised distribution. This model, however, does not include plasma effects (interaction between charged particles) and may be applied for lower positron densities.

  2. Application of quasi-steady state methods to molecular motor transport on microtubules in fungal hyphae.

    Science.gov (United States)

    Dauvergne, Duncan; Edelstein-Keshet, Leah

    2015-08-21

    We consider bidirectional transport of cargo by molecular motors dynein and kinesin that walk along microtubules, and/or diffuse in the cell. The motors compete to transport cargo in opposite directions with respect to microtubule polarity (towards the plus or minus end of the microtubule). In recent work, Gou et al. (2014) used a hierarchical set of models, each consisting of continuum transport equations to track the evolution of motors and their cargo (early endosomes) in the specific case of the fungus Ustilago maydis. We complement their work using a framework of quasi-steady state analysis developed by Newby and Bressloff (2010) and Bressloff and Newby (2013) to reduce the models to an approximating steady state Fokker-Plank equation. This analysis allows us to find analytic approximations to the steady state solutions in many cases where the full models are not easily solved. Consequently, we can make predictions about parameter dependence of the resulting spatial distributions. We also characterize the overall rates of bulk transport and diffusion, and how these are related to state transition parameters, motor speeds, microtubule polarity distribution, and specific assumptions made. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Equilibrium Limit of Boundary Scattering in Carbon Nanostructures: Molecular Dynamics Calculations of Thermal Transport

    Science.gov (United States)

    Haskins, Justin; Kinaci, Alper; Sevik, Cem; Cagin, Tahir

    2012-01-01

    It is widely known that graphene and many of its derivative nanostructures have exceedingly high reported thermal conductivities (up to 4000 W/mK at 300 K). Such attractive thermal properties beg the use of these structures in practical devices; however, to implement these materials while preserving transport quality, the influence of structure on thermal conductivity should be thoroughly understood. For graphene nanostructures, having average phonon mean free paths on the order of one micron, a primary concern is how size influences the potential for heat conduction. To investigate this, we employ a novel technique to evaluate the lattice thermal conductivity from the Green-Kubo relations and equilibrium molecular dynamics in systems where phonon-boundary scattering dominates heat flow. Specifically, the thermal conductivities of graphene nanoribbons and carbon nanotubes are calculated in sizes up to 3 microns, and the relative influence of boundary scattering on thermal transport is determined to be dominant at sizes less than 1 micron, after which the thermal transport largely depends on the quality of the nanostructure interface. The method is also extended to carbon nanostructures (fullerenes) where phonon confinement, as opposed to boundary scattering, dominates, and general trends related to the influence of curvature on thermal transport in these materials are discussed.

  4. Effect of sulfur passivation of InSb (0 0 1) substrates on molecular-beam homoepitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Solov’ev, V.A., E-mail: vasol@beam.ioffe.ru; Sedova, I.V.; Lvova, T.V.; Lebedev, M.V.; Dement’ev, P.A.; Sitnikova, A.A.; Semenov, A.N.; Ivanov, S.V.

    2015-11-30

    Highlights: • Treatment of InSb (0 0 1) substrate with 1 M aqueous Na{sub 2}S solution results in nearly complete removal of native oxides. • A sulfide protective layer formed by the S-treatment is desorbed at much lower temperatures than the native oxide layer. • The bulk InSb epilayers grown on the S-treated substrates have very smooth surface (RMS ∼0.1 nm). • Good structural quality of the homointerfaces formed at the S-treated substrates is confirmed by TEM. - Abstract: The aqueous sodium sulfide solution has been used for pre-epitaxial preparation of epi-ready InSb (0 0 1) substrates for molecular beam epitaxy (MBE) of InSb layers. X-ray photoemission spectroscopy study shows that the S-treated surface of InSb (0 0 1) substrate generally does not contain a native oxide layer and is covered with a sulfide protecting overlayer. Atomic-force microscopy and transmission electron microscopy have been applied to compare surface topography and structural properties of InSb layers grown by MBE on S-treated and untreated epi-ready InSb (0 0 1) substrates. The MBE growth of InSb layers with very smooth surface possessing the root-mean-square roughness as low as 0.1 nm and good structural quality has been demonstrated on the S-treated substrates.

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

    Science.gov (United States)

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

    2008-07-02

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

  6. Energetics of Transport through the Nuclear Pore Complex

    NARCIS (Netherlands)

    Ghavami, Ali; van der Giessen, Erik; Onck, Patrick R

    2016-01-01

    Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown

  7. Correlation between Photoluminescence and Carrier Transport and a Simple In Situ Passivation Method for High-Bandgap Hybrid Perovskites.

    Science.gov (United States)

    Stoddard, Ryan J; Eickemeyer, Felix T; Katahara, John K; Hillhouse, Hugh W

    2017-07-20

    High-bandgap mixed-halide hybrid perovskites have higher open-circuit voltage deficits and lower carrier diffusion lengths than their lower-bandgap counterparts. We have developed a ligand-assisted crystallization (LAC) technique that introduces additives in situ during the solvent wash and developed a new method to dynamically measure the absolute intensity steady-state photoluminescence and the mean carrier diffusion length simultaneously. The measurements reveal four distinct regimes of material changes and show that photoluminescence brightening often coincides with losses in carrier transport, such as in degradation or phase segregation. Further, the measurements enabled optimization of LAC on the 1.75 eV bandgap FA 0.83 Cs 0.17 Pb(I 0.66 Br 0.34 ) 3 , resulting in an enhancement of the photoluminescence quantum yield (PLQY) of over an order of magnitude, an increase of 80 meV in the quasi-Fermi level splitting (to 1.29 eV), an increase in diffusion length by a factor of 3.5 (to over 1 μm), and enhanced open-circuit voltage and short-circuit current from photovoltaics fabricated from the LAC-treated films.

  8. Molecular analysis of interactions between dendrimers and asymmetric membranes at different transport stages.

    Science.gov (United States)

    He, XiaoCong; Qu, ZhiGuo; Xu, Feng; Lin, Min; Wang, JiuLing; Shi, XingHua; Lu, TianJian

    2014-01-07

    Studying dendrimer-biomembrane interactions is important for understanding drug and gene delivery. In this study, coarse-grained molecular dynamics simulations were performed to investigate the behaviors of polyamidoamine (PAMAM) dendrimers (G4 and G5) as they interacted with asymmetric membranes from different sides of the bilayer, thus mimicking different dendrimer transport stages. The G4 dendrimer could insert into the membrane during an equilibrated state, and the G5 dendrimer could induce pore formation in the membrane when the dendrimers interacted with the outer side (outer interactions) of an asymmetric membrane [with 10% dipalmitoyl phosphatidylserine (DPPS) in the inner leaflet of the membrane]. During the interaction with the inner side of the asymmetric membrane (inner interactions), the G4 and G5 dendrimers only adsorbed onto the membrane. As the membrane asymmetry increased (e.g., increased DPPS percentage in the inner leaflet of the membrane), the G4 and G5 dendrimers penetrated deeper into the membrane during the outer interactions and the G4 and G5 dendrimers were adsorbed more tightly onto the membrane for the inner interactions. When the DPPS content reached 50%, the G4 dendrimer could completely penetrate through the membrane from the outer side to the inner side. Our study provides molecular understanding and reference information about different dendrimer transport stages during drug and gene delivery.

  9. Semiquantum molecular dynamics simulation of thermal properties and heat transport in low-dimensional nanostructures

    Science.gov (United States)

    Savin, Alexander V.; Kosevich, Yuriy A.; Cantarero, Andres

    2012-08-01

    We present a detailed description of semiquantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the effects of phonon quantum statistics are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of thermal properties and heat transport in different low-dimensional nanostructures. We describe the determination of temperature in quantum lattice systems, to which the equipartition limit is not applied. We show that one can determine the temperature of such a system from the measured power spectrum and temperature- and relaxation-rate-independent density of vibrational (phonon) states. We simulate the specific heat and heat transport in carbon nanotubes, as well as the heat transport in molecular nanoribbons with perfect (atomically smooth) and rough (porous) edges, and in nanoribbons with strongly anharmonic periodic interatomic potentials. We show that the effects of quantum statistics of phonons are essential for the carbon nanotube in the whole temperature range T<500K, in which the values of the specific heat and thermal conductivity of the nanotube are considerably less than that obtained within the description based on classical statistics of phonons. This conclusion is also applicable to other carbon-based materials and systems with high Debye temperature like graphene, graphene nanoribbons, fullerene, diamond, diamond nanowires, etc. We show that the existence of rough edges and quantum statistics of phonons change drastically the low-temperature thermal conductivity of the nanoribbon in comparison with that of the nanoribbon with perfect edges and classical phonon dynamics and statistics. The semiquantum molecular

  10. Passive House Solutions

    Energy Technology Data Exchange (ETDEWEB)

    Strom, I.; Joosten, L.; Boonstra, C. [DHV Sustainability Consultants, Eindhoiven (Netherlands)

    2006-05-15

    PEP stands for 'Promotion of European Passive Houses' and is a consortium of European partners, supported by the European Commission, Directorate General for Energy and Transport. In this working paper an overview is given of Passive House solutions. An inventory has been made of Passive House solutions for new build residences applied in each country. Based on this, the most common basic solutions have been identified and described in further detail, including the extent to which solutions are applied in common and best practice and expected barriers for the implementation in each country. An inventory per country is included in the appendix. The analysis of Passive House solutions in partner countries shows high priority with regard to the performance of the thermal envelope, such as high insulation of walls, roofs, floors and windows/ doors, thermal bridge-free construction and air tightness. Due to the required air tightness, special attention must be paid to indoor air quality through proper ventilation. Finally, efficient ((semi-)solar) heating systems for combined space and DHW heating still require a significant amount of attention in most partner countries. Other basic Passive House solutions show a smaller discrepancy with common practice and fewer barriers have been encountered in partner countries. In the next section, the general barriers in partner countries have been inventoried. For each type of barrier a suggested approach has been given. Most frequently encountered barriers in partner countries are: limited know-how; limited contractor skills; and acceptation of Passive Houses in the market. Based on the suggested approaches to overcoming barriers, this means that a great deal of attention must be paid to providing practical information and solutions to building professionals, providing practical training to installers and contractors and communication about the Passive House concept to the market.

  11. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    International Nuclear Information System (INIS)

    Matsubara, Hiroki; Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

    2015-01-01

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T c ) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

  12. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    Energy Technology Data Exchange (ETDEWEB)

    Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  14. Molecular mechanism of pH-dependent substrate transport by an arginine-agmatine antiporter.

    Science.gov (United States)

    Wang, Sheng; Yan, Renhong; Zhang, Xi; Chu, Qi; Shi, Yigong

    2014-09-02

    Enteropathogenic bacteria, exemplified by Escherichia coli, rely on acid-resistance systems (ARs) to survive the acidic environment of the stomach. AR3 consumes intracellular protons through decarboxylation of arginine (Arg) in the cytoplasm and exchange of the reaction product agmatine (Agm) with extracellular Arg. The latter process is mediated by the Arg:Agm antiporter AdiC, which is activated in response to acidic pH and remains fully active at pH 6.0 and below. Despite our knowledge of structural information, the molecular mechanism by which AdiC senses acidic pH remains completely unknown. Relying on alanine-scanning mutagenesis and an in vitro proteoliposome-based transport assay, we have identified Tyr74 as a critical pH sensor in AdiC. The AdiC variant Y74A exhibited robust transport activity at all pH values examined while maintaining stringent substrate specificity for Arg:Agm. Replacement of Tyr74 by Phe, but not by any other amino acid, led to the maintenance of pH-dependent substrate transport. These observations, in conjunction with structural information, identify a working model for pH-induced activation of AdiC in which a closed conformation is disrupted by cation-π interactions between proton and the aromatic side chain of Tyr74.

  15. Effects of electron-phonon interaction on thermal and electrical transport through molecular nano-conductors

    Energy Technology Data Exchange (ETDEWEB)

    Lü, Jing-Tao, E-mail: jtlu@hust.edu.cn [School of Physics, Huazhong University of Science and Technology, 430074 Wuhan (China); Zhou, Hangbo [Department of Physics and Center for Computational Science and Engineering, National University of Singapore, 117551 Singapore (Singapore); NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456 Singapore (Singapore); Jiang, Jin-Wu [Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, 200072 Shanghai (China); Wang, Jian-Sheng [Department of Physics and Center for Computational Science and Engineering, National University of Singapore, 117551 Singapore (Singapore)

    2015-05-15

    The topic of this review is the effects of electron-phonon interaction (EPI) on the transport properties of molecular nano-conductors. A nano-conductor connects to two electron leads and two phonon leads, possibly at different temperatures or chemical potentials. The EPI appears only in the nano-conductor. We focus on its effects on charge and energy transport. We introduce three approaches. For weak EPI, we use the nonequilibrium Green’s function method to treat it perturbatively. We derive the expressions for the charge and heat currents. For weak system-lead couplings, we use the quantum master equation approach. In both cases, we use a simple single level model to study the effects of EPI on the system’s thermoelectric transport properties. It is also interesting to look at the effect of currents on the dynamics of the phonon system. For this, we derive a semi-classical generalized Langevin equation to describe the nano-conductor’s atomic dynamics, taking the nonequilibrium electron system, as well as the rest of the atomic degrees of freedom as effective baths. We show simple applications of this approach to the problem of energy transfer between electrons and phonons.

  16. Effects of electron-phonon interaction on thermal and electrical transport through molecular nano-conductors

    International Nuclear Information System (INIS)

    Lü, Jing-Tao; Zhou, Hangbo; Jiang, Jin-Wu; Wang, Jian-Sheng

    2015-01-01

    The topic of this review is the effects of electron-phonon interaction (EPI) on the transport properties of molecular nano-conductors. A nano-conductor connects to two electron leads and two phonon leads, possibly at different temperatures or chemical potentials. The EPI appears only in the nano-conductor. We focus on its effects on charge and energy transport. We introduce three approaches. For weak EPI, we use the nonequilibrium Green’s function method to treat it perturbatively. We derive the expressions for the charge and heat currents. For weak system-lead couplings, we use the quantum master equation approach. In both cases, we use a simple single level model to study the effects of EPI on the system’s thermoelectric transport properties. It is also interesting to look at the effect of currents on the dynamics of the phonon system. For this, we derive a semi-classical generalized Langevin equation to describe the nano-conductor’s atomic dynamics, taking the nonequilibrium electron system, as well as the rest of the atomic degrees of freedom as effective baths. We show simple applications of this approach to the problem of energy transfer between electrons and phonons

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

    International Nuclear Information System (INIS)

    Tang, Gaomin; Yu, Zhizhou; Wang, Jian

    2017-01-01

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

  18. Proton transport properties of poly(aspartic acid) with different average molecular weights

    Energy Technology Data Exchange (ETDEWEB)

    Nagao, Yuki, E-mail: ynagao@kuchem.kyoto-u.ac.j [Department of Mechanical Systems and Design, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Imai, Yuzuru [Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-cho, Aoba-ku, Sendai 980-8575 (Japan); Matsui, Jun [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); Ogawa, Tomoyuki [Department of Electronic Engineering, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Miyashita, Tokuji [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)

    2011-04-15

    Research highlights: Seven polymers with different average molecular weights were synthesized. The proton conductivity depended on the number-average degree of polymerization. The difference of the proton conductivities was more than one order of magnitude. The number-average molecular weight contributed to the stability of the polymer. - Abstract: We synthesized seven partially protonated poly(aspartic acids)/sodium polyaspartates (P-Asp) with different average molecular weights to study their proton transport properties. The number-average degree of polymerization (DP) for each P-Asp was 30 (P-Asp30), 115 (P-Asp115), 140 (P-Asp140), 160 (P-Asp160), 185 (P-Asp185), 205 (P-Asp205), and 250 (P-Asp250). The proton conductivity depended on the number-average DP. The maximum and minimum proton conductivities under a relative humidity of 70% and 298 K were 1.7 . 10{sup -3} S cm{sup -1} (P-Asp140) and 4.6 . 10{sup -4} S cm{sup -1} (P-Asp250), respectively. Differential thermogravimetric analysis (TG-DTA) was carried out for each P-Asp. The results were classified into two categories. One exhibited two endothermic peaks between t = (270 and 300) {sup o}C, the other exhibited only one peak. The P-Asp group with two endothermic peaks exhibited high proton conductivity. The high proton conductivity is related to the stability of the polymer. The number-average molecular weight also contributed to the stability of the polymer.

  19. Theoretical Study of Molecular Transport Through a Permeabilized Cell Membrane in a Microchannel.

    Science.gov (United States)

    Mahboubi, Masoumeh; Movahed, Saeid; Hosseini Abardeh, Reza; Hoshyargar, Vahid

    2017-06-01

    A two-dimensional model is developed to study the molecular transport into an immersed cell in a microchannel and to investigate the effects of finite boundary (a cell is suspended in a microchannel), amplitude of electric pulse, and geometrical parameter (microchannel height and size of electrodes) on cell uptake. Embedded electrodes on the walls of the microchannel generate the required electric pulse to permeabilize the cell membrane, pass the ions through the membrane, and transport them into the cell. The shape of electric pulses is square with the time span of 6 ms; their intensities are in the range of 2.2, 2.4, 2.6, 3 V. Numerical simulations have been performed to comprehensively investigate the molecular uptake into the cell. The obtained results of the current study demonstrate that calcium ions enter the cell from the anodic side (the side near positive electrode); after a while, the cell faces depletion of the calcium ions on a positive electrode-facing side within the microchannel; the duration of depletion depends on the amplitude of electric pulse and geometry that lasts from microseconds to milliseconds. By keeping geometrical parameters and time span constant, increment of a pulse intensity enhances molecular uptake and rate of propagation inside the cell. If a ratio of electrode size to cell diameter is larger than 1, the transported amount of Ca 2+ into the cell, as well as the rate of propagation, will be significantly increased. By increasing the height of the microchannel, the rate of uptake is decreased. In an infinite domain, the peak concentration becomes constant after reaching the maximum value; this value depends on the intra-extracellular conductivity and diffusion coefficient of interior and exterior domains of the cell. In comparison, the maximum concentration is changed by geometrical parameters in the microchannel. After reaching the maximum value, the peak concentration reduces due to the depletion of Ca 2+ ions within the

  20. An Electronic Structure Approach to Charge Transfer and Transport in Molecular Building Blocks for Organic Optoelectronics

    Science.gov (United States)

    Hendrickson, Heidi Phillips

    A fundamental understanding of charge separation in organic materials is necessary for the rational design of optoelectronic devices suited for renewable energy applications and requires a combination of theoretical, computational, and experimental methods. Density functional theory (DFT) and time-dependent (TD)DFT are cost effective ab-initio approaches for calculating fundamental properties of large molecular systems, however conventional DFT methods have been known to fail in accurately characterizing frontier orbital gaps and charge transfer states in molecular systems. In this dissertation, these shortcomings are addressed by implementing an optimally-tuned range-separated hybrid (OT-RSH) functional approach within DFT and TDDFT. The first part of this thesis presents the way in which RSH-DFT addresses the shortcomings in conventional DFT. Environmentally-corrected RSH-DFT frontier orbital energies are shown to correspond to thin film measurements for a set of organic semiconducting molecules. Likewise, the improved RSH-TDDFT description of charge transfer excitations is benchmarked using a model ethene dimer and silsesquioxane molecules. In the second part of this thesis, RSH-DFT is applied to chromophore-functionalized silsesquioxanes, which are currently investigated as candidates for building blocks in optoelectronic applications. RSH-DFT provides insight into the nature of absorptive and emissive states in silsesquioxanes. While absorption primarily involves transitions localized on one chromophore, charge transfer between chromophores and between chromophore and silsesquioxane cage have been identified. The RSH-DFT approach, including a protocol accounting for complex environmental effects on charge transfer energies, was tested and validated against experimental measurements. The third part of this thesis addresses quantum transport through nano-scale junctions. The ability to quantify a molecular junction via spectroscopic methods is crucial to their

  1. The riboflavin transporter RibU in Lactococcus lactis : Molecular characterization of gene expression and the transport mechanism

    NARCIS (Netherlands)

    Burgess, CM; Slotboom, DJ; Geertsma, ER; Duurkens, Hinderika; Poolman, B; van Sinderen, D

    This study describes the characterization of the riboflavin transport protein RibU in the lactic acid bacterium Lactococcus lactis subsp. cremoris NZ9000. RibU is predicted to contain five membrane-spanning segments and is a member of a novel transport protein family, not described in the Transport

  2. Electromagnetic probes of molecular motors in the electron transport chains of mitochondria and chloroplasts

    Science.gov (United States)

    Miller, J. H., Jr.; Nawarathna, D.; Vajrala, V.; Gardner, J.; Widger, W. R.

    2005-12-01

    We report on measurements of harmonics generated by whole cells, mitochondria, and chloroplasts in response to applied sinusoidal electric fields. The frequency- and amplitude-dependence of the induced harmonics exhibit features that correlate with physiological processes. Budding yeast (S. cerevisiae) cells produce numerous harmonics, the amplitudes of which depend strongly on frequency. When the second or third harmonic amplitude is plotted vs. applied frequency, we observe two peaks, around 3 kHz and 12 kHz, which are suppressed by respiratory inhibitors. We observe similar peaks when measuring the harmonic response of B. indicas, a relative of the mitochondrial ancestor. In uncoupled mitochondria, in which most of the electron transport chain is active but the ATP-synthase molecular turbine is inactive, only one (lower frequency) of the two peaks is present. Finally, we find that harmonics generated by chloroplasts depend dramatically on incident light, and vanish in the absence of light.

  3. Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Chattaraj, D.; Dash, Smruti

    2013-01-01

    The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

  4. Equilibrium and Transport Properties of Primary, Secondary and Tertiary Amines by Molecular Simulation

    International Nuclear Information System (INIS)

    Orozco, Gustavo A.; Nieto-Draghi, Carlos; Lachet, Veronique; Mackie, Allan D.

    2014-01-01

    Using molecular simulation techniques such as Monte Carlo (MC) and molecular dynamics (MD), we present several simulation results of thermodynamic and transport properties for primary, secondary and tertiary amines. These calculations are based on a recently proposed force field for amines that follows the Anisotropic United Atom approach (AUA). Different amine molecules have been studied, including n-Butylamine, di-n-Butylamine, tri-n-Butylamine and 1,4-Butanediamine for primary, secondary, tertiary and multi-functional amines respectively. For the transport properties, we have calculated the viscosity coefficients as a function of temperature using the isothermal-isobaric (NPT) ensemble. In the case of the pure components, we have investigated different thermodynamic properties using NVT Gibbs ensemble simulations such as liquid-vapor phase equilibrium diagrams, vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures and critical densities. We have also calculated the excess enthalpies for water-n-Butylamine and n-heptane-n-Butylamine mixtures using Monte Carlo simulations in the NPT ensemble. In addition, we present the calculation of liquid-vapor surface tensions of n-Butylamine using a two-phase NVT simulation as well as the radial distribution functions. Finally, we have investigated the physical Henry constants of nitrous oxide (N 2 O) and nitrogen (N 2 ) in an aqueous solutions of n-Butylamine. In general, we found a good agreement between the available experimental information and our simulation results for all the studied properties, ratifying the predictive capability of the AUA force field for amines. (authors)

  5. Assessing the Impact of Electrostatic Drag on Processive Molecular Motor Transport.

    Science.gov (United States)

    Smith, J Darby; McKinley, Scott A

    2018-06-04

    The bidirectional movement of intracellular cargo is usually described as a tug-of-war among opposite-directed families of molecular motors. While tug-of-war models have enjoyed some success, recent evidence suggests underlying motor interactions are more complex than previously understood. For example, these tug-of-war models fail to predict the counterintuitive phenomenon that inhibiting one family of motors can decrease the functionality of opposite-directed transport. In this paper, we use a stochastic differential equations modeling framework to explore one proposed physical mechanism, called microtubule tethering, that could play a role in this "co-dependence" among antagonistic motors. This hypothesis includes the possibility of a trade-off: weakly bound trailing molecular motors can serve as tethers for cargoes and processing motors, thereby enhancing motor-cargo run lengths along microtubules; however, this introduces a cost of processing at a lower mean velocity. By computing the small- and large-time mean-squared displacement of our theoretical model and comparing our results to experimental observations of dynein and its "helper protein" dynactin, we find some supporting evidence for microtubule tethering interactions. We extrapolate these findings to predict how dynein-dynactin might interact with the opposite-directed kinesin motors and introduce a criterion for when the trade-off is beneficial in simple systems.

  6. Density scaling of the transport properties of molecular and ionic liquids.

    Science.gov (United States)

    López, Enriqueta R; Pensado, Alfonso S; Comuñas, María J P; Pádua, Agílio A H; Fernández, Josefa; Harris, Kenneth R

    2011-04-14

    Casalini and Roland [Phys. Rev. E 69, 062501 (2004); J. Non-Cryst. Solids 353, 3936 (2007)] and other authors have found that both the dielectric relaxation times and the viscosity, η, of liquids can be expressed solely as functions of the group (TV (γ)), where T is the temperature, V is the molar volume, and γ a state-independent scaling exponent. Here we report scaling exponents γ, for the viscosities of 46 compounds, including 11 ionic liquids. A generalization of this thermodynamic scaling to other transport properties, namely, the self-diffusion coefficients for ionic and molecular liquids and the electrical conductivity for ionic liquids is examined. Scaling exponents, γ, for the electrical conductivities of six ionic liquids for which viscosity data are available, are found to be quite close to those obtained from viscosities. Using the scaling exponents obtained from viscosities it was possible to correlate molar conductivity over broad ranges of temperature and pressure. However, application of the same procedures to the self-diffusion coefficients, D, of six ionic and 13 molecular liquids leads to superpositioning of poorer quality, as the scaling yields different exponents from those obtained with viscosities and, in the case of the ionic liquids, slightly different values for the anion and the cation. This situation can be improved by using the ratio (D∕T), consistent with the Stokes-Einstein relation, yielding γ values closer to those of viscosity.

  7. Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes.

    Science.gov (United States)

    Jean, Bernandie; Surratt, Christopher K; Madura, Jeffry D

    2017-09-01

    The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation. The 3β-aryltropane cocaine analogs LX10 and LX11, however, differ only in stereochemistry and share a preference for the outward-facing DAT, yet are reported to vary widely in abuse potential in an animal model. In search of the molecular basis for DAT conformation preference, complexes of cocaine, benztropine, LX10 or LX11 bound to each DAT conformation were subjected to 100ns of all-atom molecular dynamics simulation. Results were consistent with previous findings from cysteine accessibility assays used to assess an inhibitor's DAT conformation preference. The respective 2β- and 2α-substituted phenyltropanes of LX10 and LX11 interacted with hydrophobic regions of the DAT S1 binding site that were inaccessible to cocaine. Solvent accessibility measurements also revealed subtle differences in inhibitor positioning within a given DAT conformation. This work serves to advance our understanding of the conformational selectivity of DAT inhibitors and suggests that MD may be useful in antipsychostimulant therapeutic design. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Mechanisms of molecular transport through the urea channel of Helicobacter pylori

    Science.gov (United States)

    McNulty, Reginald; Ulmschneider, Jakob P.; Luecke, Hartmut; Ulmschneider, Martin B.

    2013-12-01

    Helicobacter pylori survival in acidic environments relies on cytoplasmic hydrolysis of gastric urea into ammonia and carbon dioxide, which buffer the pathogen’s periplasm. Urea uptake is greatly enhanced and regulated by HpUreI, a proton-gated inner membrane channel protein essential for gastric survival of H. pylori. The crystal structure of HpUreI describes a static snapshot of the channel with two constriction sites near the center of the bilayer that are too narrow to allow passage of urea or even water. Here we describe the urea transport mechanism at atomic resolution, revealed by unrestrained microsecond equilibrium molecular dynamics simulations of the hexameric channel assembly. Two consecutive constrictions open to allow conduction of urea, which is guided through the channel by interplay between conserved residues that determine proton rejection and solute selectivity. Remarkably, HpUreI conducts water at rates equivalent to aquaporins, which might be essential for efficient transport of urea at small concentration gradients.

  9. Leukemia-Associated Mutations in Nucleophosmin Alter Recognition by CRM1: Molecular Basis of Aberrant Transport.

    Directory of Open Access Journals (Sweden)

    Igor Arregi

    Full Text Available Nucleophosmin (NPM is a nucleocytoplasmic shuttling protein, normally enriched in nucleoli, that performs several activities related to cell growth. NPM mutations are characteristic of a subtype of acute myeloid leukemia (AML, where mutant NPM seems to play an oncogenic role. AML-associated NPM mutants exhibit altered subcellular traffic, being aberrantly located in the cytoplasm of leukoblasts. Exacerbated export of AML variants of NPM is mediated by the nuclear export receptor CRM1, and due, in part, to a mutationally acquired novel nuclear export signal (NES. To gain insight on the molecular basis of NPM transport in physiological and pathological conditions, we have evaluated the export efficiency of NPM in cells, and present new data indicating that, in normal conditions, wild type NPM is weakly exported by CRM1. On the other hand, we have found that AML-associated NPM mutants efficiently form complexes with CRM1HA (a mutant CRM1 with higher affinity for NESs, and we have quantitatively analyzed CRM1HA interaction with the NES motifs of these mutants, using fluorescence anisotropy and isothermal titration calorimetry. We have observed that the affinity of CRM1HA for these NESs is similar, which may help to explain the transport properties of the mutants. We also describe NPM recognition by the import machinery. Our combined cellular and biophysical studies shed further light on the determinants of NPM traffic, and how it is dramatically altered by AML-related mutations.

  10. Thermal transport characterization of hexagonal boron nitride nanoribbons using molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Asir Intisar Khan

    2017-10-01

    Full Text Available Due to similar atomic bonding and electronic structure to graphene, hexagonal boron nitride (h-BN has broad application prospects such as the design of next generation energy efficient nano-electronic devices. Practical design and efficient performance of these devices based on h-BN nanostructures would require proper thermal characterization of h-BN nanostructures. Hence, in this study we have performed equilibrium molecular dynamics (EMD simulation using an optimized Tersoff-type interatomic potential to model the thermal transport of nanometer sized zigzag hexagonal boron nitride nanoribbons (h-BNNRs. We have investigated the thermal conductivity of h-BNNRs as a function of temperature, length and width. Thermal conductivity of h-BNNRs shows strong temperature dependence. With increasing width, thermal conductivity increases while an opposite pattern is observed with the increase in length. Our study on h-BNNRs shows considerably lower thermal conductivity compared to GNRs. To elucidate these aspects, we have calculated phonon density of states for both h-BNNRs and GNRs. Moreover, using EMD we have explored the impact of different vacancies, namely, point vacancy, edge vacancy and bi-vacancy on the thermal conductivity of h-BNNRs. With varying percentages of vacancies, significant reduction in thermal conductivity is observed and it is found that, edge and point vacancies are comparatively more destructive than bi-vacancies. Such study would contribute further into the growing interest for accurate thermal transport characterization of low dimensional nanostructures.

  11. Contributions of different degrees of freedom to thermal transport in the C60 molecular crystal

    Science.gov (United States)

    Kumar, Sushant; Shao, Cheng; Lu, Simon; McGaughey, Alan J. H.

    2018-03-01

    Three models of the C60 molecular crystal are studied using molecular dynamics simulations to resolve the roles played by intermolecular and intramolecular degrees of freedom (DOF) in its structural, mechanical, and thermal properties at temperatures between 35 and 400 K. In the full DOF model, all DOF are active. In the rigid body model, the intramolecular DOF are frozen, such that only center of mass (COM) translations and molecular rotations/librations are active. In the point mass model, the molecule is replaced by a point mass, such that only COM translations are active. The zero-pressure lattice constants and bulk moduli predicted from the three models fall within ranges of 0.15 and 20%. The thermal conductivity of the point mass model is the largest across the temperature range, showing a crystal-like temperature dependence (i.e., it decreases with increasing temperature) due to the presence of phonon modes associated with the COM translations. The rigid body model thermal conductivity is the smallest and follows two distinct regimes. It is crystal-like at low temperatures and becomes temperature invariant at high temperatures. The latter is typical of the behavior of an amorphous material. By calculating the rotational diffusion coefficient, the transition between the two regimes is found to occur at the temperature where the molecules begin to rotate freely. Above this temperature, phonons related to COM translations are scattered by the rotational DOF. The full DOF model thermal conductivity is larger than that of the rigid body model, indicating that intramolecular DOF contribute to thermal transport.

  12. Molecular cloning and expression analysis of the sucrose transporter gene family from Theobroma cacao L.

    Science.gov (United States)

    Li, Fupeng; Wu, Baoduo; Qin, Xiaowei; Yan, Lin; Hao, Chaoyun; Tan, Lehe; Lai, Jianxiong

    2014-08-10

    In this study, we performed cloning and expression analysis of six putative sucrose transporter genes, designated TcSUT1, TcSUT2, TcSUT3, TcSUT4, TcSUT5 and TcSUT6, from the cacao genotype 'TAS-R8'. The combination of cDNA and genomic DNA sequences revealed that the cacao SUT genes contained exon numbers ranging from 1 to 14. The average molecular mass of all six deduced proteins was approximately 56 kDa (range 52 to 66 kDa). All six proteins were predicted to exhibit typical features of sucrose transporters with 12 trans-membrane spanning domains. Phylogenetic analysis revealed that TcSUT2 and TcSUT4 belonged to Group 2 SUT and Group 4 SUT, respectively, and the other TcSUT proteins were belonging to Group 1 SUT. Real-time PCR was conducted to investigate the expression pattern of each member of the SUT family in cacao. Our experiment showed that TcSUT1 was expressed dominantly in pods and that, TcSUT3 and TcSUT4 were highly expressed in both pods and in bark with phloem. Within pods, TcSUT1 and TcSUT4 were expressed more in the seed coat and seed from the pod enlargement stage to the ripening stage. TcSUT5 expression sharply increased to its highest expression level in the seed coat during the ripening stage. Expression pattern analysis indicated that TcSUT genes may be associated with photoassimilate transport into developing seeds and may, therefore, have an impact on seed production. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Molecular dynamics studies of transport properties and equation of state of supercritical fluids

    Science.gov (United States)

    Nwobi, Obika C.

    Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the

  14. Invariance of molecular charge transport upon changes of extended molecule size and several related issues

    Directory of Open Access Journals (Sweden)

    Ioan Bâldea

    2016-03-01

    Full Text Available As a sanity test for the theoretical method employed, studies on (steady-state charge transport through molecular devices usually confine themselves to check whether the method in question satisfies the charge conservation. Another important test of the theory’s correctness is to check that the computed current does not depend on the choice of the central region (also referred to as the “extended molecule”. This work addresses this issue and demonstrates that the relevant transport and transport-related properties are indeed invariant upon changing the size of the extended molecule, when the embedded molecule can be described within a general single-particle picture (namely, a second-quantized Hamiltonian bilinear in the creation and annihilation operators. It is also demonstrates that the invariance of nonequilibrium properties is exhibited by the exact results but not by those computed approximately within ubiquitous wide- and flat-band limits (WBL and FBL, respectively. To exemplify the limitations of the latter, the phenomenon of negative differential resistance (NDR is considered. It is shown that the exactly computed current may exhibit a substantial NDR, while the NDR effect is absent or drastically suppressed within the WBL and FBL approximations. The analysis done in conjunction with the WBLs and FBLs reveals why general studies on nonequilibrium properties require a more elaborate theoretical than studies on linear response properties (e.g., ohmic conductance and thermopower at zero temperature. Furthermore, examples are presented that demonstrate that treating parts of electrodes adjacent to the embedded molecule and the remaining semi-infinite electrodes at different levels of theory (which is exactly what most NEGF-DFT approaches do is a procedure that yields spurious structures in nonlinear ranges of current–voltage curves.

  15. Size Effect on Transport Properties of Gaseous Argon: A Molecular Dynamics Simulation Study

    International Nuclear Information System (INIS)

    Lee, Songhi

    2014-01-01

    We have carried out a series of equilibrium molecular dynamics (EMD) simulations of gaseous argon at 273.15 K and 1.00 atm for the calculation of transport properties as a function of the number of argon molecules (N). While the diffusion coefficients (D) of gaseous argon approach to the experimental measure with increasing N, the viscosities (η) and thermal conductivities (λ) obtained for N = 432 are unreliable due to the high fluctuation of the time correlation functions and those for N = 1728 are rather acceptable. Increasing further to N = 6912 has improved the MD results a little closer to the experimental measures for η and λ. Both the EMD results for η and λ for N = 6912 underestimate the experimental measures and it is not expected that the more increasing N makes the closer results to the experimental measures. One possible explanation for the large disagreement between MD results and the experimental measures for η and λ may be due to the use of LJ parameters which were used for liquid argon. In a recent study, we have examined the Green-Kubo formula for the calculation of transport properties (diffusion coefficient, viscosity, and thermal conductivity) of noble gases (He, Ne, Ar, Kr, and Xe) by carrying out a series of equilibrium molecular dynamics (EMD) simulations for the system of N=1728 at 273.15 K and 1.00 atm.1 While the diffusion coefficients (D) of noble gases were obtained through the original Green-Kubo formula, the viscosities (η) and thermal conductivities (λ) were obtained by utilizing the revised Green-Kubo formulas. The structural and dynamic properties of gaseous argon are completely different from those of liquid argon at 94.4 K and 1.374 g/cm 3 . The results for transport properties (D, η, and λ) at 273.15 K and 1.00 atm obtained from our EMD simulations are in general agreement with the experimental data and superior to the rigorous results of the kinetic theory

  16. Molecular determinants of transport stimulation of EAAT2 are located at interface between the trimerization and substrate transport domains.

    Science.gov (United States)

    Mortensen, Ole V; Liberato, José L; Coutinho-Netto, Joaquim; Dos Santos, Wagner F; Fontana, Andréia C K

    2015-04-01

    Excitatory amino acid transporters (EAATs) regulate glutamatergic signal transmission by clearing extracellular glutamate. Dysfunction of these transporters has been implicated in the pathogenesis of various neurological disorders. Previous studies have shown that venom from the spider Parawixia bistriata and a purified compound (Parawixin1) stimulate EAAT2 activity and protect retinal tissue from ischemic damage. In the present study, the EAAT2 subtype specificity of this compound was explored, employing chimeric proteins between EAAT2 and EAAT3 transporter subtypes and mutants to characterize the structural region targeted by the compound. This identified a critical residue (Histidine-71 in EAAT2 and Serine-45 in EAAT3) in transmembrane domain 2 (TM2) to be important for the selectivity between EAAT2 and EAAT3 and for the activity of the venom. Using the identified residue in TM2 as a structural anchor, several neighboring amino acids within TM5 and TM8 were identified to also be important for the activity of the venom. This structural domain of the transporter lies at the interface of the rigid trimerization domain and the central substrate-binding transport domain. Our studies suggest that the mechanism of glutamate transport enhancement involves an interaction with the transporter that facilitates the movement of the transport domain. We identified a domain (purple star) in the glutamate transporter EAAT2 that is important for transport stimulation through a spider venom, and suggest a mechanism for enhanced transporter function through facilitated substrate translocation (arrow). Because the dysfunction of glutamate transporters is implicated in the pathogenesis of neurological disorders, understanding the mechanisms of enhanced transport could have therapeutic implications. © 2015 International Society for Neurochemistry.

  17. Emerging treatments in lung cancer – targeting the RLIP76 molecular transporter

    Directory of Open Access Journals (Sweden)

    Goldfinger LE

    2013-11-01

    Full Text Available Lawrence E Goldfinger,1,2 Seunghyung Lee1 1Department of Anatomy and Cell Biology, The Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, PA, USA; 2Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA Abstract: Multidrug resistance in lung cancer cells is a significant obstacle in the treatment of lung cancer. Resistance to chemotherapeutic agents is often the result of efflux of the drugs from cancer cells, mediated by adenosine triphosphate (ATP-dependent drug transport across the plasma membrane. Thus, identifying molecular targets in the cancer cell transport machinery could be a key factor in successful combinatorial therapy, along with chemotherapeutic drugs. The transport protein Ral-interacting protein of 76 kDa (RLIP76, also known as Ral-binding protein 1 (RalBP1, is a highly promising target for lung cancer treatment. RLIP76 is an ATP-dependent non-ATP-binding cassette (ABC transporter, responsible for the major transport function in many cells, including many cancer cell lines, causing efflux of glutathione-electrophile conjugates of both endogenous metabolites and environmental toxins. RLIP76 is expressed in most human tissues, and is overexpressed in non-small-cell lung cancer cell lines and in many tumor types. The blockade of RLIP76 by various approaches has been shown to increase the sensitivity to radiation and chemotherapeutic drugs, and leads to apoptosis in cells. In xenograft tumor models in mice, RLIP76 blockade or depletion results in complete and sustained regression across many cancer cell types, including lung cancer cells. In addition to its transport function, RLIP76 has many other cellular and physiological functions based on its domain structure, which includes a unique Ral-binding domain and a Rho GTPase activating protein (RhoGAP-catalytic domain as well as docking sites for multiple signaling proteins. As a Ral effector, RhoGAP, and adapter protein, RLIP76

  18. Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes

    Science.gov (United States)

    Zhang, Yong; Green, Christopher T.; Tick, Geoffrey R.

    2015-01-01

    This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.

  19. Molecular Doping of the Hole-Transporting Layer for Efficient, Single-Step Deposited Colloidal Quantum Dot Photovoltaics

    KAUST Repository

    Kirmani, Ahmad R.

    2017-07-31

    Employment of thin perovskite shells and metal halides as surface-passivants for colloidal quantum dots (CQDs) have been important, recent developments in CQD optoelectronics. These have opened the route to single-step deposited high-performing CQD solar cells. These promising architectures employ a QD hole-transporting layer (HTL) whose intrinsically shallow Fermi level (EF) restricts band-bending at maximum power-point during solar cell operation limiting charge collection. Here, we demonstrate a generalized approach to effectively balance band-edge energy levels of the main CQD absorber and charge-transport layer for these high-performance solar cells. Briefly soaking the QD HTL in a solution of the metal-organic p-dopant, molybdenum tris(1-(trifluoroacetyl)-2-(trifluoromethyl)ethane-1,2-dithiolene), effectively deepens its Fermi level, resulting in enhanced band bending at the HTL:absorber junction. This blocks the back-flow of photo-generated electrons, leading to enhanced photocurrent and fill factor compared to undoped devices. We demonstrate 9.0% perovskite-shelled and 9.5% metal-halide-passivated CQD solar cells, both achieving ca. 10% relative enhancements over undoped baselines.

  20. Surface passivation process of compound semiconductor material using UV photosulfidation

    Science.gov (United States)

    Ashby, Carol I. H.

    1995-01-01

    A method for passivating compound semiconductor surfaces by photolytically disrupting molecular sulfur vapor with ultraviolet radiation to form reactive sulfur which then reacts with and passivates the surface of compound semiconductors.

  1. Assembled microneedle arrays enhance the transport of compounds varying over a large range of molecular weight across human dermatomed skin

    NARCIS (Netherlands)

    Verbaan, F.J.; Bal, S.M.; van den Berg, D.J.; Groenink, W.H.H.; Verpoorten, H.; Lüttge, Regina; Bouwstra, J.A.

    2007-01-01

    In this study, we demonstrate the feasibility to use microneedle arrays manufactured from commercially available 30G hypodermal needles to enhance the transport of compounds up to a molecular weight of 72 kDa. Piercing of human dermatomed skin with microneedle arrays was studied by Trypan Blue

  2. Method for delivery of small molecules and proteins across the cell wall of algae using molecular transporters

    Science.gov (United States)

    Geihe, Erika; Trantow, Brian; Wender, Paul; Hyman, Joel M.; Parvin, Bahram

    2017-11-14

    The introduction of tools to study, control or expand the inner-workings of algae has been slow to develop. Provided are embodiments of a molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing molecular cargos into algal cells. The methods of the disclosure have been shown to work in wild-type algae that have an intact cell wall. Developed using Chlamydomonas reinhardtii, this method is also successful with less studied algae, including Neochloris oleoabundans and Scenedesmus dimorphus, thus providing a new and versatile tool for algal research and modification. The method of delivering a cargo compound to an algal cell comprises contacting an algal cell with a guanidinium-rich delivery vehicle comprising a guanidinium-rich molecular transporter (GR-MoTr) linked to a cargo compound desired to be delivered to the algal cell, whereby the guanidinium-rich molecular transporter can traverse the algal cell wall, thereby delivering the cargo compound to the algal cell.

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

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2018-03-01

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

  4. How molecular motors are arranged on a cargo is important for vesicular transport.

    Directory of Open Access Journals (Sweden)

    Robert P Erickson

    2011-05-01

    Full Text Available The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin, dynein, and myosin. Although much is known about how single motors function, there is significant evidence that cargos in vivo are carried by multiple motors. While some aspects of multiple motor function have received attention, how the cargo itself--and motor organization on the cargo--affects transport has not been considered. To address this, we have developed a three-dimensional Monte Carlo simulation of motors transporting a spherical cargo, subject to thermal fluctuations that produce both rotational and translational diffusion. We found that these fluctuations could exert a load on the motor(s, significantly decreasing the mean travel distance and velocity of large cargos, especially at large viscosities. In addition, the presence of the cargo could dramatically help the motor to bind productively to the microtubule: the relatively slow translational and rotational diffusion of moderately sized cargos gave the motors ample opportunity to bind to a microtubule before the motor/cargo ensemble diffuses out of range of that microtubule. For rapidly diffusing cargos, the probability of their binding to a microtubule was high if there were nearby microtubules that they could easily reach by translational diffusion. Our simulations found that one reason why motors may be approximately 100 nm long is to improve their 'on' rates when attached to comparably sized cargos. Finally, our results suggested that to efficiently regulate the number of active motors, motors should be clustered together rather than spread randomly over the surface of the cargo. While our simulation uses the specific parameters for kinesin, these effects result from generic properties of the motors, cargos, and filaments, so they should apply to other motors as well.

  5. Transport coefficients of hard-sphere mixtures: Theory and Monte Carlo molecular-dynamics calculations for an isotopic mixture

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.

    1989-01-01

    The thermal transport properties of mixtures can be formulated in a number of ways, depending on the choice of driving forces for the transport of heat and matter, without violating the Onsager conditions. Here we treat transport in mixtures based on the driving forces -del ln T and -T del(μ/sub a//T), with T the temperature and μ/sub a/ the specific chemical potential, to obtain the Green-Kubo expressions and the Enskog theory for the corresponding transport coefficients which seem most amenable to molecular-dynamics evaluation. The transport properties of a hard-sphere mixture (mass ratio of 0.1, diameter ratio of 1.0, at a volume of three times close-packed volume), calculated by a Monte Carlo, molecular-dynamics method based on the Green-Kubo formulas, are compared with the predictions of the Enskog theory. The long-time behavior of the Green-Kubo time-correlation functions for shear viscosity, thermal conductivity, thermal diffusion, and mutual diffusion are found to be in good agreement with the predictions of mode-coupling theory. Except for viscosity, the contribution of the long-time tails to the transport coefficients is found to be significant. We obtain values, relative to Enskog, of 1.016 +- 0.007 for shear viscosity, 1.218 +- 0.009 for thermal conductivity, 1.267 +- 0.026 for thermal diffusion, and 1.117 +- 0.008 for mutual diffusion

  6. Sorbate Transport in Carbon Molecular Sieve Membranes and FAU/EMT Intergrowth by Diffusion NMR

    Directory of Open Access Journals (Sweden)

    John J. Low

    2012-02-01

    Full Text Available In this paper we present and discuss selected results of our recent studies of sorbate self-diffusion in microporous materials. The main focus is given to transport properties of carbon molecular sieve (CMS membranes as well as of the intergrowth of FAU-type and EMT-type zeolites. CMS membranes show promise for applications in separations of mixtures of small gas molecules, while FAU/EMT intergrowth can be used as an active and selective cracking catalyst. For both types of applications diffusion of guest molecules in the micropore networks of these materials is expected to play an important role. Diffusion studies were performed by a pulsed field gradient (PFG NMR technique that combines advantages of high field (17.6 T NMR and high magnetic field gradients (up to 30 T/m. This technique has been recently introduced at the University of Florida in collaboration with the National Magnet Lab. In addition to a more conventional proton PFG NMR, also carbon-13 PFG NMR was used.

  7. Anomalous transport of charged dust grains in a magnetized collisional plasma: A molecular dynamics study

    Science.gov (United States)

    Bezbaruah, Pratikshya; Das, Nilakshi

    2018-05-01

    Anomalous diffusion of charged dust grains immersed in a plasma in the presence of strong ion-neutral collision, flowing ions, and a magnetic field has been observed. Molecular Dynamics simulation confirms the deviation from normal diffusion in an ensemble of dust grains probed in laboratory plasma chambers. Collisional effects are significant in governing the nature of diffusion. In order to have a clear idea on the transport of particles in a real experimental situation, the contribution of streaming ions and the magnetic field along with collision is considered through the relevant interaction potential. The nonlinear evolution of Mean Square Displacement is an indication of the modification in particle trajectories due to several effects as mentioned above. It is found that strong collision and ion flow significantly affect the interparticle interaction potential in the presence of the magnetic field and lead to the appearance of the asymmetric type of Debye Hückel (D H) potential. Due to the combined effect of the magnetic field, ion flow, and collision, dusty plasma exhibits a completely novel behavior. The coupling parameter Γ enhances the asymmetric D H type potential arising due to ion flow, and this may drive the system to a disordered state.

  8. Proposal of flexible atomic and molecular process management for Monte Carlo impurity transport code based on object oriented method

    International Nuclear Information System (INIS)

    Asano, K.; Ohno, N.; Takamura, S.

    2001-01-01

    Monte Carlo simulation code on impurity transport has been developed by several groups to be utilized mainly for fusion related edge plasmas. State of impurity particle is determined by atomic and molecular processes such as ionization, charge exchange in plasma. A lot of atomic and molecular processes have been considered because the edge plasma has not only impurity atoms, but also impurity molecules mainly related to chemical erosion of carbon materials, and their cross sections have been given experimentally and theoretically. We need to reveal which process is essential in a given edge plasma condition. Monte Carlo simulation code, which takes such various atomic and molecular processes into account, is necessary to investigate the behavior of impurity particle in plasmas. Usually, the impurity transport simulation code has been intended for some specific atomic and molecular processes so that the introduction of a new process forces complicated programming work. In order to evaluate various proposed atomic and molecular processes, a flexible management of atomic and molecular reaction should be established. We have developed the impurity transport simulation code based on object-oriented method. By employing object-oriented programming, we can handle each particle as 'object', which enfolds data and procedure function itself. A user (notice, not programmer) can define property of each particle species and the related atomic and molecular processes and then each 'object' is defined by analyzing this information. According to the relation among plasma particle species, objects are connected with each other and change their state by themselves. Dynamic allocation of these objects to program memory is employed to adapt for arbitrary number of species and atomic/molecular reactions. Thus we can treat arbitrary species and process starting from, for instance, methane and acetylene. Such a software procedure would be useful also for industrial application plasmas

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  10. Micromechanism of oxygen transport during initial stage oxidation in Si(100) surface: A ReaxFF molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Yu, E-mail: yu.sun@xjtu.edu.cn [State Key Laboratory for Manufacturing Systems Engineering, School of Mechanical Engineering, Xi’an Jiaotong University, Xi’an 710049 (China); Institute for Computational Mechanics and Its Applications, Northwestern Polytechnical University, Xi’an 710072 (China); Liu, Yilun [State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi’an Jiaotong University, Xi’an 710049 (China); Chen, Xuefeng; Zhai, Zhi [State Key Laboratory for Manufacturing Systems Engineering, School of Mechanical Engineering, Xi’an Jiaotong University, Xi’an 710049 (China); Xu, Fei [Institute for Computational Mechanics and Its Applications, Northwestern Polytechnical University, Xi’an 710072 (China); Liu, Yijun [Institute for Computational Mechanics and Its Applications, Northwestern Polytechnical University, Xi’an 710072 (China); Mechanical Engineering, University of Cincinnati, Cincinnati, OH 45221-0072 (United States)

    2017-06-01

    Highlights: • A competition mechanism between thermal actuation and compressive stress blocking was found for the oxygen transport. • At low temperature, a compressive stress was generated in the oxide layer which blocked oxygen transport into the deeper region. • O atoms gained larger possibility to go deeper inward as temperature increase. • The related film quality was well explained by the competition mechanism. - Abstract: The early stage oxidation in Si(100) surface has been investigated in this work by a reactive force field molecular dynamics (ReaxFF MD) simulation, manifesting that the oxygen transport acted as a dominant issue for initial oxidation process. Due to the oxidation, a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Si(100) surface and further prevented oxidation in the deeper layer. In contrast, thermal actuation was beneficial to the oxygen transport into deeper layer as temperature increases. Therefore, a competition mechanism was found for the oxygen transport during early stage oxidation in Si(100) surface. At room temperature, the oxygen transport was governed by the blocking effect of compressive stress, so a better quality oxide film with more uniform interface and more stoichiometric oxide structure was obtained. Indeed, the mechanism presented in this work is also applicable for other self-limiting oxidation (e.g. metal oxidation) and is helpful for the design of high-performance electronic devices.

  11. Micromechanism of oxygen transport during initial stage oxidation in Si(100) surface: A ReaxFF molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Sun, Yu; Liu, Yilun; Chen, Xuefeng; Zhai, Zhi; Xu, Fei; Liu, Yijun

    2017-01-01

    Highlights: • A competition mechanism between thermal actuation and compressive stress blocking was found for the oxygen transport. • At low temperature, a compressive stress was generated in the oxide layer which blocked oxygen transport into the deeper region. • O atoms gained larger possibility to go deeper inward as temperature increase. • The related film quality was well explained by the competition mechanism. - Abstract: The early stage oxidation in Si(100) surface has been investigated in this work by a reactive force field molecular dynamics (ReaxFF MD) simulation, manifesting that the oxygen transport acted as a dominant issue for initial oxidation process. Due to the oxidation, a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Si(100) surface and further prevented oxidation in the deeper layer. In contrast, thermal actuation was beneficial to the oxygen transport into deeper layer as temperature increases. Therefore, a competition mechanism was found for the oxygen transport during early stage oxidation in Si(100) surface. At room temperature, the oxygen transport was governed by the blocking effect of compressive stress, so a better quality oxide film with more uniform interface and more stoichiometric oxide structure was obtained. Indeed, the mechanism presented in this work is also applicable for other self-limiting oxidation (e.g. metal oxidation) and is helpful for the design of high-performance electronic devices.

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

    International Nuclear Information System (INIS)

    Li Zongliang; Zou Bin; Wang Chuankui; Luo Yi

    2006-01-01

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

  13. Compositional properties of passivity

    NARCIS (Netherlands)

    Kerber, Florian; van der Schaft, Arjan

    2011-01-01

    The classical passivity theorem states that the negative feedback interconnection of passive systems is again passive. The converse statement, - passivity of the interconnected system implies passivity of the subsystems -, turns out to be equally valid. This result implies that among all feasible

  14. The role of biomembrane lipids in the molecular mechanism of ion transport radiation damage

    International Nuclear Information System (INIS)

    Medvedev, B.I.; Evtodienko, Yu.V.; Yaguzhinsky, L.S.; Kuzin, A.M.

    1977-01-01

    Increase in the rate of ATP synthesis (I.4-I.6 times), Ca 2+ -capacity (I.4-I.8 times), membrane potential (by 20-50 mv) and decrease in K - -conductivity (2.5-3 times) in rat liver mitochondria was observed three hours after γ-irradiation at a dose of 1000r. The process of oxidative phosphorylation was normalized 24 hours later, whereas damages of Ca 2+ -accumulation and K + -conductivity remain. The molecular mechanism of reduction in K + -permeability of mitochondrial membranes has been studied. The endogenous regulators of ionic transport in the lipid phase of mitochondrial biomembranes were investigated before and after γ-irradiation. It was revealed that K + -conductivity of the artificial phospholipid membranes (APM) formed of the phospholipids from irradiated mitochondria was substantially lower than that in the control. Using thin-layer chromatography the minor phospholipid fraction which increases K + -conductivity of APM was isolated from the lipids of unirradiated mitochondria. In the lipid preparations of irradiated mitochondria the minor phospholipid fraction content is sharply lowered (or absent at all). Besides the content of lysoforms of phosphatidylcholine and phosphatidylethanolamine as well as that of fatty acids and cholesterol esters were reduced 24 hours after irradiation. Three compounds with different capability to increase the APM conductivity for monovalent ions were revealed in the composition of the minor fraction. One of these components was shown to be lysopolyglycerophosphatide (lysodiphosphatidylglycerol). The role of the enzyme systems involved in radiational changes of the membrane lipid components and the importance of these phenomena for cell radiosensitivity will be discussed

  15. Molecular evidence for an involvement of organic anion transporters (OATs) in aristolochic acid nephropathy

    International Nuclear Information System (INIS)

    Bakhiya, Nadiya; Arlt, Volker M.; Bahn, Andrew; Burckhardt, Gerhard; Phillips, David H.; Glatt, Hansruedi

    2009-01-01

    Aristolochic acid (AA), present in Aristolochia species, is the major causative agent in the development of severe renal failure and urothelial cancers in patients with AA nephropathy. It may also be a cause of Balkan endemic nephropathy. Epithelial cells of the proximal tubule are the primary cellular target of AA. To study whether organic anion transporters (OATs) expressed in proximal tubule cells are involved in uptake of AA, we used human epithelial kidney (HEK293) cells stably expressing human (h) OAT1, OAT3 or OAT4. AA potently inhibited the uptake of characteristic substrates, p-aminohippurate for hOAT1 and estrone sulfate for hOAT3 and hOAT4. Aristolochic acid I (AAI), the more cytotoxic and genotoxic AA congener, exhibited high affinity for hOAT1 (K i = 0.6 μM) as well as hOAT3 (K i = 0.5 μM), and lower affinity for hOAT4 (K i = 20.6 μM). Subsequently, AAI-DNA adduct formation (investigated by 32 P-postlabelling) was used as a measure of AAI uptake. Significantly higher levels of adducts occurred in hOAT-expressing cells than in control cells: this effect was abolished in the presence of the OAT inhibitor probenecid. In Xenopus laevis oocytes hOAT-mediated efflux of p-aminohippurate was trans-stimulated by extracellular AA, providing further molecular evidence for AA translocation by hOATs. Our study indicates that OATs can mediate the uptake of AA into proximal tubule cells and thereby participate in kidney cell damage by this toxin.

  16. Molecular features contributing to virus-independent intracellular localization and dynamic behavior of the herpesvirus transport protein US9.

    Directory of Open Access Journals (Sweden)

    Manuela Pedrazzi

    Full Text Available Reaching the right destination is of vital importance for molecules, proteins, organelles, and cargoes. Thus, intracellular traffic is continuously controlled and regulated by several proteins taking part in the process. Viruses exploit this machinery, and viral proteins regulating intracellular transport have been identified as they represent valuable tools to understand and possibly direct molecules targeting and delivery. Deciphering the molecular features of viral proteins contributing to (or determining this dynamic phenotype can eventually lead to a virus-independent approach to control cellular transport and delivery. From this virus-independent perspective we looked at US9, a virion component of Herpes Simplex Virus involved in anterograde transport of the virus inside neurons of the infected host. As the natural cargo of US9-related vesicles is the virus (or its parts, defining its autonomous, virus-independent role in vesicles transport represents a prerequisite to make US9 a valuable molecular tool to study and possibly direct cellular transport. To assess the extent of this autonomous role in vesicles transport, we analyzed US9 behavior in the absence of viral infection. Based on our studies, Us9 behavior appears similar in different cell types; however, as expected, the data we obtained in neurons best represent the virus-independent properties of US9. In these primary cells, transfected US9 mostly recapitulates the behavior of US9 expressed from the viral genome. Additionally, ablation of two major phosphorylation sites (i.e. Y32Y33 and S34ES36 have no effect on protein incorporation on vesicles and on its localization on both proximal and distal regions of the cells. These results support the idea that, while US9 post-translational modification may be important to regulate cargo loading and, consequently, virion export and delivery, no additional viral functions are required for US9 role in intracellular transport.

  17. Double path integral method for obtaining the mobility of the one-dimensional charge transport in molecular chain.

    Science.gov (United States)

    Yoo-Kong, Sikarin; Liewrian, Watchara

    2015-12-01

    We report on a theoretical investigation concerning the polaronic effect on the transport properties of a charge carrier in a one-dimensional molecular chain. Our technique is based on the Feynman's path integral approach. Analytical expressions for the frequency-dependent mobility and effective mass of the carrier are obtained as functions of electron-phonon coupling. The result exhibits the crossover from a nearly free particle to a heavily trapped particle. We find that the mobility depends on temperature and decreases exponentially with increasing temperature at low temperature. It exhibits large polaronic-like behaviour in the case of weak electron-phonon coupling. These results agree with the phase transition (A.S. Mishchenko et al., Phys. Rev. Lett. 114, 146401 (2015)) of transport phenomena related to polaron motion in the molecular chain.

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

    Science.gov (United States)

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

    2017-11-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  20. Charge transport in organic molecular semiconductors from first principles: The bandlike hole mobility in a naphthalene crystal

    Science.gov (United States)

    Lee, Nien-En; Zhou, Jin-Jian; Agapito, Luis A.; Bernardi, Marco

    2018-03-01

    Predicting charge transport in organic molecular crystals is notoriously challenging. Carrier mobility calculations in organic semiconductors are dominated by quantum chemistry methods based on charge hopping, which are laborious and only moderately accurate. We compute from first principles the electron-phonon scattering and the phonon-limited hole mobility of naphthalene crystal in the framework of ab initio band theory. Our calculations combine GW electronic bandstructures, ab initio electron-phonon scattering, and the Boltzmann transport equation. The calculated hole mobility is in very good agreement with experiment between 100 -300 K , and we can predict its temperature dependence with high accuracy. We show that scattering between intermolecular phonons and holes regulates the mobility, though intramolecular phonons possess the strongest coupling with holes. We revisit the common belief that only rigid molecular motions affect carrier dynamics in organic molecular crystals. Our paper provides a quantitative and rigorous framework to compute charge transport in organic crystals and is a first step toward reconciling band theory and carrier hopping computational methods.

  1. Mechanical and charge transport properties of alkanethiol self-assembled monolayers on Au (111) surface: The Role of Molecular Tilt

    Energy Technology Data Exchange (ETDEWEB)

    Mulleregan, Alice; Qi, Yabing; Ratera, Imma; Park, Jeong Y.; Ashby, Paul D.; Quek, Su Ying; Neaton, J. B.; Salmeron, Miquel

    2007-11-12

    The relationship between charge transport and mechanical properties of alkanethiol self-assembled monolayers (SAM) on Au(111) films has been investigated using an atomic force microscope with a conductive tip. Molecular tilts induced by the pressure applied by the tip cause stepwise increases in film conductivity. A decay constant {beta} = 0.57 {+-} 0.03 {angstrom}{sup -1} was found for the current passing through the film as a function of tip-substrate separation due to this molecular tilt. This is significantly smaller than the value of {approx} 1 {angstrom}{sup -1} found when the separation is changed by changing the length of the alkanethiol molecules. Calculations indicate that for isolated dithiol molecules S-bonded to hollow sites, the junction conductance does not vary significantly as a function of molecular tilt. The impact of S-Au bonding on SAM conductance is discussed.

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

    Science.gov (United States)

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

    2017-05-01

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

  3. Passive heat removal in CANDU

    International Nuclear Information System (INIS)

    Hart, R.S.

    1997-01-01

    CANDU has a tradition of incorporating passive systems and passive components whenever they are shown to offer performance that is equal to or better than that of active systems, and to be economic. Examples include the two independent shutdown systems that employ gravity and stored energy respectively, the dousing subsystem of the CANDU 6 containment system, and the ability of the moderator to cool the fuel in the event that all coolant is lost from the fuel channels. CANDU 9 continues this tradition, incorporating a reserve water system (RWS) that increases the inventory of water in the reactor building and profiles a passive source of makeup water and/or heat sinks to various key process systems. The key component of the CANDU 9 reserve water system is a large (2500 cubic metres) water tank located at a high elevation in the reactor building. The reserve water system, while incorporating the recovery system functions, and the non-dousing functions of the dousing tank in CANDU 6, embraces other key systems to significantly extend the passive makeup/heat sink capability. The capabilities of the reserve water system include makeup to the steam generators secondary side if all other sources of water are lost; makeup to the heat transport system in the event of a leak in excess of the D 2 O makeup system capability; makeup to the moderator in the event of a moderator leak when the moderator heat sink is required; makeup to the emergency core cooling (ECC) system to assure NPSH to the ECC pumps during a loss of coolant accident (LOCA), and provision of a passive heat sink for the shield cooling system. Other passive designs are now being developed by AECL. These will be incorporated in future CANDU plants when their performance has been fully proven. This paper reviews the passive heat removal systems and features of current CANDU plants and the CANDU 9, and briefly reviews some of the passive heat removal concepts now being developed. (author)

  4. Transport of sewage molecular markers through saturated soil column and effect of easily biodegradable primary substrate on their removal.

    Science.gov (United States)

    Foolad, Mahsa; Ong, Say Leong; Hu, Jiangyong

    2015-11-01

    Pharmaceutical and personal care products (PPCPs) and artificial sweeteners (ASs) are emerging organic contaminants (EOCs) in the aquatic environment. The presence of PPCPs and ASs in water bodies has an ecologic potential risk and health concern. Therefore, it is needed to detect the pollution sources by understanding the transport behavior of sewage molecular markers in a subsurface area. The aim of this study was to evaluate transport of nine selected molecular markers through saturated soil column experiments. The selected sewage molecular markers in this study were six PPCPs including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), crotamiton (CTMT), diethyltoluamide (DEET), salicylic acid (SA) and three ASs including acesulfame (ACF), cyclamate (CYC), and saccharine (SAC). Results confirmed that ACF, CBZ, CTMT, CYC and SAC were suitable to be used as sewage molecular markers since they were almost stable against sorption and biodegradation process during soil column experiments. In contrast, transport of ACT, CF and DEET were limited by both sorption and biodegradation processes and 100% removal efficiency was achieved in the biotic column. Moreover, in this study the effect of different acetate concentration (0-100mg/L) as an easily biodegradable primary substrate on a removal of PPCPs and ASs was also studied. Results showed a negative correlation (r(2)>0.75) between the removal of some selected sewage chemical markers including ACF, CF, ACT, CYC, SAC and acetate concentration. CTMT also decreased with the addition of acetate, but increasing acetate concentration did not affect on its removal. CBZ and DEET removal were not dependent on the presence of acetate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Stochastic models of intracellular transport

    KAUST Repository

    Bressloff, Paul C.; Newby, Jay M.

    2013-01-01

    mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually

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

    Science.gov (United States)

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

    2017-12-06

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

  7. Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

    Science.gov (United States)

    Bosko, Jaroslaw T.; Ravi Prakash, J.

    2008-01-01

    Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

  8. Transportation

    National Research Council Canada - National Science Library

    Adams, James; Carr, Ron; Chebl, Maroun; Coleman, Robert; Costantini, William; Cox, Robert; Dial, William; Jenkins, Robert; McGovern, James; Mueller, Peter

    2006-01-01

    ...., trains, ships, etc.) and maximizing intermodal efficiency. A healthy balance must be achieved between the flow of international commerce and security requirements regardless of transportation mode...

  9. DELINEATING THE MOLECULAR BASIS FOR CONSTITUTIVE INTERNALIZATION AND DEGRADATION OF THE DOPAMINE TRANSPORTER

    DEFF Research Database (Denmark)

    Fog, Jacob; (Vægter), Christian Bjerggaard; Gether, Ulrik

    The human dopamine transporter (hDAT) was transiently expressed in N2A neuroblastoma cells. Confocal fluorescence microscopy revealed efficient surface targeting of the transporter in undifferentiated cells as well as in differentiated cells. In the differentiated cells the hDAT displayed...

  10. Large modulation of carrier transport by grain-boundary molecular packing and microstructure in organic thin films

    KAUST Repository

    Rivnay, Jonathan

    2009-11-08

    Solution-processable organic semiconductors are central to developing viable printed electronics, and performance comparable to that of amorphous silicon has been reported for films grown from soluble semiconductors. However, the seemingly desirable formation of large crystalline domains introduces grain boundaries, resulting in substantial device-to-device performance variations. Indeed, for films where the grain-boundary structure is random, a few unfavourable grain boundaries may dominate device performance. Here we isolate the effects of molecular-level structure at grain boundaries by engineering the microstructure of the high-performance n-type perylenediimide semiconductor PDI8-CN 2 and analyse their consequences for charge transport. A combination of advanced X-ray scattering, first-principles computation and transistor characterization applied to PDI8-CN 2 films reveals that grain-boundary orientation modulates carrier mobility by approximately two orders of magnitude. For PDI8-CN 2 we show that the molecular packing motif (that is, herringbone versus slip-stacked) plays a decisive part in grain-boundary-induced transport anisotropy. The results of this study provide important guidelines for designing device-optimized molecular semiconductors. © 2009 Macmillan Publishers Limited. All rights reserved.

  11. Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

    Science.gov (United States)

    Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

    2017-09-14

    The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

  12. Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Liping eSun

    2016-02-01

    Full Text Available Sucrose-specific porin (ScrY is a transmembrane protein that allows for the uptake of sucrose under growth-limiting conditions. The crystal structure of ScrY was resolved before by X-ray crystallography, both in its uncomplexed form and with bound sucrose. However, little is known about the molecular characteristics of the transport mechanism of ScrY. To date, there has not yet been any clear demonstration for sucrose transport through the ScrY.Here, the dynamics of the ScrY trimer embedded in a phospholipid bilayer as well as the characteristics of sucrose translocation were investigated by means of atomistic molecular dynamics (MD simulations. The potential of mean force (PMF for sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Energy decomposition allowed to pinpoint three aspartic acids as key residues opposing the passage of sucrose, all located within the L3 loop. Mutation of two aspartic acids to uncharged residues resulted in an accordingly modified electrostatics and decreased PMF barrier. The chosen methodology and results will aid in the design of porins with modified transport specificities.

  13. Transportation

    International Nuclear Information System (INIS)

    Anon.

    1998-01-01

    Here is the decree of the thirtieth of July 1998 relative to road transportation, to trade and brokerage of wastes. It requires to firms which carry out a road transportation as well as to traders and to brokers of wastes to declare their operations to the prefect. The declaration has to be renewed every five years. (O.M.)

  14. Passive solar technology

    Energy Technology Data Exchange (ETDEWEB)

    Watson, D

    1981-04-01

    The present status of passive solar technology is summarized, including passive solar heating, cooling and daylighting. The key roles of the passive solar system designer and of innovation in the building industry are described. After definitions of passive design and a summary of passive design principles are given, performance and costs of passive solar technology are discussed. Passive energy design concepts or methods are then considered in the context of the overall process by which building decisions are made to achieve the integration of new techniques into conventional design. (LEW).

  15. Coarse-grained molecular dynamics simulation of transport through the nuclear pore complex

    NARCIS (Netherlands)

    Ghavami, Ali

    2014-01-01

    Dit proefschrift is gewijd aan het mechanisme van Nucleo - cytoplasmatisch transport openbaren door grofkorrelige moleculaire dynamica simulaties van ontvouwen eiwitten in de nucleaire porie complex (NPC) . NPC's zijn zeer selectief poorten, die alle transporten over nucleaire envelop controleren .

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

    OpenAIRE

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

    2005-01-01

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

  17. Molecular mechanism of α-tocopheryl-phosphate transport across the cell membrane

    International Nuclear Information System (INIS)

    Negis, Yesim; Meydani, Mohsen; Zingg, Jean-Marc; Azzi, Angelo

    2007-01-01

    α-Tocopheryl-phosphate (α-TP) is synthesized and hydrolyzed in animal cells and tissues where it modulates several functions. α-TP is more potent than α-T in inhibiting cell proliferation, down-regulating CD36 transcription, inhibiting atherosclerotic plaque formation. Administration of α-TP to cells or animals requires its transfer through membranes, via a transporter. We show here that α-TP is passing the plasma membrane via a system that is inhibited by glibenclamide and probenecid, inhibitors of a number of transporters. Glibenclamide and probenecid prevent dose-dependently α-TP inhibition of cell proliferation. The two inhibitors act on ATP binding cassette (ABC) and organic anion transporters (OAT). Since ABC transporters function to export solutes and α-TP is transported into cells, it may be concluded that α-TP transport may occur via an OAT family member. Due to the protection by glibenclamide and probenecid on the α-TP induced cell growth inhibition it appears that α-TP acts after its uptake inside cells

  18. Molecular Cloning and Functional Analysis of a Na+-Insensitive K+ Transporter of Capsicum chinense Jacq

    Science.gov (United States)

    Ruiz-Lau, Nancy; Bojórquez-Quintal, Emanuel; Benito, Begoña; Echevarría-Machado, Ileana; Sánchez-Cach, Lucila A.; Medina-Lara, María de Fátima; Martínez-Estévez, Manuel

    2016-01-01

    High-affinity K+ (HAK) transporters are encoded by a large family of genes and are ubiquitous in the plant kingdom. These HAK-type transporters participate in low- and high-affinity potassium (K+) uptake and are crucial for the maintenance of K+ homeostasis under hostile conditions. In this study, the full-length cDNA of CcHAK1 gene was isolated from roots of the habanero pepper (Capsicum chinense). CcHAK1 expression was positively regulated by K+ starvation in roots and was not inhibited in the presence of NaCl. Phylogenetic analysis placed the CcHAK1 transporter in group I of the HAK K+ transporters, showing that it is closely related to Capsicum annuum CaHAK1 and Solanum lycopersicum LeHAK5. Characterization of the protein in a yeast mutant deficient in high-affinity K+ uptake (WΔ3) suggested that CcHAK1 function is associated with high-affinity K+ uptake, with Km and Vmax for Rb of 50 μM and 0.52 nmol mg−1 min−1, respectively. K+ uptake in yeast expressing the CcHAK1 transporter was inhibited by millimolar concentrations of the cations ammonium (NH4+) and cesium (Cs+) but not by sodium (Na+). The results presented in this study suggest that the CcHAK1 transporter may contribute to the maintenance of K+ homeostasis in root cells in C. chinense plants undergoing K+-deficiency and salt stress. PMID:28083010

  19. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

    Science.gov (United States)

    Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

    2018-04-01

    Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. A new approach to calculate charge carrier transport mobility in organic molecular crystals from imaginary time path integral simulations

    International Nuclear Information System (INIS)

    Song, Linze; Shi, Qiang

    2015-01-01

    We present a new non-perturbative method to calculate the charge carrier mobility using the imaginary time path integral approach, which is based on the Kubo formula for the conductivity, and a saddle point approximation to perform the analytic continuation. The new method is first tested using a benchmark calculation from the numerical exact hierarchical equations of motion method. Imaginary time path integral Monte Carlo simulations are then performed to explore the temperature dependence of charge carrier delocalization and mobility in organic molecular crystals (OMCs) within the Holstein and Holstein-Peierls models. The effects of nonlocal electron-phonon interaction on mobility in different charge transport regimes are also investigated

  1. Transportation

    National Research Council Canada - National Science Library

    Allshouse, Michael; Armstrong, Frederick Henry; Burns, Stephen; Courts, Michael; Denn, Douglas; Fortunato, Paul; Gettings, Daniel; Hansen, David; Hoffman, D. W; Jones, Robert

    2007-01-01

    .... The ability of the global transportation industry to rapidly move passengers and products from one corner of the globe to another continues to amaze even those wise to the dynamics of such operations...

  2. An exact approach for studying cargo transport by an ensemble of molecular motors

    International Nuclear Information System (INIS)

    Materassi, Donatello; Roychowdhury, Subhrajit; Hays, Thomas; Salapaka, Murti

    2013-01-01

    Intracellular transport is crucial for many cellular processes where a large fraction of the cargo is transferred by motor-proteins over a network of microtubules. Malfunctions in the transport mechanism underlie a number of medical maladies. Existing methods for studying how motor-proteins coordinate the transfer of a shared cargo over a microtubule are either analytical or are based on Monte-Carlo simulations. Approaches that yield analytical results, while providing unique insights into transport mechanism, make simplifying assumptions, where a detailed characterization of important transport modalities is difficult to reach. On the other hand, Monte-Carlo based simulations can incorporate detailed characteristics of the transport mechanism; however, the quality of the results depend on the number and quality of simulation runs used in arriving at results. Here, for example, it is difficult to simulate and study rare-events that can trigger abnormalities in transport. In this article, a semi-analytical methodology that determines the probability distribution function of motor-protein behavior in an exact manner is developed. The method utilizes a finite-dimensional projection of the underlying infinite-dimensional Markov model, which retains the Markov property, and enables the detailed and exact determination of motor configurations, from which meaningful inferences on transport characteristics of the original model can be derived. Under this novel probabilistic approach new insights about the mechanisms of action of these proteins are found, suggesting hypothesis about their behavior and driving the design and realization of new experiments. The advantages provided in accuracy and efficiency make it possible to detect rare events in the motor protein dynamics, that could otherwise pass undetected using standard simulation methods. In this respect, the model has allowed to provide a possible explanation for possible mechanisms under which motor proteins could

  3. Fundamental studies of passivity and passivity breakdown

    International Nuclear Information System (INIS)

    Macdonald, D.D.; Urquidi-Macdonald, M.; Song, H.; Biaggio-Rocha, S.; Searson, P.

    1991-11-01

    This report summarizes the findings of our fundamental research program on passivity and passivity breakdown. During the past three and one half years in this program (including the three year incrementally-funded grant prior to the present grant), we developed and experimentally tested various physical models for the growth and breakdown of passive films on metal surfaces. These models belong to a general class termed ''point defects models'' (PDMs), in which the growth and breakdown of passive films are described in terms of the movement of anion and cation vacancies

  4. Adaptive Green-Kubo estimates of transport coefficients from molecular dynamics based on robust error analysis

    Science.gov (United States)

    Jones, Reese E.; Mandadapu, Kranthi K.

    2012-04-01

    We present a rigorous Green-Kubo methodology for calculating transport coefficients based on on-the-fly estimates of: (a) statistical stationarity of the relevant process, and (b) error in the resulting coefficient. The methodology uses time samples efficiently across an ensemble of parallel replicas to yield accurate estimates, which is particularly useful for estimating the thermal conductivity of semi-conductors near their Debye temperatures where the characteristic decay times of the heat flux correlation functions are large. Employing and extending the error analysis of Zwanzig and Ailawadi [Phys. Rev. 182, 280 (1969)], 10.1103/PhysRev.182.280 and Frenkel [in Proceedings of the International School of Physics "Enrico Fermi", Course LXXV (North-Holland Publishing Company, Amsterdam, 1980)] to the integral of correlation, we are able to provide tight theoretical bounds for the error in the estimate of the transport coefficient. To demonstrate the performance of the method, four test cases of increasing computational cost and complexity are presented: the viscosity of Ar and water, and the thermal conductivity of Si and GaN. In addition to producing accurate estimates of the transport coefficients for these materials, this work demonstrates precise agreement of the computed variances in the estimates of the correlation and the transport coefficient with the extended theory based on the assumption that fluctuations follow a Gaussian process. The proposed algorithm in conjunction with the extended theory enables the calculation of transport coefficients with the Green-Kubo method accurately and efficiently.

  5. Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

    Science.gov (United States)

    Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

    2018-04-01

    The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

  6. Molecular and functional characterization of riboflavin specific transport system in rat brain capillary endothelial cells

    Science.gov (United States)

    Patel, Mitesh; Vadlapatla, Ramya Krishna; Pal, Dhananjay; Mitra, Ashim K.

    2012-01-01

    Riboflavin is an important water soluble vitamin (B2) required for metabolic reactions, normal cellular growth, differentiation and function. Mammalian brain cells cannot synthesize riboflavin and must import from systemic circulation. However, the uptake mechanism, cellular translocation and intracellular trafficking of riboflavin in brain capillary endothelial cells are poorly understood. The primary objective of this study is to investigate the existence of riboflavin-specific transport system and delineate the uptake and intracellular regulation of riboflavin in immortalized rat brain capillary endothelial cells (RBE4). The uptake of [3H]-Riboflavin is sodium, temperature and energy dependent but pH independent. [3H]-Riboflavin uptake is saturable with Km and Vmax values of 19 ± 3 µM and 0.235 ± 0.012 picomoles/min/mg protein, respectively. The uptake process is inhibited by unlabelled structural analogs (lumiflavin, lumichrome) but not by structurally unrelated vitamins. Ca++/calmodulin and protein kinase A (PKA) pathways are found to play an important role in the intracellular regulation of [3H]-Riboflavin. Apical and baso-lateral uptake of [3H]-Riboflavin clearly indicate that riboflavin specific transport system is predominantly localized on the apical side of RBE4 cells. A 628 bp band corresponding to riboflavin transporter is revealed in RT-PCR analysis. These findings, for the first time report the existence of a specialized and high affinity transport system for riboflavin in RBE4 cells. Blood-brain barrier (BBB) is a major obstacle limiting drug transport inside the brain as it regulates drug permeation from systemic circulation. This transporter can be utilized for targeted delivery in enhancing brain permeation of highly potent drugs on systemic administration. PMID:22683359

  7. Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model.

    Science.gov (United States)

    Patel, Saumya K; Khedkar, Vijay M; Jha, Prakash C; Jasrai, Yogesh T; Pandya, Himanshu A; George, Linz-Buoy; Highland, Hyacinth N; Skelton, Adam A

    2016-01-01

    Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to chloroquine (CQ), a widely used antimalarial drug, is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein and development of charged environment to mimic a condition of resistance. The model of PfCRT was developed using Protein homology/analogy engine (PHYRE ver 0.2) and was validated based on the results obtained using PSI-PRED. Subsequently, molecular interactions of selected phytochemicals extracted from C. roseus Linn. and T. indica were studied using multiple-iterated genetic algorithm-based docking protocol in order to investigate the translocation of these legends across the PfCRT protein. Further, molecular dynamics studies exhibiting interaction energy estimates of these compounds within the active site of the protein showed that compounds are more selective toward PfCRT. Clusters of conformations with the free energy of binding were estimated which clearly demonstrated the potential channel and by this means the translocation across the PfCRT is anticipated.

  8. A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

    Science.gov (United States)

    Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

    2018-05-08

    Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

  9. Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

    DEFF Research Database (Denmark)

    Obersteiner, Veronika; Huhs, Georg; Papior, Nick Rübner

    2017-01-01

    Metal-molecule-metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution we highlight the fundamental differences between single-molecule and ensemble ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M. [Department of Mechanical Engineering Bangladesh University of Engineering and Technology (BUET) Dhaka (Bangladesh)

    2016-07-12

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

  11. Fabrication and Molecular Transport Studies of Highly c-Oriented AFI Membranes

    KAUST Repository

    Liu, Yang; Zhang, Bing; Liu, Defei; Sheng, Ping; Lai, Zhiping

    2017-01-01

    -packed and c-oriented monolayer of plate-like seeds that is manually assembled on a porous alumina support. The straight channels in the membrane are not only aligned vertically along the membrane depth, but are also continuous without disruption. The transport

  12. Nanostructured ZnO films: A study of molecular influence on transport properties by impedance spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sappia, Luciano D.; Trujillo, Matias R. [Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET, Chacabuco 461, T4000ILI San Miguel de Tucumán (Argentina); Laboratorio de Medios e Interfases (LAMEIN), Departamento de Bioingeniería, Fac. de Cs. Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, 4000 San Miguel de Tucumán (Argentina); Lorite, Israel [Division of Superconductivity and Magnetism, Institute for Experimental Physics II, University of Leipzig, Linnéstrasse 5, 04103 Leipzig (Germany); Madrid, Rossana E., E-mail: rmadrid@herrera.unt.edu.ar [Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET, Chacabuco 461, T4000ILI San Miguel de Tucumán (Argentina); Laboratorio de Medios e Interfases (LAMEIN), Departamento de Bioingeniería, Fac. de Cs. Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, 4000 San Miguel de Tucumán (Argentina); Tirado, Monica [NanoProject and Laboratorio de Nanomateriales y Propiedades Dieléctricas, Departamento de Física, Universidad Nacional de Tucumán, Avenida Independencia 1800, Tucumán (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Argentina); and others

    2015-10-15

    Graphical abstract: - Highlights: • We study electrical transport in nanostructured ZnO films by impedance spectroscopy. • Bioaggregates on the surface produce strong changes in film transport properties. • This behavior is explained by modeling data with RC parallel circuits. • Electrical responses of ZnO films to aggregates are promising for biosensing. - Abstract: Nanomaterials based on ZnO have been used to build glucose sensors due to its high isoelectric point, which is important when a protein like Glucose Oxidase (GOx) is attached to a surface. It also creates a biologically friendly environment to preserve the activity of the enzyme. In this work we study the electrical transport properties of ZnO thin films (TFs) and single crystals (SC) in contact with different solutions by using impedance spectroscopy. We have found that the composition of the liquid, by means of the charge of the ions, produces strong changes in the transport properties of the TF. The enzyme GOx and phosphate buffer solutions have the major effect in the conduction through the films, which can be explained by the entrapment of carriers at the grain boundaries of the TFs. These results can help to design a new concept in glucose biosensing.

  13. Electron-phonon scattering from Green’s function transport combined with molecular dynamics

    DEFF Research Database (Denmark)

    Markussen, Troels; Palsgaard, Mattias Lau Nøhr; Stradi, Daniele

    2017-01-01

    approach by comparing to mobilities and conductivities obtained by the Boltzmann transport equation for different bulk and one-dimensional systems. For bulk silicon and gold we compare against experimental values. We discuss limitations and advantages of each of the computational approaches....

  14. Molecular Engineering of Non-Halogenated Solution-Processable Bithiazole based Electron Transport Polymeric Semiconductors

    KAUST Repository

    Fu, Boyi; Wang, Cheng-Yin; Rose, Bradley Daniel; Jiang, Yundi; Chang, Mincheol; Chu, Ping-Hsun; Yuan, Zhibo; Fuentes-Hernandez, Canek; Bernard, Kippelen; Bredas, Jean-Luc; Collard, David M.; Reichmanis, Elsa

    2015-01-01

    The electron deficiency and trans planar conformation of bithiazole is potentially beneficial for the electron transport performance of organic semiconductors. However, the incorporation of bithiazole into polymers through a facile synthetic strategy remains a challenge. Herein, 2,2’-bithiazole was synthesized in one step and copolymerized with dithienyldiketopyrrolopyrrole to afford poly(dithienyldiketopyrrolopyrrole-bithiazole), PDBTz. PDBTz exhibited electron mobility reaching 0.3 cm2V-1s-1 in organic field-effect transistor (OFET) configuration; this contrasts with a recently discussed isoelectronic conjugated polymer comprising an electron rich bithiophene and dithienyldiketopyrrolopyrrole, which displays merely hole transport characteristics. This inversion of charge carrier transport characteristics confirms the significant potential for bithiazole in the development of electron transport semiconducting materials. Branched 5-decylheptacyl side chains were incorporated into PDBTz to enhance polymer solubility, particularly in non-halogenated, more environmentally compatible solvents. PDBTz cast from a range of non-halogenated solvents exhibited film morphologies and field-effect electron mobility similar to those cast from halogenated solvents.

  15. Molecular Engineering of Non-Halogenated Solution-Processable Bithiazole based Electron Transport Polymeric Semiconductors

    KAUST Repository

    Fu, Boyi

    2015-04-01

    The electron deficiency and trans planar conformation of bithiazole is potentially beneficial for the electron transport performance of organic semiconductors. However, the incorporation of bithiazole into polymers through a facile synthetic strategy remains a challenge. Herein, 2,2’-bithiazole was synthesized in one step and copolymerized with dithienyldiketopyrrolopyrrole to afford poly(dithienyldiketopyrrolopyrrole-bithiazole), PDBTz. PDBTz exhibited electron mobility reaching 0.3 cm2V-1s-1 in organic field-effect transistor (OFET) configuration; this contrasts with a recently discussed isoelectronic conjugated polymer comprising an electron rich bithiophene and dithienyldiketopyrrolopyrrole, which displays merely hole transport characteristics. This inversion of charge carrier transport characteristics confirms the significant potential for bithiazole in the development of electron transport semiconducting materials. Branched 5-decylheptacyl side chains were incorporated into PDBTz to enhance polymer solubility, particularly in non-halogenated, more environmentally compatible solvents. PDBTz cast from a range of non-halogenated solvents exhibited film morphologies and field-effect electron mobility similar to those cast from halogenated solvents.

  16. Phonon-affected steady-state transport through molecular quantum dots

    Czech Academy of Sciences Publication Activity Database

    Koch, T.; Fehske, H.; Loos, Jan

    T151, č. 1 (2012), 1-10 ISSN 0031-8949 Institutional research plan: CEZ:AV0Z10100521 Keywords : the ory of electron ic transport * scattering mechanisms * polarons and electron -phonon interactions Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.032, year: 2012

  17. The molecular mechanism of ion-dependent gating in secondary transporters.

    Directory of Open Access Journals (Sweden)

    Chunfeng Zhao

    2013-10-01

    Full Text Available LeuT-like fold Na-dependent secondary active transporters form a large family of integral membrane proteins that transport various substrates against their concentration gradient across lipid membranes, using the free energy stored in the downhill concentration gradient of sodium ions. These transporters play an active role in synaptic transmission, the delivery of key nutrients, and the maintenance of osmotic pressure inside the cell. It is generally believed that binding of an ion and/or a substrate drives the conformational dynamics of the transporter. However, the exact mechanism for converting ion binding into useful work has yet to be established. Using a multi-dimensional path sampling (string-method followed by all-atom free energy simulations, we established the principal thermodynamic and kinetic components governing the ion-dependent conformational dynamics of a LeuT-like fold transporter, the sodium/benzyl-hydantoin symporter Mhp1, for an entire conformational cycle. We found that inward-facing and outward-facing states of Mhp1 display nearly the same free energies with an ion absent from the Na2 site conserved across the LeuT-like fold transporters. The barrier separating an apo-state from inward-facing or outward-facing states of the transporter is very low, suggesting stochastic gating in the absence of ion/substrate bound. In contrast, the binding of a Na2 ion shifts the free energy stabilizing the outward-facing state and promoting substrate binding. Our results indicate that ion binding to the Na2 site may also play a key role in the intracellular thin gate dynamics modulation by altering its interactions with the transmembrane helix 5 (TM5. The Potential of Mean Force (PMF computations for a substrate entrance displays two energy minima that correspond to the locations of the main binding site S1 and proposed allosteric S2 binding site. However, it was found that substrate's binds to the site S1 ∼5 kcal/mol more favorable

  18. Rational Design of Molecular Hole-Transporting Materials for Perovskite Solar Cells: Direct versus Inverted Device Configurations.

    Science.gov (United States)

    Grisorio, Roberto; Iacobellis, Rosabianca; Listorti, Andrea; De Marco, Luisa; Cipolla, Maria Pia; Manca, Michele; Rizzo, Aurora; Abate, Antonio; Gigli, Giuseppe; Suranna, Gian Paolo

    2017-07-26

    Due to a still limited understanding of the reasons making 2,2',7,7'-tetrakis(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (Spiro-OMeTAD) the state-of-the-art hole-transporting material (HTM) for emerging photovoltaic applications, the molecular tailoring of organic components for perovskite solar cells (PSCs) lacks in solid design criteria. Charge delocalization in radical cationic states can undoubtedly be considered as one of the essential prerequisites for an HTM, but this aspect has been investigated to a relatively minor extent. In marked contrast with the 3-D structure of Spiro-OMeTAD, truxene-based HTMs Trux1 and Trux2 have been employed for the first time in PSCs fabricated with a direct (n-i-p) or inverted (p-i-n) architecture, exhibiting a peculiar behavior with respect to the referential HTM. Notwithstanding the efficient hole extraction from the perovskite layer exhibited by Trux1 and Trux2 in direct configuration devices, their photovoltaic performances were detrimentally affected by their poor hole transport. Conversely, an outstanding improvement of the photovoltaic performances in dopant-free inverted configuration devices compared to Spiro-OMeTAD was recorded, ascribable to the use of thinner HTM layers. The rationalization of the photovoltaic performances exhibited by different configuration devices discussed in this paper can provide new and unexpected prospects for engineering the interface between the active layer of perovskite-based solar cells and the hole transporters.

  19. Multixenobiotic resistance in Mytilus edulis: Molecular and functional characterization of an ABCG2- type transporter in hemocytes and gills.

    Science.gov (United States)

    Ben Cheikh, Yosra; Xuereb, Benoit; Boulangé-Lecomte, Céline; Le Foll, Frank

    2018-02-01

    Among the cellular protection arsenal, ABC transporters play an important role in xenobiotic efflux in marine organisms. Two pumps belonging to B and C subfamily has been identified in Mytilus edulis. In this study, we investigated the presence of the third major subtype ABCG2/BCRP protein in mussel tissues. Transcript was expressed in hemocytes and with higher level in gills. Molecular characterization revealed that mussel ABCG2 transporter shares the sequence and organizational structure with mammalian and molluscan orthologs. Overall identity of the predicted amino acid sequence with corresponding homologs from other organisms was between 49% and 98%. Moreover, protein efflux activity was demonstrated using a combination of fluorescent allocrites and specific inhibitors. The accumulation of bodipy prazosin and pheophorbide A was heterogeneous in gills and hemocytes. Most of the used blockers enhanced probe accumulation at different levels, most significantly for bodipy prazosin. Moreover, Mrp classical blocker MK571 showed a polyspecificity. In conclusion, our data demonstrate that several ABC transporters contribute to MXR phenotype in the blue mussel including ABCG2 that forms an active pump in hemocytes and gills. Efforts are needed to distinguish between the different members and to explore their single function and specificity towards allocrites and chemosensitizers. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2005-06-21

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

  1. Isolation and molecular characterization of methicillin-resistant Staphylococcus aureus from public transport.

    Science.gov (United States)

    Iwao, Yasuhisa; Yabe, Shizuka; Takano, Tomomi; Higuchi, Wataru; Nishiyama, Akihito; Yamamoto, Tatsuo

    2012-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) not only causes disease in hospitals, but also in the community. The characteristics of MRSA transmission in the environment remain uncertain. In this study, MRSA were isolated from public transport in Tokyo and Niigata, Japan. Of 349 trains examined, eight (2.3%) were positive for MRSA. The MRSA isolated belonged to sequence types (STs) 5, 8, 88, and 89, and included community infection-associated ST8 MRSA (with novel type IV staphylococcal cassette chromosome mec) and the ST5 New York/Japan hospital clone. The data indicate that public transport could contribute to the spread of community-acquired MRSA, and awareness of this mode of transmission is necessary. © 2012 The Societies and Blackwell Publishing Asia Pty Ltd.

  2. Branchial osmoregulation in the euryhaline bull shark, Carcharhinus leucas: a molecular analysis of ion transporters.

    Science.gov (United States)

    Reilly, Beau D; Cramp, Rebecca L; Wilson, Jonathan M; Campbell, Hamish A; Franklin, Craig E

    2011-09-01

    Bull sharks, Carcharhinus leucas, are one of only a few species of elasmobranchs that live in both marine and freshwater environments. Osmoregulation in euryhaline elasmobranchs is achieved through the control and integration of various organs (kidney, rectal gland and liver) in response to changes in environmental salinity. However, little is known regarding the mechanisms of ion transport in the gills of euryhaline elasmobranchs and how they are affected by osmoregulatory challenges. This study was conducted to gain insight into the branchial ion and acid-base regulatory mechanisms of C. leucas by identifying putative ion transporters and determining whether their expression is influenced by environmental salinity. We hypothesised that expression levels of the Na(+)/K(+)-ATPase (NKA) pump, Na(+)/H(+) exchanger 3 (NHE3), vacuolar-type H(+)-ATPase (VHA) and anion exchanger pendrin (PDN) would be upregulated in freshwater (FW) C. leucas. Immunohistochemistry was used to localise all four ion transporters in gills of bull sharks captured in both FW and estuarine/seawater (EST/SW) environments. NHE3 immunoreactivity occurred in the apical region of cells with basolateral NKA expression whereas PDN was apically expressed in cells that also exhibited basolateral VHA immunoreactivity. In accordance with our hypotheses, quantitative real-time PCR showed that the mRNA expression of NHE3 and NKA was significantly upregulated in gills of FW-captured C. leucas relative to EST/SW-captured animals. These data suggest that NHE3 and NKA together may be important in mediating branchial Na(+) uptake in freshwater environments, whereas PDN and VHA might contribute to Cl(-)/HCO(3)(-) transport in marine and freshwater bull shark gills.

  3. Methylmercury transport across the blood-brain barrier by molecular mimicry

    International Nuclear Information System (INIS)

    Kerper, L.E.; Ballatori, N.; Clarkson, T.W.

    1990-01-01

    The mechanism by which methylmercury (MeHg) crosses the blood-brain barrier is not known. Co-administration of MeHg with L-cysteine by intravenous injection has been shown to accelerate MeHg uptake into brain tissue in rats. Since the complex of MeHg with L-cysteine is structurally similar to L-methionine, a substrate for the L (leucine-preferring) neutral amino acid transport system, this amino acid carrier may be involved in MeHg uptake into brain. To examine this hypothesis, the rapid carotid infusion technique was used in the rat. The concentration-dependence of initial rates of Me 203 Hg uptake into rat brains following injection of Me 203 Hg-L-cysteine complex was non-linear, exhibiting characteristics of saturable transport (K m 250 μM, V max 700 pmol·g -1 ·15 s -1 ). A slower, nonsaturable uptake was seen following MeHg-D-cysteine injection. MeHg-L-cysteine uptake was inhibited by co-injection of L-methionine (K i 200 μM), D-methionine (K i 600 μM), and amino acid analog 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (K i 1.4 mM), but not by amino acid analog α-methylaminoisobutyric acid. Transport of 14 C-L-phenylalanine was inhibited by MeHg-L-cysteine, but not by MeHgCl. The results suggest that MeHg may enter brain capillary endothelial cells as a cysteine complex, via amino acid transport system L

  4. Immunizations: Active vs. Passive

    Science.gov (United States)

    ... Issues Health Issues Health Issues Conditions Injuries & Emergencies Vaccine Preventable Diseases ... Children > Safety & Prevention > Immunizations > Immunizations: Active vs. Passive Safety & ...

  5. Sorption of PAHs to humic acid- and iron(III)carbon ate particles by using passive dosing vials for investigating the transport of organic contamination in stormwater runoff

    DEFF Research Database (Denmark)

    Nielsen, Katrine; Mikkelsen, Peter Steen; Baun, Anders

    2013-01-01

    ) has been foun d to facilitate transport of organic contaminants and metals in stormwater runoff system s, but little is known about the role of the colloidal fraction including nano-sized particl es (0.001-1 μm). Based on the large specific surface area of colloids and nanosized particles, t heir...... abundance, and knowledge about their facilitated transport of persistent organic polluti on in natural waters, they are likely to diminish the efficiency of engineered treatment sys tems unless appropriately accounted for. In this work organic and inorganic nanosized partic les were investigated......(III)carbo nate particles (22 nm) sorption experiments are ongoing. Based on these results and a literature review, the importance of including particulate fractions for surface water q uality assessment in relation to the WFD will be discussed....

  6. Stable High-Performance Perovskite Solar Cells via Grain Boundary Passivation.

    Science.gov (United States)

    Niu, Tianqi; Lu, Jing; Munir, Rahim; Li, Jianbo; Barrit, Dounya; Zhang, Xu; Hu, Hanlin; Yang, Zhou; Amassian, Aram; Zhao, Kui; Liu, Shengzhong Frank

    2018-04-01

    The trap states at grain boundaries (GBs) within polycrystalline perovskite films deteriorate their optoelectronic properties, making GB engineering particularly important for stable high-performance optoelectronic devices. It is demonstrated that trap states within bulk films can be effectively passivated by semiconducting molecules with Lewis acid or base functional groups. The perovskite crystallization kinetics are studied using in situ synchrotron-based grazing-incidence X-ray scattering to explore the film formation mechanism. A model of the passivation mechanism is proposed to understand how the molecules simultaneously passivate the Pb-I antisite defects and vacancies created by under-coordinated Pb atoms. In addition, it also explains how the energy offset between the semiconducting molecules and the perovskite influences trap states and intergrain carrier transport. The superior optoelectronic properties are attained by optimizing the molecular passivation treatments. These benefits are translated into significant enhancements of the power conversion efficiencies to 19.3%, as well as improved environmental and thermal stability of solar cells. The passivated devices without encapsulation degrade only by ≈13% after 40 d of exposure in 50% relative humidity at room temperature, and only ≈10% after 24 h at 80 °C in controlled environment. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Stable High-Performance Perovskite Solar Cells via Grain Boundary Passivation

    KAUST Repository

    Niu, Tianqi

    2018-03-12

    The trap states at grain boundaries (GBs) within polycrystalline perovskite films deteriorate their optoelectronic properties, making GB engineering particularly important for stable high-performance optoelectronic devices. It is demonstrated that trap states within bulk films can be effectively passivated by semiconducting molecules with Lewis acid or base functional groups. The perovskite crystallization kinetics are studied using in situ synchrotron-based grazing-incidence X-ray scattering to explore the film formation mechanism. A model of the passivation mechanism is proposed to understand how the molecules simultaneously passivate the Pb-I antisite defects and vacancies created by under-coordinated Pb atoms. In addition, it also explains how the energy offset between the semiconducting molecules and the perovskite influences trap states and intergrain carrier transport. The superior optoelectronic properties are attained by optimizing the molecular passivation treatments. These benefits are translated into significant enhancements of the power conversion efficiencies to 19.3%, as well as improved environmental and thermal stability of solar cells. The passivated devices without encapsulation degrade only by ≈13% after 40 d of exposure in 50% relative humidity at room temperature, and only ≈10% after 24 h at 80 °C in controlled environment.

  8. Transport Deficiency Is the Molecular Basis of Candida albicans Resistance to Antifungal Oligopeptides

    Directory of Open Access Journals (Sweden)

    Marta Schielmann

    2017-11-01

    Full Text Available Oligopeptides incorporating N3-(4-methoxyfumaroyl-L-2,3-diaminopropanoic acid (FMDP, an inhibitor of glucosamine-6-phosphate synthase, exhibited growth inhibitory activity against Candida albicans, with minimal inhibitory concentration values in the 0.05–50 μg mL-1 range. Uptake by the peptide permeases was found to be the main factor limiting an anticandidal activity of these compounds. Di- and tripeptide containing FMDP (F2 and F3 were transported by Ptr2p/Ptr22p peptide transporters (PTR and FMDP-containing hexa-, hepta-, and undecapeptide (F6, F7, and F11 were taken up by the oligopeptide transporters (OPT oligopeptide permeases, preferably by Opt2p/Opt3p. A phenotypic, apparent resistance of C. albicans to FMDP-oligopeptides transported by OPT permeases was triggered by the environmental factors, whereas resistance to those taken up by the PTR system had a genetic basis. Anticandidal activity of longer FMDP-oligopeptides was strongly diminished in minimal media containing easily assimilated ammonium sulfate or L-glutamine as the nitrogen source, both known to downregulate expression of the OPT genes. All FMDP-oligopeptides tested were more active at lower pH and this effect was slightly more remarkable for peptides F6, F7, and F11, compared to F2 and F3. Formation of isolated colonies was observed inside the growth inhibitory zones induced by F2 and F3 but not inside those induced by F6, F7, and F11. The vast majority (98% of those colonies did not originate from truly resistant cells. The true resistance of 2% of isolates was due to the impaired transport of di- and to a lower extent, tripeptides. The resistant cells did not exhibit a lower expression of PTR2, PTR22, or OPT1–3 genes, but mutations in the PTR2 gene resulting in T422H, A320S, D119V, and A320S substitutions in the amino acid sequence of Ptr2p were found.

  9. Hydrogenation of passivated contacts

    Energy Technology Data Exchange (ETDEWEB)

    Nemeth, William; Yuan, Hao-Chih; LaSalvia, Vincenzo; Stradins, Pauls; Page, Matthew R.

    2018-03-06

    Methods of hydrogenation of passivated contacts using materials having hydrogen impurities are provided. An example method includes applying, to a passivated contact, a layer of a material, the material containing hydrogen impurities. The method further includes subsequently annealing the material and subsequently removing the material from the passivated contact.

  10. Molecular docking simulations provide insights in the substrate binding sites and possible substrates of the ABCC6 transporter.

    Directory of Open Access Journals (Sweden)

    Mohammad Jakir Hosen

    Full Text Available The human ATP-binding cassette family C member 6 (ABCC6 gene encodes an ABC transporter protein (ABCC6, primarily expressed in liver and kidney. Mutations in the ABCC6 gene cause pseudoxanthoma elasticum (PXE, an autosomal recessive connective tissue disease characterized by ectopic mineralization of the elastic fibers. The pathophysiology underlying PXE is incompletely understood, which can at least partly be explained by the undetermined nature of the ABCC6 substrates as well as the unknown substrate recognition and binding sites. Several compounds, including anionic glutathione conjugates (N-ethylmaleimide; NEM-GS and leukotriene C4 (LTC4 were shown to be modestly transported in vitro; conversely, vitamin K3 (VK3 was demonstrated not to be transported by ABCC6. To predict the possible substrate binding pockets of the ABCC6 transporter, we generated a 3D homology model of ABCC6 in both open and closed conformation, qualified for molecular docking and virtual screening approaches. By docking 10 reported in vitro substrates in our ABCC6 3D homology models, we were able to predict the substrate binding residues of ABCC6. Further, virtual screening of 4651 metabolites from the Human Serum Metabolome Database against our open conformation model disclosed possible substrates for ABCC6, which are mostly lipid and biliary secretion compounds, some of which are found to be involved in mineralization. Docking of these possible substrates in the closed conformation model also showed high affinity. Virtual screening expands this possibility to explore more compounds that can interact with ABCC6, and may aid in understanding the mechanisms leading to PXE.

  11. Transportation

    Science.gov (United States)

    2007-01-01

    Faculty ii INDUSTRY TRAVEL Domestic Assistant Deputy Under Secretary of Defense (Transportation Policy), Washington, DC Department of...developed between the railroad and trucking industries. Railroads: Today’s seven Class I freight railroad systems move 42% of the nation’s intercity ...has been successfully employed in London to reduce congestion and observed by this industry study during its travels . It is currently being

  12. A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

    Science.gov (United States)

    Parker, Christian R; Leary, Edmund; Frisenda, Riccardo; Wei, Zhongming; Jennum, Karsten S; Glibstrup, Emil; Abrahamsen, Peter Bæch; Santella, Marco; Christensen, Mikkel A; Della Pia, Eduardo Antonio; Li, Tao; Gonzalez, Maria Teresa; Jiang, Xingbin; Morsing, Thorbjørn J; Rubio-Bollinger, Gabino; Laursen, Bo W; Nørgaard, Kasper; van der Zant, Herre; Agrait, Nicolas; Nielsen, Mogens Brøndsted

    2014-11-26

    Cruciform-like molecules with two orthogonally placed π-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof.

  13. Experimental study of electronic transport in single molecular contacts and surface modification via STM

    OpenAIRE

    Costa Milán, David

    2016-01-01

    El procesamiento de información usado hoy en día, está basado fundamentalmente en la industria de los semiconductores. Los imanes moleculares están siendo estudiados actualmente como una gran alternativa o complemento a la electrónica de semiconductores por sus grandes aplicaciones en el desarrollo de los sistemas electrónicos, informáticos y en el campo de la biomedicina entre otros, debido a su fácil miniaturización y posibilidad de formar puertas lógicas de tamaños inferiores a 10 nanómetr...

  14. Molecular mechanisms regulating oxygen transport and consumption in high altitude and hibernating mammals

    DEFF Research Database (Denmark)

    Revsbech, Inge Grønvall

    2016-01-01

    The aim of this thesis is to broaden the knowledge of molecular mechanisms of adjustment in oxygen (O2) uptake, conduction, delivery and consumption in mammals adapted to extreme conditions. For this end, I have worked with animals living at high altitude as an example of environmental hypoxia...... of the repeatedly found adaptive traits in animals living at high altitude and in hibernating mammals during hibernation compared with the active state. Factors that affect O2 affinity of Hb include temperature, H+/CO2 via the Bohr effect as well as Cl- and organic phosphates, in mammals mainly 2...

  15. Electron-phonon interaction in quantum transport through quantum dots and molecular systems

    Science.gov (United States)

    Ojeda, J. H.; Duque, C. A.; Laroze, D.

    2016-12-01

    The quantum transport and effects of decoherence properties are studied in quantum dots systems and finite homogeneous chains of aromatic molecules connected to two semi-infinite leads. We study these systems based on the tight-binding approach through Green's function technique within a real space renormalization and polaron transformation schemes. In particular, we calculate the transmission probability following the Landauer-Büttiker formalism, the I - V characteristics and the noise power of current fluctuations taken into account the decoherence. Our results may explain the inelastic effects through nanoscopic systems.

  16. Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases

    Science.gov (United States)

    Assenza, Salvatore; Mezzenga, Raffaele

    2018-02-01

    We perform a simulation study of the diffusion of small solutes in the confined domains imposed by inverse bicontinuous cubic phases for the primitive, diamond, and gyroid symmetries common to many lipid/water mesophase systems employed in experiments. For large diffusing domains, the long-time diffusion coefficient shows universal features when the size of the confining domain is renormalized by the Gaussian curvature of the triply periodic minimal surface. When bottlenecks are widely present, they become the most relevant factor for transport, regardless of the connectivity of the cubic phase.

  17. Method for efficient storage and transportation of sputum specimens for molecular testing of tuberculosis.

    Science.gov (United States)

    Guio, H; Okayama, H; Ashino, Y; Saitoh, H; Xiao, P; Miki, M; Yoshihara, N; Nakanowatari, S; Hattori, T

    2006-08-01

    The polymerase chain reaction (PCR) is a highly sensitive method for the detection of Mycobacterium tuberculosis and is available in most countries, though to a lesser extent in rural areas. To amplify M. tuberculosis DNA sequences of sputum spotted on FTA cards and compare them with the results of microscopic examination among culture-positive samples. A total of 102 sputum specimens of TB patients in treatment were spotted on FTA cards and stored at room temperature until DNA analysis. We assessed the IS6110 region of M. tuberculosis. The efficacy of the PCR assay for the direct detection of M. tuberculosis was evaluated and compared with the results of cultures (Middlebrook 7H9 broth) and smears of fresh sputum specimens. We were able to detect 10 fg/microl of mycobacterial DNA even after 6 months in storage. The PCR sensitivity and specificity using the FTA card system were 82% and 96%, while microscopic examination showed 41% and 95%, respectively. The FTA card system for the storage of bacterial DNA from sputum samples should be considered for the molecular diagnosis of tuberculosis. Samples can easily be obtained from geographically isolated populations and shipped by mail for accurate molecular diagnosis.

  18. The relation between molecular properties of drugs and their transport across the intestinal membrane

    Directory of Open Access Journals (Sweden)

    Zakeri-Milani P.

    2006-07-01

    Full Text Available The aim of this study was to investigate the relationship between the intestinal absorption of structurally diverse model drugs across the rat intestinal mucosa and their molecular properties. Permeability coefficients for 13 compounds were determined in anaesthetized rats. Drug solution in phosphate buffered saline (PBS was perfused through the intestinal segment with flow rate of 0.21 ml/min and samples were taken from outlet tubing at different time points up to 90 min. The permeability values ranged from 1.6×10-5 to 2 ×10-4 cm/sec for atenolol and ibuprofen respectively. Molecular properties of drugs including the number of hydrogen bond donors and acceptors, log P, logD, topological polar surface area and number of rotatable bonds were considered. The results indicated that compounds which meet 10 or fewer number of rotatable bonds and topological surface area equal to or less than 140 A◦ have a high probability of good intestinal permeability and fraction of dose which is absorbed in human. Moreover the results indicated that lower number of hydrogen bond counts and higher logD and logP values are associated with higher permeability and bioavailabilty of drugs. Therefore the experimental and computational methods could be used for the prediction of intestinal drug permeability.

  19. The molecular dynamics simulation of structure and transport properties of sheared super-cooled liquid metal

    International Nuclear Information System (INIS)

    Wang Li; Liu Xiangfa; Zhang Yanning; Yang Hua; Chen Ying; Bian Xiufang

    2003-01-01

    Much more attention has been paid to the microstructure of liquid metal under non-ordinary condition recently. In this Letter, the pair correlation function (PCF), together with internal energy of sheared super-cooled liquid Co as a function of temperature has been calculated by molecular dynamics simulation based upon the embedded atom method (EAM) and analyzed compared to that under normal condition. The finding indicates that there exist three obvious peaks of PCF for liquid Co; while as the shear stress is applied to the liquid, the first and second peaks of PCF become lower, the third peak disappeared. The concentric shell structure representing short-range order of liquid still exists, however, it is weakened by the addition of shear stress, leading to the increases of disordering degree of liquid metal. The curves of energy versus temperature suggest the higher crystalline temperature compared to that under normal condition at the same cooling rate. In addition, the viscosity of super-liquid Co is calculated by non-equilibrium molecular dynamics (NEMD)

  20. Study of the charge transport characteristics of dendrimer molecular thin films

    Energy Technology Data Exchange (ETDEWEB)

    Li, J.C., E-mail: jcli@mail.neu.edu.cn; Han, N.; Wang, S.S.; Ba, D.C.

    2011-05-31

    In this work, we systematically studied the electrical characteristics of two types of dendritic arylamine thin film devices. We observed that, for devices with different interfacial structures, their charge injection barriers and transport properties are obviously different. The smallest charge injection barrier is observed in dendrimer devices without charge-transfer interfacial layers. The Richardson-Schottky thermionic emission model can be well used to fit the experimental current-voltage characteristics at a lower voltage region. The charge injection barrier increases about 0.4 eV and 0.5 eV when a 1-decanethiol self-assembly layer and -CN terminated dendrimer thin films are inserted as the interfacial layer, respectively. It is shown that the molecule/electrode charge-transfer interfaces can largely affect the device charge injection/transport process and consequently change the device performance. In this case, the space charge limited conduction theory is more applicable to simulate the device conduction mechanism. Owing to its ultra-thin thickness, the self-assembly monolayer technique is proved to be an efficient approach in engineering the interfacial electronic structures of dendrimer thin film devices.

  1. Study of the charge transport characteristics of dendrimer molecular thin films

    International Nuclear Information System (INIS)

    Li, J.C.; Han, N.; Wang, S.S.; Ba, D.C.

    2011-01-01

    In this work, we systematically studied the electrical characteristics of two types of dendritic arylamine thin film devices. We observed that, for devices with different interfacial structures, their charge injection barriers and transport properties are obviously different. The smallest charge injection barrier is observed in dendrimer devices without charge-transfer interfacial layers. The Richardson-Schottky thermionic emission model can be well used to fit the experimental current-voltage characteristics at a lower voltage region. The charge injection barrier increases about 0.4 eV and 0.5 eV when a 1-decanethiol self-assembly layer and -CN terminated dendrimer thin films are inserted as the interfacial layer, respectively. It is shown that the molecule/electrode charge-transfer interfaces can largely affect the device charge injection/transport process and consequently change the device performance. In this case, the space charge limited conduction theory is more applicable to simulate the device conduction mechanism. Owing to its ultra-thin thickness, the self-assembly monolayer technique is proved to be an efficient approach in engineering the interfacial electronic structures of dendrimer thin film devices.

  2. Dynamical properties and transport coefficients of one-dimensional Lennard-Jones fluids: A molecular dynamics study

    Science.gov (United States)

    Bazhenov, Alexiev M.; Heyes, David M.

    1990-01-01

    The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.

  3. Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

    Science.gov (United States)

    Hoheisel, C.

    1989-01-01

    For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.

  4. Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

    International Nuclear Information System (INIS)

    Hoheisel, C.

    1989-01-01

    For several liquid states of CF 4 and SF 6 , the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints were chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3 x 10 5 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF 4 , while for SF 6 the transport coefficients fall below the experimental ones by about 30%

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

    Directory of Open Access Journals (Sweden)

    Bui Thanh-Tuan

    2013-10-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  7. Exploring the energy landscape of the charge transport levels in organic semiconductors at the molecular scale.

    Science.gov (United States)

    Cornil, J; Verlaak, S; Martinelli, N; Mityashin, A; Olivier, Y; Van Regemorter, T; D'Avino, G; Muccioli, L; Zannoni, C; Castet, F; Beljonne, D; Heremans, P

    2013-02-19

    strongly interacting electron-hole pairs can potentially escape from their Coulomb well, a process that is at the heart of photoconversion or molecular doping. Yet they do, with near-quantitative yield in some cases. Limited screening by the low dielectric medium in organic materials leads to subtle static and dynamic electronic polarization effects that strongly impact the energy landscape for charges, which offers a rationale for this apparent inconsistency. In this Account, we use different theoretical approaches to predict the energy landscape of charge carriers at the molecular level and review a few case studies highlighting the role of electrostatic interactions in conjugated organic molecules. We describe the pros and cons of different theoretical approaches that provide access to the energy landscape defining the motion of charge carriers. We illustrate the applications of these approaches through selected examples involving OFETs, OLEDs, and solar cells. The three selected examples collectively show that energetic disorder governs device performances and highlights the relevance of theoretical tools to probe energy landscapes in molecular assemblies.

  8. Molecular Characterization of CTR-type Copper Transporters in an Oceanic Diatom, Thalassiosira oceanica 1005

    Science.gov (United States)

    Kong, L.; Price, N. M.

    2016-02-01

    Copper is an essential micronutrient for phytoplankton growth because of its role as a redox cofactor in electron transfer proteins in photosynthesis and respiration, and a potentially limiting resource in parts of the open sea. Thalassiosira oceanica 1005 can grow at inorganic copper concentrations varying from 10 fmol/L to 10 nmol/L by regulating copper uptake across plasma membrane. Four putative CTR-type copper transporter genes (ToCTR1, ToCTR2, ToCTR3.1 and ToCTR3.2) were identified by BLASTP search against the T. oceanica genome. Predicted gene models were revised by assembled mRNA sequencing transcripts and updated gene models contained all conserved features of characterized CTR-type copper transporters. ToCTR3.1 and ToCTR3.2 may arise from one another by gene duplication as they shared a sequence similarity of 97.6% with a peptide insertion of 5 amino acids at N-terminus of ToCTR3.1. The expression of ToCTR1, ToCTR2 and ToCTR3.1/3.2 was upregulated in low copper concentrations, but only ToCTR3.1/3.2 showed a significant increase (2.5 fold) in copper-starved cells. Both ToCTR3.1 and ToCTR3.2 restored growth of a yeast double mutant, Saccharomyces cerevisiae ctr1Δctr3Δ, in copper deficient medium. GFP-fused ToCTR expression showed that some ToCTR3.1 localized to the plasma membrane but a large portion was retained in the endoplasmic reticulum. Inefficient targeting of ToCTR3.1 to the yeast outer membrane may explain poorer growth compared to the Saccharomyces native ScCTR1 transformant. Thus, diatom CTR genes encoding CTR-type copper transporters show high-affinity copper uptake and their regulation may enable diatoms to survive in ocean environments containing a wide range of copper concentrations.

  9. Electronic transport of molecular nanowires by considering of electron hopping energy between the second neighbors

    Directory of Open Access Journals (Sweden)

    H Rabani

    2015-07-01

    Full Text Available In this paper, we study the electronic conductance of molecular nanowires by considering the electron hopping between the first and second neighbors with the help Green’s function method at the tight-binding approach. We investigate three types of structures including linear uniform and periodic chains as well as poly(p-phenylene molecule which are embedded between two semi-infinite metallic leads. The results show that in the second neighbor approximation, the resonance, anti-resonance and Fano phenomena occur in the conductance spectra of these structures. Moreover, a new gap is observed at edge of the lead energy band wich its width depends on the value of the electron hopping energy between the second neighbors. In the systems including intrinsic gap, this hopping energy shifts the gap in the energy spectra.

  10. Gas-Transport-Property Performance of Hybrid Carbon Molecular Sieve−Polymer Materials

    KAUST Repository

    Das, Mita

    2010-10-06

    High-performance hybrid materials using carbon molecular sieve materials and 6FDA-6FpDA were produced. A detailed analysis of the effects of casting processes and the annealing temperature is reported. Two existing major obstacles, sieve agglomeration and residual stress, were addressed in this work, and subsequently a new membrane formation technique was developed to produce high-performing membranes. The successfully improved interfacial region of the hybrid membranes allows the sieves to increase the selectivity of the membranes above the neat polymer properties. Furthermore, an additional performance enhancement was seen with increased sieve loading in the hybrid membranes, leading to an actual performance above the upper bound for pure polymer membranes. The membranes were also tested under a mixed-gas environment, which further demonstrated promising results. © 2010 American Chemical Society.

  11. Thermodynamic and transport properties of nitrogen fluid: Molecular theory and computer simulations

    Science.gov (United States)

    Eskandari Nasrabad, A.; Laghaei, R.

    2018-04-01

    Computer simulations and various theories are applied to compute the thermodynamic and transport properties of nitrogen fluid. To model the nitrogen interaction, an existing potential in the literature is modified to obtain a close agreement between the simulation results and experimental data for the orthobaric densities. We use the Generic van der Waals theory to calculate the mean free volume and apply the results within the modified Cohen-Turnbull relation to obtain the self-diffusion coefficient. Compared to experimental data, excellent results are obtained via computer simulations for the orthobaric densities, the vapor pressure, the equation of state, and the shear viscosity. We analyze the results of the theory and computer simulations for the various thermophysical properties.

  12. Charge transport and magnetoresistance of G4-DNA molecular device modulated by counter ions and dephasing effect

    International Nuclear Information System (INIS)

    Kang, Da-wei; Sun, Meng-le; Zuo, Zheng-wei; Wang, Hui-xian; Lv, Shi-jie; Li, Xin-zhong; Li, Li-ben

    2016-01-01

    The charge transport properties of the G4-DNA molecular device in the presence of counter ions and dephasing effect are investigated based on the Green function method and Landauer–Büttiker theory. The currents through the G4-DNA molecular device depend on the interference patterns at different coupling configurations. There is an effective electrostatic interaction between the counter ions and the G4-DNA molecule which introduces disorder into the on-site energies of G bases. The current through the device can be enhanced by the small disorder which avoids the strong interference of electrons at the same energy in some coupling configurations, however the diagonal disorder can suppress the overall current due to the Anderson localization of charge carriers when the disorder is large. In the presence of dephasing effect the current through the device at all coupling configurations can be enhanced as a result of the phase coherence losing of electron. As for the magnetic field response, the magnetoresistance of the device is always suppressed by the counter ions and dephasing effect. - Highlights: • The counter ions can some times enhance the current through G4-DNA molecule. • The dephasing effect can enhance the current of the device at all four coupling configurations. • The magnetoresistance is always suppressed by the counter ions and dephasing effect.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-03-01

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

  14. Molecular structure of the discotic liquid crystalline phase of hexa-peri-hexabenzocoronene/oligothiophene hybrid and their charge transport properties

    International Nuclear Information System (INIS)

    Bag, Saientan; Maingi, Vishal; Maiti, Prabal K.; Yelk, Joe; Glaser, Matthew A.; Clark, Noel A.; Walba, David M.

    2015-01-01

    Using atomistic molecular dynamics simulation, we study the discotic columnar liquid crystalline (LC) phases formed by a new organic compound having hexa-peri-Hexabenzocoronene (HBC) core with six pendant oligothiophene units recently synthesized by Nan Hu et al. [Adv. Mater. 26, 2066 (2014)]. This HBC core based LC phase was shown to have electric field responsive behavior and has important applications in organic electronics. Our simulation results confirm the hexagonal arrangement of columnar LC phase with a lattice spacing consistent with that obtained from small angle X-ray diffraction data. We have also calculated various positional and orientational correlation functions to characterize the ordering of the molecules in the columnar arrangement. The molecules in a column are arranged with an average twist of 25° having an average inter-molecular separation of ∼5 Å. Interestingly, we find an overall tilt angle of 43° between the columnar axis and HBC core. We also simulate the charge transport through this columnar phase and report the numerical value of charge carrier mobility for this liquid crystal phase. The charge carrier mobility is strongly influenced by the twist angle and average spacing of the molecules in the column

  15. Energetics of Transport through the Nuclear Pore Complex.

    Directory of Open Access Journals (Sweden)

    Ali Ghavami

    Full Text Available Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC. The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles.

  16. Bronchial Mucus as a Complex Fluid: Molecular Interactions and Influence of Nanostructured Particles on Rheological and Transport Properties

    Directory of Open Access Journals (Sweden)

    Odziomek Marcin

    2017-06-01

    Full Text Available Transport properties of bronchial mucus are investigated by two-stage experimental approach focused on: (a rheological properties and (b mass transfer rate through the stagnant layer of solutions of mucus components (mucine, DNA, proteins and simulated multi-component mucus. Studies were done using thermostated horizontal diffusion cells with sodium cromoglycate and carminic acid as transferred solutes. Rheological properties of tested liquids was studied by a rotational viscometer and a cone-plate rheometer (dynamic method. First part of the studies demonstrated that inter-molecular interactions in these complex liquids influence both rheological and permeability characteristics. Transfer rate is governed not only by mucus composition and concentration but also by hydrophobic/hydrophilic properties of transported molecules. Second part was focused on the properties of such a layer in presence of selected nanostructured particles (different nanoclays and graphene oxide which may be present in lungs after inhalation. It was shown that most of such particles increase visco-elasticity of the mucus and reduce the rate of mass transfer of model drugs. Measured effects may have adverse impact on health, since they will reduce mucociliary clearance in vivo and slow down drug penetration to the bronchial epithelium during inhalation therapy.

  17. Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues.

    Directory of Open Access Journals (Sweden)

    Eva-Maria Krammer

    Full Text Available Commensal and pathogenic enteric bacteria have developed several systems to adapt to proton leakage into the cytoplasm resulting from extreme acidic conditions. One such system involves arginine uptake followed by export of the decarboxylated product agmatine, carried out by the arginine/agmatine antiporter (AdiC, which thus works as a virtual proton pump. Here, using classical and targeted molecular dynamics, we investigated at the atomic level the mechanism of arginine transport through AdiC of E. coli. Overall, our MD simulation data clearly demonstrate that global rearrangements of several transmembrane segments are necessary but not sufficient for achieving transitions between structural states along the arginine translocation pathway. In particular, local structural changes, namely rotameric conversions of two aromatic residues, are needed to regulate access to both the outward- and inward-facing states. Our simulations have also enabled identification of a few residues, overwhelmingly aromatic, which are essential to guiding arginine in the course of its translocation. Most of them belong to gating elements whose coordinated motions contribute to the alternating access mechanism. Their conservation in all known E. coli acid resistance antiporters suggests that the transport mechanisms of these systems share common features. Last but not least, knowledge of the functional properties of AdiC can advance our understanding of the members of the amino acid-carbocation-polyamine superfamily, notably in eukaryotic cells.

  18. Impact of tensile strain on the thermal transport of zigzag hexagonal boron nitride nanoribbon: An equilibrium molecular dynamics study

    Science.gov (United States)

    Navid, Ishtiaque Ahmed; Intisar Khan, Asir; Subrina, Samia

    2018-02-01

    The thermal conductivity of single layer strained hexagonal boron nitride nanoribbon (h-BNNR) has been computed using the Green—Kubo formulation of Equilibrium Molecular Dynamics (EMD) simulation. We have investigated the impact of strain on thermal transport of h-BNNR by varying the applied tensile strain from 1% upto 5% through uniaxial loading. The thermal conductivity of h-BNNR decreases monotonically with the increase of uniaxial tensile strain keeping the sample size and temperature constant. The thermal conductivity can be reduced upto 86% for an applied uniaxial tensile strain of 5%. The impact of temperature and width variation on the thermal conductivity of h-BNNR has also been studied under different uniaxial tensile strain conditions. With the increase in temperature, the thermal conductivity of strained h-BNNR exhibits a decaying characteristics whereas it shows an opposite pattern with the increasing width. Such study would provide a good insight on the strain tunable thermal transport for the potential device application of boron nitride nanostructures.

  19. Altered interregional molecular associations of the serotonin transporter in attention deficit/hyperactivity disorder assessed with PET.

    Science.gov (United States)

    Vanicek, Thomas; Kutzelnigg, Alexandra; Philippe, Cecile; Sigurdardottir, Helen L; James, Gregory M; Hahn, Andreas; Kranz, Georg S; Höflich, Anna; Kautzky, Alexander; Traub-Weidinger, Tatjana; Hacker, Marcus; Wadsak, Wolfgang; Mitterhauser, Markus; Kasper, Siegfried; Lanzenberger, Rupert

    2017-02-01

    Altered serotonergic neurotransmission has been found to cause impulsive and aggressive behavior, as well as increased motor activity, all exemplifying key symptoms of ADHD. The main objectives of this positron emission tomography (PET) study were to investigate the serotonin transporter binding potential (SERT BP ND ) in patients with ADHD and to assess associations of SERT BP ND between the brain regions. 25 medication-free patients with ADHD (age ± SD; 32.39 ± 10.15; 10 females) without any psychiatric comorbidity and 25 age and sex matched healthy control subjects (33.74 ± 10.20) were measured once with PET and the highly selective and specific radioligand [ 11 C]DASB. SERT BP ND maps in nine a priori defined ROIs exhibiting high SERT binding were compared between groups by means of a linear mixed model. Finally, adopted from structural and functional connectivity analyses, we performed correlational analyses using regional SERT binding potentials to examine molecular interregional associations between all selected ROIs. We observed significant differences in the interregional correlations between the precuneus and the hippocampus in patients with ADHD compared to healthy controls, using SERT BP ND of the investigated ROIs (P < 0.05; Bonferroni corrected). When correlating SERT BP ND and age in the ADHD and the healthy control group, we confirmed an age-related decline in brain SERT binding in the thalamus and insula (R 2  = 0.284, R 2  = 0.167, Ps < 0.05; Bonferroni corrected). The results show significantly different interregional molecular associations of the SERT expression for the precuneus with hippocampus in patients with ADHD, indicating presumably altered functional coupling. Altered interregional coupling between brain regions might be a sensitive approach to demonstrate functional and molecular alterations in psychiatric conditions. Hum Brain Mapp 38:792-802, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley

  20. Charge Transport in 4 nm Molecular Wires with Interrupted Conjugation: Combined Experimental and Computational Evidence for Thermally Assisted Polaron Tunneling.

    Science.gov (United States)

    Taherinia, Davood; Smith, Christopher E; Ghosh, Soumen; Odoh, Samuel O; Balhorn, Luke; Gagliardi, Laura; Cramer, Christopher J; Frisbie, C Daniel

    2016-04-26

    We report the synthesis, transport measurements, and electronic structure of conjugation-broken oligophenyleneimine (CB-OPI 6) molecular wires with lengths of ∼4 nm. The wires were grown from Au surfaces using stepwise aryl imine condensation reactions between 1,4-diaminobenzene and terephthalaldehyde (1,4-benzenedicarbaldehyde). Saturated spacers (conjugation breakers) were introduced into the molecular backbone by replacing the aromatic diamine with trans-1,4-diaminocyclohexane at specific steps during the growth processes. FT-IR and ellipsometry were used to follow the imination reactions on Au surfaces. Surface coverages (∼4 molecules/nm(2)) and electronic structures of the wires were determined by cyclic voltammetry and UV-vis spectroscopy, respectively. The current-voltage (I-V) characteristics of the wires were acquired using conducting probe atomic force microscopy (CP-AFM) in which an Au-coated AFM probe was brought into contact with the wires to form metal-molecule-metal junctions with contact areas of ∼50 nm(2). The low bias resistance increased with the number of saturated spacers, but was not sensitive to the position of the spacer within the wire. Temperature dependent measurements of resistance were consistent with a localized charge (polaron) hopping mechanism in all of the wires. Activation energies were in the range of 0.18-0.26 eV (4.2-6.0 kcal/mol) with the highest belonging to the fully conjugated OPI 6 wire and the lowest to the CB3,5-OPI 6 wire (the wire with two saturated spacers). For the two other wires with a single conjugation breaker, CB3-OPI 6 and CB5-OPI 6, activation energies of 0.20 eV (4.6 kcal/mol) and 0.21 eV (4.8 kcal/mol) were found, respectively. Computational studies using density functional theory confirmed the polaronic nature of charge carriers but predicted that the semiclassical activation energy of hopping should be higher for CB-OPI molecular wires than for the OPI 6 wire. To reconcile the experimental and

  1. On the density scaling of pVT data and transport properties for molecular and ionic liquids.

    Science.gov (United States)

    López, Enriqueta R; Pensado, Alfonso S; Fernández, Josefa; Harris, Kenneth R

    2012-06-07

    In this work, a general equation of state (EOS) recently derived by Grzybowski et al. [Phys. Rev. E 83, 041505 (2011)] is applied to 51 molecular and ionic liquids in order to perform density scaling of pVT data employing the scaling exponent γ(EOS). It is found that the scaling is excellent in most cases examined. γ(EOS) values range from 6.1 for ammonia to 13.3 for the ionic liquid [C(4)C(1)im][BF(4)]. These γ(EOS) values are compared with results recently reported by us [E. R. López, A. S. Pensado, M. J. P. Comuñas, A. A. H. Pádua, J. Fernández, and K. R. Harris, J. Chem. Phys. 134, 144507 (2011)] for the scaling exponent γ obtained for several different transport properties, namely, the viscosity, self-diffusion coefficient, and electrical conductivity. For the majority of the compounds examined, γ(EOS) > γ, but for hexane, heptane, octane, cyclopentane, cyclohexane, CCl(4), dimethyl carbonate, m-xylene, and decalin, γ(EOS) liquids. For viscosities and the self-diffusion coefficient-temperature ratio, we have tested the relation linking EOS and dynamic scaling parameters, proposed by Paluch et al. [J. Phys. Chem. Lett. 1, 987-992 (2010)] and Grzybowski et al. [J. Chem. Phys. 133, 161101 (2010); Phys. Rev. E 82, 013501 (2010)], that is, γ = (γ(EOS)/φ) + γ(G), where φ is the stretching parameter of the modified Avramov relation for the density scaling of a transport property, and γ(G) is the Grüneisen constant. This relationship is based on data for structural relaxation times near the glass transition temperature for seven molecular liquids, including glass formers, and a single ionic liquid. For all the compounds examined in our much larger database the ratio (γ(EOS)/φ) is actually higher than γ, with the only exceptions of propylene carbonate and 1-methylnaphthalene. Therefore, it seems the relation proposed by Paluch et al. applies only in certain cases, and is really not generally applicable to liquid transport properties such as

  2. Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.

    Science.gov (United States)

    França, João M P; Nieto de Castro, Carlos A; Pádua, Agílio A H

    2017-07-05

    We used molecular dynamics simulation to study the effect of suspended carbon nanomaterials, nanotubes and graphene sheets, on the thermal conductivity of ionic liquids, an issue related to understanding the properties of nanofluids. One important aspect that we developed is an atomistic model of the interactions between the organic ions and carbon nanomaterials, so we did not rely on existing force fields for small organic molecules or assume simple combining rules to describe the interactions at the liquid/material interface. Instead, we used quantum calculations with a density functional suitable for non-covalent interactions to parameterize an interaction model, including van der Waals terms and also atomic partial charges on the materials. We fitted a n-m interaction potential function with n values of 9 or 10 and m values between 5 and 8, so a 12-6 Lennard-Jones function would not fit the quantum calculations. For the atoms of ionic liquids and carbon nanomaterials interacting among themselves, we adopted existing models from the literature. We studied the imidazolium ionic liquids [C 4 C 1 im][SCN], [C 4 C 1 im][N(CN) 2 ], [C 4 C 1 im][C(CN) 3 ] and [C 4 C 1 im][(CF 3 SO 2 ) 2 N]. Attraction is stronger for cations (than for anions) above and below the π-system of the nanomaterials, whereas anions show stronger attraction for the hydrogenated edges. The ordering of ions around and inside (7,7) and (10,10) single-walled nanotubes, and near a stack of graphene sheets, was analysed in terms of density distribution functions. We verified that anions are found, as well as cations, in the first interfacial layer interacting with the materials, which is surprising given the interaction potential surfaces. The thermal conductivity of the ionic liquids and of composite systems containing one nanotube or one graphene stack in suspension was calculated using non-equilibrium molecular dynamics. Thermal conductivity was calculated along the axis of the nanotube and

  3. 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.

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

    KAUST Repository

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

    2013-01-01

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

  5. Surface transport mechanisms in molecular glasses probed by the exposure of nano-particles

    Science.gov (United States)

    Ruan, Shigang; Musumeci, Daniele; Zhang, Wei; Gujral, Ankit; Ediger, M. D.; Yu, Lian

    2017-05-01

    For a glass-forming liquid, the mechanism by which its surface contour evolves can change from bulk viscous flow at high temperatures to surface diffusion at low temperatures. We show that this mechanistic change can be conveniently detected by the exposure of nano-particles native in the material. Despite its high chemical purity, the often-studied molecular glass indomethacin contains low-concentration particles approximately 100 nm in size and 0.3% in volume fraction. Similar particles are present in polystyrene, another often-used model. In the surface-diffusion regime, particles are gradually exposed in regions vacated by host molecules, for example, the peak of a surface grating and the depletion zone near a surface crystal. In the viscous-flow regime, particle exposure is not observed. The surface contour around an exposed particle widens over time in a self-similar manner as 3 (Bt)1/4, where B is a surface mobility constant and the same constant obtained by surface grating decay. This work suggests that in a binary system composed of slow- and fast-diffusing molecules, slow-diffusing molecules can be stranded in surface regions vacated by fast-diffusing molecules, effectively leading to phase separation.

  6. Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhi-Guo [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China); National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621900 (China); Key Laboratory of High Energy Density Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Cheng, Yan [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China); Key Laboratory of High Energy Density Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Chen, Qi-Feng, E-mail: chenqf01@gmail.com, E-mail: xrchen@scu.edu.cn [National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621900 (China); Chen, Xiang-Rong, E-mail: chenqf01@gmail.com, E-mail: xrchen@scu.edu.cn [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China)

    2016-05-15

    The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm{sup 3} along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.

  7. Energy level alignment and electron transport through metal/organic contacts. From interfaces to molecular electronics

    Energy Technology Data Exchange (ETDEWEB)

    Abad, Enrique

    2013-07-01

    A new calculational approach to describing metal/organic interfaces. A valuable step towards a better understanding of molecular electronics. Nominated as an outstanding contribution by the Autonomous University of Madrid. In recent years, ever more electronic devices have started to exploit the advantages of organic semiconductors. The work reported in this thesis focuses on analyzing theoretically the energy level alignment of different metal/organic interfaces, necessary to tailor devices with good performance. Traditional methods based on density functional theory (DFT), are not appropriate for analyzing them because they underestimate the organic energy gap and fail to correctly describe the van der Waals forces. Since the size of these systems prohibits the use of more accurate methods, corrections to those DFT drawbacks are desirable. In this work a combination of a standard DFT calculation with the inclusion of the charging energy (U) of the molecule, calculated from first principles, is presented. Regarding the dispersion forces, incorrect long range interaction is substituted by a van der Waals potential. With these corrections, the C60, benzene, pentacene, TTF and TCNQ/Au(111) interfaces are analyzed, both for single molecules and for a monolayer. The results validate the induced density of interface states model.

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

    KAUST Repository

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

    2013-01-01

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

  9. Molecular dynamics simulations for transport coefficients of liquid argon: new approaches

    International Nuclear Information System (INIS)

    Lee, Song Hi; Park, Dong Kue; Kang, Dae Bok

    2003-01-01

    The stress and the heat-flux auto-correlation functions in the Green-Kubo formulas for shear viscosity and thermal conductivity have non-decaying long-time tails. This problem can be overcome by improving the statistical accuracy by N (number of particles)times, considering the stress and the heat-flux of the system as properties of each particle. The mean square stress and the heat-flux displacements in the Einstein formulas for shear viscosity and thermal conductivity are non linear functions of time since the quantities in the mean square stress and the heat-flux displacements are not continuous under periodic boundary conditions. An alternative to these quantities is to integrate the stress and the heat-flux with respect to time, but the resulting mean square stress and heat-flux displacements are still not linear versus time. This problem can be also overcome by improving the statistical accuracy. The results for transport coefficients of liquid argon obtained are discussed

  10. In silico investigation of molecular effects caused by missense mutations in creatine transporter protein

    Science.gov (United States)

    Zhang, Zhe; Schwatz, Charles; Alexov, Emil

    2011-03-01

    Creatine transporter (CT) protein, which is encoded by SLC6A8 gene, is essential for taking up the creatine in the cell, which in turn plays a key role in the spatial and temporal maintenance of energy in skeletal and cardiac muscle cells. It was shown that some missense mutations in CT cause mental retardation, while others are harmless non-synonymous single nucleoside polymorphism (nsSNP). Currently fifteen missense mutations in CT are known, among which twelve are disease-causing. Sequence analysis reveals that there is no clear trend distinguishing disease-causing from harmless missense mutations. Because of that, we built 3D model of the CT using highly homologous template and use the model to investigate the effects of mutations of CT stability and hydrogen bond network. It is demonstrated that disease-causing mutations affect the folding free energy and ionization states of titratable group in much greater extend as compared with harmless mutations. Supported by grants from NLM, NIH, grant numbers 1R03LM009748 and 1R03LM009748-S1.

  11. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    KAUST Repository

    Stevens, Loah A.; Goetz, Katelyn P.; Fonari, Alexandr; Shu, Ying; Williamson, Rachel M.; Bredas, Jean-Luc; Coropceanu, Veaceslav P.; Jurchescu, Oana D.; Collis, Gavin E.

    2015-01-01

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  12. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    KAUST Repository

    Stevens, Loah A.

    2015-01-13

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  13. Reverse Cholesterol Transport: Molecular Mechanisms and the Non-medical Approach to Enhance HDL Cholesterol

    Directory of Open Access Journals (Sweden)

    Leandro R. Marques

    2018-05-01

    Full Text Available Dyslipidemia (high concentrations of LDL-c and low concentrations of HDL-c is a major cause of cardiovascular events, which are the leading cause of death in the world. On the other hand, nutrition and regular exercise can be an interesting strategy to modulate lipid profile, acting as prevention or treatment, inhibiting the risk of diseases due to its anti-inflammatory and anti-atherogenic characteristics. Additionally, the possibility of controlling different training variables, such as type, intensity and recovery interval, can be used to maximize the benefits of exercise in promoting cardiovascular health. However, the mechanisms by which exercise and nutrients act in the regulation of cholesterol and its fractions, such as reverse cholesterol transport, receptors and transcription factors involved, such as PPARs and their role related to exercise, deserve further discussion. Therefore, the objective of this review is to debate about non-medical approaches to increase HDL-c, such as nutritional and training strategies, and to discuss the central mechanisms involved in the modulation of lipid profile during exercise, as well as that can be controlled by physical trainers or sports specialists in attempt to maximize the benefits promoted by exercise. The search for papers was performed in the databases: Medline (Pubmed, Science Direct, Scopus, Sport Discus, Web of Science, Scielo and Lilacs until February 2016.

  14. Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability

    Directory of Open Access Journals (Sweden)

    Chen-Peng Chen

    2018-04-01

    Full Text Available The skin permeability (Kp defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical’s skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.

  15. Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability.

    Science.gov (United States)

    Chen, Chen-Peng; Chen, Chan-Cheng; Huang, Chia-Wen; Chang, Yen-Ching

    2018-04-15

    The skin permeability ( Kp ) defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR) based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical's skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.

  16. Surface potential, charging and local current transport of individual Ge quantum dots grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Singha, R.K. [Department of Physics, Visva-Bharati, Santiniketan 731235 (India); Manna, S.; Bar, R.; Das, S. [Department of Physics, Indian Institute of Technology-Kharagpur, Kharagpur 721302 (India); Ray, S.K., E-mail: physkr@phy.iitkgp.ernet.in [Department of Physics, Indian Institute of Technology-Kharagpur, Kharagpur 721302 (India)

    2017-06-15

    Highlights: We have elaborately explained the individual Ge QD charging phenomena and current transport, which is very important to understand the Ge/Si nano devices. This paper will give a flavor to properly understand these phenomena linked together along with the photocurrent mechanism which is related to the Ge/Si valence band offset. • Both the CAFM and KPFM techniques point out the functionality of doping nature of the underneath Si substrate on the aforementioned characteristics of Ge QDs. • Analysis of the surface potential mapping using KPFM technique yields an approximate valence band offset measurement which is required to understand the intra-valence transition of holes for the realization of long wavelength infrared photodetector. • KPFM and CAFM can be utilized to explore the charging/discharging phenomena of dots and their composition variations. • Current-voltage (I–V) characteristics of the individual Ge QD strongly depends on the individual QD size. • Energy band diagrams for diamond tip and Ge QD shows the higher barrier for electrons and lower barrier for holes allowing the easy tunneling for holes to dominate the transport. - Abstract: It is fundamentally important to understand the nanoscale electronic properties of a single quantum dot (QD) contrary to an ensemble of QDs. Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy (CAFM) are two important tools, which could be employed to probe surface potential, charging phenomena, and current transport mechanism of individual QD. We demonstrate the aforementioned characteristics of self-assembled Ge QDs, which was grown on Si substrates by solid source molecular beam epitaxy driven by the Stranski-Krastanov method. Study reveals that each Ge QD acts as charge storage node even at zero applied bias. The shape, size and density of QDs could be well probed by CAFM and KPFM, whereas QD facets could be better resolved by the conductive tip. The CAFM investigation

  17. Inward open characterization of EmrD transporter with molecular dynamics simulation

    International Nuclear Information System (INIS)

    Tan, Xianwei; Wang, Boxiong

    2016-01-01

    EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

  18. Inward open characterization of EmrD transporter with molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Xianwei [School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Boxiong, E-mail: boxiong_wang@yahoo.com [Department of Precision Instrument, Tsinghua University, Beijing 100084 (China)

    2016-06-10

    EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

  19. Methane and CO2 Adsorption and Transport in Carbon-based Systems from Experiments and Molecular Simulation

    Science.gov (United States)

    Wilcox, Jennifer; Firouzi, Mahnaz; Rupp, Erik; Haghapanah, Reza; Wang, Beibei

    2013-04-01

    Carbon capture and sequestration is one strategy that could potentially mitigate gigatons of CO2 emissions per year; however, technical obstacles have thus far hindered wide-scale deployment of this strategy. To design efficient and reliable strategies for either carbon capture or sequestration at the full-scale, one needs to understand the chemical and physical properties of CO2 and its interaction with its local surroundings at the molecular-scale. To investigate the chemical and physical properties of CO2 and its local surroundings at the molecular-scale, surface characterization studies are carried out alongside theoretical model efforts. Experimental investigation of CO2 interactions with organic-based porous materials ranging in complexity from functionalized graphene and activated carbon to various-rank coal and gas shale samples to create a set of realistic models that take into account both surface and pore heterogeneity. Integration of theory and experiments takes place to allow for the relevant physics at the molecular-level to be revealed. Determining adsorption and transport phenomena of CO2 (and mixtures, including H2O, and CH4) within the model pore systems can be used to understand the complex pore matrices of carbon-based sorbents, coal, and the organic components of gas shale that are crucial to determining their carbon capture or sequestration potential. Non-equilibrium molecular dynamics (NEMD) simulations of pure carbon dioxide, methane, helium and their mixtures have been carried out in carbon slit pores to investigate gas slippage and Klinkenberg effects in the organic matrices of coal and gas shale rocks. NEMD techniques are ideally suited for the experimental situation in which an external driving force, such as a chemical potential or pressure gradient, are applied on the system. Simulations have been conducted to determine the effect of pore size and exposure to an external potential on the velocity profile and slip-stick boundary

  20. The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni) molecular devices based on zigzag graphene nanoribbon electrodes

    Science.gov (United States)

    Li, Dongde; Wu, Di; Zhang, Xiaojiao; Zeng, Bowen; Li, Mingjun; Duan, Haiming; Yang, Bingchu; Long, Mengqiu

    2018-05-01

    The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni; dcdmp = 2,3-dicyano-5,6-dimercaptopyrazyne) molecular devices based on zigzag graphene nanoribbon (ZGNR) electrodes were investigated by density functional theory combined nonequilibrium Green's function method (DFT-NEGF). Our results show that the spin-dependent transport properties of the M(dcdmp)2 molecular devices can be controlled by the spin configurations of the ZGNR electrodes, and the central 3d-transition metal atom can introduce a larger magnetism than that of the nonferrous metal one. Moreover, the perfect spin filtering effect, negative differential resistance, rectifying effect and magnetic resistance phenomena can be observed in our proposed M(dcdmp)2 molecular devices.

  1. Molecular cloning, characterization and expression analysis of two members of the Pht1 family of phosphate transporters in Glycine max.

    Directory of Open Access Journals (Sweden)

    Zhaoyun Wu

    Full Text Available BACKGROUND: Phosphorus is one of the macronutrients essential for plant growth and development. The acquisition and translocation of phosphate are pivotal processes of plant growth. In a large number of plants, phosphate uptake by roots and translocation within the plant are presumed to occur via a phosphate/proton cotransport mechanism. PRINCIPAL FINDINGS: We cloned two cDNAs from soybean (Glycine max, GmPT1 and GmPT2, which show homology to the phosphate/proton cotransporter PHO84 from the budding yeast Saccharomyces cerevisiae. The amino acid sequence of the products predicted from GmPT1 and GmPT2 share 61% and 63% identity, respectively, with the PHO84 in amino acid sequence. The deduced structure of the encoded proteins revealed 12 membrane-spanning domains with a central hydrophilic region. The molecular mass values are ∼58.7 kDa for GmPT1 and ∼58.6 kDa for GmPT2. Transiently expressed GFP-protein fusions provide direct evidence that the two Pi transporters are located in the plasma membrane. Uptake of radioactive orthophosphate by the yeast mutant MB192 showed that GmPT1 and GmPT2 are dependent on pH and uptake is reduced by the addition of uncouplers of oxidative phosphorylation. The K(m for phosphate uptake by GmPT1 and GmPT2 is 6.65 mM and 6.63 mM, respectively. A quantitative real time RT-PCR assay indicated that these two genes are expressed in the roots and shoots of seedlings whether they are phosphate-deficient or not. Deficiency of phosphorus caused a slight change of the expression levels of GmPT1 and GmPT2. CONCLUSIONS: The results of our experiments show that the two phosphate transporters have low affinity and the corresponding genes are constitutively expressed. Thereby, the two phosphate transporters can perform translocation of phosphate within the plant.

  2. Passive magnetic bearing configurations

    Science.gov (United States)

    Post, Richard F [Walnut Creek, CA

    2011-01-25

    A journal bearing provides vertical and radial stability to a rotor of a passive magnetic bearing system when the rotor is not rotating and when it is rotating. In the passive magnetic bearing system, the rotor has a vertical axis of rotation. Without the journal bearing, the rotor is vertically and radially unstable when stationary, and is vertically stable and radially unstable when rotating.

  3. Passive solar construction handbook

    Energy Technology Data Exchange (ETDEWEB)

    Levy, E.; Evans, D.; Gardstein, C.

    1981-08-01

    Many of the basic elements of passive solar design are reviewed. The unique design constraints presented in passive homes are introduced and many of the salient issues influencing design decisions are described briefly. Passive solar construction is described for each passive system type: direct gain, thermal storage wall, attached sunspace, thermal storage roof, and convective loop. For each system type, important design and construction issues are discussed and case studies illustrating designed and built examples of the system type are presented. Construction details are given and construction and thermal performance information is given for the materials used in collector components, storage components, and control components. Included are glazing materials, framing systems, caulking and sealants, concrete masonry, concrete, brick, shading, reflectors, and insulators. The Load Collector Ratio method for estimating passive system performance is appended, and other analysis methods are briefly summarized. (LEW)

  4. Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

    KAUST Repository

    Turgman-Cohen, Salomon; Araque, Juan C.; Hoek, Eric M. V.; Escobedo, Fernando A.

    2013-01-01

    We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

  5. Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

    KAUST Repository

    Turgman-Cohen, Salomon

    2013-10-08

    We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

  6. From boiling point to glass transition temperature: transport coefficients in molecular liquids follow three-parameter scaling.

    Science.gov (United States)

    Schmidtke, B; Petzold, N; Kahlau, R; Hofmann, M; Rössler, E A

    2012-10-01

    The phenomenon of the glass transition is an unresolved problem in condensed matter physics. Its prominent feature, the super-Arrhenius temperature dependence of the transport coefficients, remains a challenge to be described over the full temperature range. For a series of molecular glass formers, we combined τ(T) collected from dielectric spectroscopy and dynamic light scattering covering a range 10(-12) s < τ(T) < 10(2) s. Describing the dynamics in terms of an activation energy E(T), we distinguish a high-temperature regime characterized by an Arrhenius law with a constant activation energy E(∞) and a low-temperature regime for which E(coop)(T) ≡ E(T)-E(∞) increases exponentially while cooling. A scaling is introduced, specifically E(coop)(T)/E(∞) [proportionality] exp[-λ(T/T(A)-1)], where λ is a fragility parameter and T(A) a reference temperature proportional to E(∞). In order to describe τ(T) still the attempt time τ(∞) has to be specified. Thus, a single interaction parameter E(∞) describing the high-temperature regime together with λ controls the temperature dependence of low-temperature cooperative dynamics.

  7. Electrical transport in n-type ZnMgSSe grown by molecular beam epitaxy on GaAs

    International Nuclear Information System (INIS)

    Marshall, T.; Petruzzello, J.A.; Herko, S.P.

    1994-01-01

    Significant progress in improving the Performance of blue-green II-VI semiconductor injection lasers has come about from advances in the epitaxial growth and doping of ZnMgSSe on GaAs substrates. This paper investigates electrical transport and its relation to structural quality in n-type Zn 1-y Mg y S x Se 1-x epilayers doped with Cl, grown by molecular beam epitaxy. The composition parameters x and y vary from about 0.12-0.18 and 0.08-0.15, respectively. The quaternary epilayers studied are lattice-matched (or nearly so) to the GaAs substrate. Temperature-dependent Hall-effect measurements are performed on seven n-type ZnMgSSe:Cl epilayers, and a technique is presented whereby the resulting mobility-vs-temperature data is compared with data for ZnSe to obtain a structural figure of merit that is useful in characterizing the quaternary epilayer. 29 refs., 4 figs

  8. Performance of the PBX-M passive plate stabilization system

    International Nuclear Information System (INIS)

    Kugel, H.W.; Bell, R.; Bernabei, S.

    1994-02-01

    The PBX-M passive plate stabilization system provides significant stabilization of long-wavelength external kink modes, the slowing of vertical instability growth rates, and the amelioration of disruption characteristics. The passive plate stabilization system has allowed the use of LHCD and IBW to induce current density and pressure profile modifications, and m = 1 divertor biasing for modifying edge plasma transport. Improvements in the passive plate system insulators and support structures have provided reliable operation. Impurity influxes with the close-fitting passive plates are low. Solid target boronization is applied routinely to reduce conditioning time and maintain clean conditions

  9. Nanopolaritonics with a continuum of molecules: simulations of molecular-induced selectivity in plasmonics transport through a continuous Y-shape.

    Science.gov (United States)

    Neuhauser, Daniel

    2011-11-28

    Using the recent NF (near-field) formulation for electrodynamics on the nanoscale, we simulate transport in a Y-shape gold nanostructure in the presence of 2-level molecules. NF is shown to be easily integrated with the Liouville equation, producing a simple and efficient nanopolaritons (plasmons-excitons) solver, with a large time step. Two cases are considered: coating of the gold structure with molecular layers thinner than the structure, and filling space with aligned molecules. In both cases significant effects on the radiation transport are obtained even for low molecular densities. At low densities the effects are primarily an overall reduction of the plasmonics peak, but at higher densities there is a significant selectivity control by the molecules. A redshift is predicted, especially for the space-filling case. The combined nanopolariton shows qualitative hybridization, and the spectral peaks separate with increasing coupling, i.e., with increasing molecular densities. The results open the way to "control of light by light," i.e., controlling plasmonic light transport by inducing a change in the direction of the guiding molecular dipoles through radiation or other means.

  10. The anchoring effect on the spin transport properties and I-V characteristics of pentacene molecular devices suspended between nickel electrodes.

    Science.gov (United States)

    Caliskan, S; Laref, A

    2014-07-14

    Spin-polarized transport properties are determined for pentacene sandwiched between Ni surface electrodes with various anchoring ligands. These calculations are carried out using spin density functional theory in tandem with a non-equilibrium Green's function technique. The presence of a Se atom at the edge of the pentacene molecule significantly modifies the transport properties of the device because Se has a different electronegativity than S. Our theoretical results clearly show a larger current for spin-up electrons than for spin-down electrons in the molecular junction that is attached asymmetrically across the Se linker at one side of the Ni electrodes (in an APL magnetic orientation). Moreover, this molecular junction exhibits pronounced NDR as the bias voltage is increased from 0.8 to 1.0 V. However, this novel NDR behavior is only detected in this promising pentacene molecular device. The NDR in the current-voltage (I-V) curve results from the narrowness of the density of states for the molecular states. The feasibility of controlling the TMR is also predicted in these molecular device nanostructures. Spin-dependent transmission calculations show that the sign and strength of the current-bias voltage characteristics and the TMR could be tailored for the organic molecule devices. These molecular junctions are joined symmetrically and asymmetrically between Ni metallic probes across the S and Se atoms (at the ends of the edges of the pentacene molecule). Our theoretical findings show that spin-valve phenomena can occur in these prototypical molecular junctions. The TMR and NDR results show that nanoscale junctions with spin valves could play a vital role in the production of novel functional molecular devices.

  11. The link between exercise and titin passive stiffness.

    Science.gov (United States)

    Lalande, Sophie; Mueller, Patrick J; Chung, Charles S

    2017-09-01

    What is the topic of this review? This review focuses on how in vivo and molecular measurements of cardiac passive stiffness can predict exercise tolerance and how exercise training can reduce cardiac passive stiffness. What advances does it highlight? This review highlights advances in understanding the relationship between molecular (titin-based) and in vivo (left ventricular) passive stiffness, how passive stiffness modifies exercise tolerance, and how exercise training may be therapeutic for cardiac diseases with increased passive stiffness. Exercise can help alleviate the negative effects of cardiovascular disease and cardiovascular co-morbidities associated with sedentary behaviour; this may be especially true in diseases that are associated with increased left ventricular passive stiffness. In this review, we discuss the inverse relationship between exercise tolerance and cardiac passive stiffness. Passive stiffness is the physical property of cardiac muscle to produce a resistive force when stretched, which, in vivo, is measured using the left ventricular end diastolic pressure-volume relationship or is estimated using echocardiography. The giant elastic protein titin is the major contributor to passive stiffness at physiological muscle (sarcomere) lengths. Passive stiffness can be modified by altering titin isoform size or by post-translational modifications. In both human and animal models, increased left ventricular passive stiffness is associated with reduced exercise tolerance due to impaired diastolic filling, suggesting that increased passive stiffness predicts reduced exercise tolerance. At the same time, exercise training itself may induce both short- and long-term changes in titin-based passive stiffness, suggesting that exercise may be a treatment for diseases associated with increased passive stiffness. Direct modification of passive stiffness to improve exercise tolerance is a potential therapeutic approach. Titin passive stiffness itself may

  12. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu; Shamma, Jeff S.; Martins, Nuno C.

    2018-01-01

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  13. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu

    2018-03-21

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  14. Surface passivation technology for III-V semiconductor nanoelectronics

    International Nuclear Information System (INIS)

    Hasegawa, Hideki; Akazawa, Masamichi

    2008-01-01

    The present status and key issues of surface passivation technology for III-V surfaces are discussed in view of applications to emerging novel III-V nanoelectronics. First, necessities of passivation and currently available surface passivation technologies for GaAs, InGaAs and AlGaAs are reviewed. Then, the principle of the Si interface control layer (ICL)-based passivation scheme by the authors' group is introduced and its basic characterization is presented. Ths Si ICL is a molecular beam epitaxy (MBE)-grown ultrathin Si layer inserted between III-V semiconductor and passivation dielectric. Finally, applications of the Si ICL method to passivation of GaAs nanowires and GaAs nanowire transistors and to realization of pinning-free high-k dielectric/GaAs MOS gate stacks are presented

  15. Development of the relaxation-assisted 2DIR method for accessing structures of molecules and its application for studying the energy transport on a molecular level

    Science.gov (United States)

    Kasyanenko, Valeriy Mitrofanovich

    Measuring the three-dimensional structure of molecules, dynamics of structural changes, and energy transport on a molecular scale is important for many areas of natural science. Supplementing the widely used methods of x-ray diffraction, NMR, and optical spectroscopies, a two-dimensional infrared spectroscopy (2DIR) method was introduced about a decade ago. The 2DIR method measures pair-wise interactions between vibrational modes in molecules, thus acquiring molecular structural constraints such as distances between vibrating groups and the angles between their transition dipoles. The 2DIR method has been applied to a variety of molecular systems but in studying larger molecules such as proteins and peptides the method is facing challenges associated with the congestion of their vibrational spectra and delocalized character of their vibrational modes. To help extract structural information from such spectra and make efficient use of vibrational modes separated by large distances, a novel relaxation-assisted 2DIR method (RA 2DIR) has recently been proposed, which exploits the transport of excess vibrational energy from the initially excited mode. With the goal of further development of RA 2DIR, we applied it to a variety of molecular systems, including model compounds, transition-metal complexes, and isomers. The experiments revealed several novel effects which both enhance the power of RA 2DIR and bring a deeper understanding to the fundamental process of energy transport on a molecular level. We demonstrated that RA 2DIR can enhance greatly (27-fold) the cross-peak amplitude among spatially remote modes, which leads to an increase of the range of distances accessible for structural measurements by several fold. We demonstrated that the energy transport time correlates with the intermode distance. This correlation offers a new way for identifying connectivity patterns in molecules. We developed two models of energy transport in molecules. In one, a spatial overlap

  16. Aktiv kontra passiv forvaltning

    DEFF Research Database (Denmark)

    Bechmann, Ken L.; Pedersen, Lasse Heje

    2017-01-01

    Fordele og ulemper ved aktiv og passiv forvaltning har fået fornyet opmærksomhed blandt andet i forbindelse med den forestående implementering af MiFID II. Som bidrag til denne diskussion indeholder dette nummer af Finans/Invest tre artikler, der behandler aktiv og passiv forvaltning fra...... forskellige vinkler. Denne leder forklarer, hvorfor valget mellem aktiv og passiv forvaltning er mere kompliceret, end hvad man kunne tro ved første øjekast, og konkluderer, at der vil være plads til - og behov for - begge typer forvaltning....

  17. Most energetic passive states.

    Science.gov (United States)

    Perarnau-Llobet, Martí; Hovhannisyan, Karen V; Huber, Marcus; Skrzypczyk, Paul; Tura, Jordi; Acín, Antonio

    2015-10-01

    Passive states are defined as those states that do not allow for work extraction in a cyclic (unitary) process. Within the set of passive states, thermal states are the most stable ones: they maximize the entropy for a given energy, and similarly they minimize the energy for a given entropy. Here we find the passive states lying in the other extreme, i.e., those that maximize the energy for a given entropy, which we show also minimize the entropy when the energy is fixed. These extremal properties make these states useful to obtain fundamental bounds for the thermodynamics of finite-dimensional quantum systems, which we show in several scenarios.

  18. Molecular simulation of thermodynamic and transport properties for the H{sub 2}O+NaCl system

    Energy Technology Data Exchange (ETDEWEB)

    Orozco, Gustavo A.; Jiang, Hao; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Moultos, Othonas A.; Economou, Ioannis G. [Chemical Engineering Program, Texas A and M University at Qatar, P.O. Box 23874, Doha (Qatar)

    2014-12-21

    Molecular dynamics and Monte Carlo simulations have been carried out to obtain thermodynamic and transport properties of the binary mixture H{sub 2}O+NaCl at temperatures from T = 298 to 473 K. In particular, vapor pressures, liquid densities, viscosities, and vapor-liquid interfacial tensions have been obtained as functions of pressure and salt concentration. Several previously proposed fixed-point-charge models that include either Lennard-Jones (LJ) 12-6 or exponential-6 (Exp6) functional forms to describe non-Coulombic interactions were studied. In particular, for water we used the SPC and SPC/E (LJ) models in their rigid forms, a semiflexible version of the SPC/E (LJ) model, and the Errington-Panagiotopoulos Exp6 model; for NaCl, we used the Smith-Dang and Joung-Cheatham (LJ) parameterizations as well as the Tosi-Fumi (Exp6) model. While none of the model combinations are able to reproduce simultaneously all target properties, vapor pressures are well represented using the SPC plus Joung-Cheathem model combination, and all LJ models do well for the liquid density, with the semiflexible SPC/E plus Joung-Cheatham combination being the most accurate. For viscosities, the combination of rigid SPC/E plus Smith-Dang is the best alternative. For interfacial tensions, the combination of the semiflexible SPC/E plus Smith-Dang or Joung-Cheatham gives the best results. Inclusion of water flexibility improves the mixture densities and interfacial tensions, at the cost of larger deviations for the vapor pressures and viscosities. The Exp6 water plus Tosi-Fumi salt model combination was found to perform poorly for most of the properties of interest, in particular being unable to describe the experimental trend for the vapor pressure as a function of salt concentration.

  19. Use of FTA gene guard filter paper for the storage and transportation of tumor cells for molecular testing.

    Science.gov (United States)

    Dobbs, Larry J; Madigan, Merle N; Carter, Alexis B; Earls, Lori

    2002-01-01

    Efficient methods of storing tumor specimens for molecular testing are needed in the modern surgical pathology laboratory. The FTA Gene Guard system is a novel method for the collection and room temperature storage of blood samples for DNA testing. The method uses index card-sized filter papers that provide an ideal medium on which to store tumor specimens for DNA testing. To determine whether FTA filter paper can be used in the surgical pathology laboratory to store tumor cells for DNA testing. Cell suspensions were prepared from 60 surgical specimens, and DNA was extracted either immediately or after storage on FTA paper. The DNA extracted by each method was tested by polymerase chain reaction (PCR) for the beta-globin and interferon gamma genes, and the results were compared. Fifteen lymph node specimens stored on FTA paper were then tested for immunoglobulin heavy chain (IgH) gene rearrangement by PCR, and these results were compared with those obtained for immediately extracted DNA. University medical center. The DNA extracted from cells stored on FTA paper performed as well in the PCR as the freshly extracted DNA in nearly all cases (>95%). The results of tests for IgH gene rearrangements showed 100% concordance between the 2 methods of DNA extraction.Conclusion.-Cells from surgical specimens can be stored on FTA paper for extended lengths of time, and DNA can be extracted from these cells for PCR-based testing. FTA filter paper is a reliable medium for the storage and/or transport of tumor cells for PCR-based DNA analysis.

  20. Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study.

    Science.gov (United States)

    Cáceres-Delpiano, Javier; Teneb, Jaime; Mansilla, Rodrigo; García, Apolinaria; Salas-Burgos, Alexis

    2015-06-26

    Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Althought the existance of several protonable residues in the periplasmic loops are related to the pH-dependent activity, we find interesting to have a clear view of the conformational changes involved in this phenomena through a molecular dynamic study. Molecular dynamic simulations of the UreI transporter at three different pH conditions were performed, revealing two main pH-dependent conformations, which we present as the open and close states. We find that salt bridges between the periplasmic loops are crucial interactions that stabilize these conformations. Besides, a cooperative behaviour exists between the six subunits of the system that is necessary to fulfill the activity of this transporter. We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions. The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system. We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations.

  1. Techniques for active passivation

    Science.gov (United States)

    Roscioli, Joseph R.; Herndon, Scott C.; Nelson, Jr., David D.

    2016-12-20

    In one embodiment, active (continuous or intermittent) passivation may be employed to prevent interaction of sticky molecules with interfaces inside of an instrument (e.g., an infrared absorption spectrometer) and thereby improve response time. A passivation species may be continuously or intermittently applied to an inlet of the instrument while a sample gas stream is being applied. The passivation species may have a highly polar functional group that strongly binds to either water or polar groups of the interfaces, and once bound presents a non-polar group to the gas phase in order to prevent further binding of polar molecules. The instrument may be actively used to detect the sticky molecules while the passivation species is being applied.

  2. Passive radon daughter dosimeters

    International Nuclear Information System (INIS)

    McElroy, R.G.C.; Johnson, J.R.

    1986-03-01

    On the basis of an extensive review of the recent literature concerning passive radon daughter dosimeters, we have reached the following conclusions: 1) Passive dosimeters for measuring radon are available and reliable. 2) There does not presently exist an acceptable passive dosimeter for radon daughters. There is little if any hope for the development of such a device in the foreseeable future. 3) We are pessimistic about the potential of 'semi-passive dosimeters' but are less firm about stating categorically that these devices cannot be developed into a useful radon daughter dosimeter. This report documents and justifies these conclusions. It does not address the question of the worker's acceptance of these devices because at the present time, no device is sufficiently advanced for this question to be meaningful. 118 refs

  3. Passive Mixing inside Microdroplets

    Directory of Open Access Journals (Sweden)

    Chengmin Chen

    2018-04-01

    Full Text Available Droplet-based micromixers are essential units in many microfluidic devices for widespread applications, such as diagnostics and synthesis. The mixers can be either passive or active. When compared to active methods, the passive mixer is widely used because it does not require extra energy input apart from the pump drive. In recent years, several passive droplet-based mixers were developed, where mixing was characterized by both experiments and simulation. A unified physical understanding of both experimental processes and simulation models is beneficial for effectively developing new and efficient mixing techniques. This review covers the state-of-the-art passive droplet-based micromixers in microfluidics, which mainly focuses on three aspects: (1 Mixing parameters and analysis method; (2 Typical mixing element designs and the mixing characters in experiments; and, (3 Comprehensive introduction of numerical models used in microfluidic flow and diffusion.

  4. Microfluidic technology platforms for synthesizing, labeling and measuring the kinetics of transport and biochemical reactions for developing molecular imaging probes

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, Michael E. [Univ. of California, Los Angeles, CA (United States)

    2009-09-01

    Radiotracer techniques are used in environmental sciences, geology, biology and medicine. Radiotracers with Positron Emission Tomography (PET) provided biological examinations of ~3 million patients 2008. Despite the success of positron labeled tracers in many sciences, there is limited access in an affordable and convenient manner to develop and use new tracers. Integrated microfluidic chips are a new technology well matched to the concentrations of tracers. Our goal is to develop microfluidic chips and new synthesis approaches to enable wide dissemination of diverse types of tracers at low cost, and to produce new generations of radiochemists for which there are many unfilled jobs. The program objectives are to: 1. Develop an integrated microfluidic platform technology for synthesizing and 18F-labeling diverse arrays of different classes of molecules. 2. Incorporate microfluidic chips into small PC controlled devices (“Synthesizer”) with a platform interfaced to PC for electronic and fluid input/out control. 3. Establish a de-centralized model with Synthesizers for discovering and producing molecular imaging probes, only requiring delivery of inexpensive [18F]fluoride ion from commercial PET radiopharmacies vs the centralized approach of cyclotron facilities synthesizing and shipping a few different types of 18F-probes. 4. Develop a position sensitive avalanche photo diode (PSAPD) camera for beta particles embedded in a microfluidic chip for imaging and measuring transport and biochemical reaction rates to valid new 18F-labeled probes in an array of cell cultures. These objectives are met within a research and educational program integrating radio-chemistry, synthetic chemistry, biochemistry, engineering and biology in the Crump Institute for Molecular Imaging. The Radiochemistry Training Program exposes PhD and post doctoral students to molecular imaging in vitro in cells and microorganisms in microfluidic chips and in vivo with PET, from new technologies

  5. CANDU passive shutdown systems

    Energy Technology Data Exchange (ETDEWEB)

    Hart, R S; Olmstead, R A [AECL CANDU, Sheridan Park Research Community, Mississauga, ON (Canada)

    1996-12-01

    CANDU incorporates two diverse, passive shutdown systems, independent of each other and from the reactor regulating system. Both shutdown systems function in the low pressure, low temperature, moderator which surrounds the fuel channels. The shutdown systems are functionally different, physically separate, and passive since the driving force for SDS1 is gravity and the driving force for SDS2 is stored energy. The physics of the reactor core itself ensures a degree of passive safety in that the relatively long prompt neutron generation time inherent in the design of CANDU reactors tend to retard power excursions and reduces the speed required for shutdown action, even for large postulated reactivity increases. All passive systems include a number of active components or initiators. Hence, an important aspect of passive systems is the inclusion of fail safe (activated by active component failure) operation. The mechanisms that achieve the fail safe action should be passive. Consequently the passive performance of the CANDU shutdown systems extends beyond their basic modes of operation to include fail safe operation based on natural phenomenon or stored energy. For example, loss of power to the SDS1 clutches results in the drop of the shutdown rods by gravity, loss of power or instrument air to the injection valves of SDS2 results in valve opening via spring action, and rigorous self checking of logic, data and timing by the shutdown systems computers assures a fail safe reactor trip through the collapse of a fluctuating magnetic field or the discharge of a capacitor. Event statistics from operating CANDU stations indicate a significant decrease in protection system faults that could lead to loss of production and elimination of protection system faults that could lead to loss of protection. This paper provides a comprehensive description of the passive shutdown systems employed by CANDU. (author). 4 figs, 3 tabs.

  6. Mass Transport Properties of LiD-U Mixtures from Orbital FreeMolecular Dynamics Simulations and a Pressure-Matching Mixing Rule

    International Nuclear Information System (INIS)

    Burakovsky, Leonid; Kress, Joel D.; Collins, Lee A.

    2012-01-01

    Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD) x U (1-x) compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, ρ, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk B T/V + P e , is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species α, D α , the mutual diffusion coefficient for species α and β, Dαβ, and the shear viscosity, η, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.

  7. Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores.

    Science.gov (United States)

    Elosegui-Artola, Alberto; Andreu, Ion; Beedle, Amy E M; Lezamiz, Ainhoa; Uroz, Marina; Kosmalska, Anita J; Oria, Roger; Kechagia, Jenny Z; Rico-Lastres, Palma; Le Roux, Anabel-Lise; Shanahan, Catherine M; Trepat, Xavier; Navajas, Daniel; Garcia-Manyes, Sergi; Roca-Cusachs, Pere

    2017-11-30

    YAP is a mechanosensitive transcriptional activator with a critical role in cancer, regeneration, and organ size control. Here, we show that force applied to the nucleus directly drives YAP nuclear translocation by decreasing the mechanical restriction of nuclear pores to molecular transport. Exposure to a stiff environment leads cells to establish a mechanical connection between the nucleus and the cytoskeleton, allowing forces exerted through focal adhesions to reach the nucleus. Force transmission then leads to nuclear flattening, which stretches nuclear pores, reduces their mechanical resistance to molecular transport, and increases YAP nuclear import. The restriction to transport is further regulated by the mechanical stability of the transported protein, which determines both active nuclear transport of YAP and passive transport of small proteins. Our results unveil a mechanosensing mechanism mediated directly by nuclear pores, demonstrated for YAP but with potential general applicability in transcriptional regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Molecular Events Involved in a Single Cycle of Ligand Transfer from an ATP Binding Cassette Transporter, LolCDE, to a Molecular Chaperone, LolA*

    OpenAIRE

    Taniguchi, Naohiro; Tokuda, Hajime

    2008-01-01

    An ATP binding cassette transporter LolCDE complex releases lipoproteins from the inner membrane of Escherichia coli in an ATP-dependent manner, leading to the formation of a complex between a lipoprotein and a periplasmic chaperone, LolA. LolA is proposed to undergo a conformational change upon the lipoprotein binding. The lipoprotein is then transferred from the LolA-lipoprotein complex to the outer membrane via LolB. Unlike most ATP binding cassette transporters med...

  9. Molecular Aspects of Structure, Gating, and Physiology of pH-Sensitive Background K2P and Kir K+-Transport Channels

    Science.gov (United States)

    Sepúlveda, Francisco V.; Pablo Cid, L.; Teulon, Jacques; Niemeyer, María Isabel

    2015-01-01

    K+ channels fulfill roles spanning from the control of excitability to the regulation of transepithelial transport. Here we review two groups of K+ channels, pH-regulated K2P channels and the transport group of Kir channels. After considering advances in the molecular aspects of their gating based on structural and functional studies, we examine their participation in certain chosen physiological and pathophysiological scenarios. Crystal structures of K2P and Kir channels reveal rather unique features with important consequences for the gating mechanisms. Important tasks of these channels are discussed in kidney physiology and disease, K+ homeostasis in the brain by Kir channel-equipped glia, and central functions in the hearing mechanism in the inner ear and in acid secretion by parietal cells in the stomach. K2P channels fulfill a crucial part in central chemoreception probably by virtue of their pH sensitivity and are central to adrenal secretion of aldosterone. Finally, some unorthodox behaviors of the selectivity filters of K2P channels might explain their normal and pathological functions. Although a great deal has been learned about structure, molecular details of gating, and physiological functions of K2P and Kir K+-transport channels, this has been only scratching at the surface. More molecular and animal studies are clearly needed to deepen our knowledge. PMID:25540142

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  11. Neurotransmitter transporters

    DEFF Research Database (Denmark)

    Gether, Ulrik; Andersen, Peter H; Larsson, Orla M

    2006-01-01

    The concentration of neurotransmitters in the extracellular space is tightly controlled by distinct classes of membrane transport proteins. This review focuses on the molecular function of two major classes of neurotransmitter transporter that are present in the cell membrane of neurons and....... Recent research has provided substantial insight into the structure and function of these transporters. In particular, the recent crystallizations of bacterial homologs are of the utmost importance, enabling the first reliable structural models of the mammalian neurotransmitter transporters...

  12. Molecular mechanisms of the epithelial transport of toxic metal ions, particularly mercury, cadmium, lead, arsenic, zinc, and copper. Progress report, January 1, 1979-December 31, 1979

    International Nuclear Information System (INIS)

    Wasserman, R.H.

    1979-01-01

    The mechanism of lead transport is presented, and especially the particular similarities or dissimilarities between lead and calcium in this process. The absorption of these metals was determined cockerels, raised on a commercial diet or on a specified diet, using in vivo ligated loop procedure. The dose administered into the loop contained 0.5 μCi 203 Pb (and/or 0.1 μCi 47 Ca), and 0.01 mM lead acetate (and/or mM CaCl 2 ) in 0.5 ml 0.15 M NaCl,pH 6.5. It was shown that lead is rapidly taken up by the mucosal tissue, and slowly transferred into the body, whereas less calcium is retained by the tissue and the transfer of calcium is many times as effective as that for lead. They appear to respond in a similar manner to a low calcium intake and vitamin D treatment. Increasing luminal stable lead concentration significantly reduced the percentage of radiolead significantly reduced the percentage of radiolead absorbed, but did not affect the absorption of calcium. Also, vitamin D enhanced the transfer of plasma 47 Ca into the lumen but did not affect the transfer of plasma 203 Pb. Intravenous administration of 1,25(OH) 2 CC to rachitic chicks enhanced calcium and lead absorption, but the maximal absorption of these metals occurred at slightly different times after administering this metabolite, indicating that two different transport systems may be involved. It was concluded that lead is transported across the epithelial wall by a passive diffusion and this process is affected by vitamin D in a similar manner as this vitamin affects the diffusional component of calcium transport

  13. A Portable Passive Physiotherapeutic Exoskeleton

    Directory of Open Access Journals (Sweden)

    Dasheek Naidu

    2012-10-01

    Full Text Available The public healthcare system in South Africa is in need of urgent attention in no small part because there has been an escalation in the number of stroke victims which could be due to the increase in hypertension in this urbanizing society. There is a growing need for physiotherapists and occupational therapists in the country, which is further hindered by the division between urban and rural areas. A possible solution is a portable passive physiotherapeutic exoskeleton device. The exoskeleton device has been formulated to encapsulate methodologies that enable the anthropomorphic integration between a biological and mechatronic limb. A physiotherapeutic mechanism was designed to be portable and adjustable, without limiting the spherical motion and workspace of the human arm. The exoskeleton was designed to be portable in the sense that it could be transported geographically. It is a complete device allowing for motion in the shoulder, elbow, wrist and hand joints. The inverse kinematics was solved iteratively via the Damped Least Squares (DLS method. The electronic and computer system allowed for professional personnel to either change an individual joint or a combination of joints angles via the kinematic models. A ramp PI controller was established to provide a smooth response to simulate the passive therapy motion.

  14. Passive Magnetic Latching Mechanisms For Robotic Applications

    KAUST Repository

    Fiaz, Usman

    2017-04-01

    This thesis investigates the passive magnetic latching mechanism designs for autonomous aerial grasping and programmable self-assembly. The enormous latching potential of neodymium magnets is a well-established fact when it comes to their ability to interact with ferrous surfaces in particular. The force of attraction or repulsion among the magnets is strong enough to keep the levitation trains, and high speed transportation pods off the rails. But such utilization of these desirable magnetic properties in commercial applications, comes at a cost of high power consumption since the magnets used are usually electromagnets. On the other hand, we explore some useful robotic applications of passive (and hence low cost) magnetic latching; which are of vital importance in autonomous aerial transportation, automated drone-based package deliveries, and programmable self-assembly and self-reconfigurable systems. We propose, and implement a novel, attach/detach mechatronic mechanism, based on passive magnetic latching of permanent magnets for usBots; our indige- nously built programmable self-assembly robots, and show that it validates the game theoretic self-assembly algorithms. Another application addressed in this thesis is the utilization of permanent magnets in autonomous aerial grasping for Unmanned Aerial Vehicles (UAVs). We present a novel gripper design for ferrous objects with a passive magnetic pick up and an impulse based drop. For both the applications, we highlight the importance, simplicity and effectiveness of the proposed designs while providing a brief comparison with the other technologies out there.

  15. Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.

    Science.gov (United States)

    Liu, Henry C; Goldenberg, Anne; Chen, Yuchen; Lun, Christina; Wu, Wei; Bush, Kevin T; Balac, Natasha; Rodriguez, Paul; Abagyan, Ruben; Nigam, Sanjay K

    2016-10-01

    Statistical analysis was performed on physicochemical descriptors of ∼250 drugs known to interact with one or more SLC22 "drug" transporters (i.e., SLC22A6 or OAT1, SLC22A8 or OAT3, SLC22A1 or OCT1, and SLC22A2 or OCT2), followed by application of machine-learning methods and wet laboratory testing of novel predictions. In addition to molecular charge, organic anion transporters (OATs) were found to prefer interacting with planar structures, whereas organic cation transporters (OCTs) interact with more three-dimensional structures (i.e., greater SP3 character). Moreover, compared with OAT1 ligands, OAT3 ligands possess more acyclic tetravalent bonds and have a more zwitterionic/cationic character. In contrast, OCT1 and OCT2 ligands were not clearly distinquishable form one another by the methods employed. Multiple pharmacophore models were generated on the basis of the drugs and, consistent with the machine-learning analyses, one unique pharmacophore created from ligands of OAT3 possessed cationic properties similar to OCT ligands; this was confirmed by quantitative atomic property field analysis. Virtual screening with this pharmacophore, followed by transport assays, identified several cationic drugs that selectively interact with OAT3 but not OAT1. Although the present analysis may be somewhat limited by the need to rely largely on inhibition data for modeling, wet laboratory/in vitro transport studies, as well as analysis of drug/metabolite handling in Oat and Oct knockout animals, support the general validity of the approach-which can also be applied to other SLC and ATP binding cassette drug transporters. This may make it possible to predict the molecular properties of a drug or metabolite necessary for interaction with the transporter(s), thereby enabling better prediction of drug-drug interactions and drug-metabolite interactions. Furthermore, understanding the overlapping specificities of OATs and OCTs in the context of dynamic transporter tissue

  16. Measure Guideline: Passive Vents

    Energy Technology Data Exchange (ETDEWEB)

    Berger, David [Consortium for Advanced Residential Buildings, Norwalk, CT (United States); Neri, Robin [Consortium for Advanced Residential Buildings, Norwalk, CT (United States)

    2016-02-05

    This document addresses the use of passive vents as a source of outdoor air in multifamily buildings. The challenges associated with implementing passive vents and the factors affecting performance are outlined. A comprehensive design methodology and quantified performance metrics are provided. Two hypothetical design examples are provided to illustrate the process. This document is intended to be useful to designers, decision-makers, and contractors implementing passive ventilation strategies. It is also intended to be a resource for those responsible for setting high-performance building program requirements, especially pertaining to ventilation and outdoor air. To ensure good indoor air quality, a dedicated source of outdoor air is an integral part of high-performance buildings. Presently, there is a lack of guidance pertaining to the design and installation of passive vents, resulting in poor system performance. This report details the criteria necessary for designing, constructing, and testing passive vent systems to enable them to provide consistent and reliable levels of ventilation air from outdoors.

  17. Final Report, University of California Merced: Uranium and strontium fate in waste-weathered sediments: Scaling of molecular processes to predict reactive transport (DE-SC0007095)

    Energy Technology Data Exchange (ETDEWEB)

    O' Day, Peggy Anne [University of California Merced; Chorover, Jon [University of Arizona; Steefel, Carl [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Mueller, Karl [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Um, Wooyong [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-30

    Objectives of the Project: 1. Determine the process coupling that occurs between mineral transformation and contaminant (U and Sr) speciation in acid-uranium waste weathered Hanford sediments. 2. Establish linkages between molecular-scale contaminant speciation and meso-scale contaminant lability, release and reactive transport. 3. Make conjunctive use of molecular- to bench-scale data to constrain the development of a mechanistic, reactive transport model that includes coupling of contaminant sorption-desorption and mineral transformation reactions. Hypotheses Tested: Uranium and strontium speciation in legacy sediments from the U-8 and U-12 Crib sites can be reproduced in bench-scale weathering experiments conducted on unimpacted Hanford sediments from the same formations; Reactive transport modeling of future uranium and strontium releases from the vadose zone of acid-waste weathered sediments can be effectively constrained by combining molecular-scale information on contaminant bonding environment with grain-scale information on contaminant phase partitioning, and meso-scale kinetic data on contaminant release from the waste-weathered porous media; Although field contamination and laboratory experiments differ in their diagenetic time scales (decades for field vs. months to years for lab), sediment dissolution, neophase nucleation, and crystal growth reactions that occur during the initial disequilibrium induced by waste-sediment interaction leave a strong imprint that persists over subsequent longer-term equilibration time scales and, therefore, give rise to long-term memory effects. Enabling Capabilities Developed: Our team developed an iterative measure-model approach that is broadly applicable to elucidate the mechanistic underpinnings of reactive contaminant transport in geomedia subject to active weathering.

  18. Method for Biochar Passivation Using Low Percent Oxygen

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kristin; Dupuis, Dan; Wilcox, Esther

    2016-06-06

    The thermochemical process development unit may be configured for pyrolysis or gasification. The pyrolysis unit operations include: feed transport system; entrained flow reactor; solids removal and collection; and liquid scrubbing, collection, and filtration. Char accumulates in the collection drums at a rate of ~1.5 kg/hr and must be passivated before it is stored or transported.

  19. Molecular structure, photoluminescent and electroluminescent properties of bis(2-(4-methyl-2-hydroxyphenyl)benzothiazolate) zinc with excellent electron-transport characteristics

    International Nuclear Information System (INIS)

    Xu Huixia; Xu Bingshe; Fang Xiaohong; Yue Yan; Chen Liuqing; Wang Hua; Hao Yuying

    2011-01-01

    Highlights: → The synthesis, crystal structure and photophysical properties of Zn(4-MeBTZ) 2 were reported. → The electron-transport property was investigated by theoretical calculations and experimental. → We found that Zn(4-MeBTZ) 2 has a higher electron mobility than that of [Zn(BTZ) 2 ] 2 and the devices based on it have a lower turn-on voltage. - Abstract: In this article, the molecular structure, photoluminescent and electroluminescent properties of bis(2-(4-methyl-2-hydroxyphenyl) benzothiazolate) zinc (Zn(4-MeBTZ) 2 ) with good electron-transport characteristics were reported. This complex was identified as triclinic structure with the strong intermolecular π-π stacking interactions between the benzothiazolate/phenoxido rings and weak intramolecular hydrogen bonds by X-ray single-crystal diffraction. Quantum chemical method has been employed to investigate electron structure and charge transport property. The blue-green light emission was observed by fabricating double-layer devices using Zn(4-MeBTZ) 2 as electron-transport and NPB as hole-transport material. The performance of organic light-emitting devices based on Zn(4-MeBTZ) 2 is much better than that of the devices based on [Zn(BTZ) 2 ] 2 .

  20. Constructing passive houses

    Energy Technology Data Exchange (ETDEWEB)

    Oehler, S. [Oehler Faigle Archkom Solar Architektur, Bretten (Germany)

    2005-07-01

    Everybody can learn to build energy-efficient. It needs theoretical and practical experience. 1997 we built the first freestanding Passive House in Europe, the Passive House Oehler. There had been a lot of questions, starting with the insecurity, whether the calculation program of the Passive House Institute, the PHPP, is working properly in our case. Nobody knew at that time because nobody tried it out before. It took us a lot of time to find out and every detail of the construction hat to be invented to meet the very high demand of thermal quality. All the following houses needed less time and had fewer open questions, adding one piece of experience with every building. 2002 we realised the biggest Passive House, the office building Energon Ulm with 420 working spaces. In the meantime we have learned a lot like how to produce prefabricated timber elements for the facades, providing good insulation, air tightness and avoiding serious thermal bridges. We have proofed, that any kind of building type can be a Passive House. And with increasing experience the freedom of design and construction is growing. Even the economical efficiency increased. The Energon Ulm is providing a much better indoor climate than any other office building and was build 10 % cheaper than an average German office building. At present the Passive House Standard is the most efficient solution for the user to live in the desired comfort zone between 20 C and 25 C. This zone of individual feeling-well can be described with the term ''operative temperature''. This term is defined by factors like air temperature, radiation temperature of warm and cold surfaces, air speed and humidity. The result of all these factors has to be within 18 C to 25 C without accepting one of the factors getting extreme.

  1. Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays.

    NARCIS (Netherlands)

    Kirchberger, S.; Leroch, M.; Huynen, M.A.; Wahl, M.; Neuhaus, H.E.; Tjaden, J.

    2007-01-01

    Physiological studies on the Brittle1 maize mutant have provided circumstantial evidence that ZmBT1 (Zea mays Brittle1 protein) is involved in the ADP-Glc transport into maize endosperm plastids, but up to now, no direct ADP-Glc transport mediated by ZmBT1 has ever been shown. The heterologous

  2. Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays

    NARCIS (Netherlands)

    Kirchberger, S.; Leroch, M.; Huynen, M.A.; Wahl, M.; Neuhaus, H.E.; Tjaden, J.

    2007-01-01

    Physiological studies on the Brittle1 maize mutant have provided circumstantial evidence that ZmBT1 (Zea mays Brittle1 protein) is involved in the ADP-Glc transport into maize endosperm plastids, but up to now, no direct ADP-Glc transport mediated by ZmBT1 has ever been shown. The heterologous

  3. Molecular response to imatinib & its correlation with mRNA expression levels of imatinib influx & efflux transporters in patients with chronic myeloid leukaemia in chronic phase

    Directory of Open Access Journals (Sweden)

    Hemant Malhotra

    2015-01-01

    Full Text Available Background & objectives: Imatinib is the standard first-line treatment for chronic myeloid leukaemia (CML patients. About 20 to 30 per cent patients develop resistance to imatinib and fail imatinib treatment. One of the mechanisms proposed is varying expression levels of the drug transporters. This study was aimed to determine the expression levels of imatinib transporter genes (OCT1, ABCB1, ABCG2 in CML patients and to correlate these levels with molecular response. Methods: Sixty three CML chronic phase patients who were on 400 mg/day imatinib for more than two years were considered for gene expression analysis study for OCT1, ABCB1 and ABCG2 genes. These were divided into responders and non-responders. The relative transcript expression levels of the three genes were compared between these two categories. The association between the expression values of these three genes was also determined. Results: No significant difference in the expression levels of OCT1, ABCB1 and ABCG2 was found between the two categories. The median transcript expression levels of OCT1, ABCB1 and ABCG2 genes in responders were 26.54, 10.78 and 0.64 versus 33.48, 7.09 and 0.53 in non-responders, respectively. A positive association was observed between the expression of the ABCB1 and ABCG2 transporter genes (r=0.407, P<0.05 while no association was observed between the expression of either of the ABC transporter genes with the OCT1 gene. Interpretation & conclusions: Our findings demonstrated that the mRNA expression levels of imatinib transporter genes were not correlated with molecular response in CML patients. Further studies need to be done on a large sample of CML patients to confirm these findings.

  4. Passive containment system

    International Nuclear Information System (INIS)

    Kleimola, F.W.

    1977-01-01

    Disclosed is a containment system that provides complete protection entirely by passive means for the loss of coolant accident in a nuclear power plant and wherein all stored energy released in the coolant blowdown is contained and absorbed while the nuclear fuel is prevented from over-heating by a high containment back-pressure and a reactor vessel refill system. The primary containment vessel is restored to a high sub-atmospheric pressure within a few minutes after accident initiation and the decay heat is safely transferred to the environment while radiolytic hydrogen is contained by passive means. 20 claims, 14 figures

  5. Wireless passive radiation sensor

    Science.gov (United States)

    Pfeifer, Kent B; Rumpf, Arthur N; Yelton, William G; Limmer, Steven J

    2013-12-03

    A novel measurement technique is employed using surface acoustic wave (SAW) devices, passive RF, and radiation-sensitive films to provide a wireless passive radiation sensor that requires no batteries, outside wiring, or regular maintenance. The sensor is small (<1 cm.sup.2), physically robust, and will operate unattended for decades. In addition, the sensor can be insensitive to measurement position and read distance due to a novel self-referencing technique eliminating the need to measure absolute responses that are dependent on RF transmitter location and power.

  6. The Impact of Molecular p-Doping on Charge Transport in High-Mobility Small-Molecule/Polymer Blend Organic Transistors

    KAUST Repository

    Paterson, Alexandra F.

    2017-12-27

    Molecular doping is a powerful tool with the potential to resolve many of the issues currently preventing organic thin-film transistor (OTFT) commercialization. However, the addition of dopant molecules into organic semiconductors often disrupts the host lattice, introducing defects and harming electrical transport. New dopant-based systems that overcome practical utilization issues, while still reaping the electrical performance benefits, would therefore be extremely valuable. Here, the impact of p-doping on the charge transport in blends consisting of the small-molecule 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT), the polymer indacenodithiophene-benzothiadiazole (C16IDT-BT), and the molecular dopant C60F48 is investigated. Electrical field-effect measurements indicate that p-doping not only enhances the average saturation mobility from 1.4 to 7.8 cm2 V−1 s−1 over 50 devices (maximum values from around 4 to 13 cm2 V−1 s−1), but also improves bias–stress stability, contact resistance, threshold voltage, and the overall device-to-device performance variation. Importantly, materials characterization using X-ray diffraction, X-ray photoemission spectroscopy, and ultraviolet photoemission spectroscopy, combined with charge transport modeling, reveal that effective doping is achieved without perturbing the microstructure of the polycrystalline semiconductor film. This work highlights the remarkable potential of ternary organic blends as a simple platform for OTFTs to achieve all the benefits of doping, with none of the drawbacks.

  7. The Impact of Molecular p-Doping on Charge Transport in High-Mobility Small-Molecule/Polymer Blend Organic Transistors

    KAUST Repository

    Paterson, Alexandra F.; Lin, Yen-Hung; Mottram, Alexander D.; Fei, Zhuping; Niazi, Muhammad Rizwan; Kirmani, Ahmad R.; Amassian, Aram; Solomeshch, Olga; Tessler, Nir; Heeney, Martin; Anthopoulos, Thomas D.

    2017-01-01

    Molecular doping is a powerful tool with the potential to resolve many of the issues currently preventing organic thin-film transistor (OTFT) commercialization. However, the addition of dopant molecules into organic semiconductors often disrupts the host lattice, introducing defects and harming electrical transport. New dopant-based systems that overcome practical utilization issues, while still reaping the electrical performance benefits, would therefore be extremely valuable. Here, the impact of p-doping on the charge transport in blends consisting of the small-molecule 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT), the polymer indacenodithiophene-benzothiadiazole (C16IDT-BT), and the molecular dopant C60F48 is investigated. Electrical field-effect measurements indicate that p-doping not only enhances the average saturation mobility from 1.4 to 7.8 cm2 V−1 s−1 over 50 devices (maximum values from around 4 to 13 cm2 V−1 s−1), but also improves bias–stress stability, contact resistance, threshold voltage, and the overall device-to-device performance variation. Importantly, materials characterization using X-ray diffraction, X-ray photoemission spectroscopy, and ultraviolet photoemission spectroscopy, combined with charge transport modeling, reveal that effective doping is achieved without perturbing the microstructure of the polycrystalline semiconductor film. This work highlights the remarkable potential of ternary organic blends as a simple platform for OTFTs to achieve all the benefits of doping, with none of the drawbacks.

  8. Anchoring group effects in molecular devices: An ab initio study on the electronic transport of a carbon-dimer

    International Nuclear Information System (INIS)

    Wang, R.N.; Zheng, X.H.; Dai, Z.X.; Hao, H.; Song, L.L.; Zeng, Z.

    2011-01-01

    The conductance of a molecular device is sensitive to the contact geometry between the molecules and the probing electrodes. Taking a carbon-dimer C 2 as an example and connecting it to the electrodes by different linking atoms H, Cu and S, we investigate the anchoring group effect in molecular devices by the first-principles approaches. The results exhibit that, depending on the anchoring groups and the subsequent different metal-molecule chemical bonds, the current varies over more than two orders of magnitude under the same bias. This emphasizes the great importance of the anchoring groups in molecular devices.

  9. Passiv-Sammler

    OpenAIRE

    Fritsche, U.

    1991-01-01

    The invention relates to a passive collector for air pollution for the determination of emission rates for dry and wet deposits on construction materials such as natural stone, whereby the collector has a surrogate surface of the stone under investigation, the surrogate surface being linked to a collecting vessel such that any dry or wet contamination occurring can be collected.

  10. Passive houses in Norway

    Energy Technology Data Exchange (ETDEWEB)

    Halse, Andreas

    2008-12-15

    The paper analyzes the introduction of passive houses in the Norwegian house market. Passive houses are houses with extremely low levels of energy consumption for heating, and have not yet been built in Norway, but have started to enter the market in Germany and some other countries. The construction sector is analyzed as a sectoral innovation system. The different elements of the innovation system are studied. This includes government agencies, producers, consumers, finance and education. The analysis shows that passive and low-energy houses are on the verge of market breakthrough. This can partly be explained by economic calculations, and partly by processes of learning and change in the institutional set-up of the sector. The construction sector is a sector characterized by low innovative intensity and little interaction between different agents. Those working to promote passive houses have to some extent managed to cope with these challenges. This has happened by breaking away from the traditional focus of Norwegian energy efficiency policies on technology and the economically rational agents, by instead focusing on knowledge and institutional change at the level of the producers. (Author)

  11. Hood River Passive House

    Energy Technology Data Exchange (ETDEWEB)

    Hales, David [BA-PIRC, Spokane, WA (United States)

    2014-01-01

    The Hood River Passive Project was developed by Root Design Build of Hood River Oregon using the Passive House Planning Package (PHPP) to meet all of the requirements for certification under the European Passive House standards. The Passive House design approach has been gaining momentum among residential designers for custom homes and BEopt modeling indicates that these designs may actually exceed the goal of the U.S. Department of Energy's (DOE) Building America program to "reduce home energy use by 30%-50% (compared to 2009 energy codes for new homes). This report documents the short term test results of the Shift House and compares the results of PHPP and BEopt modeling of the project. The design includes high R-Value assemblies, extremely tight construction, high performance doors and windows, solar thermal DHW, heat recovery ventilation, moveable external shutters and a high performance ductless mini-split heat pump. Cost analysis indicates that many of the measures implemented in this project did not meet the BA standard for cost neutrality. The ductless mini-split heat pump, lighting and advanced air leakage control were the most cost effective measures. The future challenge will be to value engineer the performance levels indicated here in modeling using production based practices at a significantly lower cost.

  12. Passive THz metamaterials

    DEFF Research Database (Denmark)

    Lavrinenko, Andrei; Malureanu, Radu; Zalkovskij, Maksim

    2012-01-01

    In this work we present our activities in the fabrication and characterization of passive THz metamaterials. We use two fabrication processes to develop metamaterials either as free-standing metallic membranes or patterned metallic multi-layers on the substrates to achieve different functionalities...

  13. Passive safety of passenger cars : a pilot-study into the development of a ranking list of passengers. On behalf of the Dutch Ministry of Transport and Public Works.

    NARCIS (Netherlands)

    Kampen, L.T.B. van

    1998-01-01

    This report is the English translation of IRRD 491574 (see C 11059). The key objective of this study was to investigate the feasibility of constructing a list of individual or grouped types of cars which could be ranked according to passive safety. A ranked listing was drawn up as based on accident

  14. Molecular Doping of the Hole-Transporting Layer for Efficient, Single-Step Deposited Colloidal Quantum Dot Photovoltaics

    KAUST Repository

    Kirmani, Ahmad R.; Garcia de Arquer, F. Pelayo; Fan, James Z.; Khan, Jafar Iqbal; Walters, Grant; Hoogland, Sjoerd; Wehbe, Nimer; Said, Marcel M.; Barlow, Stephen; Laquai, Fré dé ric; Marder, Seth R.; Sargent, Edward H.; Amassian, Aram

    2017-01-01

    solar cells. These promising architectures employ a QD hole-transporting layer (HTL) whose intrinsically shallow Fermi level (EF) restricts band-bending at maximum power-point during solar cell operation limiting charge collection. Here, we demonstrate a

  15. Excitatory amino acid transporters: recent insights into molecular mechanisms, novel modes of modulation and new therapeutic possibilities

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Fahlke, Christoph; Bjørn-Yoshimoto, Walden Emil

    2015-01-01

    The five excitatory amino acid transporters (EAAT1–5) mediating the synaptic uptake of the major excitatory neurotransmitter glutamate are differently expressed throughout the CNS and at the synaptic level. Although EAATs are crucial for normal excitatory neurotransmission, explorations into the ......The five excitatory amino acid transporters (EAAT1–5) mediating the synaptic uptake of the major excitatory neurotransmitter glutamate are differently expressed throughout the CNS and at the synaptic level. Although EAATs are crucial for normal excitatory neurotransmission, explorations...

  16. Modulating Hole Transport in Multilayered Photocathodes with Derivatized p-Type Nickel Oxide and Molecular Assemblies for Solar-Driven Water Splitting

    Energy Technology Data Exchange (ETDEWEB)

    Shan, Bing [Department; Sherman, Benjamin D. [Department; Klug, Christina M. [Center; Nayak, Animesh [Department; Marquard, Seth L. [Department; Liu, Qing [Department; Bullock, R. Morris [Center; Meyer, Thomas J. [Department

    2017-08-31

    We report here a new photocathode composed of a bi-layered doped NiO film topped by a macro-mesoporous ITO (ioITO) layer with molecular assemblies attached to the ioITO surface. The NiO film containing a 2% K+ doped NiO inner layer and a 2% Cu2+ doped NiO outer layer provides sufficient driving force for hole transport after injection to NiO by the molecular assembly. The tri-layered oxide, NiK0.02O | NiCu0.02O | ioITO, sensitized by a ruthenium polypyridyl dye and functionalized with a nickel-based hydrogen evolution catalyst, outperforms its counterpart, NiO | NiO | ioITO, in photocatalytic hydrogen evolution from water over a period of several hours with a Faradaic yield of ~90%.

  17. Tuning carrier mobility of phosphorene nanoribbons by edge passivation and strain

    International Nuclear Information System (INIS)

    Zhang, Xiaoou; Li, Qingfang; Xu, Bo; Wan, Bo; Yin, Jiang; Wan, X.G.

    2016-01-01

    Using first-principles calculations, we have studied the effects of different edge passivation groups on the carrier mobility of the phosphorene nanoribbons (PNRs) and strain effect on the transport property in passivated PNRs. The numerical results show that the size-dependent carrier mobility of passivated PNRs is not very sensitive to the different passivation groups, such as hydrogen (H), fluorine (F) and chlorine (Cl), but strongly associated with the orientation of nanoribbons. Passivated armchair-PNR has much larger carrier mobility than passivated zigzag-PNR at the similar ribbon width. With increasing ribbon width, the electron mobility of passivated PNRs can be further enhanced. We also find that the anisotropy of carrier mobility in passivated PNRs can be reversed by applying tensile strain resulting from order switching of the conduction bands around Fermi level.

  18. Tuning carrier mobility of phosphorene nanoribbons by edge passivation and strain

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiaoou [National Laboratory of Solid State Microstructures, College of Physics, Nanjing University, Nanjing 210093 (China); Li, Qingfang, E-mail: qingfangli@nuist.edu.cn [National Laboratory of Solid State Microstructures, College of Physics, Nanjing University, Nanjing 210093 (China); Department of Physics, Nanjing University of Information Science & Technology, Nanjing 210044 (China); Xu, Bo, E-mail: xubonju@gmail.com [National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering, Nanjing University, Nanjing 210093 (China); Wan, Bo [National Laboratory of Solid State Microstructures, College of Physics, Nanjing University, Nanjing 210093 (China); Yin, Jiang [National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering, Nanjing University, Nanjing 210093 (China); Wan, X.G. [National Laboratory of Solid State Microstructures, College of Physics, Nanjing University, Nanjing 210093 (China)

    2016-02-05

    Using first-principles calculations, we have studied the effects of different edge passivation groups on the carrier mobility of the phosphorene nanoribbons (PNRs) and strain effect on the transport property in passivated PNRs. The numerical results show that the size-dependent carrier mobility of passivated PNRs is not very sensitive to the different passivation groups, such as hydrogen (H), fluorine (F) and chlorine (Cl), but strongly associated with the orientation of nanoribbons. Passivated armchair-PNR has much larger carrier mobility than passivated zigzag-PNR at the similar ribbon width. With increasing ribbon width, the electron mobility of passivated PNRs can be further enhanced. We also find that the anisotropy of carrier mobility in passivated PNRs can be reversed by applying tensile strain resulting from order switching of the conduction bands around Fermi level.

  19. A corrected NEGF + DFT approach for calculating electronic transport through molecular devices: Filling bound states and patching the non-equilibrium integration

    International Nuclear Information System (INIS)

    Li Rui; Zhang Jiaxing; Hou Shimin; Qian Zekan; Shen Ziyong; Zhao Xingyu; Xue Zengquan

    2007-01-01

    We discuss two problems in the conventional approach for studying charge transport in molecular electronic devices that is based on the non-equilibrium Green's function formalism and density functional theory, i.e., the bound states and the numerical integration of the non-equilibrium density matrix. A scheme of filling the bound states in the bias window and a method of patching the non-equilibrium integration are proposed, both of which are referred to as the non-equilibrium correction. The discussion is illustrated by means of calculations on a model system consisting of a 4,4 bipyridine molecule connected to two semi-infinite gold monatomic chains

  20. Intrinsically Passive Handling and Grasping

    NARCIS (Netherlands)

    Stramigioli, Stefano; Scherpen, Jacquelien M.A.; Khodabandehloo, Koorosh

    2000-01-01

    The paper presents a control philosophy called Intrinsically Passive Control, which has the feature to properly behave during interaction with any passive objects. The controlled robot will never become unstable due to the physical structure of the controller.

  1. Significantly enhanced thermal conductivity of indium arsenide nanowires via sulfur passivation.

    Science.gov (United States)

    Xiong, Yucheng; Tang, Hao; Wang, Xiaomeng; Zhao, Yang; Fu, Qiang; Yang, Juekuan; Xu, Dongyan

    2017-10-16

    In this work, we experimentally investigated the effect of sulfur passivation on thermal transport in indium arsenide (InAs) nanowires. Our measurement results show that thermal conductivity can be enhanced by a ratio up to 159% by sulfur passivation. Current-voltage (I-V) measurements were performed on both unpassivated and S-passivated InAs nanowires to understand the mechanism of thermal conductivity enhancement. We observed a remarkable improvement in electrical conductivity upon sulfur passivation and a significant contribution of electrons to thermal conductivity, which account for the enhanced thermal conductivity of the S-passivated InAs nanowires.

  2. Passive cyclotron current drive for fusion plasmas

    International Nuclear Information System (INIS)

    Kernbichler, W.

    1995-01-01

    The creation of toroidal current using cyclotron radiation in a passive way is, together with the well known bootstrap current, an interesting method for stationary current drive in high-temperature fusion reactors. Here, instead of externally applied RF-waves, fish-scale like structures at the first wall help to create enough asymmetry in the self generated cyclotron radiation intensity to drive a current within the plasma. The problem of computing passive cyclotron current drive consists of actually two linked problems, which are the computation of the electron equilibrium under the presence of self-generated radiation, and the computation of the photon equilibrium in a bounded system with a distorted electron distribution. This system of integro-differential equations cannot be solved directly in an efficient way. Therefore a linearization procedure was developed to decouple both sets of equations, finally linked through a generalized local current drive efficiency. The problem of the exact accounting for the wall profile effects was reduced to the solution of a Fredholm-type integral equation of the 2 nd -kind. Based on all this an extensive computer code was developed to compute the passively driven current as well as radiation losses, radiation transport and overall efficiencies. The results therefrom give an interesting and very detailed insight into the problems related to passive cyclotron current drive

  3. Molecular mechanisms of the epithelial transport of toxic metal ions. Final report, September 1, 1975-December 31, 1985

    International Nuclear Information System (INIS)

    Wasserman, R.H.; Fullmer, C.S.

    1986-01-01

    Studies were undertaken to examine the effects of various factors on the intestinal absorption of cadmium, zinc, arsenate and lead as well as the toxic effects of cadmium and lead on the intestinal transport of calcium. Intestinal cadmium absorption was influenced by many of the same factors which influence calcium transport, although there was no direct evidence for a common transport pathway. Cadmium inhibited the intestinal absorption of calcium, primarily at the intestinal level, since no effect on the cholecalciferol endocrine system was observed. Many similarities and differences were documented for intestinal lead and calcium transport, suggesting that these two cations share some of the same transport components. The effect of dietary lead was far more severe under conditions of dietary calcium restriction, effectively eliminating the adaptation response via the cholecalciferol endocrine system. This effect was attributed partially to lead inhibition of renal production of the active hormone, although direct inhibition, at the intestinal level, was also suggested. Several members of the troponin C family of calcium-binding proteins were shown to bind lead in preference to calcium, suggesting that many of the toxic manifestations of lead may be related to perturbation of calcium-mediated cellular processes. 110 refs

  4. Molecular characterization of ABC transporters in marine ciliate, Euplotes crassus: Identification and response to cadmium and benzo[a]pyrene.

    Science.gov (United States)

    Kim, Hokyun; Yim, Bora; Kim, Jisoo; Kim, Haeyeon; Lee, Young-Mi

    2017-11-30

    ATP-binding cassette (ABC) transporters participate in transporting various substances, including xenobiotics, in or out of cells. However, their genetic information and function in ciliates remain still unclear. In this study, we sequenced and characterized two ABC transporter genes (EcABCB and EcABCC), and investigated the effect of cadmium (Cd) and benzo[a]pyrene (B[a]P) on their function and gene expression, using efflux assay and real-time reverse transcription-polymerase chain reaction (qRT-PCR), respectively, in the marine ciliate, Euplotes crassus. Sequencing analysis and efflux assay showed that EcABCB and EcABCC are typical ABC transporters, possessing conserved function. Exposure to Cd (≥5mg/L) and B[a]P (≥50.5μg/L) enhanced accumulation of a substrate. A significant increase in the expression of EcABCB and EcABC mRNA was observed at lower concentration in response to Cd and B[a]P. Our findings indicate that Cd and B[a]P could inhibit the efflux function of ABC transporters, leading to cellular toxicity in the ciliate. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Passive solar heating

    Energy Technology Data Exchange (ETDEWEB)

    Wiberg, K

    1981-11-10

    The present work treats the possibilities for heating according to the passive solar heating method. Problems of 'spatial organization in an energy-saving society' are distinguished from among other social problems. The final delimination of the actual problems under investigation consists of the use of passive solar heating and especially the 'consequences of such solar heating exploitation upon the form and structures' of planning and construction. In the concluding chapter an applied example shows how this method can be used in designing an urban area and what are its limitations. The results indicate the possibilities and difficulties in attempting to transfer this ideal and general method into models and directives for form and structure from which examples of the actual possibilities in practical planning can be given.

  6. Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)-A Molecular Dynamics Approach.

    Science.gov (United States)

    Kamaraj, Balu; Purohit, Rituraj

    2016-11-01

    Oculocutaneous albinism type IV (OCA4) is an autosomal recessive inherited disorder which is characterized by reduced biosynthesis of melanin pigmentation in skin, hair, and eyes and caused by the genetic mutations in the membrane-associated transporter protein (MATP) encoded by SLC45A2 gene. The MATP protein consists of 530 amino acids which contains 12 putative transmembrane domains and plays an important role in pigmentation and probably functions as a membrane transporter in melanosomes. We scrutinized the most OCA4 disease-associated mutation and their structural consequences on SLC45A2 gene. To understand the atomic arrangement in 3D space, the native and mutant structures were modeled. Further the structural behavior of native and mutant MATP protein was investigated by molecular dynamics simulation (MDS) approach in explicit lipid and water background. We found Y317C as the most deleterious and disease-associated SNP on SLC45A2 gene. In MDS, mutations in MATP protein showed loss of stability and became more flexible, which alter its structural conformation and function. This phenomenon has indicated a significant role in inducing OCA4. Our study explored the understanding of molecular mechanism of MATP protein upon mutation at atomic level and further helps in the field of pharmacogenomics to develop a personalized medicine for OCA4 disorder. J. Cell. Biochem. 117: 2608-2619, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Qademah Fault Passive Data

    KAUST Repository

    Hanafy, Sherif M.

    2014-01-01

    OBJECTIVE: In this field trip we collect passive data to 1. Convert passive to surface waves 2. Locate Qademah fault using surface wave migration INTRODUCTION: In this field trip we collected passive data for several days. This data will be used to find the surface waves using interferometry and then compared to active-source seismic data collected at the same location. A total of 288 receivers are used. A 3D layout with 5 m inline intervals and 10 m cross line intervals is used, where we used 12 lines with 24 receivers at each line. You will need to download the file (rec_times.mat), it contains important information about 1. Field record no 2. Record day 3. Record month 4. Record hour 5. Record minute 6. Record second 7. Record length P.S. 1. All files are converted from original format (SEG-2) to matlab format P.S. 2. Overlaps between records (10 to 1.5 sec.) are already removed from these files

  8. Influence of Low Molecular Weight Organic Acids on Transport of Cadmium and Copper Ions across Model Phospholipid Membranes

    Czech Academy of Sciences Publication Activity Database

    Parisová, Martina; Navrátil, Tomáš; Šestáková, Ivana; Jaklová Dytrtová, Jana; Mareček, Vladimír

    2013-01-01

    Roč. 8, č. 1 (2013), s. 27-44 ISSN 1452-3981 R&D Projects: GA AV ČR IAA400400806 Institutional support: RVO:61388963 ; RVO:61388955 Keywords : cadmium * copper * low molecular weight organic acid Subject RIV: CG - Electrochemistry Impact factor: 1.956, year: 2013

  9. Concept research on general passive system

    International Nuclear Information System (INIS)

    Han Xu; Yang Yanhua; Zheng Mingguang

    2009-01-01

    This paper summarized the current passive techniques used in nuclear power plants. Through classification and analysis, the functional characteristics and inherent identification of passive systems were elucidated. By improving and extending the concept of passive system, the general passive concept was proposed, and space and time relativity was discussed and assumption of general passive system were illustrated. The function of idealized general passive system is equivalent with the current passive system, but the design of idealized general passive system is more flexible. (authors)

  10. Effect of dialysate osmolarity on the transport of low-molecular weight solutes and proteins during CAPD

    NARCIS (Netherlands)

    Imholz, A. L.; Koomen, G. C.; Struijk, D. G.; Arisz, L.; Krediet, R. T.

    1993-01-01

    Osmotic-induced fluid and solute transport was studied in ten stable CAPD patients, who were examined twice within one week, using dialysate with 1.36% glucose on the first and 3.86% glucose on the second day. Peritoneal fluid kinetics were determined using intraperitoneally administered dextran 70

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  12. Enhancing the intestinal absorption of low molecular weight chondroitin sulfate by conjugation with α-linolenic acid and the transport mechanism of the conjugates.

    Science.gov (United States)

    Xiao, Yuliang; Li, Pingli; Cheng, Yanna; Zhang, Xinke; Sheng, Juzheng; Wang, Decai; Li, Juan; Zhang, Qian; Zhong, Chuanqing; Cao, Rui; Wang, Fengshan

    2014-04-25

    The purpose of this report was to demonstrate the effect of amphiphilic polysaccharides-based self-assembling micelles on enhancing the oral absorption of low molecular weight chondroitin sulfate (LMCS) in vitro and in vivo, and identify the transepithelial transport mechanism of LMCS micelles across the intestinal barrier. α-Linolenic acid-low molecular weight chondroitin sulfate polymers(α-LNA-LMCS) were successfully synthesized, and characterized by FTIR, (1)HNMR, TGA/DSC, TEM, laser light scattering and zeta potential. The significant oral absorption enhancement and elimination half-life (t₁/₂) extension of LNA-LMCS2 in rats were evidenced by intragastric administration in comparison with CS and LMCS. Caco-2 transport studies demonstrated that the apparent permeability coefficient (Papp) of LNA-LMCS2 was significantly higher than that of CS and LMCS (p<0.001), and no significant effects on the overall integrity of the monolayer were observed during the transport process. In addition, α-LNA-LMCS micelles accumulated around the cell membrane and intercellular space observed by confocal laser scanning microscope (CLSM). Furthermore, evident alterations in the F-actin cytoskeleton were detected by CLSM observation following the treatment of the cell monolayers with α-LNA-LMCS micelles, which further certified the capacity of α-LNA-LMCS micelles to open the intercellular tight junctions rather than disrupt the overall integrity of the monolayer. Therefore, LNA-LMCS2 with low cytotoxicity and high bioavailability might be a promising substitute for CS in clinical use, such as treating osteoarthritis, atherosclerosis, etc. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. [Levels and molecular heterogeneity of serotonin transporter protein in platelets of patients with different mental diseases: a comparative analysis with the use of monoclonal and polyclonal antibodies].

    Science.gov (United States)

    Brusov, O S; Faktor, M I; Zlobina, G P; Bologov, P V; Kaleda, V G; Oleĭchik, I V; Korenev, A N; Piatnitskiĭ, A N; Dupin, A M; Katasonov, A B; Morozova, M A; Beniashvili, A G; Lozier, R Kh; Pavlova, E V; Segal, O L; Massino, Iu S; Dmitriev, A D

    2001-01-01

    Polyclonal (PAb) and monoclonal (MAb) antibodies to CT2-epitope of the C-terminal fragment of serotonin transporter (SERT) protein were used to study the levels and molecular heterogeneity of platelet SERT in healthy donors and patients with affective (AD) and somatoform (SD) disorders, schizoaffective disorder (SAD) and schizophrenia. SERT was found to exist as high molecular wight (HMW) and low molecular weight (LMW) forms separated after electrophoresis. The levels of HMW and LMW forms of SERT were significantly, decreased in mentally ill patients as compared to healthy individuals. Unlike PAb, horse radish peroxidase (HRP)-conjugated MAbs were more sensitive and specific to SERT and could detect the LMW form of SERT as a duplet protein form with MW about 40 and 43 kDa. The MAb to CT2 C-terminal fragment of SERT conjugated with HRP is considered to be a new valuable tool for further investigation of SERT expression, properties, and posttranslation modification in the controls and in patients with different psychopathology.

  14. Interplay between structure and transport properties of molten salt mixtures of ZnCl2-NaCl-KCl: A molecular dynamics study.

    Science.gov (United States)

    Manga, Venkateswara Rao; Swinteck, Nichlas; Bringuier, Stefan; Lucas, Pierre; Deymier, Pierre; Muralidharan, Krishna

    2016-03-07

    Molten mixtures of network-forming covalently bonded ZnCl2 and network-modifying ionically bonded NaCl and KCl salts are investigated as high-temperature heat transfer fluids for concentrating solar power plants. Specifically, using molecular dynamics simulations, the interplay between the extent of the network structure, composition, and the transport properties (viscosity, thermal conductivity, and diffusion) of ZnCl2-NaCl-KCl molten salts is characterized. The Stokes-Einstein/Eyring relationship is found to break down in these network-forming liquids at high concentrations of ZnCl2 (>63 mol. %), while the Eyring relationship is seen with increasing KCl concentration. Further, the network modification due to the addition of K ions leads to formation of non-bridging terminal Cl ions, which in turn lead to a positive temperature dependence of thermal conductivity in these melts. This new understanding of transport in these ternary liquids enables the identification of appropriate concentrations of the network formers and network modifiers to design heat transfer fluids with desired transport properties for concentrating solar power plants.

  15. Excitation energy transfer in molecular complexes: transport processes, optical properties and effects of nearby placed metal nano-particles

    Science.gov (United States)

    May, Volkhard; Megow, Jörg; Zelinskyi, Iaroslav

    2012-04-01

    Excitation energy transfer (EET) in molecular systems is studied theoretically. Chromophore complexes are considered which are formed by a butanediamine dendrimer with four pheophorbide-a molecules. To achieve a description with an atomic resolution and to account for the effect of an ethanol solvent a mixed quantum classical methodology is utilized. Details of the EET and spectra of transient anisotropy showing signatures of EET are presented. A particular control of intermolecular EET is achieved by surface plasmons of nearby placed metal nanoparticles (MNP). To attain a quantum description of the molecule-MNP system a microscopic theory is introduced. As a particular application surface plasmon affected absorption spectra of molecular complexes placed in the proximity of a spherical MNP are discussed.

  16. Destructive quantum interference in electron transport: A reconciliation of the molecular orbital and the atomic orbital perspective

    Science.gov (United States)

    Zhao, Xin; Geskin, Victor; Stadler, Robert

    2017-03-01

    Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.

  17. Thermal transport in UO2 with defects and fission products by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xiang-Yang [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mcclellan, Kenneth James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lashley, Jason Charles [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Byler, Darrin David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stanek, Christopher Richard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-14

    The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO2 due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO2 thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U5+ and Zr4+ in UO2 have been developed for the EAM potential. The thermal conductivity results from MD simulations are then corrected for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO2+x samples.

  18. Molecular cloning and expression profile of an ATP-binding cassette (ABC) transporter gene from the hemipteran insect Nilaparvata lugens.

    Science.gov (United States)

    Zha, W J; Li, S H; Zhou, L; Chen, Z J; Liu, K; Yang, G C; Hu, G; He, G C; You, A Q

    2015-03-30

    The ATP-binding cassette (ABC) transporters belong to a large superfamily of proteins that have important physiological functions in all living organisms. In insects, ABC transporters have important functions in the transport of molecules, and are also involved in insecticide resistance, metabolism, and development. In this study, the Nilaparvata lugens Stal (Hemiptera: Delphacidae) ABCG (NlABCG) gene was identified and characterized. The complete mRNA sequence of NlABCG was 2608-bp long, with an open reading frame of 2064 bp encoding a protein comprised of 687 amino acids. The conserved regions include three N-glycosylation and 34 phosphorylation sites, as well as seven transmembrane domains. The amino acid identity with the closely related species Acyrthosiphon pisum was 42.8%. Developmental expression analysis using quantitative real-time reverse transcriptase PCR suggested that the NlABCG transcript was expressed at all developmental stages of N. lugens. The lowest expression of NlABCG was in the 1st instar, and levels increased with larval growth. The transcript profiles of NlABCG were analyzed in various tissues from a 5th instar nymph, and the highest expression was observed in the midgut. These results suggest that the sequence, characteristics, and expression of NlABCG are highly conserved, and basic information is provided for its functional analysis.

  19. Analysis of the structural and functional roles of coupling helices in the ATP-binding cassette transporter MsbA through enzyme assays and molecular dynamics simulations.

    Science.gov (United States)

    Furuta, Tadaomi; Yamaguchi, Tomohiro; Kato, Hiroaki; Sakurai, Minoru

    2014-07-08

    ATP-binding cassette (ABC) transporters are constructed from some common structural units: the highly conserved nucleotide-binding domains (NBDs), which work as a nucleotide-dependent engine for driving substrate transport, the diverse transmembrane domains (TMDs), which create the translocation pathway, and the coupling helices (CHs), which are located at the NBD-TMD interface. Although the CHs are believed to be essential for NBD-TMD communication, their roles remain unclear. In this study, we performed enzyme assays and molecular dynamics (MD) simulations of the ABC transporter MsbA and two MsbA mutants in which the amino acid residues of one of the CHs were mutated to alanines: (i) wild type (Wt), (ii) CH1 mutant (Mt1), and (iii) CH2 mutant (Mt2). The experiments show that the CH2 mutation decreases the ATPase activity (kcat) compared with that of the Wt (a decrease of 32%), and a nearly equal degree of decrease in the ATP binding affinity (Km) was observed for both Mt1 and Mt2. The MD simulations successfully accounted for several structural and dynamical origins for these experimental observations. In addition, on the basis of collective motion and morphing analyses, we propose that the reverse-rotational motions and noddinglike motions between the NBDs and TMDs are indispensable for the conformational transition between the inward- and outward-facing conformations. In particular, CH2 is significantly important for the occurrence of the noddinglike motion. These findings provide important insights into the structure-function relationship of ABC transporters.

  20. Passive Power Filters

    CERN Document Server

    Künzi, R.

    2015-06-15

    Power converters require passive low-pass filters which are capable of reducing voltage ripples effectively. In contrast to signal filters, the components of power filters must carry large currents or withstand large voltages, respectively. In this paper, three different suitable filter struc tures for d.c./d.c. power converters with inductive load are introduced. The formulas needed to calculate the filter components are derived step by step and practical examples are given. The behaviour of the three discussed filters is compared by means of the examples. P ractical aspects for the realization of power filters are also discussed.

  1. Role of passive valves & devices in poison injection system of advanced heavy water reactor

    International Nuclear Information System (INIS)

    Sapra, M.K.; Kundu, S.; Vijayan, P.K.; Vaze, K.K.; Sinha, R.K.

    2014-01-01

    The Advanced Heavy Water Reactor (AHWR) is a 300 MWe pressure tube type boiling light water (H 2 O) cooled, heavy water (D 2 O) moderated reactor. The reactor design is based on well-proven water reactor technologies and incorporates a number of passive safety features such as natural circulation core cooling; direct in-bundle injection of light water coolant during a Loss of Coolant Accident (LOCA) from Advanced Accumulators and Gravity Driven Water Pool by passive means; Passive Decay Heat Removal using Isolation Condensers, Passive Containment Cooling System and Passive Containment Isolation System. In addition to above, there is another passive safety system named as Passive Poison Injection System (PPIS) which is capable of shutting down the reactor for a prolonged time. It is an additional safety system in AHWR to fulfill the shutdown function in the event of failure of wired shutdown systems i.e. primary and secondary shut down systems of the reactor. When demanded, PPIS injects the liquid poison into the moderator by passive means using passive valves and devices. On increase of main heat transport (MHT) system pressure beyond a predetermined value, a set of rupture disks burst, which in-turn actuate the passive valve. The opening of passive valve initiates inrush of high pressure helium gas into poison tanks to push the poison into the moderator system, thereby shutting down the reactor. This paper primarily deals with design and development of Passive Poison Injection System (PPIS) and its passive valves & devices. Recently, a prototype DN 65 size Poison Injection Passive Valve (PIPV) has been developed for AHWR usage and tested rigorously under simulated conditions. The paper will highlight the role of passive valves & devices in PPIS of AHWR. The design concept and test results of passive valves along with rupture disk performance will also be covered. (author)

  2. Expansion of passive safety function

    International Nuclear Information System (INIS)

    Inai, Nobuhiko; Nei, Hiromichi; Kumada, Toshiaki.

    1995-01-01

    Expansion of the use of passive safety functions is proposed. Two notions are presented. One is that, in the design of passive safety nuclear reactors where aversion of active components is stressed, some active components are purposely introduced, by which a system is built in such a way that it behaves in an apparently passive manner. The second notion is that, instead of using a passive safety function alone, a passive safety function is combined with some active components, relating the passivity in the safety function with enhanced controllability in normal operation. The nondormant system which the authors propose is one example of the first notion. This is a system in which a standby safety system is a portion of the normal operation system. An interpretation of the nondormant system via synergetics is made. As an example of the second notion, a PIUS density lock aided with active components is proposed and is discussed

  3. Molecular cloning and functional characterization of an ATP-binding cassette transporter OtrC from Streptomyces rimosus

    Directory of Open Access Journals (Sweden)

    Yu Lan

    2012-08-01

    Full Text Available Abstract Background The otrC gene of Streptomyces rimosus was previously annotated as an oxytetracycline (OTC resistance protein. However, the amino acid sequence analysis of OtrC shows that it is a putative ATP-binding cassette (ABC transporter with multidrug resistance function. To our knowledge, none of the ABC transporters in S. rimosus have yet been characterized. In this study, we aimed to characterize the multidrug exporter function of OtrC and evaluate its relevancy to OTC production. Results In order to investigate OtrC’s function, otrC is cloned and expressed in E. coli The exporter function of OtrC was identified by ATPase activity determination and ethidium bromide efflux assays. Also, the susceptibilities of OtrC-overexpressing cells to several structurally unrelated drugs were compared with those of OtrC-non-expressing cells by minimal inhibitory concentration (MIC assays, indicating that OtrC functions as a drug exporter with a broad range of drug specificities. The OTC production was enhanced by 1.6-fold in M4018 (P = 0.000877 and 1.4-fold in SR16 (P = 0.00973 duplication mutants, while it decreased to 80% in disruption mutants (P = 0.0182 and 0.0124 in M4018 and SR16, respectively. Conclusions The results suggest that OtrC is an ABC transporter with multidrug resistance function, and plays an important role in self-protection by drug efflux mechanisms. This is the first report of such a protein in S. rimosus, and otrC could be a valuable target for genetic manipulation to improve the production of industrial antibiotics.

  4. Passive cooling containment study

    International Nuclear Information System (INIS)

    Shin, J.J.; Iotti, R.C.; Wright, R.F.

    1993-01-01

    Pressure and temperature transients of nuclear reactor containment following postulated loss of coolant accident with a coincident station blackout due to total loss of all alternating current power are studied analytically and experimentally for the full scale NPR (New Production Reactor). All the reactor and containment cooling under this condition would rely on the passive cooling system which removes reactor decay heat and provides emergency core and containment cooling. Containment passive cooling for this study takes place in the annulus between containment steel shell and concrete shield building by natural convection air flow and thermal radiation. Various heat transfer coefficients inside annular air space were investigated by running the modified CONTEMPT code CONTEMPT-NPR. In order to verify proper heat transfer coefficient, temperature, heat flux, and velocity profiles were measured inside annular air space of the test facility which is a 24 foot (7.3m) high, steam heated inner cylinder of three foot (.91m) diameter and five and half foot (1.7m) diameter outer cylinder. Comparison of CONTEMPT-NPR and WGOTHIC was done for reduced scale NPR

  5. Fly ash carbon passivation

    Science.gov (United States)

    La Count, Robert B; Baltrus, John P; Kern, Douglas G

    2013-05-14

    A thermal method to passivate the carbon and/or other components in fly ash significantly decreases adsorption. The passivated carbon remains in the fly ash. Heating the fly ash to about 500 and 800 degrees C. under inert gas conditions sharply decreases the amount of surfactant adsorbed by the fly ash recovered after thermal treatment despite the fact that the carbon content remains in the fly ash. Using oxygen and inert gas mixtures, the present invention shows that a thermal treatment to about 500 degrees C. also sharply decreases the surfactant adsorption of the recovered fly ash even though most of the carbon remains intact. Also, thermal treatment to about 800 degrees C. under these same oxidative conditions shows a sharp decrease in surfactant adsorption of the recovered fly ash due to the fact that the carbon has been removed. This experiment simulates the various "carbon burnout" methods and is not a claim in this method. The present invention provides a thermal method of deactivating high carbon fly ash toward adsorption of AEAs while retaining the fly ash carbon. The fly ash can be used, for example, as a partial Portland cement replacement in air-entrained concrete, in conductive and other concretes, and for other applications.

  6. Pronounced low-frequency vibrational thermal transport in C60 fullerite realized through pressure-dependent molecular dynamics simulations

    Science.gov (United States)

    Giri, Ashutosh; Hopkins, Patrick E.

    2017-12-01

    Fullerene condensed-matter solids can possess thermal conductivities below their minimum glassy limit while theorized to be stiffer than diamond when crystallized under pressure. These seemingly disparate extremes in thermal and mechanical properties raise questions into the pressure dependence on the thermal conductivity of C60 fullerite crystals, and how the spectral contributions to vibrational thermal conductivity changes under applied pressure. To answer these questions, we investigate the effect of strain on the thermal conductivity of C60 fullerite crystals via pressure-dependent molecular dynamics simulations under the Green-Kubo formalism. We show that the thermal conductivity increases rapidly with compressive strain, which demonstrates a power-law relationship similar to their stress-strain relationship for the C60 crystals. Calculations of the density of states for the crystals under compressive strains reveal that the librational modes characteristic in the unstrained case are diminished due to densification of the molecular crystal. Over a large compression range (0-20 GPa), the Leibfried-Schlömann equation is shown to adequately describe the pressure dependence of thermal conductivity, suggesting that low-frequency intermolecular vibrations dictate heat flow in the C60 crystals. A spectral decomposition of the thermal conductivity supports this hypothesis.

  7. Surface Passivation in Empirical Tight Binding

    OpenAIRE

    He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

    2015-01-01

    Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameter...

  8. Molecular cloning and characterization of a gene encoding the proline transporter protein in common bean(Phaseolus vulgaris L.)

    Institute of Scientific and Technical Information of China (English)

    Jibao; Chen; Jing; Wu; Yunfeng; Lu; Yuannan; Cao; Hui; Zeng; Zhaoyuan; Zhang; Lanfen; Wang; Shumin; Wang

    2016-01-01

    As a typical compatible solute, proline is accumulated in plants under environmental stresses. Proline transporter(Pro T) plays an important role in proline distribution between plant organs. Using a candidate gene approach, we cloned a c DNA sequence for Pro T from common bean(Phaseolus vulgaris L.) and designated the gene Pv Pro T. The deduced amino acid sequence of Pv Pro T showed high similarity to Bet/Pro T proteins from other leguminous plants, and the highest similarity was observed with mothbean(Vigna aconitifolia L.) Vu Pro T.Relative quantification of the m RNA level of Pv Pro T using real-time PCR analysis showed that the Pv Pro T transcript level was higher in leaves than in stems and roots of common bean plants subjected to drought and salt stress. Under 20%(w/w) PEG-6000 treatment,drought-resistant plants expressed a higher level of Pv Pro T transcripts than droughtsensitive plants. Although heterologous expression of Pv Pro T in the Escherichia coli mutant mkh13 showed that Pv Pro T exhibited uptake activities for proline and betaine, no betaine content was detected in the common bean. These findings suggest that Pv Pro T plays an important role in the transportation of proline in common bean plants exposed to drought and salt stress.

  9. Controlling Microstructure-Transport Interplay in Highly Phase-Separated Perfluorosulfonated Aromatic Multiblock Ionomers via Molecular Architecture Design.

    Science.gov (United States)

    Nguyen, Huu-Dat; Assumma, Luca; Judeinstein, Patrick; Mercier, Regis; Porcar, Lionel; Jestin, Jacques; Iojoiu, Cristina; Lyonnard, Sandrine

    2017-01-18

    Proton-conducting multiblock polysulfones bearing perfluorosulfonic acid side chains were designed to encode nanoscale phase-separation, well-defined hydrophilic/hydrophobic interfaces, and optimized transport properties. Herein, we show that the superacid side chains yield highly ordered morphologies that can be tailored by best compromising ion-exchange capacity and block lengths. The obtained microstructures were extensively characterized by small-angle neutron scattering (SANS) over an extended range of hydration. Peculiar swelling behaviors were evidenced at two different scales and attributed to the dilution of locally flat polymer particles. We evidence the direct correlation between the quality of interfaces, the topology and connectivity of ionic nanodomains, the block superstructure long-range organization, and the transport properties. In particular, we found that the proton conductivity linearly depends on the microscopic expansion of both ionic and block domains. These findings indicate that neat nanoscale phase-separation and block-induced long-range connectivity can be optimized by designing aromatic ionomers with controlled architectures to improve the performances of polymer electrolyte membranes.

  10. Triphenylamine-Thienothiophene Organic Charge-Transport Molecular Materials: Effect of Substitution Pattern on their Thermal, Photoelectrochemical, and Photovoltaic Properties.

    Science.gov (United States)

    Le, Thi Huong; Dao, Quang-Duy; Nghiêm, Mai-Phuong; Péralta, Sébastien; Guillot, Regis; Pham, Quoc Nghi; Fujii, Akihiko; Ozaki, Masanori; Goubard, Fabrice; Bui, Thanh-Tuân

    2018-04-25

    Two readily accessible thienothiophene-triphenylamine charge-transport materials have been synthesized by simply varying the substitution pattern of the triphenylamine groups on a central thienothiophene π-linker. The impact of the substitution pattern on the thermal, photoelectrochemical, and photovoltaic properties of these materials was evaluated and, based on theoretical and experimental studies, we found that the isomer in which the triphenylamine groups were located at the 2,5-positions of the thienothiophene core (TT-2,5-TPA) had better π-conjugation than the 3,6-isomer (TT-3,6-TPA). Whilst the thermal, morphological, and hydrophobic properties of the two materials were similar, their optoelectrochemical and photovoltaic properties were noticeably impacted. When applied as hole-transport materials in hybrid perovskite solar cells, the 2,5-isomer exhibited a power-conversion efficiency of 13.6 %, much higher than that of its 3,6-counterpart (0.7 %) under the same standard conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Mesoscopic spin-flip transport through a hybrid system with a single molecular dot system applied with ac magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Chen Qiao, E-mail: cqhy1127@yahoo.com.c [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Liu Jin [Institute of Theoretical Physics, Chinese Academy of Science, Beijing 100190 (China); Wang Zhiyong [School of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054 (China)

    2011-01-17

    We have investigated the current for the system of vibrating quantum dot irradiated with a rotating magnetic field and an oscillating magnetic field by nonequilibrium Green's function. The rotating magnetic field rotates with the angular frequency {omega}{sub r} around the z-axis with the tilt angle {theta}, and the time-oscillating magnetic field is located in the z-axis with the angular frequency {omega}. Different behaviors have been shown in the presence of electron-phonon interaction (EPI) which plays a significant role in the transport. The current displays asymmetric behavior as the source-drain bias eV=0, novel side peaks or shoulders can be found due to the phonon absorption and emission procedure, and the negative differential resistance becomes stronger as the parameter g increases. Furthermore, the strong EPI also destroys the quasiperiodic oscillations of current in the region {mu}{sub 0}B{sub 1}>2.5{Delta}. The electron transport properties are also significantly influenced by the linewidth function {Gamma}.

  12. Molecular cloning and characterization of a gene encoding the proline transporter protein in common bean (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Jibao Chen

    2016-10-01

    Full Text Available As a typical compatible solute, proline is accumulated in plants under environmental stresses. Proline transporter (ProT plays an important role in proline distribution between plant organs. Using a candidate gene approach, we cloned a cDNA sequence for ProT from common bean (Phaseolus vulgaris L. and designated the gene PvProT. The deduced amino acid sequence of PvProT showed high similarity to Bet/ProT proteins from other leguminous plants, and the highest similarity was observed with mothbean (Vigna aconitifolia L. VuProT. Relative quantification of the mRNA level of PvProT using real-time PCR analysis showed that the PvProT transcript level was higher in leaves than in stems and roots of common bean plants subjected to drought and salt stress. Under 20% (w/w PEG-6000 treatment, drought-resistant plants expressed a higher level of PvProT transcripts than drought-sensitive plants. Although heterologous expression of PvProT in the Escherichia coli mutant mkh13 showed that PvProT exhibited uptake activities for proline and betaine, no betaine content was detected in the common bean. These findings suggest that PvProT plays an important role in the transportation of proline in common bean plants exposed to drought and salt stress.

  13. Passive-solar construction handbook

    Energy Technology Data Exchange (ETDEWEB)

    Levy, E.; Evans, D.; Gardstein, C.

    1981-02-01

    Many of the basic elements of passive solar design are reviewed. Passive solar construction is covered according to system type, each system type discussion including a general discussion of the important design and construction issues which apply to the particular system and case studies illustrating designed and built examples of the system type. The three basic types of passive solar systems discussed are direct gain, thermal storage wall, and attached sunspace. Thermal performance and construction information is presented for typical materials used in passive solar collector components, storage components, and control components. Appended are an overview of analysis methods and a technique for estimating performance. (LEW)

  14. Local structure of scalar flux in turbulent passive scalar mixing

    Science.gov (United States)

    Konduri, Aditya; Donzis, Diego

    2012-11-01

    Understanding the properties of scalar flux is important in the study of turbulent mixing. Classical theories suggest that it mainly depends on the large scale structures in the flow. Recent studies suggest that the mean scalar flux reaches an asymptotic value at high Peclet numbers, independent of molecular transport properties of the fluid. A large DNS database of isotropic turbulence with passive scalars forced with a mean scalar gradient with resolution up to 40963, is used to explore the structure of scalar flux based on the local topology of the flow. It is found that regions of small velocity gradients, where dissipation and enstrophy are small, constitute the main contribution to scalar flux. On the other hand, regions of very small scalar gradient (and scalar dissipation) become less important to the scalar flux at high Reynolds numbers. The scaling of the scalar flux spectra is also investigated. The k - 7 / 3 scaling proposed by Lumley (1964) is observed at high Reynolds numbers, but collapse is not complete. A spectral bump similar to that in the velocity spectrum is observed close to dissipative scales. A number of features, including the height of the bump, appear to reach an asymptotic value at high Schmidt number.

  15. Revealing the Molecular Structure and the Transport Mechanism at the Base of Primary Cilia Using Superresolution STED Microscopy

    Science.gov (United States)

    Yang, Tung-Lin

    The primary cilium is an organelle that serves as a signaling center of the cell and is involved in the hedgehog signaling, cAMP pathway, Wnt pathways, etc. Ciliary function relies on the transportation of molecules between the primary cilium and the cell, which is facilitated by intraflagellar transport (IFT). IFT88, one of the important IFT proteins in complex B, is known to play a role in the formation and maintenance of cilia in various types of organisms. The ciliary transition zone (TZ), which is part of the gating apparatus at the ciliary base, is home to a large number of ciliopathy molecules. Recent studies have identified important regulating elements for TZ gating in cilia. However, the architecture of the TZ region and its arrangement relative to intraflagellar transport (IFT) proteins remain largely unknown, hindering the mechanistic understanding of the regulation processes. One of the major challenges comes from the tiny volume at the ciliary base packed with numerous proteins, with the diameter of the TZ close to the diffraction limit of conventional microscopes. Using a series of stimulated emission depletion (STED) superresolution images mapped to electron microscopy images, we analyzed the structural organization of the ciliary base. Subdiffraction imaging of TZ components defines novel geometric distributions of RPGRIP1L, MKS1, CEP290, TCTN2 and TMEM67, shedding light on their roles in TZ structure, assembly, and function. We found TCTN2 at the outmost periphery of the TZ close to the ciliary membrane, with a 227+/-18 nm diameter. TMEM67 was adjacent to TCTN2, with a 205+/-20 nm diameter. RPGRIP1L was localized toward the axoneme at the same axial level as TCTN2 and TMEM67, with a 165+/-8 nm diameter. MKS1 was situated between TMEM67 and RPGRIP1L, with an 186+/-21 nm diameter. Surprisingly, CEP290 was localized at the proximal side of the TZ close to the distal end of the centrin-labeled basal body. The lateral width was unexpectedly close to

  16. Passivation of MBE grown InGaSb/InAs superlattice photodiodes

    Science.gov (United States)

    Hill, Cory J.; Keo, Sam S.; Mumolo, Jason M.; Gunapala, Sarath D.

    2005-01-01

    We have performed wet chemical passivation tests on InGaSb/InAs superlattice photodiode structures grown molecular beam epitaxy. The details of the devices growth and characterization as well as the results of chemical passivation involving RuCl3 and H2SO4 with SiO2 dielectric depositions are presented.

  17. Contamination of public transports by Staphylococcus aureus and its carriage by biomedical students: point-prevalence, related risk factors and molecular characterization of methicillin-resistant strains.

    Science.gov (United States)

    Mendes, Â; Martins da Costa, P; Rego, D; Beça, N; Alves, C; Moreira, T; Conceição, T; Aires-de-Sousa, M

    2015-08-01

    To analyse the contamination of public transports by Staphylococcus aureus and assess its carriage by biomedical students, focussing on the point-prevalence, related risk factors and molecular characterization of methicillin-resistant strains. Cross-sectional survey. Methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) isolated from handrails of buses (n = 112) and trains (n = 79) circulating in Porto and from nasal swabs of local university students (n = 475) were quantified, characterized by molecular typing methods and related to possible risk factors. The MRSA prevalence in buses (16.1%) was not significantly different from trains (8.9%). There was also no identifiable association between the counts of MSSA and MRSA in buses and trains and the number of travellers in each sampling day, specific routes (including those passing by main hospitals) or other risk factors. Of the students, 37.1% carried S. aureus, and having a part-time job or smoking were found to be risk factors for carriage. EMRSA-15 (ST22-SCCmecIVh) was the prevalent MRSA clonal lineage, found not only in the buses (n = 14) and trains (n = 2) but also in the single MRSA-carrier among the students. The characteristics of the community-associated Southwest Pacific MRSA clone were found in a single ST30-IVa isolate, which may suggest a recent SCCmec acquisition by an MSSA background in the community. The spread of EMRSA-15, a common hospital-associated lineage, among different public transports and as a nasal coloniser is of concern and warrants adequate public health control measures. Copyright © 2015 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  18. Active and passive control of zinc phthalocyanine photodynamics

    NARCIS (Netherlands)

    Sharma, Divya; Huijser, Jannetje Maria; Savolainen, Janne; Steen, Gerrit Willem; Herek, Jennifer Lynn

    2013-01-01

    In this work we report on the ultrafast photodynamics of the photosensitizer zinc phthalocyanine (ZnPc) and manipulation thereof. Two approaches are followed: active control via pulse shaping and passive control via strategic manipulation in the periphery of the molecular structure. The objective of

  19. Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter in Bacillus subtilis.

    Science.gov (United States)

    Charbonnier, Teddy; Le Coq, Dominique; McGovern, Stephen; Calabre, Magali; Delumeau, Olivier; Aymerich, Stéphane; Jules, Matthieu

    2017-10-03

    At the heart of central carbon metabolism, pyruvate is a pivotal metabolite in all living cells. Bacillus subtilis is able to excrete pyruvate as well as to use it as the sole carbon source. We herein reveal that ysbAB (renamed pftAB ), the only operon specifically induced in pyruvate-grown B. subtilis cells, encodes a hetero-oligomeric membrane complex which operates as a facilitated transport system specific for pyruvate, thereby defining a novel class of transporter. We demonstrate that the LytST two-component system is responsible for the induction of pftAB in the presence of pyruvate by binding of the LytT response regulator to a palindromic region upstream of pftAB We show that both glucose and malate, the preferred carbon sources for B. subtilis , trigger the binding of CcpA upstream of pftAB , which results in its catabolite repression. However, an additional CcpA-independent mechanism represses pftAB in the presence of malate. Screening a genome-wide transposon mutant library, we find that an active malic enzyme replenishing the pyruvate pool is required for this repression. We next reveal that the higher the influx of pyruvate, the stronger the CcpA-independent repression of pftAB , which suggests that intracellular pyruvate retroinhibits pftAB induction via LytST. Such a retroinhibition challenges the rational design of novel nature-inspired sensors and synthetic switches but undoubtedly offers new possibilities for the development of integrated sensor/controller circuitry. Overall, we provide evidence for a complete system of sensors, feed-forward and feedback controllers that play a major role in environmental growth of B. subtilis IMPORTANCE Pyruvate is a small-molecule metabolite ubiquitous in living cells. Several species also use it as a carbon source as well as excrete it into the environment. The bacterial systems for pyruvate import/export have yet to be discovered. Here, we identified in the model bacterium Bacillus subtilis the first import

  20. Transport Measurements and Synchrotron-Based X-Ray Absorption Spectroscopy of Iron Silicon Germanide Grown by Molecular Beam Epitaxy

    Science.gov (United States)

    Elmarhoumi, Nader; Cottier, Ryan; Merchan, Greg; Roy, Amitava; Lohn, Chris; Geisler, Heike; Ventrice, Carl, Jr.; Golding, Terry

    2009-03-01

    Some of the iron-based metal silicide and germanide phases have been predicted to be direct band gap semiconductors. Therefore, they show promise for use as optoelectronic materials. We have used synchrotron-based x-ray absorption spectroscopy to study the structure of iron silicon germanide films grown by molecular beam epitaxy. A series of Fe(Si1-xGex)2 thin films (2000 -- 8000å) with a nominal Ge concentration of up to x = 0.04 have been grown. X-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) measurements have been performed on the films. The nearest neighbor co-ordination corresponding to the β-FeSi2 phase of iron silicide provides the best fit with the EXAFS data. Temperature dependent (20 coefficient was calculated. Results suggest semiconducting behavior of the films which is consistent with the EXAFS results.

  1. Thermal transport property of Ge34 and d-Ge investigated by molecular dynamics and the Slack's equation

    International Nuclear Information System (INIS)

    Han-Fu, Wang; Wei-Guo, Chu; Yan-Jun, Guo; Hao, Jin

    2010-01-01

    In this study, we evaluate the values of lattice thermal conductivity κ L of type II Ge clathrate (Ge 34 ) and diamond phase Ge crystal (d-Ge) with the equilibrium molecular dynamics (EMD) method and the Slack's equation. The key parameters of the Slack's equation are derived from the thermodynamic properties obtained from the lattice dynamics (LD) calculations. The empirical Tersoff's potential is used in both EMD and LD simulations. The thermal conductivities of d-Ge calculated by both methods are in accordance with the experimental values. The predictions of the Slack's equation are consistent with the EMD results above 250 K for both Ge 34 and d-Ge. In a temperature range of 200–1000 K, the κ L value of d-Ge is about several times larger than that of Ge 34 . (condensed matter: structure, thermal and mechanical properties)

  2. Self and transport diffusivity of CO2 in the metal-organic framework MIL-47(V) explored by quasi-elastic neutron scattering experiments and molecular dynamics simulations.

    Science.gov (United States)

    Salles, Fabrice; Jobic, Hervé; Devic, Thomas; Llewellyn, Philip L; Serre, Christian; Férey, Gérard; Maurin, Guillaume

    2010-01-26

    Quasi-elastic neutron scattering measurements are combined with molecular dynamics simulations to determine the self-diffusivity, corrected diffusivity, and transport diffusivity of CO(2) in the metal-organic framework MIL-47(V) (MIL = Materials Institut Lavoisier) over a wide range of loading. The force field used for describing the host/guest interactions is first validated on the thermodynamics of the MIL-47(V)/CO(2) system, prior to being transferred to the investigations of the dynamics. A decreasing profile is then deduced for D(s) and D(o) whereas D(t) presents a non monotonous evolution with a slight decrease at low loading followed by a sharp increase at higher loading. Such decrease of D(t) which has never been evidenced in any microporous systems comes from the atypical evolution of the thermodynamic correction factor that reaches values below 1 at low loading. This implies that, due to intermolecular interactions, the CO(2) molecules in MIL-47(V) do not behave like an ideal gas. Further, molecular simulations enabled us to elucidate unambiguously a 3D diffusion mechanism within the pores of MIL-47(V).

  3. Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter in Bacillus subtilis

    Directory of Open Access Journals (Sweden)

    Teddy Charbonnier

    2017-10-01

    Full Text Available At the heart of central carbon metabolism, pyruvate is a pivotal metabolite in all living cells. Bacillus subtilis is able to excrete pyruvate as well as to use it as the sole carbon source. We herein reveal that ysbAB (renamed pftAB, the only operon specifically induced in pyruvate-grown B. subtilis cells, encodes a hetero-oligomeric membrane complex which operates as a facilitated transport system specific for pyruvate, thereby defining a novel class of transporter. We demonstrate that the LytST two-component system is responsible for the induction of pftAB in the presence of pyruvate by binding of the LytT response regulator to a palindromic region upstream of pftAB. We show that both glucose and malate, the preferred carbon sources for B. subtilis, trigger the binding of CcpA upstream of pftAB, which results in its catabolite repression. However, an additional CcpA-independent mechanism represses pftAB in the presence of malate. Screening a genome-wide transposon mutant library, we find that an active malic enzyme replenishing the pyruvate pool is required for this repression. We next reveal that the higher the influx of pyruvate, the stronger the CcpA-independent repression of pftAB, which suggests that intracellular pyruvate retroinhibits pftAB induction via LytST. Such a retroinhibition challenges the rational design of novel nature-inspired sensors and synthetic switches but undoubtedly offers new possibilities for the development of integrated sensor/controller circuitry. Overall, we provide evidence for a complete system of sensors, feed-forward and feedback controllers that play a major role in environmental growth of B. subtilis.

  4. A novel Usher protein network at the periciliary reloading point between molecular transport machineries in vertebrate photoreceptor cells.

    Science.gov (United States)

    Maerker, Tina; van Wijk, Erwin; Overlack, Nora; Kersten, Ferry F J; McGee, Joann; Goldmann, Tobias; Sehn, Elisabeth; Roepman, Ronald; Walsh, Edward J; Kremer, Hannie; Wolfrum, Uwe

    2008-01-01

    The human Usher syndrome (USH) is the most frequent cause of combined deaf-blindness. USH is genetically heterogeneous with at least 12 chromosomal loci assigned to three clinical types, USH1-3. Although these USH types exhibit similar phenotypes in human, the corresponding gene products belong to very different protein classes and families. The scaffold protein harmonin (USH1C) was shown to integrate all identified USH1 and USH2 molecules into protein networks. Here, we analyzed a protein network organized in the absence of harmonin by the scaffold proteins SANS (USH1G) and whirlin (USH2D). Immunoelectron microscopic analyses disclosed the colocalization of all network components in the apical inner segment collar and the ciliary apparatus of mammalian photoreceptor cells. In this complex, whirlin and SANS directly interact. Furthermore, SANS provides a linkage to the microtubule transport machinery, whereas whirlin may anchor USH2A isoform b and VLGR1b (very large G-protein coupled receptor 1b) via binding to their cytodomains at specific membrane domains. The long ectodomains of both transmembrane proteins extend into the gap between the adjacent membranes of the connecting cilium and the apical inner segment. Analyses of Vlgr1/del7TM mice revealed the ectodomain of VLGR1b as a component of fibrous links present in this gap. Comparative analyses of mouse and Xenopus photoreceptors demonstrated that this USH protein network is also part of the periciliary ridge complex in Xenopus. Since this structural specialization in amphibian photoreceptor cells defines a specialized membrane domain for docking and fusion of transport vesicles, we suggest a prominent role of the USH proteins in cargo shipment.

  5. Molecular Dynamics Simulation for Surface and Transport Properties of Fluorinated Silica Nanoparticles in Water or Decane: Application to Gas Recovery Enhancement

    Directory of Open Access Journals (Sweden)

    Sepehrinia Kazem

    2017-05-01

    Full Text Available Determination of surface and transport properties of nanoparticles (NPs is essential for a variety of applications in enhanced oil and gas recoveries. In this paper, the impact of the surface chemistry of silica NPs on their hydro- and oleo-phobic properties as well as their transport properties are investigated in water or decane using molecular dynamics simulation. Trifluoromethyl or pentafluoroethyl groups as water and oil repellents are placed on the NPs. It is found that the density and residence time of liquid molecules around the NPs are modulated considerably with the existence of the functional groups on the NPs’ surfaces. Also, much larger density fluctuations for liquids close to the surface of the NPs are observed when the number of the groups on the NPs increases, indicating increased hydrophobicity. In addition, the diffusion coefficient of the NPs in either water or decane increases with increasing the number or length of the fluorocarbon chains, demonstrating non-Brownian behavior for the NPs. The surface chemistry imparts a considerable contribution on the diffusion coefficient of the NPs. Finally, potential of mean force calculations are undertaken. It is observed that the free energy of adsorption of the NPs on a mineral surface is more favorable than that of the aggregation of the NPs, which suggests the NPs adsorb preferably on the mineral surface.

  6. Transport and optical properties of c-axis oriented wedge shaped GaN nanowall network grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Bhasker, H. P.; Dhar, S. [Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra-400076 (India); Thakur, Varun; Kesaria, Manoj; Shivaprasad, S. M. [Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore- 560064 (India)

    2014-02-21

    The transport and optical properties of wedge-shaped nanowall network of GaN grown spontaneously on cplane sapphire substrate by Plasma-Assisted Molecular Beam Epitaxy (PAMBE) show interesting behavior. The electron mobility at room temperature in these samples is found to be orders of magnitude higher than that of a continuous film. Our study reveals a strong correlation between the mobility and the band gap in these nanowall network samples. However, it is seen that when the thickness of the tips of the walls increases to an extent such that more than 70% of the film area is covered, it behaves close to a flat sample. In the sample with lower surface coverage (≈40% and ≈60%), it was observed that the conductivity, mobility as well as the band gap increase with the decrease in the average tip width of the walls. Photoluminescence (PL) experiments show a strong and broad band edge emission with a large (as high as ≈ 90 meV) blue shift, compared to that of a continuous film, suggesting a confinement of carriers on the top edges of the nanowalls. The PL peak width remains wide at all temperatures suggesting the existence of a high density of tail states at the band edge, which is further supported by the photoconductivity result. The high conductivity and mobility observed in these samples is believed to be due to a “dissipation less” transport of carriers, which are localized at the top edges (edge states) of the nanowalls.

  7. Transport and optical properties of c-axis oriented wedge shaped GaN nanowall network grown by molecular beam epitaxy

    International Nuclear Information System (INIS)

    Bhasker, H. P.; Dhar, S.; Thakur, Varun; Kesaria, Manoj; Shivaprasad, S. M.

    2014-01-01

    The transport and optical properties of wedge-shaped nanowall network of GaN grown spontaneously on cplane sapphire substrate by Plasma-Assisted Molecular Beam Epitaxy (PAMBE) show interesting behavior. The electron mobility at room temperature in these samples is found to be orders of magnitude higher than that of a continuous film. Our study reveals a strong correlation between the mobility and the band gap in these nanowall network samples. However, it is seen that when the thickness of the tips of the walls increases to an extent such that more than 70% of the film area is covered, it behaves close to a flat sample. In the sample with lower surface coverage (≈40% and ≈60%), it was observed that the conductivity, mobility as well as the band gap increase with the decrease in the average tip width of the walls. Photoluminescence (PL) experiments show a strong and broad band edge emission with a large (as high as ≈ 90 meV) blue shift, compared to that of a continuous film, suggesting a confinement of carriers on the top edges of the nanowalls. The PL peak width remains wide at all temperatures suggesting the existence of a high density of tail states at the band edge, which is further supported by the photoconductivity result. The high conductivity and mobility observed in these samples is believed to be due to a “dissipation less” transport of carriers, which are localized at the top edges (edge states) of the nanowalls

  8. Passive cooling of condensate chambers as retrofitting measure in boiling water reactors; Passive Kuehlung der Kondensationskammern in Siedewasserreaktoren als Nachruestmassnahme

    Energy Technology Data Exchange (ETDEWEB)

    Freis, Daniel; Nachtrodt, Frederik; Sporn, Michael; Tietsch, Wolfgang; Sassen, Felix [Westinghouse Electric Germany GmbH, Mannheim (Germany)

    2012-11-01

    Westinghouse Electric Germany GmbH has developed a concept for passive cooling of condensate chambers of BWR-type reactors. Due to its compactness the system is feasible as retrofitting measure. The passive condensate chamber cooling system is based on a cooling module with ascending and down pipe that are connected with the evaporation condenser to form a cooling circuit. Based on the consequent use of high-effective heat transport mechanisms, as boiling, condensation without non-condensable gases and mass transport a high cooling performance and compact construction is possible. The system is completely passive and completely diverse to existing active cooling systems. In the frame of a true-scale experiment the significant cooling performance was demonstrated. RELAP5 calculations confirmed the functionality of the cooling module.

  9. Passive acoustic monitoring of bed load for fluvial applications

    Science.gov (United States)

    The sediment transported as bed load in streams and rivers is notoriously difficult to monitor cheaply and accurately. Passive acoustic methods are relatively simple, inexpensive, and provide spatial integration along with high temporal resolution. In 1963 work began on monitoring emissions from par...

  10. Passive Wireless Sensor System for Space and Structural Health Monitoring, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Aviana Molecular (Aviana) and the University of Central Florida (UCF) propose to develop a Passive Wireless Sensor System (PWSS) for Structural Health Monitoring...

  11. Passive magnetic bearing system

    Science.gov (United States)

    Post, Richard F.

    2014-09-02

    An axial stabilizer for the rotor of a magnetic bearing provides external control of stiffness through switching in external inductances. External control also allows the stabilizer to become a part of a passive/active magnetic bearing system that requires no external source of power and no position sensor. Stabilizers for displacements transverse to the axis of rotation are provided that require only a single cylindrical Halbach array in its operation, and thus are especially suited for use in high rotation speed applications, such as flywheel energy storage systems. The elimination of the need of an inner cylindrical array solves the difficult mechanical problem of supplying support against centrifugal forces for the magnets of that array. Compensation is provided for the temperature variation of the strength of the magnetic fields of the permanent magnets in the levitating magnet arrays.

  12. European vehicle passive safety network

    NARCIS (Netherlands)

    Wismans, J.S.H.M.; Janssen, E.G.

    1999-01-01

    The general objective of the European Vehicle Passive Safety Network is to contribute to the reduction of the number of road traffic victims in Europe by passive safety measures. The aim of the road safety policy of the European Commission is to reduce the annual total of fatalities to 18000 in

  13. Passive films at the nanoscale

    International Nuclear Information System (INIS)

    Maurice, Vincent; Marcus, Philippe

    2012-01-01

    Highlights: ► Nanoscale data on growth, structure and local properties of passive films reviewed. ► Preferential role of defects of passive films on the corrosion resistance emphasized. ► Effect of grain boundaries on local electronic properties shown by new data. ► Use of atomistic modeling to test mechanistic hypotheses illustrated. - Abstract: The nanometer scale chemical and structural aspects of ultrathin oxide passive films providing self-protection against corrosion to metals and alloys in aqueous environments are reviewed. Data on the nucleation and growth of 2D anodic oxide films, details on the atomic structure and nanostructure of 3D passive films, the preferential role of surface step edges in dissolution in the passive state and the preferential role of grain boundaries of the passive films in passivity breakdown are presented. Future perspectives are discussed, and exemplified by new data obtained on the relationship between the nanostructure of oxide passive films and their local electronic properties. Atomistic corrosion modeling by ab initio density functional theory (DFT) is illustrated by the example of interactions of chloride ions with hydroxylated oxide surfaces, including the role of surface step edges. Data obtained on well-defined substrate surfaces with surface analytical techniques are emphasized.

  14. Udviklingen i bilers passive sikkerhed

    DEFF Research Database (Denmark)

    Hels, Tove; Lyckegaard, Allan; Prato, Carlo Giacomo

    man mellem aktiv og passiv sikkerhed, det vil sige faktorer, der nedsætter • risikoen for, at der sker et uheld (aktiv sikkerhed), henholdsvis • graden af alvorlighed, givet at uheldet er sket (passiv sikkerhed). Rapporten begrænser sig til at undersøge, om der kan påvises en generel sammenhæng mellem...

  15. The Passive in Singapore English.

    Science.gov (United States)

    Bao, Zhiming; Wee, Lionel

    1999-01-01

    Presents an analysis of the two passive (or passive-like) constructions in Singapore English which exhibit substrate influence from Malay and Chinese. The paper shows that while substrate languages contribute to the grammar of Singapore English, the continued prestige of standard English exerts normative pressure and mitigates the effect of…

  16. Molecular characterization of free tropospheric aerosol collected at the Pico Mountain Observatory: a case study with a long-range transported biomass burning plume

    Science.gov (United States)

    Dzepina, K.; Mazzoleni, C.; Fialho, P.; China, S.; Zhang, B.; Owen, R. C.; Helmig, D.; Hueber, J.; Kumar, S.; Perlinger, J. A.; Kramer, L. J.; Dziobak, M. P.; Ampadu, M. T.; Olsen, S.; Wuebbles, D. J.; Mazzoleni, L. R.

    2015-05-01

    Free tropospheric aerosol was sampled at the Pico Mountain Observatory located at 2225 m above mean sea level on Pico Island of the Azores archipelago in the North Atlantic. The observatory is located ~ 3900 km east and downwind of North America, which enables studies of free tropospheric air transported over long distances. Aerosol samples collected on filters from June to October 2012 were analyzed to characterize organic carbon, elemental carbon, and inorganic ions. The average ambient concentration of aerosol was 0.9 ± 0.7 μg m-3. On average, organic aerosol components represent the largest mass fraction of the total measured aerosol (60 ± 51%), followed by sulfate (23 ± 28%), nitrate (13 ± 10%), chloride (2 ± 3%), and elemental carbon (2 ± 2%). Water-soluble organic matter (WSOM) extracted from two aerosol samples (9/24 and 9/25) collected consecutively during a pollution event were analyzed using ultrahigh-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Approximately 4000 molecular formulas were assigned to each of the mass spectra in the range of m/z 100-1000. The majority of the assigned molecular formulas had unsaturated structures with CHO and CHNO elemental compositions. FLEXPART retroplume analyses showed the sampled air masses were very aged (average plume age > 12 days). These aged aerosol WSOM compounds had an average O/C ratio of ~ 0.45, which is relatively low compared to O/C ratios of other aged aerosol. The increase in aerosol loading during the measurement period of 9/24 was linked to biomass burning emissions from North America by FLEXPART retroplume analysis and Moderate Resolution Imaging Spectroradiometer (MODIS) fire counts. This was confirmed with biomass burning markers detected in the WSOM and with the morphology and mixing state of particles as determined by scanning electron microscopy. The presence of markers characteristic of aqueous-phase reactions of phenolic species suggests

  17. Statistics of an advected passive scalar

    International Nuclear Information System (INIS)

    Kimura, Y.; Kraichnan, R.H.

    1993-01-01

    An elementary argument shows that non-Gaussian fluctuations in the temperature at a point in space are induced by random advection of a passive temperature field that has a nonlinear mean gradient, whether or not there is molecular diffusion. This is corroborated by exact analysis for the nondiffusive case and by direct numerical simulation for diffusive cases. Eulerian mapping closure gives results close to the simulation data. Non-Gaussian fluctuations of temperature at a point also are induced by a more subtle mechanism that requires both advection and molecular diffusion and is effective even when the statistics are strictly homogeneous. It operates through selectively strong dissipation of regions where intense temperature gradients have been induced by advective straining. This phenomenon is demonstrated by simulations and explored by means of an idealized analytical model

  18. Solvent vapor annealing in the molecular regime drastically improves carrier transport in small-molecule thin-film transistors

    KAUST Repository

    Khan, Hadayat Ullah

    2013-04-10

    We demonstrate a new way to investigate and control the solvent vapor annealing of solution-cast organic semiconductor thin films. Solvent vapor annealing of spin-cast films of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-Pn) is investigated in situ using quartz crystal microbalance with dissipation (QCM-D) capability, allowing us to monitor both solvent mass uptake and changes in the mechanical rigidity of the film. Using time-resolved grazing incidence wide angle X-ray scattering (GIWAXS) and complementary static atomic force microscopy (AFM), we demonstrate that solvent vapor annealing in the molecular regime can cause significant performance improvements in organic thin film transistors (OTFTs), whereas allowing the solvent to percolate and form a liquid phase results in catastrophic reorganization and dewetting of the film, making the process counterproductive. Using these lessons we devise processing conditions which prevent percolation of the adsorbed solvent vapor molecules for extended periods, thus extending the benefits of solvent vapor annealing and improving carrier mobility by nearly two orders of magnitude. Ultimately, it is demonstrated that QCM-D is a very powerful sensor of the state of the adsorbed solvent as well as the thin film, thus making it suitable for process development as well as in-line process monitoring both in laboratory and in future manufacturing settings. © 2013 American Chemical Society.

  19. Vertical transport in isotype InAlN/GaN dipole induced diodes grown by molecular beam epitaxy

    Science.gov (United States)

    Fireman, M. N.; Li, Haoran; Keller, Stacia; Mishra, Umesh K.; Speck, James S.

    2017-05-01

    InAlN dipole diodes were developed and fabricated on both (0001) Ga-Face and (" separators="| 000 1 ¯) N-face oriented GaN on sapphire templates by molecular beam epitaxy. The orientation and direction of the InAlN polarization dipole are functions of the substrate orientation and composition, respectively. Special consideration was taken to minimize growth differences and impurity uptake during growth on these orientations of opposite polarity. Comparison of devices on similarly grown structures with In compositions in excess of 50% reveals that dipole diodes shows poorer forward bias performance and exhibited an increase in reverse bias leakage, regardless of orientation. Similarly, (0001) Ga-face oriented InAlN at a lowered 40% In composition had poor device characteristics, namely, the absence of expected exponential turn on in forward bias. By contrast, at In compositions close to 40%, (" separators="| 000 1 ¯) N-face oriented InAlN devices had excellent performance, with over five orders of magnitude of rectification and extracted barrier heights of 0.53- 0.62 eV; these values are in close agreement with simulation. Extracted ideality factors ranging from 1.08 to 1.38 on these devices are further evidence of their optimal performance. Further discussion focuses on the growth and orientation conditions that may lead to this discrepancy yet emphasizes that with proper design and growth strategy, the rectifying dipole diodes can be achieved with InAlN nitride dipole layers.

  20. Solvent vapor annealing in the molecular regime drastically improves carrier transport in small-molecule thin-film transistors

    KAUST Repository

    Khan, Hadayat Ullah; Li, Ruipeng; Ren, Yi; Chen, Long; Payne, Marcia M.; Bhansali, Unnat Sampatraj; Smilgies, Detlef Matthias; Anthony, John Edward; Amassian, Aram

    2013-01-01

    We demonstrate a new way to investigate and control the solvent vapor annealing of solution-cast organic semiconductor thin films. Solvent vapor annealing of spin-cast films of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-Pn) is investigated in situ using quartz crystal microbalance with dissipation (QCM-D) capability, allowing us to monitor both solvent mass uptake and changes in the mechanical rigidity of the film. Using time-resolved grazing incidence wide angle X-ray scattering (GIWAXS) and complementary static atomic force microscopy (AFM), we demonstrate that solvent vapor annealing in the molecular regime can cause significant performance improvements in organic thin film transistors (OTFTs), whereas allowing the solvent to percolate and form a liquid phase results in catastrophic reorganization and dewetting of the film, making the process counterproductive. Using these lessons we devise processing conditions which prevent percolation of the adsorbed solvent vapor molecules for extended periods, thus extending the benefits of solvent vapor annealing and improving carrier mobility by nearly two orders of magnitude. Ultimately, it is demonstrated that QCM-D is a very powerful sensor of the state of the adsorbed solvent as well as the thin film, thus making it suitable for process development as well as in-line process monitoring both in laboratory and in future manufacturing settings. © 2013 American Chemical Society.