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Sample records for fluctuation-driven molecular transport

  1. Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study

    Directory of Open Access Journals (Sweden)

    Marcel Aguilella-Arzo

    2017-03-01

    Full Text Available Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise.

  2. 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...

  3. Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

    Directory of Open Access Journals (Sweden)

    Andrea Maesani

    2015-11-01

    Full Text Available The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

  4. Photoinduced diffusion molecular transport

    Science.gov (United States)

    Rozenbaum, Viktor M.; Dekhtyar, Marina L.; Lin, Sheng Hsien; Trakhtenberg, Leonid I.

    2016-08-01

    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).

  5. Electron transport in molecular junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun

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

  6. Fluctuation-driven mechanotransduction regulates mitochondrial-network structure and function

    Science.gov (United States)

    Bartolák-Suki, Erzsébet; Imsirovic, Jasmin; Parameswaran, Harikrishnan; Wellman, Tyler J.; Martinez, Nuria; Allen, Philip G.; Frey, Urs; Suki, Béla

    2015-10-01

    Cells can be exposed to irregular mechanical fluctuations, such as those arising from changes in blood pressure. Here, we report that ATP production, assessed through changes in mitochondrial membrane potential, is downregulated in vascular smooth muscle cells in culture exposed to monotonous stretch cycles when compared with cells exposed to a variable cyclic stretch that incorporates physiological levels of cycle-by-cycle variability in stretch amplitude. Variable stretch enhances ATP production by increasing the expression of ATP synthase’s catalytic domain, cytochrome c oxidase and its tyrosine phosphorylation, mitofusins and PGC-1α. Such a fluctuation-driven mechanotransduction mechanism is mediated by motor proteins and by the enhancement of microtubule-, actin- and mitochondrial-network complexity. We also show that, in aorta rings isolated from rats, monotonous stretch downregulates--whereas variable stretch maintains--physiological vessel-wall contractility through mitochondrial ATP production. Our results have implications for ATP-dependent and mechanosensitive intracellular processes.

  7. Quantum Transport Through Tunable Molecular Diodes

    KAUST Repository

    Obodo, Joshua Tobechukwu

    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.

  8. Monoamine transporters: Insights from molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Julie eGrouleff

    2015-10-01

    Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.

  9. Molecular aspects of hepatobiliary transport

    NARCIS (Netherlands)

    Muller, M; Jansen, PLM

    1997-01-01

    Generation of bile flow is a regulated, ATP-dependent process and depends on the coordinated action of a number of transporter proteins in the sinusoidal and canalicular domains of the hepatocyte. Dysfunction of any of these proteins leads to retention of substrates, with conjugated hyperbilirubinem

  10. Monoamine transporters: insights from molecular dynamics simulations

    Science.gov (United States)

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  11. Vibrational Heat Transport in Molecular Junctions

    Science.gov (United States)

    Segal, Dvira; Agarwalla, Bijay Kumar

    2016-05-01

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

  12. Molecular model of the neural dopamine transporter

    Science.gov (United States)

    Ravna, Aina Westrheim; Sylte, Ingebrigt; Dahl, Svein G.

    2003-05-01

    The dopamine transporter (DAT) regulates the action of dopamine by reuptake of the neurotransmitter into presynaptic neurons, and is the main molecular target of amphetamines and cocaine. DAT and the Na+/H+ antiporter (NhaA) are secondary transporter proteins that carry small molecules across a cell membrane against a concentration gradient, using ion gradients as energy source. A 3-dimensional projection map of the E. coli NhaA has confirmed a topology of 12 membrane spanning domains, and was previously used to construct a 3-dimensional NhaA model with 12 trans-membrane α-helices (TMHs). The NhaA model, and site directed mutagenesis data on DAT, were used to construct a detailed 3-dimensional DAT model using interactive molecular graphics and empiric force field calculations. The model proposes a dopamine transport mechanism involving TMHs 1, 3, 4, 5, 7 and 11. Asp79, Tyr252 and Tyr274 were the primary cocaine binding residues. Binding of cocaine or its analogue, (-)-2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), seemed to lock the transporter in an inactive state, and thus inhibit dopamine transport. The present model may be used to design further experimental studies of the molecular structure and mechanisms of DAT and other secondary transporter proteins.

  13. Charge transport network dynamics in molecular aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Nicholas E. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry; Chen, Lin X. [Argonne National Lab. (ANL), Argonne, IL (United States). Chemical Science and Engineering Division; Ratner, Mark A. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry

    2016-07-20

    Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed.

  14. Charge Transport Phenomena in Peptide Molecular Junctions

    Directory of Open Access Journals (Sweden)

    Alessandra Luchini

    2008-01-01

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

  15. Molecular modeling of inelastic electron transport in molecular junctions

    Science.gov (United States)

    Jiang, Jun; Kula, Mathias; Luo, Yi

    2008-09-01

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

  16. Molecular modeling of inelastic electron transport in molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-09-17

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

  17. 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

  18. Electron and Phonon Transport in Molecular Junctions

    DEFF Research Database (Denmark)

    Li, Qian

    transmission at the Fermi energy. We propose and analyze a way of using π   stacking to design molecular junctions to control heat transport. We develop a simple model system to identify optimal parameter regimes and then use density functional theory (DFT) to extract model parameters for a number of specific....... The system we are interested in here are π-stacked molecules connected with two semi-infinite leads. π-stacked aromatic rings, connected via π-π electronic coupling, provides a rather soft mechanical bridge while maintaining high electronic conductivity. We investigate electron transport...... and the thermoelectric response of five representative π-stacked systems. We find that the transmission and power factor are both enhanced by increasing the conjugation length or adding substituent groups. The local transmission shows that several extra paths are added by cyano groups, which increases the total...

  19. 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...... is applied to a hydrogen molecule in an infinite Pt wire and a benzene-dithiol (BDT) molecule between Au(111) surfaces. We show that the transmission function of BDT in a wide energy window around the Fermi level can be completely accounted for by only two molecular orbitals. (c) 2005 Elsevier B.V. All...

  20. Electronic transport properties of phenylacetylene molecular junctions

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  1. 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.

  2. Physiological and molecular aspects of cobalamin transport.

    Science.gov (United States)

    Fedosov, Sergey N

    2012-01-01

    Minute doses of a complex cofactor cobalamin (Cbl, vitamin B12) are essential for metabolism. The nutritional chain for humans includes: (1) production of Cbl by bacteria in the intestinal tract of herbivores; (2) accumulation of the absorbed Cbl in animal tissues; (3) consumption of food of animal origin. Most biological sources contain both Cbl and its analogues, i.e. Cbl-resembling compounds physiologically inactive in animal cells. Selective assimilation of the true vitamin requires an interplay between three transporting proteins - haptocorrin (HC), intrinsic factor (IF), transcobalamin (TC) - and several receptors. HC is present in many biological fluids, including gastric juice, where it assists in disposal of analogues. Gastric IF selectively binds dietary Cbl and enters the intestinal cells via receptor-mediated endocytosis. Absorbed Cbl is transmitted to TC and delivered to the tissues with blood flow. The complex transport system guarantees a very efficient uptake of the vitamin, but failure at any link causes Cbl-deficiency. Early detection of a negative B12 balance is highly desirable to prevent irreversible neurological damages, anaemia and death in aggravated cases. The review focuses on the molecular mechanisms of cobalamin transport with emphasis on interaction of corrinoids with the specific proteins and protein-receptor recognition. The last section briefly describes practical aspects of recent basic research concerning early detection of B12-related disorders, medical application of Cbl-conjugates, and purification of corrinoids from biological samples.

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

    Science.gov (United States)

    Troisi, Alessandro; Ratner, Mark A

    2006-02-01

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

  4. Velocity Fluctuations Driven by the Damped, Aperiodic Mode in the Intergalactic Medium

    Science.gov (United States)

    Kolberg, U.; Schlickeiser, R.; Yoon, P. H.

    2017-08-01

    On account of its finite temperature, the unmagnetized intergalactic medium (IGM) is subject to thermal fluctuations. Due to the fundamental coupling between particles and fields in a plasma, the field fluctuations generate current densities by means of the Lorentz force and thereby affect both the density and the velocity fluctuations of the particles. Recently, a new damped, aperiodic mode was discovered that dominates field fluctuations in the IGM. Apart from its impact on the transport properties of the IGM that determine the propagation of cosmic rays, previous research has shown that this mode provides turbulent magnetic seed fields of 6× {10}-18 {{G}} that are an essential ingredient in the generation of cosmic magnetic fields. The current investigation addresses the influence of the mode on the particle motion. In order to describe the corresponding state of the turbulence, both the spectrum and the integrated total value of the mode-driven proton velocity fluctuations are computed. It is found that the latter amounts to 1.16× {10}8{ T}47/2{n}-7-1/2 {cm} {{{s}}}-1 assuming a temperature of {T}e={T}p={10}4{T}4 {{K}} and a density of {n}e={n}p={10}-7{n}-7 {{cm}}-3. This value is two orders of magnitude larger than the thermal velocity. If the IGM neutrals adopt the same velocities as the protons by mutual charge exchange and elastic collisions (ambipolar diffusion), atomic lines propagating through the IGM are expected to display spectral broadening, enhanced by a factor of 90 beyond the thermal level in the case of hydrogen. This opens the window to a first direct observation of the damped aperiodic mode. Other observational techniques such as dispersion measure, rotation measure, and scintillation data are not applicable in this case because the mode is a transverse one, and, as such, it does not induce the required density fluctuations, as is shown here.

  5. Transport properties of a novel molecular rotor

    Science.gov (United States)

    Xue, Mei; Wang, K. L.; Kabehie, Sanaz; Zink, Jeffrey I.

    2008-03-01

    Rotary motion around a molecular axis has been controlled by electron transfer process and by photoexcitation. The basis of the motion is intramolecular rotation of a ligand (3,8-di-ethynyltrityl-1, 10-phenanthroline) around a copper axle. The asymmetric copper system is synthesized by immobilizing a ``stator'' to a silicon support. The ``rotator,'' 3,8-di-ethynyltrityl-1, 10-phenanthroline is complexed to the metal center, Cu (I) or Cu (II) serving as an ``axle''. The Cu (I) system structure is tetrahedral, but that of Cu (II) is square planar. The interconversion of the two provides the basis for controlled, rotational motion. Hysteresis is observed in the different region of the applied voltage for different stators. The peak of the bisP-Si shifts to the left compared to that of the phen-Si stator because of the larger energy gap of phen-Si. The energy states of the Cu (I) and Cu (II) are extracted from the transport measurement results.

  6. Cooperative transport by small teams of molecular motors

    OpenAIRE

    Klumpp, Stefan; Muller, Melanie J. I.; Lipowsky, Reinhard

    2006-01-01

    Molecular motors power directed transport of cargoes within cells. Even if a single motor is sufficient to transport a cargo, motors often cooperate in small teams. We discuss the cooperative cargo transport by several motors theoretically and explore some of its properties. In particular we emphasize how motor teams can drag cargoes through a viscous environment.

  7. 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.

  8. Molecular motor transport through hollow nanowires

    DEFF Research Database (Denmark)

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

    2014-01-01

    Biomolecular motors offer self-propelled, directed transport in designed microscale networks and can potentially replace pump-driven nanofluidics. However, in existing systems, transportation is limited to the two-dimensional plane. Here we demonstrate fully one-dimensional (1D) myosin-driven mot......Biomolecular motors offer self-propelled, directed transport in designed microscale networks and can potentially replace pump-driven nanofluidics. However, in existing systems, transportation is limited to the two-dimensional plane. Here we demonstrate fully one-dimensional (1D) myosin......-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...

  9. Porous carbon nanotubes: Molecular absorption, transport, and separation

    Science.gov (United States)

    Yzeiri, Irena; Patra, Niladri; Král, Petr

    2014-03-01

    We use classical molecular dynamics simulations to study nanofluidic properties of porous carbon nanotubes. We show that saturated water vapor condenses on the porous nanotubes, can be absorbed by them and transported in their interior. When these nanotubes are charged and placed in ionic solutions, they can selectively absorb ions in their interior and transport them. Porous carbon nanotubes can also be used as selective molecular sieves, as illustrated on a room temperature separation of benzene and ethanol.

  10. Macroscopic transport by synthetic molecular machines

    NARCIS (Netherlands)

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

    2005-01-01

    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

  11. 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

  12. 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 go

  13. 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 p

  14. The molecular mechanism for nuclear transport and its application.

    Science.gov (United States)

    Kim, Yun Hak; Han, Myoung-Eun; Oh, Sae-Ock

    2017-06-01

    Transportation between the cytoplasm and the nucleoplasm is critical for many physiological and pathophysiological processes including gene expression, signal transduction, and oncogenesis. So, the molecular mechanism for the transportation needs to be studied not only to understand cell physiological processes but also to develop new diagnostic and therapeutic targets. Recent progress in the research of the nuclear transportation (import and export) via nuclear pore complex and four important factors affecting nuclear transport (nucleoporins, Ran, karyopherins, and nuclear localization signals/nuclear export signals) will be discussed. Moreover, the clinical significance of nuclear transport and its application will be reviewed. This review will provide some critical insight for the molecular design of therapeutics which need to be targeted inside the nucleus.

  15. Quantum transport in molecular devices and graphene

    NARCIS (Netherlands)

    Heersche, H.B.

    2006-01-01

    As a result of progress in nanotechnology, smaller and smaller electronic circuits can be made. The stage of electrically contacting even a single molecule has now been reached. This stimulates both fundamental and applied research alike. Molecular electronics is hence a booming new field that draws

  16. Quantum transport in molecular devices and graphene

    NARCIS (Netherlands)

    Heersche, H.B.

    2006-01-01

    As a result of progress in nanotechnology, smaller and smaller electronic circuits can be made. The stage of electrically contacting even a single molecule has now been reached. This stimulates both fundamental and applied research alike. Molecular electronics is hence a booming new field that draws

  17. Controlled Electronic Transport through Branched Molecular Conductors

    OpenAIRE

    2008-01-01

    Abstract The conductance through a branched conductor placed between two electrodes is analyzed using the Landauer transport formulation within the framework of the single electron, and the tight binding approximations. Terminal side chains are expressed as self energy terms which map the branched conductor onto an effective linear chain Hamiltonian. The effect of uniform side branches on resonant zero-bias conductance is shown to be analytically solvable and particularly simple, w...

  18. Molecular transport in collagenous tissues measured by gel electrophoresis.

    Science.gov (United States)

    Hunckler, Michael D; Tilley, Jennifer M R; Roeder, Ryan K

    2015-11-26

    Molecular transport in tissues is important for drug delivery, nutrient supply, waste removal, cell signaling, and detecting tissue degeneration. Therefore, the objective of this study was to investigate gel electrophoresis as a simple method to measure molecular transport in collagenous tissues. The electrophoretic mobility of charged molecules in tissue samples was measured from relative differences in the velocity of a cationic dye passing through an agarose gel in the absence and presence of a tissue section embedded within the gel. Differences in electrophoretic mobility were measured for the transport of a molecule through different tissues and tissue anisotropy, or the transport of different sized molecules through the same tissue. Tissue samples included tendon and fibrocartilage from the proximal (tensile) and distal (compressive) regions of the bovine flexor tendon, respectively, and bovine articular cartilage. The measured electrophoretic mobility was greatest in the compressive region of the tendon (fibrocartilage), followed by the tensile region of tendon, and lowest in articular cartilage, reflecting differences in the composition and organization of the tissues. The anisotropy of tendon was measured by greater electrophoretic mobility parallel compared with perpendicular to the predominate collagen fiber orientation. Electrophoretic mobility also decreased with increased molecular size, as expected. Therefore, the results of this study suggest that gel electrophoresis may be a useful method to measure differences in molecular transport within various tissues, including the effects of tissue type, tissue anisotropy, and molecular size. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Molecular mechanisms of water transport in the eye

    DEFF Research Database (Denmark)

    Hamann, Steffen; Hamann, Steffen Ellitsgaard

    2002-01-01

    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......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...

  20. Cooperative behavior of molecular motors: Cargo transport and traffic phenomena

    Science.gov (United States)

    Lipowsky, Reinhard; Beeg, Janina; Dimova, Rumiana; Klumpp, Stefan; Müller, Melanie J. I.

    2010-01-01

    All eukaryotic cells including those of our own body contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and make discrete mechanical steps with a step size of the order of 10 nm but are able to pull cargo particles over much larger distances, from micrometers up to meters. In vivo, the intracellular cargos include large membrane-bounded organelles, smaller vesicles, a subset of mRNAs, cytoskeletal filaments, and various protein building blocks, which are transported between different cell compartments. This cargo transport is usually performed by teams of motors. If all motors belong to the same molecular species, the cooperative action of the motors leads to uni-directional transport with a strongly increased run length and with a characteristic force dependence of the velocity distributions. If two antagonistic teams of motors pull on the same cargo particle, they perform a stochastic tug-of-war, which is characterized by a subtle force balance between the two motor teams and leads to several distinct patterns of bi-directional transport. So far, all experimental observations on bi-directional transport are consistent with such a tug-of-war. If many motors and/or cargo particles are transported along the filaments, one encounters various traffic phenomena. Depending on their mutual interactions and the compartment geometry, the motors form various spatio-temporal patterns such as traffic jams, and undergo nonequilibrium phase transitions between different patterns of transport.

  1. 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)

  2. Transport Phenomena of Water in Molecular Fluidic Channels

    Science.gov (United States)

    Vo, Truong Quoc; Kim, Bohung

    2016-09-01

    In molecular-level fluidic transport, where the discrete characteristics of a molecular system are not negligible (in contrast to a continuum description), the response of the molecular water system might still be similar to the continuum description if the time and ensemble averages satisfy the ergodic hypothesis and the scale of the average is enough to recover the classical thermodynamic properties. However, even in such cases, the continuum description breaks down on the material interfaces. In short, molecular-level liquid flows exhibit substantially different physics from classical fluid transport theories because of (i) the interface/surface force field, (ii) thermal/velocity slip, (iii) the discreteness of fluid molecules at the interface and (iv) local viscosity. Therefore, in this study, we present the result of our investigations using molecular dynamics (MD) simulations with continuum-based energy equations and check the validity and limitations of the continuum hypothesis. Our study shows that when the continuum description is subjected to the proper treatment of the interface effects via modified boundary conditions, the so-called continuum-based modified-analytical solutions, they can adequately predict nanoscale fluid transport phenomena. The findings in this work have broad effects in overcoming current limitations in modeling/predicting the fluid behaviors of molecular fluidic devices.

  3. Charge Transport by Superexchange in Molecular Host-Guest Systems

    Science.gov (United States)

    Symalla, Franz; Friederich, Pascal; Massé, Andrea; Meded, Velimir; Coehoorn, Reinder; Bobbert, Peter; Wenzel, Wolfgang

    2016-12-01

    Charge transport in disordered organic semiconductors is generally described as a result of incoherent hopping between localized states. In this work, we focus on multicomponent emissive host-guest layers as used in organic light-emitting diodes (OLEDs), and show using multiscale ab initio based modeling that charge transport can be significantly enhanced by the coherent process of molecular superexchange. Superexchange increases the rate of emitter-to-emitter hopping, in particular if the emitter molecules act as relatively deep trap states, and allows for percolation path formation in charge transport at low guest concentrations.

  4. Scaling theory for percolative charge transport in disordered molecular semiconductors

    NARCIS (Netherlands)

    Cottaar, J.; Koster, L.J.A; Coehoorn, R.; Bobbert, P.A.

    2011-01-01

    We present a scaling theory for charge transport in molecular semiconductors with Gaussian energy disorder, which extends standard percolation theory by including bonds with conductances close to the percolating one in the random-resistor network of bonds representing charge hopping. A general and c

  5. Scaling Theory for Percolative Charge Transport in Disordered Molecular Semiconductors

    NARCIS (Netherlands)

    Cottaar, J.; Koster, L. J. A.; Coehoorn, R.; Bobbert, P. A.

    2011-01-01

    We present a scaling theory for charge transport in disordered molecular semiconductors that extends percolation theory by including bonds with conductances close to the percolating one in the random-resistor network representing charge hopping. A general and compact expression is given for the char

  6. 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-c...

  7. Coulomb Traps and Charge Transport in Molecular Solids

    Science.gov (United States)

    Scher, Harvey

    2000-03-01

    A major result of experimental studies of a diverse assortment of disordered molecular solids is the observation of a common pattern in the charge transport properties. The transport ranges from charge transfer between molecules doped in an inert polymer to motion along the silicon backbone of polysilylenes. The pattern is the unusual combination of Poole Frenkel-like electric field dependence and non-Arrhenius temperature dependence of the mobility. The latter feature has been especially puzzling. We study the drift mobility of a molecular polaron in the presence of an applied field and Coulomb traps. The model is based on one previously developed for geminate recombination of photogenerated charge carriers. The key electric field and temperature dependencies of the mobility measurements are well reproduced by this model. Our conclusion is that this nearly universal transport behavior arises from competition between rates of polaron trapping and release from a very low density of Coulomb traps.

  8. Water and Molecular Transport across Nanopores in Monolayer Graphene Membranes

    Science.gov (United States)

    Jang, Doojoon; O'Hern, Sean; Kidambi, Piran; Boutilier, Michael; Song, Yi; Idrobo, Juan-Carlos; Kong, Jing; Laoui, Tahar; Karnik, Rohit

    2015-11-01

    Graphene's atomic thickness and high tensile strength allow it to outstand as backbone material for next-generation high flux separation membrane. Molecular dynamics simulations predicted that a single-layer graphene membrane could exhibit high permeability and selectivity for water over ions/molecules, qualifying as novel water desalination membranes. However, experimental investigation of water and molecular transport across graphene nanopores had remained barely explored due to the presence of intrinsic defects and tears in graphene. We introduce two-step methods to seal leakage across centimeter scale single-layer graphene membranes create sub-nanometer pores using ion irradiation and oxidative etching. Pore creation parameters were varied to explore the effects of created pore structures on water and molecular transport driven by forward osmosis. The results demonstrate the potential of nanoporous graphene as a reliable platform for high flux nanofiltration membranes.

  9. Generic Transport Mechanisms for Molecular Traffic in Cellular Protrusions

    Science.gov (United States)

    Graf, Isabella R.; Frey, Erwin

    2017-03-01

    Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice-gas model we study how the interplay between active and diffusive transport and mass conservation leads to localized domain walls and tip localization of the motors. We identify a mechanism for task sharing between the active motors (maintaining a gradient) and the diffusive motion (transport to the tip), which ensures that energy consumption is low and motor exchange mostly happens at the tip. These features are attributed to strong nearest-neighbor correlations that lead to a strong reduction of active currents, which we calculate analytically using an exact moment identity, and might prove useful for the understanding of correlations and active transport also in more elaborate systems.

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

    Science.gov (United States)

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

    2014-01-01

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

  11. Investigation of the charge transport through disordered organic molecular heterojunctions

    Science.gov (United States)

    Houili, H.; Tutiš, E.; Batistić, I.; Zuppiroli, L.

    2006-08-01

    We present a three-dimensional multiparticle Monte Carlo (3DMPMC) simulation of hopping transport in disordered organic molecular media. We used this approach in order to study the charge transport across an energetically disordered organic molecular heterojunction which is known to strongly influence the characteristics of the multilayer devices based on thin organic films. The role of the energetic disorder and its spatial correlations, which govern the transport in the bulk, are examined here for the bilayer homopolar system where the heterojunction represents the bottleneck for the transport. We study the effects of disorder on both sides of the heterojunction, including the effects of the spatial correlation within each material and among the layers. The 3DMPMC approach allowed us to correctly tackle the effects of the Coulomb interaction among carriers in the region where the charge accumulation in the device is particularly important and the Coulomb interaction most pronounced. The Coulomb interaction enhances the current by increasing the electric field at the heterojunction as well as by affecting the thermalization of the carriers in front of the barrier. In order to build a rather comprehensive picture of the hopping transport over the homopolar heterojunction, we supplemented the MC simulations by a master equation (ME) calculation.

  12. The molecular interactions of buspirone analogues with the serotonin transporter.

    Science.gov (United States)

    Jarończyk, Małgorzata; Chilmonczyk, Zdzisław; Mazurek, Aleksander P; Nowak, Gabriel; Ravna, Aina W; Kristiansen, Kurt; Sylte, Ingebrigt

    2008-10-15

    A major problem with the selective serotonin reuptake inhibitors (SSRIs) is the delayed onset of action. A reason for that may be that the initial SSRI-induced increase in serotonin levels activates somatodendritic 5-HT(1A) autoreceptors, causing a decrease in serotonin release in major forebrain areas. It has been suggested that compounds combining inhibition of the serotonin transport protein with antagonistic effects on the 5-HT(1A) receptor will shorten the onset time. The anxiolytic drug buspirone is known as 5-HT(1A) partial agonist. In the present work, we are studying the inhibition of the serotonin transporter protein by a series of buspirone analogues by molecular modelling and by experimental affinity measurements. Models of the transporter protein were constructed using the crystal structure of the Escherichia coli major facilitator family transporter-LacY and the X-ray structure of the neurotransmitter symporter family (NSS) transporter-LeuT(Aa) as templates. The buspirone analogues were docked into both SERT models and the interactions with amino acids within the protein were analyzed. Two putative binding sites were identified on the LeuT(Aa) based model, one suggested to be a high-affinity site, and the other suggested to be a low-affinity binding site. Molecular dynamic simulations of the LacY based model in complex with ligands did not induce a helical architecture of the LacY based model into an arrangement more similar to that of the LeuT(Aa) based model.

  13. Distinct transport regimes for two elastically coupled molecular motors.

    Science.gov (United States)

    Berger, Florian; Keller, Corina; Klumpp, Stefan; Lipowsky, Reinhard

    2012-05-18

    Cooperative cargo transport by two molecular motors involves an elastic motor-motor coupling, which can reduce the motors' velocity and/or enhance their unbinding from the filament. We show theoretically that these interference effects lead, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive by explicit calculations and general time scale arguments, can be explored experimentally by varying the elastic coupling strength.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis...... demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can...

  15. Molecular 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.

  16. Molecular orbital theory of ballistic electron transport through molecules

    Science.gov (United States)

    Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

    2009-03-01

    Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.

  17. 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......, 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...... interacts with hydrophobic channel lining residues, whereas in the cytoplasmic half-channel key protein-substrate interactions are mediated by ionic residues. A major energy barrier against transport is found within a tight segment of the periplasmic half-channel where sugar hydration is minimal and protein-sugar...

  18. Suppression of phonon transport in molecular Christmas trees.

    Science.gov (United States)

    Lambert, Colin John; Famili, Marjan; Grace, Iain; Sadeghi, Hatef

    2017-02-27

    Minimising the phonon thermal conductance of self-assembled molecular films, whilst preserving their electrical properties, is highly desirable, both for thermal management at the nanoscale and for the design of high-efficiency thermoelectric materials. Here we highlight a new strategy for minimising the phonon thermal conductance of Christmas-tree-like molecules composed of a long trunk, along which phonons can propagate, attached to pendant molecular branches. We demonstrate that phonon transport along the trunk is suppressed by Fano resonances associated with internal vibrational modes of the branches and that thermal conductance is suppressed most-effectively in molecules with pendant branches of different lengths. As examples, we use density functional theory to demonstrate the reduction in phonon transport in tree-like molecules formed from alkane or acene trunks with various pendant branches.

  19. Direct observation of stepwise movement of a synthetic molecular transporter

    Science.gov (United States)

    Wickham, Shelley F. J.; Endo, Masayuki; Katsuda, Yousuke; Hidaka, Kumi; Bath, Jonathan; Sugiyama, Hiroshi; Turberfield, Andrew J.

    2011-03-01

    Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor and fuel, all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold, and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.

  20. 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.

  1. Molecular Dynamics Simulation on thermodynamic Properties and Transport Coefficients

    Institute of Scientific and Technical Information of China (English)

    D.X.Xiong

    1996-01-01

    Moecular dynamics simulation (MDS) is used to study the thermodynamic properties and transport coefficients of an argon system with Lennend-Jones potential.The results on the velocity distribution,mean free path,mean collison time,specific heat and self0diffusion coefficient agree well with the existing theoretical /experimental data,It shows that molecular dynamics method is another bridge to connect microworld and macreoworld.

  2. Non-equilibrium transport through a disordered molecular nanowire

    OpenAIRE

    2016-01-01

    We investigate the non-equilibrium transport properties of a disordered molecular nanowire. The nanowire is regarded as a quasi-one-dimensional organic crystal composed of self-assembled molecules. One orbital and a single random energy are assigned to each molecule while the intermolecular coupling does not fluctuate. Consequently, electronic states are expected to be spatially localized. We consider the regime of strong localization, namely, the localization length is smaller than the lengt...

  3. Charge transport in photochemically modified molecularly doped polymers

    Science.gov (United States)

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

    1995-08-01

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

  4. Electronic transport properties of a quinone-based molecular switch

    Science.gov (United States)

    Zheng, Ya-Peng; Bian, Bao-An; Yuan, Pei-Pei

    2016-09-01

    In this paper, we carried out first-principles calculations based on density functional theory and non-equilibrium Green's function to investigate the electronic transport properties of a quinone-based molecule sandwiched between two Au electrodes. The molecular switch can be reversibly switched between the reduced hydroquinone (HQ) and oxidized quinone (Q) states via redox reactions. The switching behavior of two forms is analyzed through their I- V curves, transmission spectra and molecular projected self-consistent Hamiltonian at zero bias. Then we discuss the transmission spectra of the HQ and Q forms at different bias, and explain the oscillation of current according to the transmission eigenstates of LUMO energy level for Q form. The results suggest that this kind of a quinone-based molecule is usable as one of the good candidates for redox-controlled molecular switches.

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

    Science.gov (United States)

    Tada, Tomofumi; Yoshizawa, Kazunari

    2015-12-28

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

  6. Molecular Mechanisms of Phosphorus Metabolism and Transport during Leaf Senescence

    Directory of Open Access Journals (Sweden)

    Kyla A. Stigter

    2015-12-01

    Full Text Available Leaf senescence, being the final developmental stage of the leaf, signifies the transition from a mature, photosynthetically active organ to the attenuation of said function and eventual death of the leaf. During senescence, essential nutrients sequestered in the leaf, such as phosphorus (P, are mobilized and transported to sink tissues, particularly expanding leaves and developing seeds. Phosphorus recycling is crucial, as it helps to ensure that previously acquired P is not lost to the environment, particularly under the naturally occurring condition where most unfertilized soils contain low levels of soluble orthophosphate (Pi, the only form of P that roots can directly assimilate from the soil. Piecing together the molecular mechanisms that underpin the highly variable efficiencies of P remobilization from senescing leaves by different plant species may be critical for devising effective strategies for improving overall crop P-use efficiency. Maximizing Pi remobilization from senescing leaves using selective breeding and/or biotechnological strategies will help to generate P-efficient crops that would minimize the use of unsustainable and polluting Pi-containing fertilizers in agriculture. This review focuses on the molecular mechanisms whereby P is remobilized from senescing leaves and transported to sink tissues, which encompasses the action of hormones, transcription factors, Pi-scavenging enzymes, and Pi transporters.

  7. Dynamic Gradient Directed Molecular Transport and Concentration in Hydrogel Films.

    Science.gov (United States)

    Tsai, Tsung-Han; Ali, Mohammad A; Jiang, Zhelong; Braun, Paul V

    2017-04-24

    Materials which selectively transport molecules along defined paths offer new opportunities for concentrating, processing and sensing chemical and biological agents. Here, we present the use of traveling ionic waves to drive molecular transport and concentration of hydrophilic molecules entrained within a hydrogel. The traveling ionic wave is triggered by the spatially localized introduction of ions, which through a dissipative ion exchange process, converts quaternary ammonium groups in the hydrogel from hydrophilic to hydrophobic. Through a reaction-diffusion process, the hydrophobic region expands with a sharp transition at the leading edge; it is this sharp gradient in hydrophilicity that drives the transport of hydrophilic molecules dispersed within the film. The traveling wave moved up to 450 μm within 30 min, while the gradient length remained 20 μm over this time. As an example of the potential of molecular concentration using this approach, a 70-fold concentration of a hydrophilic dye was demonstrated. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Molecular motor traffic: From biological nanomachines to macroscopic transport

    Science.gov (United States)

    Lipowsky, Reinhard; Chai, Yan; Klumpp, Stefan; Liepelt, Steffen; Müller, Melanie J. I.

    2006-12-01

    All cells of animals and plants contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and have a size of 20-100 nm but are able to pull vesicles, organelles and other types of cargo over large distances, from micrometers up to meters. There are several families of motors: kinesins, dyneins, and myosins. Most of these motors have two heads which are used as legs and perform discrete steps along the filaments. Several aspects of the motor behavior will be discussed: motor cycles of two-headed motors; walks of single motors or cargo particles which consist of directed movements interrupted by random, diffusive motion; cargo transport through tube-like compartments; active diffusion of cargo particles in slab-like compartments; cooperative transport of cargo by several motors which may be uni- or bi-directional; and systems with many interacting motors that exhibit traffic jams, self-organized density and flux patterns, and traffic phase transitions far from equilibrium. It is necessary to understand these traffic phenomena in a quantitative manner in order to construct and optimize biomimetic transport systems based on motors and filaments with many possible applications in bioengineering, pharmacology, and medicine.

  9. 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.

  10. 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

  11. Collective transport of weakly interacting molecular motors with Langmuir kinetics

    Science.gov (United States)

    Chandel, Sameep; Chaudhuri, Abhishek; Muhuri, Sudipto

    2015-04-01

    Filament-based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as kinesins weakly interact among themselves during transport and with the surrounding cellular environment. Motivated by these observations we study a driven lattice gas model for collective unidirectional transport of molecular motors on open filament. This model incorporates short-range next-nearest-neighbour (NNN) interactions between the motors and couples the transport process on filament with surrounding cellular environment through adsorption-desorption Langmuir kinetics (LK) of the motors. We analyse this model within the framework of a mean-field (MF) theory in the limit of weak interactions between the motors. We point to the mapping of this model with the non-conserved version of the Katz-Lebowitz-Spohn (KLS) model. The system exhibits rich phase behavior with a variety of inhomogeneous phases including localized shocks in the bulk of the filament. We obtain the steady-state density and current profiles, analyse their variation as a function of the strength of interaction and construct the non-equilibrium MF phase diagram. We compare these MF results with Monte Carlo simulations and find that the MF analysis shows reasonably good agreement with simulation results as long as the motors are weakly interacting. For sufficently strong NNN interaction between the motors, the mean-field results deviate significantly, and for very strong NNN interaction in the absence of LK, the current in the lattice is determined solely by the NNN interaction parameter and it becomes independent of entry and exit rates of motors at the filament boundaries.

  12. Optical and transport properties of complex molecular systems

    OpenAIRE

    2009-01-01

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

  13. Scaling Theory for Percolative Charge Transport in Disordered Molecular Semiconductors

    Science.gov (United States)

    Cottaar, J.; Koster, L. J. A.; Coehoorn, R.; Bobbert, P. A.

    2011-09-01

    We present a scaling theory for charge transport in disordered molecular semiconductors that extends percolation theory by including bonds with conductances close to the percolating one in the random-resistor network representing charge hopping. A general and compact expression is given for the charge mobility for Miller-Abrahams and Marcus hopping on different lattices with Gaussian energy disorder, with parameters determined from numerically exact results. The charge-concentration dependence is universal. The model-specific temperature dependence can be used to distinguish between the hopping models.

  14. Thermal Transport in Carbon Nanotubes using Molecular Dynamics

    Science.gov (United States)

    Moore, Andrew; Khatun, Mahfuza

    2011-10-01

    We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.

  15. Kinetic modelling of molecular hydrogen transport in microporous carbon materials.

    Science.gov (United States)

    Hankel, Marlies; Zhang, Hong; Nguyen, Thanh X; Bhatia, Suresh K; Gray, Stephen K; Smith, Sean C

    2011-05-07

    The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H(2)/D(2) and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D(2) transport is dramatically favored over H(2). However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients-implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H(2)/D(2) in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage through the pore mouth, is also

  16. Electronic Transport in Molecular Junction Based on C20 Cages

    Institute of Scientific and Technical Information of China (English)

    OUYANG Fang-Ping; XU Hui

    2007-01-01

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

  17. Transport diffusion in one dimensional molecular systems: Power law and validity of Fick's law

    Science.gov (United States)

    Xu, Zhi-cheng; Zheng, Dong-qin; Ai, Bao-quan; Hu, Bambi; Zhong, Wei-rong

    2015-10-01

    The transport diffusion in one-dimensional molecular systems is investigated through non-equilibrium molecular dynamics and Monte Carlo methods. We have proposed the power law relationship of the transport diffusion coefficient with the temperature, the mass and the transport length, D* ∝ T*m*-1L*β, where β equals to 0.8 for small systems and zero for large systems. It is found that Fick's law is valid in long transport length but invalid in short transport length. Our results can provide a new perspective for understanding the microscopic mechanism of the molecular transport phenomena in low-dimensional systems.

  18. Molecular dynamics simulation of ion transport in a nanochannel

    Institute of Scientific and Technical Information of China (English)

    CHEN Min; CHEN YunFei; ZHONG Wu; YANG JueKuan

    2008-01-01

    A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented,and the process of ion transport in the nanochannel was simulated in this paper.The model consists of two water sinks at the two ends and a pump in the middle,which is different from a single pump model in previous MD simulations.Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the en-richment of counterions in the nanochannel.A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel,and the current in the pump region is mainly induced by the motion of counterions.In addition,the ion number in the pump region rapidly decreases as the external electric field is applied.In the equilibrated system,the electrically neutral character in the pump region is destroyed and this region displays a certain electrical char-acter,which depends on the surface charge.The ion distribution is greatly different from the results predicted by the continuum theory,e.g.a smaller peak value of Na+ concentration appears near the wall.The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density.The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model.The mechanism of some special ex-perimental phenomena in a nanochannel and the effect of the surface charge den-sity on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.

  19. Molecular dynamics simulation of ion transport in a nanochannel

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented, and the process of ion transport in the nanochannel was simulated in this paper. The model consists of two water sinks at the two ends and a pump in the middle, which is different from a single pump model in previous MD simulations. Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the enrichment of counterions in the nanochannel. A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel, and the current in the pump region is mainly induced by the motion of counterions. In addition, the ion number in the pump region rapidly decreases as the external electric field is applied. In the equilibrated system, the electrically neutral character in the pump region is destroyed and this region displays a certain electrical character, which depends on the surface charge. The ion distribution is greatly different from the results predicted by the continuum theory, e.g. a smaller peak value of Na+ concentration appears near the wall. The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density. The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model. The mechanism of some special experimental phenomena in a nanochannel and the effect of the surface charge density on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.

  20. Molecular physiology of vesicular glutamate transporters in the digestive system

    Institute of Scientific and Technical Information of China (English)

    Tao Li; Fayez K. Ghishan; Liqun Bai

    2005-01-01

    Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system (CNS). Packaging and storage of glutamate into glutamatergic neuronal vesicles require ATP-dependent vesicular glutamate uptake systems, which utilize the electrochemical proton gradient as a driving force. Three vesicular glutamate transporters (VGLUT1-3) have been recently identified from neuronal tissue where they play a key role to maintain the vesicular glutamate level. Recently, it has been demonstrated that glutamate signaling is also functional in peripheral neuronal and non-neuronal tissues, and occurs in sites of pituitary, adrenal, pineal glands, bone, GI tract, pancreas,skin, and testis. The glutamate receptors and VGLUTs in digestivesystem have been found in both neuronal and endocrinal cells. The glutamate signaling in the digestive system may have significant relevance to diabetes and GI tract motility disorders. This review will focus on the most recent update of molecular physiology of digestive VGLUTs.

  1. Stochastic modeling of cargo transport by teams of molecular motors

    CERN Document Server

    Klein, Sarah; Santen, Ludger

    2014-01-01

    Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.

  2. Transport Properties of Fluids in Micropores by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    LIU, Ying-Chun(刘迎春); WANG, Qi(王琦); Lü, Ling-Hong(吕玲红)

    2004-01-01

    The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity were analyzed in micropores with pore widths from 0.8 to 4.0 nm. The results show that the diffusivity in micropores is much lower than the bulk diffusivity, and it decreases as the pore width decreases; but the viscosity in micropores is significantly larger than the bulk one, and it increases sharply in narrow micropores. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular direction. The temperature and density are important factors that obviously affect diffusivity and viscosity in micropores.

  3. A heterogeneous model for gas transport in carbon molecular sieves.

    Science.gov (United States)

    Ding, L P; Yuan, Y X; Farooq, S; Bhatia, S K

    2005-01-18

    A dual resistance model with distribution of either barrier or pore diffusional activation energy is proposed in this work for gas transport in carbon molecular sieve (CMS) micropores. This is a novel approach in which the equilibrium is homogeneous, but the kinetics is heterogeneous. The model seems to provide a possible explanation for the concentration dependence of the thermodynamically corrected barrier and pore diffusion coefficients observed in previous studies from this laboratory on gas diffusion in CMS. The energy distribution is assumed to follow the gamma distribution function. It is shown that the energy distribution model can fully capture the behavior described by the empirical model established in earlier studies to account for the concentration dependence of thermodynamically corrected barrier and pore diffusion coefficients. A methodology is proposed for extracting energy distribution parameters, and it is further shown that the extracted energy distribution parameters can effectively predict integral uptake and column breakthrough profiles over a wide range of operating pressures.

  4. Stochastic simulations of cargo transport by processive molecular motors.

    Science.gov (United States)

    Korn, Christian B; Klumpp, Stefan; Lipowsky, Reinhard; Schwarz, Ulrich S

    2009-12-28

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-07

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

  6. Molecular level water and solute transport in reverse osmosis membranes

    Science.gov (United States)

    Lueptow, Richard M.; Shen, Meng; Keten, Sinan

    2015-11-01

    The water permeability and rejection characteristics of six solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polymeric reverse osmosis (RO) membrane using non-equilibrium molecular dynamics simulations. Results indicate that water flux increases with an increasing fraction of percolated free volume in the membrane polymer structure. Solute molecules display Brownian motion and hop from pore to pore as they pass through the membrane. The solute rejection depends on both the size of the solute molecule and the chemical interaction of the solute with water and the membrane. When the open spaces in the polymeric structure are such that solutes have to shed at least one water molecule from their solvation shell to pass through the membrane molecular structure, the water-solute pair interaction energy governs solute rejection. Organic solutes more easily shed water molecules than ions to more readily pass through the membrane. Hydrogen-bonding sites for molecules like urea also lead to a higher rejection. These findings underline the importance of the solute's solvation shell and solute-water-membrane chemistry in solute transport and rejection in RO membranes. Funded by the Institute for Sustainability and Energy at Northwestern with computing resources from XSEDE (NSF grant ACI-1053575).

  7. A logic-gated nanorobot for targeted transport of molecular payloads

    National Research Council Canada - National Science Library

    Douglas, Shawn M; Bachelet, Ido; Church, George M

    2012-01-01

    We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery...

  8. Molecular transport through capillaries made with atomic-scale precision

    Science.gov (United States)

    Radha, B.; Esfandiar, A.; Wang, F. C.; Rooney, A. P.; Gopinadhan, K.; Keerthi, A.; Mishchenko, A.; Janardanan, A.; Blake, P.; Fumagalli, L.; Lozada-Hidalgo, M.; Garaj, S.; Haigh, S. J.; Grigorieva, I. V.; Wu, H. A.; Geim, A. K.

    2016-10-01

    Nanometre-scale pores and capillaries have long been studied because of their importance in many natural phenomena and their use in numerous applications. A more recent development is the ability to fabricate artificial capillaries with nanometre dimensions, which has enabled new research on molecular transport and led to the emergence of nanofluidics. But surface roughness in particular makes it challenging to produce capillaries with precisely controlled dimensions at this spatial scale. Here we report the fabrication of narrow and smooth capillaries through van der Waals assembly, with atomically flat sheets at the top and bottom separated by spacers made of two-dimensional crystals with a precisely controlled number of layers. We use graphene and its multilayers as archetypal two-dimensional materials to demonstrate this technology, which produces structures that can be viewed as if individual atomic planes had been removed from a bulk crystal to leave behind flat voids of a height chosen with atomic-scale precision. Water transport through the channels, ranging in height from one to several dozen atomic planes, is characterized by unexpectedly fast flow (up to 1 metre per second) that we attribute to high capillary pressures (about 1,000 bar) and large slip lengths. For channels that accommodate only a few layers of water, the flow exhibits a marked enhancement that we associate with an increased structural order in nanoconfined water. Our work opens up an avenue to making capillaries and cavities with sizes tunable to ångström precision, and with permeation properties further controlled through a wide choice of atomically flat materials available for channel walls.

  9. Coexistence and efficiency of normal and anomalous transport by molecular motors in living cells

    CERN Document Server

    Goychuk, Igor; Metzler, R

    2013-01-01

    Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  10. Cooperative effects enhance the transport properties of molecular spider teams

    CERN Document Server

    Rank, Matthias; Frey, Erwin

    2013-01-01

    Molecular spiders are synthetic molecular motors based on DNA nanotechnology. While natural molecular motors have evolved towards very high efficiency, it remains a major challenge to develop efficient designs for man-made molecular motors. Inspired by biological motor proteins like kinesin and myosin, molecular spiders comprise a body and several legs. The legs walk on a lattice that is coated with substrate which can be cleaved catalytically. We propose a novel molecular spider design in which n spiders form a team. Our theoretical considerations show that coupling several spiders together alters the dynamics of the resulting team significantly. Although spiders operate at a scale where diffusion is dominant, spider teams can be tuned to behave nearly ballistic, which results in fast and predictable motion. Based on the separation of time scales of substrate and product dwell times, we develop a theory which utilises equivalence classes to coarse-grain the micro-state space. In addition, we calculate diffus...

  11. 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 compris...

  12. Novel molecular pathways in renal Mg2+ transport: a guided tour along the nephron

    DEFF Research Database (Denmark)

    San-Cristobal, Pedro; Dimke, Henrik Anthony; Hoenderop, Joost Gj;

    2010-01-01

    This review highlights recent advances in renal magnesium (Mg) handling. The understanding of the molecular processes of epithelial Mg transport has expanded considerably due to the identification of novel genes involved in hypomagnesemic disorders....

  13. First-principles study of the electron transport through conjugated molecular wires with different carbon backbones

    Science.gov (United States)

    Yao, Jinhuan; Li, Yanwei; Zou, Zhengguang; Wang, Hongbo; Shen, Yufang

    2012-03-01

    The nonequilibrium Green's function approach in combination with density-functional theory is used to perform ab initio quantum-mechanical calculations of the electron transport properties of polyacetylene, polythiophene, poly(phenylene vinylene), poly(p-phenylene ethynylene), and poly(p-phenylene) molecules sandwiched between two gold electrodes. The results demonstrate that the conjugation path has a profound effect on the electron transport property of the molecular wires. Among the five molecular wires, polyacetylene is the most conductive one. The conductivities of the five molecular wires decrease with an order of polyacetylene > polythiophene > poly(phenylene vinylene) > poly(p-phenylene ethynylene) > poly(p-phenylene). The conductivities of polyacetylene and polythiophene are much higher than those of poly(phenylene vinylene), poly(p-phenylene ethynylene), and poly(p-phenylene). The difference of electron transport behaviors of these molecular wires are analyzed in terms of the electronic structures, the transmission spectra, and the spatial distributions of molecular orbitals.

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

    OpenAIRE

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

    2012-01-01

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

  15. Molecular evolution of plant AAP and LHT amino acid transporters

    Directory of Open Access Journals (Sweden)

    Mechthild eTegeder

    2012-02-01

    Full Text Available Nitrogen is an essential mineral nutrient and it is often transported within living organisms in its reduced form, as amino acids. Transport of amino acids across cellular membranes requires proteins, and here we report the phylogenetic analysis across taxa of two amino acid transporter families, the Amino Acid Permeases (AAPs and the Lysine-Histidine-like Transporters (LHTs. We found that the two transporter families form two distinct groups in plants supporting the concept that both are essential. AAP transporters seem to be restricted to land plants. They were found in Selaginella moellindorffii and Physcomitrella patens but not in Chlorophyte, Charophyte or Rhodophyte algae. AAPs were strongly represented in vascular plants, consistent with their major function in phloem (vascular tissue loading of amino acids for sink nitrogen supply. LHTs on the other hand appeared prior to land plants. LHTs were not found in chlorophyte algae Chlamydomonas reinhardtii and Volvox carterii. However, the characean alga Klebsormidium flaccidum encodes KfLHT13 and phylogenetic analysis indicates that it is basal to land plant LHTs. This is consistent with the hypothesis that characean algae are ancestral to land plants. LHTs were also found in both Selaginella moellindorffii and Physcomitrella patens as well as in monocots and eudicots. To date, AAPs and LHTs have mainly been characterized in Arabidopsis (eudicots and these studies provide clues to the functions of the newly identified homologs.

  16. 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

    are important drug targets in treating i.e. affective disorders such as depression and anxiety, and for drugs of abuse such as ecstasy and cocaine. The normal function of the SERT relies on large conformational changes and its inhibition by antidepressants represents a conformational lock. Understanding...... the molecular mechanism of inhibition and which structural elements are involved in inhibitor binding and conformational changes of the transporter will provide clues for the development of improved drugs for the treatment of depression. Guided by our previous studies, we combined different biochemical methods......-HT transport. We also find that the potency of antidepressants is improved by in SERT with a lengthened IL5. These findings support the notion that intracellular loops are important substructures with a role in both the transport mechanism and molecular pharmacology of SERT....

  17. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  18. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Science.gov (United States)

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  19. 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.

  20. Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations

    CERN Document Server

    Shen, Meng; Lueptow, Richard M

    2016-01-01

    The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics (NEMD) simulations. Results indicate that water transport increases with an increasing fraction of connected percolated free volume, or water-accessible open space, in the membrane polymer structure. This free volume is enhanced by the dynamic structure of the membrane at the molecular level as it swells when hydrated and vibrates due to molecular collisions allowing a continuous path connecting the opposite membrane surfaces. The tortuous paths available for transport of solutes result in Brownian motion of solute molecules and hopping from pore to pore as they pass through the polymer network structure of the membrane. The transport of alcohol solutes decreases for solutes with larger Van der Waals volume, which corresponds to less available percolated free volume, or sol...

  1. Optically induced transport through semiconductor-based molecular electronics

    Science.gov (United States)

    Li, Guangqi; Fainberg, Boris D.; Seideman, Tamar

    2015-04-01

    A tight binding model is used to investigate photoinduced tunneling current through a molecular bridge coupled to two semiconductor electrodes. A quantum master equation is developed within a non-Markovian theory based on second-order perturbation theory with respect to the molecule-semiconductor electrode coupling. The spectral functions are generated using a one dimensional alternating bond model, and the coupling between the molecule and the electrodes is expressed through a corresponding correlation function. Since the molecular bridge orbitals are inside the bandgap between the conduction and valence bands, charge carrier tunneling is inhibited in the dark. Subject to the dipole interaction with the laser field, virtual molecular states are generated via the absorption and emission of photons, and new tunneling channels open. Interesting phenomena arising from memory are noted. Such a phenomenon could serve as a switch.

  2. Centrosymmetry enhances quantum transport in disordered molecular networks

    Science.gov (United States)

    Zech, Tobias; Mulet, Roberto; Wellens, Thomas; Buchleitner, Andreas

    2014-05-01

    For more than 50 years we have known that photosynthetic systems harvest solar energy with almost unit quantum efficiency. However, recent experimental evidence of quantum coherence during the excitonic energy transport in photosynthetic organisms challenges our understanding of this fundamental biological function. Currently, and despite numerous efforts, the causal connection between coherence and efficiency is still a matter of debate. We show, through extensive simulations of quantum coherent transport on networks, that three dimensional structures characterized by centro-symmetric Hamiltonians are statistically more efficient than random arrangements. Moreover, a strong correlation of centro-symmetry with quantum efficiency is also observed under the coherent transport dynamics induced by experimentally estimated electronic Hamiltonians of the Fenna-Mathew-Olson complex of sulfur bacteria and of the cryptophyte PC645 complex of marine algae. The application of a genetic algorithm results in a set of optimized Hamiltonians only when seeded from the experimentally estimated Hamiltonian. These results suggest that what appears to be geometrically disordered complexes may well exhibit an inherent hidden symmetry which enhances the energy transport between chromophores. We are confident that our results will motivate research to explore the properties of nearly centro-symmetric Hamiltonians in realistic environments, and to unveil the role of symmetries for quantum effects in biology. The unravelling of such symmetries may open novel perspectives and suggest new design principles in the development of artificial devices.

  3. Molecular basis for substrate discrimination by glycine transporters.

    Science.gov (United States)

    Vandenberg, Robert J; Shaddick, Kim; Ju, Pengchu

    2007-05-11

    Glycine is an inhibitory neurotransmitter in the spinal cord and brain stem, where it acts on strychnine-sensitive glycine receptors, and is also an excitatory neurotransmitter throughout the brain and spinal cord, where it acts on the N-methyl-d-aspartate family of receptors. There are two Na(+)/Cl(-)-dependent glycine transporters, GLYT1 and GLYT2, which control extracellular glycine concentrations and these transporters show differences in substrate selectivity and blocker sensitivity. A bacterial Na(+)-dependent leucine transporter (LeuT(Aa)) has recently been crystallized and its structure determined. When the amino acid residues within the leucine binding site of LeuT(Aa) are aligned with residues of the two glycine transporters there are a number of identical residues and also some key differences. In this report, we demonstrate that the LeuT(Aa) structure represents a good working model of the Na(+)/Cl(-)-dependent neurotransmitters and that differences in substrate selectivity can be attributed to a single difference of a glycine residue in transmembrane domain 6 of GLYT1 for a serine residue at the corresponding position of GLYT2.

  4. Observation of quantum interference in molecular charge transport

    DEFF Research Database (Denmark)

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

    2012-01-01

    , phenomena such as giant magnetoresistance(5), Kondo effects(6) and conductance switching(7-11) have been observed in single molecules, and theorists have predicted that it should also be possible to observe quantum interference in molecular conductors(12-18), but until now all the evidence...

  5. Molecular-dynamics calculation of the vacancy heat of transport

    Energy Technology Data Exchange (ETDEWEB)

    Schelling, Patrick K.; Ernotte, Jacques; Shokeen, Lalit; Tucker, William C. [Advanced Material Processing and Analysis Center and Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 (United States); Woods Halley, J. [Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 555455 (United States)

    2014-07-14

    We apply the recently developed constrained-dynamics method to elucidate the thermodiffusion of vacancies in a single-component material. The derivation and assumptions used in the method are clearly explained. Next, the method is applied to compute the reduced heat of transport Q{sub v}{sup *}−h{sub fv} for vacancies in a single-component material. Results from simulations using three different Morse potentials, with one providing an approximate description of Au, and an embedded-atom model potential for Ni are presented. It is found that the reduced heat of transport Q{sub v}{sup *}−h{sub fv} may take either positive or negative values depending on the potential parameters and exhibits some dependence on temperature. It is also found that Q{sub v}{sup *}−h{sub fv} may be correlated with the activation entropy. The results are discussed in comparison with experimental and previous simulation results.

  6. [Molecular genetic studies of mitochondrial ornithine transporter deficiency (HHH syndrome)].

    Science.gov (United States)

    Tsujino, S; Miyamoto, T; Kanazawa, N

    2001-11-01

    Mitochondrial ornithine transporter deficiency has been called HHH syndrome, because this disorder is characterized by three biochemical abnormalities; hyperornithinemia, hyperammonemia, and homocitrullinuria, and presents with various neurological symptoms; mental retardation, spastic paraparesis with pyramidal signs, cerebellar ataxia and episodic disturbance of consciousness or coma due to hyperammonemia. We identified four mutations in the mitochondrial ornithine transporter gene (ORNT1) of Japanese patients with HHH syndrome. These include a nonsense mutation (R179X), associated with exon skipping, missense mutations (G27E, P126R), and an insertion of AAC between codons 228 and 229, leading to an insertion of amino acid Asn. Especially, R179X was detected 4 of 7 Japanese patients (8 of 14 alleles), implying that this is a common mutation in Japanese population.

  7. Molecular Momentum Transport at Fluid-Solid Interfaces in MEMS/NEMS: A Review

    Directory of Open Access Journals (Sweden)

    Zeng-Yuan Guo

    2009-10-01

    Full Text Available This review is focused on molecular momentum transport at fluid-solid interfaces mainly related to microfluidics and nanofluidics in micro-/nano-electro-mechanical systems (MEMS/NEMS. This broad subject covers molecular dynamics behaviors, boundary conditions, molecular momentum accommodations, theoretical and phenomenological models in terms of gas-solid and liquid-solid interfaces affected by various physical factors, such as fluid and solid species, surface roughness, surface patterns, wettability, temperature, pressure, fluid viscosity and polarity. This review offers an overview of the major achievements, including experiments, theories and molecular dynamics simulations, in the field with particular emphasis on the effects on microfluidics and nanofluidics in nanoscience and nanotechnology. In Section 1 we present a brief introduction on the backgrounds, history and concepts. Sections 2 and 3 are focused on molecular momentum transport at gas-solid and liquid-solid interfaces, respectively. Summary and conclusions are finally presented in Section 4.

  8. Molecular momentum transport at fluid-solid interfaces in MEMS/NEMS: a review.

    Science.gov (United States)

    Cao, Bing-Yang; Sun, Jun; Chen, Min; Guo, Zeng-Yuan

    2009-10-29

    This review is focused on molecular momentum transport at fluid-solid interfaces mainly related to microfluidics and nanofluidics in micro-/nano-electro-mechanical systems (MEMS/NEMS). This broad subject covers molecular dynamics behaviors, boundary conditions, molecular momentum accommodations, theoretical and phenomenological models in terms of gas-solid and liquid-solid interfaces affected by various physical factors, such as fluid and solid species, surface roughness, surface patterns, wettability, temperature, pressure, fluid viscosity and polarity. This review offers an overview of the major achievements, including experiments, theories and molecular dynamics simulations, in the field with particular emphasis on the effects on microfluidics and nanofluidics in nanoscience and nanotechnology. In Section 1 we present a brief introduction on the backgrounds, history and concepts. Sections 2 and 3 are focused on molecular momentum transport at gas-solid and liquid-solid interfaces, respectively. Summary and conclusions are finally presented in Section 4.

  9. Molecular Modeling of Interfacial Proton Transport in Polymer Electrolyte Membranes

    OpenAIRE

    2014-01-01

    The proton conductivity of polymer electrolyte membranes (PEMs) plays a crucial role for the performance of polymer electrolyte fuel cells (PEFCs). High hydration of Nafion-like membranes is crucial to high proton conduction across the PEM, which limits the operation temperature of PEFCs to <100o C. At elevated temperatures (>100o C) and minimal hydration, interfacial proton transport becomes vital for membrane operation. Along with fuel cell systems, interfacial proton conduction is of...

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

    Science.gov (United States)

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

    2013-04-01

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

  11. Molecular Transport Mechanisms for Associating and Solvating Penetrant in Polymers

    Science.gov (United States)

    2007-11-02

    PIB ) at different vapor activities in order to understand complex diffusion mechanisms and probe molecular structures above the glass tranisition. The...the individual diffusion coefficients can be separated and that they are equal to each other for the acetic acid/ PIB system. The values of the...BOH) mixtures in polyisobutylene ( PIB ) was studied at varying mixture compositions. Diffusion coefficients and hydrogen bonding interactions were

  12. 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.

  13. Graphene nanoribbon molecular sensor based on inelastic transport

    Energy Technology Data Exchange (ETDEWEB)

    Ritter, C. [School of Physics, Trinity College Dublin, Dublin 2 (Ireland); Muniz, R. B.; Latgé, A. [Instituto de Física, Universidade Federal Fluminense SN, 24210-360 Niterói-RJ (Brazil)

    2014-04-07

    Results of phonon-assisted inelastic quantum transport calculations are presented for graphene nanoribbons. We consider a single molecule attached to a carbon atom and describe the electronic structure by a tight-binding model, taking into account a local phonon mode associated with the attached molecule characteristic vibration. The calculated transmission spectra reveal a striking sensitivity for molecules attached to the edges of asymmetric zigzag graphene nanoribbons. Our results show that the differential conductance may be used to identify the presence as well as the characteristic vibration frequency of a target molecule at finite temperatures.

  14. Molecular characterization of a proline transporter from Chilo suppressalis

    Institute of Scientific and Technical Information of China (English)

    Jia Huang; Shun-Fan Wu; Gong-Yin Ye

    2011-01-01

    Proline plays an important role in regulating synaptic neurotransmission in both mammalian and insect nervous systems. The full-length complementary DNA sequences encoding the proline transporter gene (CsProT) and its alternative spliced transcript (CsProT-ST) were cloned from the striped stem borer (SSB), Chilo suppressalis,one of the most important rice pests in Asia. The comparison of amino acid sequences showed that CsProT is highly similar to the proline transporter isolated from Manduca sexta (MasProT). The developmental changes of the relative messenger RNA expression levels of CsProT and CsProT-ST genes were examined in SSB. The expression level of CsProT-ST is much higher than that of CsProT in all developmental periods, suggesting that the 3′-end spliced variant is the major transcript instead of CsProT. The highest expression level of both genes in the pupal stage means that proline may be involved in some unclear functions in the metamorphosis from pupa to adulthood.

  15. Thermal transport properties of uranium dioxide by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku; Sinnott, Susan B. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States); Tulenko, James S. [Department of Nuclear and Radiological Engineering, University of Florida, Gainesville, FL 32611 (United States); Grimes, Robin W. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Schelling, Patrick K. [AMPAC and Department of Physics, University of Central Florida, Orlando, FL 32816 (United States); Phillpot, Simon R. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States)], E-mail: sphil@mse.ufl.edu

    2008-04-30

    The thermal conductivities of single crystal and polycrystalline UO{sub 2} are calculated using molecular dynamics simulations, with interatomic interactions described by two different potential models. For single crystals, the calculated thermal conductivities are found to be strongly dependent on the size of the simulation cell. However, a scaling analysis shows that the two models predict essentially identical values for the thermal conductivity for infinite system sizes. By contrast, simulations with the two potentials for identical fine polycrystalline structures yield estimated thermal conductivities that differ by a factor of two. We analyze the origin of this difference.

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

    CERN Document Server

    Singal, J; Schindler, R

    2013-01-01

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

  17. Modulating molecular transport across peptide-modified nanoporous alumina membranes with light

    Science.gov (United States)

    Kumeria, Tushar; Yu, Jingxian; Alsawat, Mohammed; Kurkuri, Mahaveer D.; Santos, Abel; Abell, Andrew D.; Losic, Dusan

    2016-12-01

    We designed and fabricated a smart and stimuli responsive membrane to cater on demand molecular transporting applications. A novel photoswitchable peptide (PSP) was synthesized and attached inside nanoporous anodic alumina membranes (NAAMs) pores. The PSP specifically switched between its cis and trans photostationary states on exposure to 364 nm and 440 nm wavelength lights respectively, which not only provided the ability to control its pore diameter but also the surface chemistry. The switchable molecular transport properties of the PSP-NAAMs have been shown as a function of the light exposure. Most importantly, the molecular transport across PSP-NAAMs could be repeatedly switched between on and off state, which is highly significant for on-demand triggered drug release systems.

  18. Charge transport in high mobility molecular semiconductors: classical models and new theories.

    Science.gov (United States)

    Troisi, Alessandro

    2011-05-01

    The theories developed since the fifties to describe charge transport in molecular crystals proved to be inadequate for the most promising classes of high mobility molecular semiconductors identified in the recent years, including for example pentacene and rubrene. After reviewing at an elementary level the classical theories, which still provide the language for the understanding of charge transport in these systems, this tutorial review outlines the recent experimental and computational evidence that prompted the development of new theories of charge transport in molecular crystals. A critical discussion will illustrate how very rarely it is possible to assume a charge hopping mechanism for high mobility organic crystals at any temperature. Recent models based on the effect of non-local electron-phonon coupling, dynamic disorder, coexistence of localized and delocalized states are reviewed. Additionally, a few more recent avenues of theoretical investigation, including the study of defect states, are discussed.

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

    Science.gov (United States)

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

    2015-06-24

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

  20. 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.

  1. Proximity Labeling Reveals Molecular Determinants of FGFR4 Endosomal Transport.

    Science.gov (United States)

    Haugsten, Ellen Margrethe; Sørensen, Vigdis; Kunova Bosakova, Michaela; de Souza, Gustavo Antonio; Krejci, Pavel; Wiedlocha, Antoni; Wesche, Jørgen

    2016-10-07

    The fibroblast growth factor receptors (FGFRs) are important oncogenes promoting tumor progression in many types of cancer, such as breast, bladder, and lung cancer as well as multiple myeloma and rhabdomyosarcoma. However, little is known about how these receptors are internalized and down-regulated in cells. We have here applied proximity biotin labeling to identify proteins involved in FGFR4 signaling and trafficking. For this purpose we fused a mutated biotin ligase, BirA*, to the C-terminal tail of FGFR4 (FGFR4-BirA*) and the fusion protein was stably expressed in U2OS cells. Upon addition of biotin to these cells, proteins in proximity to the FGFR4-BirA* fusion protein became biotinylated and could be isolated and identified by quantitative mass spectrometry. We identified in total 291 proteins, including 80 proteins that were enriched in samples where the receptor was activated by the ligand (FGF1), among them several proteins previously found to be involved in FGFR signaling (e.g., FRS2, PLCγ, RSK2 and NCK2). Interestingly, many of the identified proteins were implicated in endosomal transport, and by precise annotation we were able to trace the intracellular pathways of activated FGFR4. Validating the data by confocal and three-dimensional structured illumination microscopy analysis, we concluded that FGFR4 uses clathrin-mediated endocytosis for internalization and is further sorted from early endosomes to the recycling compartment and the trans-Golgi network. Depletion of cells for clathrin heavy chain led to accumulation of FGFR4 at the cell surface and increased levels of active FGFR4 and PLCγ, while AKT and ERK signaling was diminished, demonstrating that functional clathrin-mediated endocytosis is required for proper FGFR4 signaling. Thus, this study reveals proteins and pathways involved in FGFR4 transport and signaling that provide possible targets and opportunities for therapeutic intervention in FGFR4 aberrant cancer.

  2. Molecular determinants for selective recognition of antidepressants in the human serotonin and norepinephrine transporters

    DEFF Research Database (Denmark)

    Andersen, Jacob; Stuhr-Hansen, Nicolai; Zachariassen, Linda

    2011-01-01

    /NET selectivity are poorly understood. In this study, the structural basis for selectivity of the SERT selective inhibitor citalopram and the structurally closely related NET selective inhibitor talopram is delineated. A systematic structure-activity relationship study allowed identification of the substituents......, these findings provide important insight into the molecular basis for SERT/NET selectivity of antidepressants, which can be used to guide rational development of unique transporter inhibitors with fine-tuned transporter selectivity....

  3. The molecular photo-cell: quantum transport and energy conversion at strong non-equilibrium.

    Science.gov (United States)

    Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan

    2015-02-09

    The molecular photo-cell is a single molecular donor-acceptor complex attached to electrodes and subject to external illumination. Besides the obvious relevance to molecular photo-voltaics, the molecular photo-cell is of interest being a paradigmatic example for a system that inherently operates in out-of-equilibrium conditions and typically far from the linear response regime. Moreover, this system includes electrons, phonons and photons, and environments which induce coherent and incoherent processes, making it a challenging system to address theoretically. Here, using an open quantum systems approach, we analyze the non-equilibrium transport properties and energy conversion performance of a molecular photo-cell, including both coherent and incoherent processes and treating electrons, photons, and phonons on an equal footing. We find that both the non-equilibrium conditions and decoherence play a crucial role in determining the performance of the photovoltaic conversion and the optimal energy configuration of the molecular system.

  4. Molecular identification and characterisation of the glycine transporter (GLYT1) and the glutamine/glutamate transporter (ASCT2) in the rat lens

    DEFF Research Database (Denmark)

    Lim, Julie; Lorentzen, Karen Axelgaard; Kistler, Joerg;

    2006-01-01

    the molecular identity of GSH transporters in the lens, we have focused on identifying transporters involved in the uptake of the precursor amino acids required for GSH synthesis. Previously, we identified an uptake system for cyst(e)ine mediated by the Xc(-) exchanger and the Excitatory Amino Acid Transporters...... in the centre of the lens raises the possibility that ASCT2 may work with the Xc(-) exchanger to accumulate cysteine where it can potentially act as a low molecular mass antioxidant....

  5. Multicomponent ballistic transport in narrow single wall carbon nanotubes: Analytic model and molecular dynamics simulations

    Science.gov (United States)

    Mutat, T.; Adler, J.; Sheintuch, M.

    2011-01-01

    The transport of gas mixtures through molecular-sieve membranes such as narrow nanotubes has many potential applications, but there remain open questions and a paucity of quantitative predictions. Our model, based on extensive molecular dynamics simulations, proposes that ballistic motion, hindered by counter diffusion, is the dominant mechanism. Our simulations of transport of mixtures of molecules between control volumes at both ends of nanotubes give quantitative support to the model's predictions. The combination of simulation and model enable extrapolation to longer tubes and pore networks.

  6. Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches.

    Science.gov (United States)

    Gutiérrez, R; Caetano, R A; Woiczikowski, B P; Kubar, T; Elstner, M; Cuniberti, G

    2009-05-22

    We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

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

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

    Molecular junctions are promising candidates for thermoelectric devices due to the potential to tune the electronic and thermal transport properties. However, a high figure of merit is hard to achieve, without reducing the phononic contribution to thermal conductance. Here, we propose a strategy...... to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...... molecular junction. Phonon transmission of pi-stacked systems is largely attenuated in the whole frequency range, and the remaining transmission occurs mainly below 5 THz, where out-of-plane channels dominate. The figure of merit (ZT) of the pi-stacked molecular junction is dramatically enhanced because...

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

    Science.gov (United States)

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

    2010-02-01

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

  9. 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.

  10. Superdiffusive transport by multivalent molecular walkers moving under load

    CERN Document Server

    Olah, Mark J

    2012-01-01

    We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo biased, superdiffusive motion, even in opposition to an external load force. The walker in the model lacks any inherent orientation of body or track, and its legs have no chemomechanical coupling other than the passive constraint imposed by their connection to a common body. Yet, under appropriate kinetic conditions the walker's motion is biased in the direction of unvisited sites, which allows the walker to move nearly ballistically away from the origin as long as a local supply of unmodified substrate sites is available. The multivalent random walker model is mathematically formulated as a continuous-time Markov process and is studied numerically. We use Monte Carlo simulations to generate ensemble estimates of the mean squared displacement and mean work done for this non-er...

  11. Molecular transport through large-diameter DNA nanopores

    Science.gov (United States)

    Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.

    2016-01-01

    DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ≈4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ≈3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration. PMID:27658960

  12. Molecular transport through large-diameter DNA nanopores

    Science.gov (United States)

    Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.

    2016-09-01

    DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ~4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ~3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ulman, Kanchan [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India); Narasimhan, Shobhana [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India); Sheikh Saqr Laboratory, ICMS, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India); Delin, Anna [Department of Materials and Nanophysics, School of Information and Communication Technology, Electrum 229, Royal Institute of Technology (KTH), SE-16440 Kista (Sweden); Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); SeRC (Swedish e-Science Research Center), KTH, SE-10044 Stockholm (Sweden)

    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%.

  14. Stochastic model for photoinduced surface relief grating formation through molecular transport in polymer films.

    Energy Technology Data Exchange (ETDEWEB)

    Juan, M.; Plain, J.; Bachelot, R.; Royer, P.; Gray, S. K.; Wiederrecht, G. P.; Univ. de Technologie de Troyes

    2008-09-01

    We use a stochastic model to study photoinduced surface relief grating (SRG) formation due to molecular transport in azobenzene polymer films. The model is shown to reproduce the essential experimental features of SRG formation. In particular, it predicts SRG formation under both p and s polarizations, and the double peaked topographies that can occur at early times of the process. The evolving molecular positions and orientations during exposure are also followed, providing a useful mechanistic picture of SRG dynamics.

  15. Molecular hole transporting materials for organic light-emitting diodes (OLEDs)

    Science.gov (United States)

    Loy, Douglas E.

    Organic light-emitting devices are rapidly becoming viable contenders in the display market. One of the major obstacles to the commercial viability of OLEDs is device stability and lifetime. Device stability has been partially, if not mostly, attributed to thermal instability of the organic charge transport layers. Some characteristics of good hole transporters for OLEDs are reversible oxidation, high thermal stability, and the ability to form amorphous films upon vacuum deposition. The main objective of this research was to design novel hole transporting materials with improved thermal stability, while retaining favorable electronic properties. Molecular structure can have drastic effects on the properties of the thin organic films of the hole transporting layers. Hole transporters with increased molecular asymmetry and rigidity have been demonstrated to give amorphous materials with higher glass transition temperatures. While asymmetry provides materials that are more thermally stable, the asymmetry must not be to an extent that would cause electronic asymmetry. Electronic asymmetry resulting from dipoles can act as local charge traps thus hindering hole transport. Increasing molecular rigidity provides materials with increased thermal stability, as well as improved hole mobility. The increased mobility is due in part to the better conjugation with materials held in a planar orientation. A direct correlation has been found between the thermal stability of a OLED and the glass transition of the hole transporting material used. Structural design, synthesis and characterization of novel hole transporting materials will be reported, as well as their performance in electroluminescent devices. Device operation and architecture will also be discussed, including the use of hole transporters as host for emitting materials.

  16. Transport of molecular fluids through three-dimensional porous media

    Science.gov (United States)

    Adler, Pierre; Pazdniakou, Aliaksei

    2014-05-01

    The main purpose of this study is to extend the analysis which has been made for the double layer theory (summarized by [1]) to situations where the distance between the solid walls is of the order of several molecular diameters. This is of a large interest from a scientific viewpoint and for various engineering applications. The intermolecular forces and their influence on fluid structure and dynamics can be taken into account by using the mesoscopic scale models based on the Boltzmann equation [2]. The numerical methods derived from these models are less demanding in computational resources than conventional molecular dynamics methods and therefore long time evolution of large samples can be considered. Three types of fluid particles are considered, namely the anions, the cations and the solvent. They possess a finite diameter which should be at least a few lattice units. The collision frequency between particles is increased by the pair correlation function for hard spheres. The lattice Boltzmann model is built in three dimensions with 19 velocities; it involves two relaxation times. The particle distribution functions are discretized over a basis of Hermite polynomial tensors. Electric forces are included and a Poisson equation is simultaneously solved by a successive over-relaxation method. The numerical algorithm is detailed; it is devised in order to be able to address any three-dimensional porous media. It involves the determination of the densities of each particle species, of the overall density and of the equilibrium distribution function. Then, the electric forces are determined. Collision operators are applied as well as the boundary conditions. Finally, the propagation step is performed and the algorithm starts a new loop. The influence of parameters can be illustrated by systematic calculations in a plane Poiseuille configuration. The drastic influence of the ratio between the channel width and the particle sizes on the local densities and the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-15

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

  18. Charge carrier transport in molecularly doped polycarbonate as a test case for the dipolar glass model.

    Science.gov (United States)

    Novikov, S V; Tyutnev, A P

    2013-03-14

    We present the results of Monte Carlo simulations of the charge carrier transport in a disordered molecular system containing spatial and energetic disorders using the dipolar glass model. Model parameters of the material were chosen to fit a typical polar organic photoconductor polycarbonate doped with 30% of aromatic hydrazone, whose transport properties are well documented in literature. Simulated carrier mobility demonstrates a usual Poole-Frenkel field dependence and its slope is very close to the experimental value without using any adjustable parameter. At room temperature transients are universal with respect to the electric field and transport layer thickness. At the same time, carrier mobility does not depend on the layer thickness and transients develop a well-defined plateau where the current does not depend on time, thus demonstrating a non-dispersive transport regime. Tails of the transients decay as power law with the exponent close to -2. This particular feature indicates that transients are close to the boundary between dispersive and non-dispersive transport regimes. Shapes of the simulated transients are in very good agreement with the experimental ones. In summary, we provide a first verification of a self-consistency of the dipolar glass transport model, where major transport parameters, extracted from the experimental transport data, are then used in the transport simulation, and the resulting mobility field dependence and transients are in very good agreement with the initial experimental data.

  19. Electronic transport in fullerene C20 bridge assisted by molecular vibrations.

    Science.gov (United States)

    Yamamoto, Takahiro; Watanabe, Kazuyuki; Watanabe, Satoshi

    2005-08-01

    The effect of molecular vibrations on electronic transport is investigated with the smallest fullerene C20 bridge, utilizing the Keldysh nonequilibrium Green's function techniques combined with the tight-binding molecular-dynamics method. Large discontinuous steps appear in the differential conductance when the applied bias voltage matches particular vibrational energies. The magnitude of the step is found to vary considerably with the vibrational mode and to depend on the local electronic states besides the strength of electron-vibration coupling. On the basis of this finding, a novel way to control the molecular motion by adjusting the gate voltage is proposed.

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

    Science.gov (United States)

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

    2013-07-03

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

  1. Molecular physiology of zinc transport in the Zn hyperaccumulator Thlaspi caerulescens.

    Science.gov (United States)

    Lasat, M M; Pence, N S; Garvin, D F; Ebbs, S D; Kochian, L V

    2000-01-01

    In this manuscript, recent research from this laboratory into physiological and molecular aspects of heavy metal (Zn) transport in the hyperaccumulating plant species, Thlaspi caerulescens is reviewed. This research is aimed at elucidating the processes that underlie the accumulation of extraordinarily high levels of Zn in the T. caerulescens shoot (up to 3% Zn dry wt.) without any associated toxicity symptom. Physiological studies focused on the use of radiotracer flux techniques (65Zn2+) to characterize zinc transport and compartmentation in the root, and translocation and accumulation in the shoot of T. caerulescens in comparison with a related non-accumulator, T. arvense. These studies indicated that Zn transport was stimulated at a number of sites in T. caerulescens, contributing to the hyperaccumulation trait. The transport processes that were stimulated included Zn influx into both root and leaf cells, and Zn loading into the xylem. The 4- to 5-fold stimulation of Zn influx into the root was hypothesized to be due to an increased abundance of Zn transporters in T. caerulescens root cells. Additionally, compartmental analysis (radiotracer wash out or efflux techniques) was used to show that Zn was sequestered in the vacuoles of T. arvense root cells which retarded Zn translocation to the shoot in this non-accumulator species. Molecular studies have focused on the cloning and characterization of Zn transport genes in T. caerulescens. Complementation of a yeast Zn transport-defective mutant with a T. caerulescens cDNA library resulted in the recovery of a cDNA, ZNT1, that encodes a Zn transporter. Sequence analysis of ZNT1 indicated it is a member of a recently discovered micronutrient transport gene family which includes the Arabidopsis Fe transporter, IRT1, and the ZIP Zn transporters. Expression of ZNT1 in yeast allowed for a physiological characterization of this transporter. It was shown to encode a high affinity Zn transporter which can also mediate low

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

    NARCIS (Netherlands)

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

    2011-01-01

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

  3. Active transport improves the precision of linear long distance molecular signalling

    Science.gov (United States)

    Godec, Aljaž; Metzler, Ralf

    2016-09-01

    Molecular signalling in living cells occurs at low copy numbers and is thereby inherently limited by the noise imposed by thermal diffusion. The precision at which biochemical receptors can count signalling molecules is intimately related to the noise correlation time. In addition to passive thermal diffusion, messenger RNA and vesicle-engulfed signalling molecules can transiently bind to molecular motors and are actively transported across biological cells. Active transport is most beneficial when trafficking occurs over large distances, for instance up to the order of 1 metre in neurons. Here we explain how intermittent active transport allows for faster equilibration upon a change in concentration triggered by biochemical stimuli. Moreover, we show how intermittent active excursions induce qualitative changes in the noise in effectively one-dimensional systems such as dendrites. Thereby they allow for significantly improved signalling precision in the sense of a smaller relative deviation in the concentration read-out by the receptor. On the basis of linear response theory we derive the exact mean field precision limit for counting actively transported molecules. We explain how intermittent active excursions disrupt the recurrence in the molecular motion, thereby facilitating improved signalling accuracy. Our results provide a deeper understanding of how recurrence affects molecular signalling precision in biological cells and novel medical-diagnostic devices.

  4. Applicability of the wide-band limit in DFT-based molecular transport calculations

    NARCIS (Netherlands)

    Verzijl, C.J.O.; Seldenthuis, J.S.; Thijssen, J.M.

    2013-01-01

    Transport properties of molecular junctions are notoriously expensive to calculate with ab initio methods, primarily due to the semi-infinite electrodes. This has led to the introduction of different approximation schemes for the electrodes. For the most popular metals used in experiments, such as g

  5. Ab initio transport calculations of molecular wires with electron-phonon couplings

    Science.gov (United States)

    Hirose, Kenji; Kobayashi, Nobuhiko

    2009-03-01

    Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  7. Molecular-dynamics of water transport through membranes - water from solvent to solute

    NARCIS (Netherlands)

    BERENDSEN, HJC; MARRINK, SJ

    1993-01-01

    An application of Molecular Dynamics computer simulation (MD) to the process of transport of water through a lipid bilayer membrane is described. The permeation process is far too slow to be modeled by straightforward MD. In stead the inverse of the permeability coefficient is expressed as an

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

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    transport and thermoelectric response in the π-stacked structures by investigating five representative stacked molecular junctions. We found that a π-stacked system of two substituted anthracenes exhibits good thermopower and a high power factor, suggesting that increased conjugation can enhance...

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  10. Modeling of the Electro-Mechanical Response of Carbon Nanotubes: Molecular Dynamics and Transport Calculations

    Science.gov (United States)

    Svizhenko, Alexel; Anantram, M. P.; Maiti, Amitesh

    2003-01-01

    This paper presents viewgraphs on the modeling of the electromechanical response of carbon nanotubes, utilizing molecular dynamics and transport calculations. The topics include: 1) Simulations of the experiment; 2) Effect of diameter, length and temperature; and 3) Study of sp3 coordination-"The Table experiment".

  11. 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...

  12. Use of a molecular decoy to segregate transport from antigenicity in the FrpB iron transporter from Neisseria meningitidis.

    Directory of Open Access Journals (Sweden)

    Muhammad Saleem

    Full Text Available FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe(3+ with high affinity. EPR spectra of the bound Fe(3+ ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe(3+ binding was reduced or abolished on mutation of the Fe(3+-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe(3+. The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a 'molecular decoy' to distract immune surveillance.

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

    Science.gov (United States)

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

    2012-07-17

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

  14. Molecular Determinants of Substrate Specificity in Sodium-coupled Glutamate Transporters.

    Science.gov (United States)

    Silverstein, Nechama; Ewers, David; Forrest, Lucy R; Fahlke, Christoph; Kanner, Baruch I

    2015-11-27

    Crystal structures of the archaeal homologue GltPh have provided important insights into the molecular mechanism of transport of the excitatory neurotransmitter glutamate. Whereas mammalian glutamate transporters can translocate both glutamate and aspartate, GltPh is only one capable of aspartate transport. Most of the amino acid residues that surround the aspartate substrate in the binding pocket of GltPh are highly conserved. However, in the brain transporters, Thr-352 and Met-362 of the reentrant hairpin loop 2 are replaced by the smaller Ala and Thr, respectively. Therefore, we have studied the effects of T352A and M362T on binding and transport of aspartate and glutamate by GltPh. Substrate-dependent intrinsic fluorescence changes were monitored in transporter constructs containing the L130W mutation. GltPh-L130W/T352A exhibited an ~15-fold higher apparent affinity for l-glutamate than the wild type transporter, and the M362T mutation resulted in an increased affinity of ~40-fold. An even larger increase of the apparent affinity for l-glutamate, around 130-fold higher than that of wild type, was observed with the T352A/M362T double mutant. Radioactive uptake experiments show that GltPh-T352A not only transports aspartate but also l-glutamate. Remarkably, GltPh-M362T exhibited l-aspartate but not l-glutamate transport. The double mutant retained the ability to transport l-glutamate, but its kinetic parameters were very similar to those of GltPh-T352A alone. The differential impact of mutation on binding and transport of glutamate suggests that hairpin loop 2 not only plays a role in the selection of the substrate but also in its translocation.

  15. A self-consistent transport model for molecular conduction based on extended Huckel theory with full three-dimensional electrostatics

    DEFF Research Database (Denmark)

    Zahid, F.; Paulsson, Magnus; Polizzi, E.;

    2005-01-01

    We present a transport model for molecular conduction involving an extended Huckel theoretical treatment of the molecular chemistry combined with a nonequilibrium Green's function treatment of quantum transport. The self-consistent potential is approximated by CNDO (complete neglect of differential...

  16. Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife.

    Science.gov (United States)

    Balkenhol, Niko; Waits, Lisette P

    2009-10-01

    Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.

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

    Science.gov (United States)

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-12-01

    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. Molecular regulation of sucrose catabolism and sugar transport for development, defence and phloem function.

    Science.gov (United States)

    Li, Jun; Wu, Limin; Foster, Ryan; Ruan, Yong-Ling

    2017-03-17

    Sucrose (Suc) is the major end product of photosynthesis in mesophyll cells of most vascular plants. It is loaded into phloem of mature leaves for long-distance translocation to non-photosynthetic organs where it is unloaded for diverse uses. Clearly, Suc transport and metabolism is central to plant growth and development and the functionality of the entire vascular system. Despite of vast information in the literature about the physiological roles of individual sugar metabolic enzymes and transporters, there is a lack of systematic evaluation about their molecular regulation from transcriptional to post-translational levels. Knowledge on this topic is essential for understanding and improving plant development, optimising resource distribution and increasing crop productivity. We therefore focused our analyses on molecular control of key players in Suc metabolism and transport, including (i) the identification of promoter elements responsive to sugars and hormones or targeted by transcription factors and microRNAs degrading transcripts of target genes and (ii) modulation of enzyme and transporter activities through protein-protein interactions and other post-translational modifications. We highlighted major remaining questions and discussed opportunities to exploit current understanding to gain new insights into molecular control of carbon partitioning for improving plant performance.

  19. How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport.

    Science.gov (United States)

    Goychuk, Igor; Kharchenko, Vasyl O; Metzler, Ralf

    2014-01-01

    Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  20. How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport.

    Directory of Open Access Journals (Sweden)

    Igor Goychuk

    Full Text Available Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  1. Investigation of Terminal Group Effect on Electron Transport Through Open Molecular Structures

    Institute of Scientific and Technical Information of China (English)

    C.Preferencial Kala; P.Aruna Priya; D.John Thiruvadigal

    2013-01-01

    The effect of terminal groups on the electron transport through metal-molecule-metal system has been investigated using nonequilibrium Green's function (NEGF) formalism combined with extended Huckel theory (EHT).Au-molecule-Au junctions are constructed with borazine and BCN unit structure as core molecule and sulphur (S),oxygen (O),selenium (Se) and cyano-group (CN) as terminal groups.The electron transport characteristics of the borazine and BCN molecular systems are analyzed through the transmission spectra and the current-voltage curve.The results demonstrate that the terminal groups modifying the transport behaviors of these systems in a controlled way.Our result shows that,selenium is the best linker to couple borazine to Au electrode and oxygen is the best one to couple BCN to Au electrode.Furthermore,the results of borazine systems are compared with that of BCN molecular systems and are discussed.Simulation results show that the conductance through BCN molecular systems is four times larger than the borazine molecular systems.Negative differential resistance behavior is observed with borazine-CN system and the saturation feature appears in BCN systems.

  2. 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.

  3. Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT.

    Science.gov (United States)

    Noskov, Sergei Y

    2008-12-01

    The recently published X-ray structure of LeuT, a Na(+)/Cl(-)-dependent neurotransmitter transporter, has provided fresh impetus to efforts directed at understanding the molecular principles governing specific neurotransmitter transport. The combination of the LeuT crystal structure with the results of molecular simulations enables the functional data on specific binding and transport to be related to molecular structure. All-atom FEP and molecular dynamics (MD) simulations of LeuT embedded in an explicit membrane were performed alongside a decomposition analysis to dissect the molecular determinants of the substrate specificity of LeuT. It was found that the ligand must be in a zwitterionic (ZW) form to bind tightly to the transporter. The theoretical results on the absolute binding-free energies for leucine, alanine, and glycine show that alanine can be a potent substrate for LeuT, although leucine is preferred, which is consistent with the recent experimental data (Singh et al., Nature 2007;448:952-956). Furthermore, LeuT displays robust specificity for leucine over glycine. Interestingly, the ability of LeuT to discriminate between substrates relies on the dynamics of residues that form its binding pocket (e.g., F253 and Q250) and the charged side chains (R30-D404) from a second coordination shell. The water-mediated R30-D404 salt bridge is thought to be part of the extracellular (EC) gate of LeuT. The introduction of a polar ligand such as glycine to the water-depleted binding pocket of LeuT gives rise to structural rearrangements of the R30-D404-Q250 hydrogen-bonding network and leads to increased hydration of the binding pocket. Conformational changes associated with the broken hydrogen bond between Q250 and R30 are shown to be important for tight and selective ligand binding to LeuT.

  4. Bidirectional transport by molecular motors: enhanced processivity and response to external forces.

    Science.gov (United States)

    Müller, Melanie J I; Klumpp, Stefan; Lipowsky, Reinhard

    2010-06-02

    Intracellular transport along cytoskeletal filaments is often mediated by two teams of molecular motors that pull on the same cargo and move in opposite directions along the filaments. We have recently shown theoretically that this bidirectional transport can be understood as a stochastic tug-of-war between the two motor teams. Here, we further develop our theory to investigate the experimentally accessible dynamic behavior of cargos transported by strong motors such as kinesin-1 or cytoplasmic dynein. By studying the run and binding times of such a cargo, we show that the properties of biological motors, such as the large ratio of stall/detachment force and the small ratio of superstall backward/forward velocity, are favorable for bidirectional cargo transport, leading to fast motion and enhanced diffusion. In addition, cargo processivity is shown to be strongly enhanced by transport via several molecular motors even if these motors are engaged in a tug-of-war. Finally, we study the motility of a bidirectional cargo under force. Frictional forces arising, e.g., from the viscous cytoplasm, lead to peaks in the velocity distribution, while external forces as exerted, e.g., by an optical trap, lead to hysteresis effects. Our results, in particular our explicit expressions for the cargo binding time and the distance of the peaks in the velocity relation under friction, are directly accessible to in vitro as well as in vivo experiments.

  5. Theoretical descriptions of electron transport through single molecules: Developing design tools for molecular electronic devices

    Science.gov (United States)

    Carroll, Natalie R.

    There are vast numbers of organic compounds that could be considered for use in molecular electronics. Hence there is a need for efficient and economical screening tools. Here we develop theoretical methods to describe electron transport through individual molecules, the ultimate goal of which is to establish design tools for molecular electronic devices. To successfully screen a compound for its use as a device component requires a proper representation of the quantum mechanics of electron transmission. In this work we report the development of tools for the description of electron transmission that are: Charge self-consistent, valid in the presence of a finite applied potential field and (in some cases) explicitly time-dependent. In addition, the tools can be extended to any molecular system, including biosystems, because they are free of restrictive parameterizations. Two approaches are explored: (1) correlation of substituent parameter values (sigma), (commonly found in organic chemistry textbooks) to properties associated with electron transport, (2) explicit tracking of the time evolution of the wave function of a nonstationary electron. In (1) we demonstrate that the a correlate strongly with features of the charge migration process, establishing them as useful indicators of electronic properties. In (2) we employ a time-dependent description of electron transport through molecular junctions. To date, the great majority of theoretical treatments of electron transport in molecular junctions have been of the time-independent variety. Time dependence, however, is critical to such properties as switching speeds in binary computer components and alternating current conductance, so we explored methods based on time-dependent quantum mechanics. A molecular junction is modeled as a single molecule sandwiched between two clusters of close-packed metal atoms or other donor and acceptor groups. The time dependence of electron transport is investigated by initially

  6. Electronic Transport Properties of a Naphthopyran-Based Optical Molecular Switch:an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    XIA Cai-Juan; LIU De-Sheng; ZHANG Ying-Tang

    2011-01-01

    The electronic transport properties of a. Naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's Function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation. Theoretical results show that the current through the open form is significantly larger than that through the closed form, which is different from other optical switches based on ring-opening reactions of the molecular bridge. The maximum on-off ratio (about 90) can be obtained at 1.4 V. The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.%@@ ronic transport properties of a naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's function formalism combined with first-principles density functional theory.The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation.Theoretical results show that the current through the open form is significantly larger than that through the closed form,which is different from other optical switches based on ring-opening reactions of the molecular bridge.The maximum on-off ratio(about 90)can be obtained at 1.4 V.The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap.Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.

  7. 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......-classical approximation. Both charge and energy transport and their interplay can be studied. We compare the MD results with those of a fully quantum mechanical nonequilibrium Green's function (NEGF) approach for the electron currents. We find a ballistic to diffusive transition of the electron conduction in one...

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

    DEFF Research Database (Denmark)

    Sinning, Steffen; Said, Saida; Malinauskaite, Lina

    structures of the bacterial homolog, LeuT, captured in a new conformation without substrate or sodium bound shows a dramatic rotation of an absolutely conserved leucine into the substrate site. Molecular dynamics simulations combined with functional studies on SERT support that this leucine must act...... 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...

  9. Light quasiparticles dominate electronic transport in molecular crystal field-effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Li, Z. Q.; Podzorov, V.; Sai, N.; Martin, Michael C.; Gershenson, M. E.; Di Ventra, M.; Basov, D. N.

    2007-03-01

    We report on an infrared spectroscopy study of mobile holes in the accumulation layer of organic field-effect transistors based on rubrene single crystals. Our data indicate that both transport and infrared properties of these transistors at room temperature are governed by light quasiparticles in molecular orbital bands with the effective masses m[small star, filled]comparable to free electron mass. Furthermore, the m[small star, filled]values inferred from our experiments are in agreement with those determined from band structure calculations. These findings reveal no evidence for prominent polaronic effects, which is at variance with the common beliefs of polaron formation in molecular solids.

  10. Vibrational effects in charge transport through a molecular double quantum dot

    CERN Document Server

    Sowa, Jakub K; Briggs, G Andrew D; Gauger, Erik M

    2016-01-01

    Recent progress in the field of molecular electronics has revealed the fundamental importance of the coupling between the electronic degrees of freedom and specific vibrational modes. Considering the examples of a molecular dimer and a carbon nanotube double quantum dot, we here theoretically investigate transport through a two-site system that is strongly coupled to a single vibrational mode. Using a quantum master equation approach, we demonstrate that, depending on the relative positions of the two dots, electron-phonon interactions can lead to negative differential conductance and suppression of the current through the system. We also discuss the experimental relevance of the presented results and possible implementations of the studied system.

  11. Coherent site-directed transport in complex molecular networks: an effective Hamiltonian approach.

    Science.gov (United States)

    Weissman, Shira; Peskin, Uri

    2010-03-21

    Defining the conditions for coherent site-directed transport from an electron donor to a specific acceptor through tunneling barriers in a network of multiple donor/acceptors sites is an important step toward controlling electronic processes in molecular networks. The required analysis is most challenging since the entire network in essentially involved in coherent transport. In this work we introduce an efficient approach for formulating an effective donor/acceptor coupling in terms of the entire network parameters. The approach is based on implementation of Feshbach projection operators to map the entire network Hamiltonian onto a subspace defined by two specific donor and acceptor sites. This nonperturbative approach enables to define regimes of network parameters in which the effective donor-acceptor coupling is optimal. This is demonstrated numerically for simple models of molecular networks.

  12. Vibration-induced inelastic effects in the electron transport through multisite molecular bridges.

    Science.gov (United States)

    Zimbovskaya, Natalya A; Kuklja, Maija M

    2009-09-21

    We theoretically analyzed inelastic effects in the electron transport through molecular junctions originating from electron-vibron interactions. The molecular bridge was simulated by a periodical chain of identical hydrogenlike atoms with the nearest neighbors interaction thus providing a set of energy states for the electron tunneling. To avoid difficulties inevitably arising when advanced computational techniques are employed to study inelastic electron transport through multilevel bridges, we propose and develop a semiphenomenological approach. The latter is based on Buttiker's dephasing model within the scattering matrix formalism. We apply the proposed approach to describe features associated with electron energy transfer to vibrational phonons that appear in the second derivative of the current in the junction with respect to the bias voltage. In the particular case of a single level bridge our results agree with those obtained by proper calculations carried out within the nonequilibrium Green's functions method indicating the usefulness of the suggested approach.

  13. Effect of Molecular Orientation, on Photovoltaic Efficiency and Carrier Transport, in a New Semiconducting Polymer

    Science.gov (United States)

    Kažukauskas, V.; Pranaitis, M.; Sentein, C.; Rocha, L.; Raimond, P.; Duyssens, I.; van, I.; Severen; Lutsen, L.; Cleij, T.; Vanderzande, D.

    2008-03-01

    New functionalized soluble poly(p-phenylene vinylene) derivative bearing polar molecules was designed and synthesized in order to investigate effects of molecular orientation in polymer photovoltaic devices. The active polar molecule is the 4-(N-butyl-N-2-hydroxyethyl)-1- nitro-benzene group. The grafting of the push-pull molecule with a donor/transmitter/acceptor structure, possessing a large ground state dipole moment, enables the molecular orientation by a dc electric field. An internal electric field stored in such system facilitates exciton dissociation and improves charge transport in single-layer devices. In our systems an increase in the external quantum efficiency by a factor of about 1.5 to 2 is estimated. The associated effects of orientation on the carrier injection and transport properties were evidenced.

  14. Verification of the dispersive charge transport in a hydrazone:polycarbonate molecularly doped polymer.

    Science.gov (United States)

    Tyutnev, Andrey P; Saenko, Vladimir S; Pozhidaev, Evgenii D; Kolesnikov, Vladislav A

    2009-03-18

    We report results of specially planned experiments intended to verify the dispersive character of the charge carrier transport in polycarbonate molecularly doped with hydrazone at 30 wt% loading, using for this purpose samples specifically featuring a well-defined plateau on a linear-linear plot. For this purpose we propose a new variant of the time-of-flight technique which allows easy changing of the generation zone width from about 0.5 µm (surface excitation) through intermediate values to full sample thickness (bulk excitation). To achieve this, we use electron pulses of 3-50 keV energy rather than traditional light pulses provided by lasers. Experimental results corroborated by numerical calculations uniquely prove that carrier transport in this molecularly doped polymer is dispersive, with the dispersion parameter equal to 0.75. Nevertheless, the mobility field dependence follows the famous Poole-Frenkel law.

  15. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti

    2011-01-01

    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  16. Transport of nanoparticles across pulmonary surfactant monolayer: a molecular dynamics study.

    Science.gov (United States)

    Xu, Yan; Deng, Li; Ren, Hao; Zhang, Xianren; Huang, Fang; Yue, Tongtao

    2017-07-21

    Pulmonary nanodrug delivery is an emerging concept, especially for targeted lung cancer therapy. Once inhaled, the nanoparticles (NPs) acting as drug carriers need to efficiently cross the pulmonary surfactant monolayer (PSM) of lung alveoli, which act as the first barrier for external particles entering the lung. Herein, by performing molecular dynamics simulations, we study how inhaled NPs interact with the PSM, particularly focusing on the transport of NPs with different properties across the PSM. While hydrophilic NPs translocate directly across the PSM, transport of hydrophobic NPs is achieved as the PSM wraps them. Intriguingly, when hydrophilic NPs are decorated with lipid molecules (LCNPs), they are wrapped by the PSM efficiently with mild PSM perturbation. Moreover, the structure formed is like a vesicle, which will likely fuse with cell membranes to accomplish the transport of hydrophilic NPs into secondary organs. This behavior makes the LCNP a prospective candidate for pulmonary nanodrug delivery. Herein, the effects of the physical properties of LCNPs on their transport are investigated. Increasing the LCNP size promotes its wrapping by reducing the PSM bending energy. The binding energy that drives transport can be strengthened by increasing the lipid coating density and the lipid tail length, both of which also reduce the risk of PSM rupture during transport. These results should help researchers understand how to better use surface decorations to achieve efficient pulmonary entry, which may provide useful guidance for the design of nano-based platforms for inhaled drug delivery.

  17. Mechanism for cocaine blocking the transport of dopamine: insights from molecular modeling and dynamics simulations.

    Science.gov (United States)

    Huang, Xiaoqin; Gu, Howard H; Zhan, Chang-Guo

    2009-11-12

    Molecular modeling and dynamics simulations have been performed to study how cocaine inhibits dopamine transporter (DAT) for the transport of dopamine. The computationally determined DAT-ligand binding mode is totally different from the previously proposed overlap binding mode in which cocaine- and dopamine-binding sites are the same (Beuming, T.; et al. Nat. Neurosci. 2008, 11, 780-789). The new cocaine-binding site does not overlap with, but is close to, the dopamine-binding site. Analysis of all results reveals that when cocaine binds to DAT, the initial binding site is likely the one modeled in this study because this binding site can naturally accommodate cocaine. Then cocaine may move to the dopamine-binding site after DAT makes some necessary conformational change and expands the binding site cavity. It has been demonstrated that cocaine may inhibit the transport of dopamine through both blocking the initial DAT-dopamine binding and reducing the kinetic turnover of the transporter following the DAT-dopamine binding. The relative contributions to the phenomenological inhibition of the transport of dopamine from blocking the initial binding and reducing the kinetic turnover can be different in different types of assays. The obtained general structural and mechanistic insights are consistent with available experimental data and could be valuable for guiding future studies toward understanding cocaine's inhibiting of other transporters.

  18. 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.

  19. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kress, Joel David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ticknor, Christopher [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Collins, Lee A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  20. Unveiling self-assembled monolayers' potential for molecular spintronics: spin transport at high voltage.

    Science.gov (United States)

    Galbiati, Marta; Barraud, Clément; Tatay, Sergio; Bouzehouane, Karim; Deranlot, Cyrile; Jacquet, Eric; Fert, Albert; Seneor, Pierre; Mattana, Richard; Petroff, Frédéric

    2012-12-18

    Molecular magnetic tunnel junctions using self-assembled monolayers (SAMs) as tunnel barriers show stable and efficient spin transport properties. Large tunnel magnetoresistance with a flat bias voltage dependence of the magnetoresistance is observed in La(2/3) Sr(1/3) MnO(3) /dodecylphosphonic acid SAM/Co nanocontacts. This opens the door to spintronic tailoring though SAM engineering and could also lead to new venues for spin injection in organic devices.

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

    Science.gov (United States)

    Kosov, Daniel S.

    2017-02-01

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

  2. Spinal traction promotes molecular transportation in a simulated degenerative intervertebral disc model.

    Science.gov (United States)

    Kuo, Ya-Wen; Hsu, Yu-Chun; Chuang, I-Ting; Chao, Pen-Hsiu Grace; Wang, Jaw-Lin

    2014-04-20

    Biomechanical experiment using an in situ porcine model. To find the effect of traction treatment on annulus microstructure, molecular convection, and cell viability of degraded discs. Spinal traction is a conservative treatment for disc disorders. The recognized biomechanical benefits include disc height recovery, foramen enlargement, and intradiscal pressure reduction. However, the influence of traction treatment on annulus microstructure, molecular transportation, and cell viability of degraded discs has not been fully investigated. A total of 48 thoracic discs were dissected from 8 porcine spines (140 kg, 6-month old) within 4 hours after killing them and then divided into 3 groups: intact, degraded without traction, and degraded with traction. Each disc was incubated in a whole-organ culture system and subjected to diurnal loadings for 7 days. Except for the intact group, discs were degraded with 0.5 mL of trypsin on day 1 and a 5-hour fatigue loading on day 2. From day 4 to day 6, half of the degraded discs received a 30-minute traction treatment per day (traction force: 20 kg; loading: unloading = 30 s: 10 s). By the end of the incubation, the discs were inspected for disc height loss, annulus microstructure, molecular (fluorescein sodium) intensity, and cell viability. Collagen fibers were crimped and delaminated, whereas the pores were occluded in the annulus fibrosus of the degraded discs. Molecular transportation and cell viability of the discs decreased after matrix degradation. With traction treatment, straightened collagen fibers increased within the degraded annulus fibrosus, and the annulus pores were less occluded. Both molecular transportation and cell viability increased, but not to the intact level. Traction treatment is effective in enhancing nutrition supply and promoting disc cell proliferation of the degraded discs. N/A.

  3. Molecular motors transporting cargos in viscoelastic cytosol: how to beat subdiffusion with a power stroke?

    CERN Document Server

    Goychuk, Igor; Metzler, Ralf

    2013-01-01

    Anomalously slow passive diffusion, $\\langle \\delta x^2(t)\\rangle\\simeq t^{\\alpha}$, with $0<\\alpha<1$, of larger tracers such as messenger RNA and endogenous submicron granules in the cytoplasm of living biological cells has been demonstrated in a number of experiments and has been attributed to the viscoelastic physical nature of the cellular cytoplasm. This finding provokes the question to which extent active intracellular transport is affected by this viscoelastic environment: does the subdiffusion of free submicron cargo such as vesicles and organelles always imply anomalously slow transport by molecular motors such as kinesins, that is, directed transport characterized by a sublinear growth of the mean distance, $\\langle x(t)\\rangle\\simeq t^{\\alpha_{\\rm eff}}$, with $0<\\alpha_{\\rm eff}<1$? Here we study a generic model approach combining the commonly accepted two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubule driven by a flashing bind...

  4. External forces influence the elastic coupling effects during cargo transport by molecular motors.

    Science.gov (United States)

    Berger, Florian; Keller, Corina; Klumpp, Stefan; Lipowsky, Reinhard

    2015-02-01

    Cellular transport is achieved by the cooperative action of molecular motors which are elastically linked to a common cargo. When the motors pull on the cargo at the same time, they experience fluctuating elastic strain forces induced by the stepping of the other motors. These elastic coupling forces can influence the motors' stepping and unbinding behavior and thereby the ability to transport cargos. Based on a generic single motor description, we introduce a framework that explains the response of two identical molecular motors to a constant external force. In particular, we relate the single motor parameters, the coupling strength and the external load force to the dynamics of the motor pair. We derive four distinct transport regimes and determine how the crossover lines between the regimes depend on the load force. Our description of the overall cargo dynamics takes into account relaxational displacements of the cargo caused by the unbinding of one motor. For large forces and weak elastic coupling these back-shifts dominate the displacements. To develop an intuitive understanding about motor cooperativity during cargo transport, we introduce a time scale for load sharing. This time scale allows us to predict how the regulation of single motor parameters influences the cooperativity. As an example, we show that up-regulating the single motor processivity enhances load sharing of the motor pair.

  5. Charge Transport through Organic Molecular Wires Embedded in Ultrathin Insulating Inorganic Layer

    Energy Technology Data Exchange (ETDEWEB)

    Edri, E; Frei, H

    2015-12-07

    Dense phase silica layers with thickness of a few nanometers featuring embedded organic molecular wires of type p-oligo(phenylenevinylene) are shown by visible light sensitized electrochemical measurements to transport charges across the insulating membrane. Here, we find that such hybrid materials combination allows electronic charge transport only through the wires, while blocking molecular transport. Embodiment of the wire molecules in the silica was accomplished by atomic layer deposition under mild temperature conditions. Grown on Co oxide films for water oxidation, with the wire molecules covalently anchored on the oxide surface, the layer functions as a proton conducting separation membrane. Characterization by XPS, FT-IR and STEM/EDX confirms the integrity of the silica-encapsulated organic wires. Cyclic voltammetry with redox couple of selected potential relative to the energy levels of the wire molecules shows that the membrane is free of pinholes. The new type of membrane allows separation of incompatible redox reaction environments on the length scale of nanometers while enabling controlled electron transport between them. Finally, this opens up the coupling of carbon dioxide reduction with water oxidation, the essential reactions of artificial photosynthesis, in an integrated nanoscale photosystem.

  6. 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.

  7. The effect of molecular mobility on electronic transport in carbon nanotube-polymer composites and networks

    Energy Technology Data Exchange (ETDEWEB)

    Shenogin, Sergei, E-mail: sergei.shenogin.ctr.ru@us.af.mil [Air Force Research Laboratory, Materials and Manufacturing Directorate, 2941 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433 (United States); University of Dayton Research Institute, 300 College Park, Dayton, Ohio 45469 (United States); Lee, Jonghoon [Air Force Research Laboratory, Materials and Manufacturing Directorate, 2941 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433 (United States); UTC, Inc., 1270 N Fairfield Rd, Dayton, Ohio 45432 (United States); Voevodin, Andrey A.; Roy, Ajit K. [Air Force Research Laboratory, Materials and Manufacturing Directorate, 2941 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433 (United States)

    2014-12-21

    A multiscale modeling approach to the prediction of electrical conductivity in carbon nanotube (CNT)–polymer composite materials is developed, which takes into account thermally activated molecular mobility of the matrix and the CNTs. On molecular level, a tight-binding density functional theory and non-equilibrium Green's function method are used to calculate the static electron transmission function in the contact between two metallic carbon nanotubes that corresponds to electron transport at 0 K. For higher temperatures, the statistical distribution of effective contact resistances is considered that originates from thermal fluctuations of intermolecular distances caused by molecular mobility of carbon nanotube and the polymer matrix. Based on this distribution and using effective medium theory, the temperature dependence of macroscopic electrical resistivity for CNT-polymer composites and CNT mats is calculated. The predicted data indicate that the electrical conductivity of the CNT-polymer composites increases linearly with temperature above 50 K, which is in a quantitative agreement with the experiments. Our model predicts a slight nonlinearity in temperature dependence of electric conductivity at low temperatures for percolated composites with small CNT loading. The model also explains the effect of glass transition and other molecular relaxation processes in the polymer matrix on the composite electrical conductivity. The developed multiscale approach integrates the atomistic charge transport mechanisms in percolated CNT-polymer composites with the macroscopic response and thus enables direct comparison of the prediction with the measurements of macroscopic material properties.

  8. Guidelines for choosing molecular "alligator clip" binding motifs in electron transport devices

    Science.gov (United States)

    Reuter, Matthew G.; Seideman, Tamar; Ratner, Mark A.

    2011-04-01

    We employ a one-electron, tight-binding model of an electrode-molecule-electrode junction to explore the fundamental relationship between adsorption geometry and electron transport, producing exact results (within this model). By varying the chemisorption location (e.g., atop a surface atom or in a hollow site between surface atoms) and the molecule-electrode coupling, we find that the largest currents are realized when the molecule (i) is highly coordinated by the surface and (ii) has favorable overlap with electrode states near the Fermi level. We also show the importance of electrode-induced molecular level shifting for certain adsorption geometries, which can cause molecular levels far from the Fermi level to conduct better than those near the Fermi level. Since all of these factors are greatly influenced by the chemical moiety used to link the molecule to an electrode, these results present a set of guidelines to help choose "alligator clips" for molecular electronic devices.

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

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

    CERN Document Server

    Kilgour, Michael

    2015-01-01

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

  11. A generalized quantum chemical approach for elastic and inelastic electron transports in molecular electronics devices

    Science.gov (United States)

    Jiang, Jun; Kula, Mathias; Luo, Yi

    2006-01-01

    A generalized quantum chemical approach for electron transport in molecular devices is developed. It allows one to treat devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. An extension to include the vibration motions of the molecule has also been implemented which has produced the inelastic electron-tunneling spectroscopy of molecular electronics devices with unprecedented accuracy. Important information about the structure of the molecule and of metal-molecule contacts that are not accessible in the experiment are revealed. The calculated current-voltage (I-V) characteristics of different molecular devices, including benzene-1,4-dithiolate, octanemonothiolate [H(CH2)8S], and octanedithiolate [S(CH2)8S] bonded to gold electrodes, are in very good agreement with experimental measurements.

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

    Science.gov (United States)

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

    2014-07-29

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

  13. Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template.

    Science.gov (United States)

    Indarte, Martín; Madura, Jeffry D; Surratt, Christopher K

    2008-02-15

    Pharmacological and behavioral studies indicate that binding of cocaine and the amphetamines by the dopamine transporter (DAT) protein is principally responsible for initiating the euphoria and addiction associated with these drugs. The lack of an X-ray crystal structure for the DAT or any other member of the neurotransmitter:sodium symporter (NSS) family has hindered understanding of psychostimulant recognition at the atomic level; structural information has been obtained largely from mutagenesis and biophysical studies. The recent publication of a crystal structure for the bacterial leucine transporter LeuT(Aa), a distantly related NSS family homolog, provides for the first time a template for three-dimensional comparative modeling of NSS proteins. A novel computational modeling approach using the capabilities of the Molecular Operating Environment program MOE 2005.06 in conjunction with other comparative modeling servers generated the LeuT(Aa)-directed DAT model. Probable dopamine and amphetamine binding sites were identified within the DAT model using multiple docking approaches. Binding sites for the substrate ligands (dopamine and amphetamine) overlapped substantially with the analogous region of the LeuT(Aa) crystal structure for the substrate leucine. The docking predictions implicated DAT side chains known to be critical for high affinity ligand binding and suggest novel mutagenesis targets in elucidating discrete substrate and inhibitor binding sites. The DAT model may guide DAT ligand QSAR studies, and rational design of novel DAT-binding therapeutics.

  14. Role of energy distribution in contacts on thermal transport in Si: A molecular dynamics study

    Science.gov (United States)

    Dunn, Jonathan; Antillon, Edwin; Maassen, Jesse; Lundstrom, Mark; Strachan, Alejandro

    2016-12-01

    We use molecular dynamics simulations to investigate how the energy input and distribution in contacts affect the thermal transport in silicon as described by the Stillinger-Webber potential. We create a temperature difference across a Si specimen by maintaining the temperature of two contacts (also made of Si) using widely used thermostats: the deterministic Nosé-Hoover approach and a stochastic Langevin bath. Quite surprisingly, the phonon thermal conductivity of the channel obtained using the two thermostats but under otherwise identical conditions can differ by a factor of up to three. The discrepancy between the two methods vanishes as the coupling strength between the thermostat and material is reduced and for long channels. A spectral analysis of the contacts and channel shows that increasing the coupling of the stochastic Langevin thermostat affects the spectral energy distribution in the contacts away from that based on the vibrational density of states, broadening peaks and smoothening the distribution. This results in contacts injecting phonons preferentially in low frequency modes and in transport through the channel away from local equilibrium. A comparison of the MD results with Boltzmann transport equation simulations provides an additional insight into the role of contacts on thermal transport in nanoscale specimens. These results stress the importance of contacts in nanoscale thermal transport in simulations and in the interpretation of experimental data.

  15. 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.

  16. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressurea)

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2012-07-01

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  17. Overcoming ABC transporter-mediated multidrug resistance: Molecular mechanisms and novel therapeutic drug strategies.

    Science.gov (United States)

    Li, Wen; Zhang, Han; Assaraf, Yehuda G; Zhao, Kun; Xu, Xiaojun; Xie, Jinbing; Yang, Dong-Hua; Chen, Zhe-Sheng

    2016-07-01

    Multidrug resistance is a key determinant of cancer chemotherapy failure. One of the major causes of multidrug resistance is the enhanced efflux of drugs by membrane ABC transporters. Targeting ABC transporters projects a promising approach to eliminating or suppressing drug resistance in cancer treatment. To reveal the functional mechanisms of ABC transporters in drug resistance, extensive studies have been conducted from identifying drug binding sites to elucidating structural dynamics. In this review article, we examined the recent crystal structures of ABC proteins to depict the functionally important structural elements, such as domains, conserved motifs, and critical amino acids that are involved in ATP-binding and drug efflux. We inspected the drug-binding sites on ABC proteins and the molecular mechanisms of various substrate interactions with the drug binding pocket. While our continuous battle against drug resistance is far from over, new approaches and technologies have emerged to push forward our frontier. Most recent developments in anti-MDR strategies include P-gp inhibitors, RNA-interference, nano-medicines, and delivering combination strategies. With the advent of the 'Omics' era - genomics, epigenomics, transcriptomics, proteomics, and metabolomics - these disciplines play an important role in fighting the battle against chemoresistance by further unraveling the molecular mechanisms of drug resistance and shed light on medical therapies that specifically target MDR. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Molecular analysis confirms the long-distance transport of Juniperus ashei pollen.

    Science.gov (United States)

    Mohanty, Rashmi Prava; Buchheim, Mark Alan; Anderson, James; Levetin, Estelle

    2017-01-01

    Although considered rare, airborne pollen can be deposited far from its place of origin under a confluence of favorable conditions. Temporally anomalous records of Cupressacean pollen collected from January air samples in London, Ontario, Canada have been cited as a new case of long-distance transport. Data on pollination season implicated Juniperus ashei (mountain cedar), with populations in central Texas and south central Oklahoma, as the nearest source of the Cupressacean pollen in the Canadian air samples. This finding is of special significance given the allergenicity of mountain cedar pollen. While microscopy is used extensively to identify particles in the air spora, pollen from all members of the Cupressaceae, including Juniperus, are morphologically indistinguishable. Consequently, we implemented a molecular approach to characterize Juniperus pollen using PCR in order to test the long-distance transport hypothesis. Our PCR results using species-specific primers confirmed that the anomalous Cupressacean pollen collected in Canada was from J. ashei. Forward trajectory analysis from source areas in Texas and the Arbuckle Mountains in Oklahoma and backward trajectory analysis from the destination area near London, Ontario were completed using models implemented in HYSPLIT4 (Hybrid Single-Particle Lagrangian Integrated Trajectory). Results from these trajectory analyses strongly supported the conclusion that the J. ashei pollen detected in Canada had its origins in Texas or Oklahoma. The results from the molecular findings are significant as they provide a new method to confirm the long-distance transport of pollen that bears allergenic importance.

  19. A Molecular Motor, KIF13A, Controls Anxiety by Transporting the Serotonin Type 1A Receptor

    Directory of Open Access Journals (Sweden)

    Ruyun Zhou

    2013-02-01

    Full Text Available Molecular motors are fundamental to neuronal morphogenesis and function. However, the extent to which molecular motors are involved in higher brain functions remains largely unknown. In this study, we show that mice deficient in the kinesin family motor protein KIF13A (Kif13a−/− mice exhibit elevated anxiety-related behavioral phenotypes, probably because of a reduction in 5HT1A receptor (5HT1AR transport. The cell-surface expression level of the 5HT1AR was reduced in KIF13A-knockdown neuroblastoma cells and Kif13a−/− hippocampal neurons. Biochemical analysis showed that the forkhead-associated (FHA domain of KIF13A and an intracellular loop of the 5HT1AR are the interface between the motor and cargo vesicles. A minimotor consisting of the motor and FHA domains is able to transport 5HT1AR-carrying organelles in in vitro reconstitution assays. Collectively, our results suggest a role for this molecular motor in anxiety control.

  20. 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

  1. 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...

  2. Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals.

    Science.gov (United States)

    Wang, Linjun; Akimov, Alexey V; Chen, Liping; Prezhdo, Oleg V

    2013-11-07

    The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

  3. Evaluation of collective transport properties of ionic melts from molecular dynamics simulations

    Indian Academy of Sciences (India)

    Manish Agarwal; Charusita Chakravarty

    2009-09-01

    Molecular dynamics simulations of beryllium fluoride (BeF2) have been carried out in the canonical (NVT) ensemble using a rigid-ion potential model. The Green-Kubo formalism has been applied to compute viscosities and ionic conductivities of BeF2 melt. The computational parameters critical for reliably estimating these collective transport properties are shown to differ significantly for viscosity and ionic conductivity. In addition to the equilibrium values of these transport properties, structural relaxation times as well as high-frequency IR-active modes are computed from the pressure and charge-flux auto correlation functions (ACFs) respectively. It is shown that a network-forming ionic melt, such as BeF2, will display persistent oscillatory behaviour of the integral of the charge-flux ACF. By suitable Fourier transformation, one can show that these persistent oscillations correspond to highfrequency, infra-red active vibrations associated with local modes of the network.

  4. Molecular basis of epithelial Ca2+ and Mg2+ transport: insights from the TRP channel family

    DEFF Research Database (Denmark)

    Dimke, Henrik Anthony; Hoenderop, Joost G J; Bindels, René J M

    2011-01-01

    potential (TRP) family identified several new ion channels acting as gatekeepers of Ca(2+) and Mg(2+) transport in these epithelia, greatly increasing our understanding of the molecular processes that facilitate the movement of these minerals. In the intestine, TRP channels contribute to the saturable...... active transcellular movement of divalent cations from the lumen into the enterocyte. Furthermore, in bone, TRPV channels play important roles by influencing the osteoclastic resorption process, thereby contributing importantly to overall bone mineral content. The divalent cation-permeable TRPV5 and TRPM......6 channels are located in the renal distal convolution, the main site of active transcellular Ca(2+) and Mg(2+) transport. The channels are regulated by a multitude of factors and hormones that contribute importantly to keeping the systemic concentrations of Ca(2+) and Mg(2+) within normal limits...

  5. Asymptotic Analysis of Microtubule-Based Transport by Multiple Identical Molecular Motors

    CERN Document Server

    McKinley, Scott A; Fricks, John; Kramer, Peter R

    2011-01-01

    We describe a system of stochastic differential equations (SDEs) which model the interaction between processive molecular motors, such as kinesin and dynein, and the biomolecular cargo they tow as part of microtubule-based intracellular transport. We show that the classical experimental environment fits within a parameter regime which is qualitatively distinct from conditions one expects to find in living cells. Through an asymptotic analysis of our system of SDEs, we develop a means for applying in vitro observations of the nonlinear response by motors to forces induced on the attached cargo to make analytical predictions for two parameter regimes that have thus far eluded direct experimental observation: 1) highly viscous in vivo transport and 2) dynamics when multiple identical motors are attached to the cargo and microtubule.

  6. 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.

  7. Molecular dynamics simulations of Na{sup +} and leucine transport by LeuT

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Rong, E-mail: rong.chen@anu.edu.au; Chung, Shin-Ho

    2015-08-14

    Molecular dynamics simulations are used to gain insight into the binding of Na{sup +} and leucine substrate to the bacterial amino acid transporter LeuT, focusing on the crystal structures of LeuT in the outward-open and inward-open states. For both conformations of LeuT, a third Na{sup +} binding site involving Glu290 in addition to the two sites identified from the crystal structures is observed. Once the negative charge from Glu290 in the inward-open LeuT is removed, the ion bound to the third site is ejected from LeuT rapidly, suggesting that the protonation state of Glu290 regulates Na{sup +} binding and release. In Cl{sup −}-dependent transporters where Glu290 is replaced by a neutral serine, a Cl{sup −} ion would be required to replace the role of Glu290. Thus, the simulations provide insights into understanding Na{sup +} and substrate transport as well as Cl{sup −}-independence of LeuT. - Highlights: • Ion binding site involving Glu290 is identified in the outward- and inward-open LeuT. • Sodium is released from inward-open LeuT once the side chain of Glu290 is protonated. • Protonation state of Glu290 regulates sodium binding and transport in LeuT.

  8. Deciphering the molecular basis of ammonium uptake and transport in maritime pine.

    Science.gov (United States)

    Castro-Rodríguez, Vanessa; Assaf-Casals, Iman; Pérez-Tienda, Jacob; Fan, Xiaorong; Avila, Concepción; Miller, Anthony; Cánovas, Francisco M

    2016-08-01

    Ammonium is the predominant form of inorganic nitrogen in the soil of coniferous forests. Despite the ecological and economic importance of conifers, the molecular basis of ammonium uptake and transport in this group of gymnosperms is largely unknown. In this study, we describe the functional characterization of members of the AMT gene family in Pinus pinaster: PpAMT1.1, PpAMT1.2 and PpAMT1.3 (subfamily 1) and PpAMT2.1 and PpAMT2.3 (subfamily 2). Our phylogenetic analysis indicates that in conifers, all members of the AMT1 subfamily evolved from a common ancestor that is evolutionarily related to the ancient PpAMT1.2 gene. Individual AMT genes are developmentally and nutritionally regulated, and their transcripts are specifically distributed in different organs. PpAMT1.3 was predominantly expressed in the roots, particularly during N starvation and mycorrhizal interaction, whereas PpAMT2.3 was preferentially expressed in lateral roots. Immunolocalization studies of roots with varied nitrogen availability revealed that PpAMT1 and PpAMT2 proteins play complementary roles in the uptake of external ammonium. Heterologous expression in yeast and Xenopus oocytes revealed that the AMT genes encode functional transporters with different kinetics and with different capacities for ammonium transport. Our results provide new insights on how nitrogen is acquired and transported in conifers.

  9. 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.

  10. Lattice-gas model for active vesicle transport by molecular motors with opposite polarities

    Science.gov (United States)

    Muhuri, Sudipto; Pagonabarraga, Ignacio

    2010-08-01

    We introduce a multispecies lattice-gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargos being carried by oppositely directed molecular motors, moving on a single biofilament. Building on a totally asymmetric exclusion process to characterize the motion of the interacting cargos, we allow for mass exchange with the environment, input, and output at filament boundaries and focus on the role of interconversion rates and how they affect the directionality of the net cargo transport. We quantify the effect of the various different competing processes in terms of nonequilibrium phase diagrams. The interplay of interconversion rates, which allow for flux reversal and evaporation-deposition processes, introduces qualitatively unique features in the phase diagrams. We observe regimes of three-phase coexistence, the possibility of phase re-entrance, and a significant flexibility in how the different phase boundaries shift in response to changes in control parameters. The moving steady-state solutions of this model allows for different possibilities for the spatial distribution of cargo vesicles, ranging from homogeneous distribution of vesicles to polarized distributions, characterized by inhomogeneities or shocks. Current reversals due to internal regulation emerge naturally within the framework of this model. We believe that this minimal model will clarify the understanding of many features of collective vesicle transport, apart from serving as the basis for building more exact quantitative models for vesicle transport relevant to various in vivo situations.

  11. 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.

  12. Role of water states on water uptake and proton transport in Nafion using molecular simulations and bimodal network

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Gi Suk [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Mechanical Engineering; Kaviany, Massoud [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Mechanical Engineering; Gostick, Jeffrey T. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Kientiz, Brian [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Weber, Adam Z. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Kim, Moo Hwan [Pohang Univ. of Science and Technology (POSTECH) (Korea, Republic of). Dept. of Mechanical Engineering

    2011-04-07

    In this paper, using molecular simulations and a bimodal-domain network, the role of water state on Nafion water uptake and water and proton transport is investigated. Although the smaller domains provide moderate transport pathways, their effectiveness remains low due to strong, resistive water molecules/domain surface interactions. Finally, the water occupancy of the larger domains yields bulk-like water, and causes the observed transition in the water uptake and significant increases in transport properties.

  13. Analytical and numerical studies of photo-injected charge transport in molecularly-doped polymers

    Science.gov (United States)

    Roy Chowdhury, Amrita

    The mobility of photo-injected charge carriers in molecularly-doped polymers (MDPs) exhibits a commonly observed, and nearly universal Poole-Frenkel field dependence, mu exp√(beta0E), that has been shown to arise from the correlated Gaussian energy distribution of transport sites encountered by charges undergoing hopping transport through the material. Analytical and numerical studies of photo-injected charge transport in these materials are presented here with an attempt to understand how specific features of the various models developed to describe these systems depend on the microscopic parameters that define them. Specifically, previously published time-of-flight mobility data for the molecularly doped polymer 30% DEH:PC (polycarbonate doped with 30 wt.% aromatic hydrazone DEH) is compared with direct analytical and numerical predictions of five disorder-based models, the Gaussian disorder model (GDM) of Bassler, and four correlated disorder models introduced by Novikov, et al., and by Parris, et al. In these numerical studies, disorder parameters describing each model were varied from reasonable starting conditions, in order to give the best overall fit. The uncorrelated GDM describes the Poole-Frenkel field dependence of the mobility only at very high fields, but fails for fields lower than about 64 V/mum. The correlated disorder models with small amounts of geometrical disorder do a good over-all job of reproducing a robust Poole-Frenkel field dependence, with correlated disorder theories that employ polaron transition rates showing qualitatively better agreement with experiment than those that employ Miller-Abrahams rates. In a separate study, the heuristic treatment of spatial or geometric disorder incorporated in existing theories is critiqued, and a randomly-diluted lattice gas model is developed to describe the spatial disorder of the transport sites in a more realistic way.

  14. Multistate APLIP and VibLIP: From molecular bond extension to atomic transport

    CERN Document Server

    Suominen, Kalle-Antti

    2013-01-01

    APLIP is a method for using a STIRAP-like three-state configuration with two laser pulses for continuous extension of a molecular bond, introduced in 1998. It is based on time-dependent light-induced potential surfaces (LIP). In VibLIP one extends the idea into a method for tailoring the vibrational state while changing the electronic state, introduced in 2000. Here I discuss the extension of both methods to situations that involve more than three electronic states, and note the possibility of using the method on adiabatic transport of atoms between microtraps or equivalent structures.

  15. QUANTUM-MECHANICAL PROPERTIES OF PROTON TRANSPORT IN THE HYDROGEN-BONDED MOLECULAR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; LI PING

    2000-01-01

    The dynamic equations of the proton transport along the hydrogen bonded molecular systems have been obtainedby using completely quantum-mechanical method to be based on new Hamiltonian and model we proposed. Somequantum-mechanical features of the proton-solitons have also been given in such a case. The alternate motion of twodefects resulting from proton transfer occurred in the systems can be explained by the results. The results obtainedshow that the proton-soliton has corpuscle feature and obey classical equations of motion, while the free soliton movesin uniform velocity along the hydrogen bonded chains.

  16. Transport properties of room temperature ionic liquids from classical molecular dynamics

    CERN Document Server

    Andreussi, Oliviero

    2012-01-01

    Room Temperature Ionic Liquids (RTILs) have attracted much of the attention of the scientific community in the past decade due the their novel and highly customizable properties. Nonetheless their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g. system size effects and choice of the interaction potential, is analyzed.

  17. Transport dynamics of molecular motors that switch between an active and inactive state.

    Science.gov (United States)

    Pinkoviezky, I; Gov, N S

    2013-08-01

    Molecular motors are involved in key transport processes in the cell. Many of these motors can switch from an active to a nonactive state, either spontaneously or depending on their interaction with other molecules. When active, the motors move processively along the filaments, while when inactive they are stationary. We treat here the simple case of spontaneously switching motors, between the active and inactive states, along an open linear track. We use our recent analogy with vehicular traffic, where we go beyond the mean-field description. We map the phase diagram of this system, and find that it clearly breaks the symmetry between the different phases, as compared to the standard total asymmetric exclusion process. We make several predictions that may be testable using molecular motors in vitro and in living cells.

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

    CERN Document Server

    Baldea, Ioan

    2015-01-01

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

  19. Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

    Science.gov (United States)

    Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

    2014-11-18

    CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium

  20. Electronic Transport Properties of an Anthraquinone-Based Molecular Switch with Carbon Nanotube Electrodes

    Institute of Scientific and Technical Information of China (English)

    ZHAO Peng; LIU De-Sheng

    2012-01-01

    Based on the nonequilibrium Green's function method and density functional theory calculations,we theoretically investigate the electronic transport properties of an anthraquinone-based molecular switch with carbon nanotube electrodes.The molecules that comprise the switch can convert between reduced hydroquinone (HQ) and oxidized anthraquinne (AQ) states via redox reactions.Our results show that the on-off ratio is increased one order of magnitude when compared to the case of gold electrodes.Moreover,an obvious negative differential resistance behavior at much low bias (0.07 V) is observed in the HQ form.%Based on the nonequilihrium Green's function method and density functional theory calculations, we theoretically investigate the electronic transport properties of an anthraquinone-based molecular switch with carbon nanotube electrodes. The molecules that comprise the switch can convert between reduced hydroquinone (HQ) and oxidized anthraquinne (AQ) states via redox reactions. Our results show that the on-off ratio is increased one order of magnitude when compared to the case of gold electrodes. Moreover, an obvious negative differential resistance behavior at much low bias (0.07 V) is observed in the HQ form.

  1. Scaling Model of Low-Temperature Transport Properties for Molecular and Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Vitaly B. Rogankov

    2015-01-01

    Full Text Available The universal scaling concept is applied to the low-temperature range of any liquid states and substances located between the melting (Tm and normal boiling (Tb points far away from the critical region. The physical reason to develop such approach is the revealed collapse of all low-temperature isotherms onto the single universal one argued by the model of fluctuational thermodynamics (FT proposed recently by author. The pressure reduced by the molecular parameters of the effective short-range Lennard-Jones (LJ potential depends here only on the reduced density. To demonstrate the extraordinary predictive abilities of the developed low-temperature scaling model it has been applied to the prediction of equilibrium and transport (kinetic and dynamic viscosity, self-diffusion, and thermal conductivity properties not only for molecular liquids but also for molten organic salts termed ionic liquids (ILs. The best argument in favor of the proposed methodology is the appropriate consistency with the scarce experiments prediction of transport coefficients for ILs on the base of universal scaling function constructed for the simplest LJ-like liquid argon. The only input data of any substance for prediction are the linear approximations of T-dependent density and isobaric heat capacity taken from the standard measurements at atmospheric pressure.

  2. Adsorption equilibrium and transport kinetics for a range of probe gases in Takeda 3A carbon molecular sieve.

    Science.gov (United States)

    Rutherford, S W; Coons, J E

    2005-04-15

    Measurements of adsorption equilibria and transport kinetics for argon, oxygen and nitrogen at 20, 50, and 80 degrees C on commercially derived Takeda carbon molecular sieve (CMS) employed for air separation have been undertaken in an effort to elucidate fundamental mechanisms of transport. Results indicate that micropore diffusion which is modeled by a Fickian diffusion process, governs the transport of oxygen molecules and the pore mouth barrier controls argon and nitrogen transport which is characterized by a linear driving force (LDF) model. For the three temperatures studied, the pressure dependence of the diffusivity and the LDF rate constant appear to be well characterized by a formulation based on the chemical potential as the driving force for transport. Isosteric heat of adsorption at zero loading and activation energy measurements are compared with predictions made from a previously proposed molecular model for characterizing CMS.

  3. Insights into molecular properties of the human monocarboxylate transporter 8 by combining functional with structural information

    Directory of Open Access Journals (Sweden)

    Kleinau Gunnar

    2011-08-01

    Full Text Available Abstract Background The monocarboxylate transporter 8 (MCT8 is a member of the major facilitator superfamily (MFS and transports specificly iodothyronines. MCT8 mutations are the underlying cause of a syndrome of severe X-linked psychomotor retardation known as the Allan-Herndon-Dudley syndrome. This syndrome is characterized by abnormally high T3, low/normal T4 serum levels and slightly elevated serum TSH. To date, more than 25 pathogenic mutations in hMCT8 are known and they are valuable indicators of important regions for structural and functional MCT8 properties. Methods We designed a structural human MCT8 model and studied reported pathogenic missense mutations with focus on the estimation of those amino acid positions which are probably sensitive for substrate transport. Furthermore, assuming similarities between determinants of T3 binding observed in the published crystal structure of the thyroid hormone receptor beta occupied by its ligand T3 and the structural MCT8 model, we explore potential T3 binding sites in the MCT8 substrate channel cavity. Results We found that all known pathogenic missense mutations are located exclusively in the transmembrane helices and to a high degree at conserved residues among the MCT family. Furthermore, mutations either of or to prolines/glycines are located mainly at helices 9-12 and are expected to cause steric clashes or structural misfolding. In contrast, several other mutations are close to the potential substrate channel and affected amino acids are likely involved in the switching mechanism between different transporter conformations. Finally, three potential substrate binding sites are predicted for MCT8. Conclusions Naturally occurring mutations of MCT8 provide molecular insights into protein regions important for protein folding, substrate binding and the switching mechanism during substrate transport. Future studies guided by this information should help to clarify structure

  4. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2013-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

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

    Science.gov (United States)

    Tang, Gaomin; Yu, Zhizhou; Wang, Jian

    2017-08-01

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

  6. Imaging ion and molecular transport at subcellular resolution by secondary ion mass spectrometry

    Science.gov (United States)

    Chandra, Subhash; Morrison, George H.

    1995-05-01

    The transport of K+, Na+, and Ca2+ were imaged in individual cells with a Cameca IMS-3f ion microscope. Strict cryogenic frozen freeze-dry sample preparations were employed. Ion redistribution artifacts in conventional chemical preparations are discussed. Cryogenically prepared freeze-fractured freeze-dried cultured cells allowed the three-dimensional ion microscopic imaging of elements. As smaller structures in calcium images can be resolved with the 0.5 [mu]m spatial resolution, correlative techniques are needed to confirm their identity. The potentials of reflected light microscopy, scanning electron microscopy and laser scanning confocal microscopy are discussed for microfeature recognition in freeze-fractured freeze-dried cells. The feasibility of using frozen freeze-dried cells for imaging molecular transport at subcellular resolution was tested. Ion microscopy successfully imaged the transport of the isotopically tagged (13C, 15N) amino acid, -arginine. The labeled amino acid was imaged at mass 28 with a Cs+ primary ion beam as the 28(13C15N)- species. After a 4 h exposure of LLC-PK1 kidney cells to 4 mM labeled arginine, the amino acid was localized throughout the cell with a preferential incorporation into the nucleus and nucleolus. An example is also shown of the ion microscopic imaging of sodium borocaptate, an experimental therapeutic drug for brain tumors, in cryogenically prepared frozen freeze-dried Swiss 3T3 cells.

  7. Molecular dynamics simulations of Na(+) and leucine transport by LeuT.

    Science.gov (United States)

    Chen, Rong; Chung, Shin-Ho

    2015-08-14

    Molecular dynamics simulations are used to gain insight into the binding of Na(+) and leucine substrate to the bacterial amino acid transporter LeuT, focusing on the crystal structures of LeuT in the outward-open and inward-open states. For both conformations of LeuT, a third Na(+) binding site involving Glu290 in addition to the two sites identified from the crystal structures is observed. Once the negative charge from Glu290 in the inward-open LeuT is removed, the ion bound to the third site is ejected from LeuT rapidly, suggesting that the protonation state of Glu290 regulates Na(+) binding and release. In Cl(-)-dependent transporters where Glu290 is replaced by a neutral serine, a Cl(-) ion would be required to replace the role of Glu290. Thus, the simulations provide insights into understanding Na(+) and substrate transport as well as Cl(-)-independence of LeuT.

  8. On the molecular mechanism of flippase- and scramblase-mediated phospholipid transport.

    Science.gov (United States)

    Montigny, Cédric; Lyons, Joseph; Champeil, Philippe; Nissen, Poul; Lenoir, Guillaume

    2016-08-01

    Phospholipid flippases are key regulators of transbilayer lipid asymmetry in eukaryotic cell membranes, critical to many trafficking and signaling pathways. P4-ATPases, in particular, are responsible for the uphill transport of phospholipids from the exoplasmic to the cytosolic leaflet of the plasma membrane, as well as membranes of the late secretory/endocytic pathways, thereby establishing transbilayer asymmetry. Recent studies combining cell biology and biochemical approaches have improved our understanding of the path taken by lipids through P4-ATPases. Additionally, identification of several protein families catalyzing phospholipid 'scrambling', i.e. disruption of phospholipid asymmetry through energy-independent bi-directional phospholipid transport, as well as the recent report of the structure of such a scramblase, opens the way to a deeper characterization of their mechanism of action. Here, we discuss the molecular nature of the mechanism by which lipids may 'flip' across membranes, with an emphasis on active lipid transport catalyzed by P4-ATPases. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Jing-Tao Lü

    2015-05-01

    Full Text Available 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.

  11. Energetic and molecular water permeation mechanisms of the human red blood cell urea transporter B.

    Directory of Open Access Journals (Sweden)

    Slim Azouzi

    Full Text Available Urea transporter B (UT-B is a passive membrane channel that facilitates highly efficient permeation of urea. In red blood cells (RBC, while the major function of UT-B is to transport urea, it is assumed that this protein is able to conduct water. Here, we have revisited this last issue by studying RBCs and ghosts from human variants with defects of aquaporin 1 (AQP1 or UT-B. We found that UT-B's osmotic water unit permeability (pfunit is similar to that of AQP1. The determination of diffusional permeability coefficient (Pd allowed the calculation of the Pf/Pd ratio, which is consistent with a single-file water transport. Molecular dynamic simulations of water conduction through human UT-B confirmed the experimental finding. From these results, we propose an atomistic description of water-protein interactions involved in this permeation. Inside the UT-B pore, five water molecules were found to form a single-file and move rapidly along a channel by hydrogen bond exchange involving two critical threonines. We further show that the energy barrier for water located in the central region coincides with a water dipole reorientation, which can be related to the proton exclusion observed experimentally. In conclusion, our results indicate that UT-B should be considered as a new member of the water channel family.

  12. Ion Transport and Structural Properties of Polymeric Electrolytes and Ionic Liquids from Molecular Dynamics Simulations

    Science.gov (United States)

    Borodin, Oleg

    2010-03-01

    Molecular dynamics simulations are well suited for exploring electrolyte structure and ion transport mechanisms on the nanometer length scale and the nanosecond time scales. In this presentation we will describe how MD simulations assist in answering fundamental questions about the lithium transport mechanisms in polymeric electrolytes and ionic liquids. In particular, in the first part of the presentation the extent of ion aggregation, the structure of ion aggregates and the lithium cation diffusion in binary polymeric electrolytes will be compared with that of single-ion conducting polymers. In the second part of the talk, the lithium transport in polymeric electrolytes will be compared with that of three ionic liquids ( [emim][FSI] doped with LiFSI , [pyr13][FSI] doped with LiFSI, [emim][BF4] doped with LiBF4). The relation between ionic liquid self-diffusion, conductivity and thermodynamic properties will be discussed in details. A number of correlations between heat of vaporization Hvap, cation-anion binding energy (E+/-), molar volume (Vm), self-diffusion coefficient (D) and ionic conductivity for 29 ionic liquids have been investigated using MD simulations. A significant correlation between D and Hvap has been found, while best correlation was found for -log((D Vm)) vs. Hvap+0.28E+/-. A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids.

  13. Transport across two interacting quantum dots: bulk Kondo, Kondo box and molecular regimes

    Science.gov (United States)

    Costa Ribeiro, Laercio; Hamad, Ignacio; Chiappe, Guillermo; Victoriano Anda, Enrique

    2014-03-01

    We analyze the transport properties of a double quantum dot device with both dots coupled to perfect conducting leads and to a finite chain of N non-interacting sites connecting both of them. The inter-dot chain strongly influences the transport across the system and the local density of states of the dots. We study the case of small number of sites, so that Kondo box effects are present. For odd N and small coupling between the inter-dot chain and the dots, a state with two coexisting Kondo regimes develops: the bulk Kondo due to the quantum dots connected to leads and the one produced by the screening of the quantum dots spins by the spin in the finite chain. As the coupling to the inter-dot chain increases, there is a crossover to a molecular Kondo effect, due to the screening of the molecule spin by the leads. For even N the two-Kondo temperatures regime does not develop and the physics is dominated by the usual competition between Kondo and antiferromagnetism. We finally study how the transport properties are affected as N is increased. We used exact multi-configurational Lanczos calculations and finite U slave-boson mean-field theory. The results obtained with both methods describe qualitatively and also quantitatively the same physics.

  14. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes.

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S; Dickson, James M

    2013-03-28

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  15. Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer.

    Science.gov (United States)

    Gedeon, Patrick C; Indarte, Martín; Surratt, Christopher K; Madura, Jeffry D

    2010-03-01

    The dopamine transporter (DAT) operates via facilitated diffusion, harnessing an inward Na(+) gradient to drive dopamine from the extracellular synaptic cleft to the neuron interior. The DAT is relevant to central nervous system disorders such as Parkinson disease and attention-deficit hyperactivity disorder and is the primary site of action for the abused psychostimulants cocaine and amphetamines. Crystallization of a DAT homolog, the bacterial leucine transporter LeuT, provided the first reliable 3-D DAT template. Here, the LeuT crystal structure and the DAT molecular model have been combined with their respective substrates, leucine and dopamine, in lipid bilayer molecular dynamics simulations toward tracking substrate movement along the protein's substrate/ion permeation pathway. Specifically, movement of residue pairs that comprise the "external gate" was followed as a function of substrate presence. The transmembrane (TM) 1 arginine-TM 10 aspartate strut formed less readily in DAT compared with LeuT, with or without substrate present. For LeuT but not DAT, the addition of substrate enhanced the chances of forming the TM 1-10 bridge. Also, movement of the fourth extracellular loop EL-4 in the presence of substrate was more pronounced for DAT, the EL-4 unwinding to a degree. The overall similarity between the LeuT and DAT molecular dynamics simulations indicated that LeuT was a legitimate model to guide DAT structure-function predictions. There were, nevertheless, differences significant enough to allow for DAT-unique insights, which may include how cocaine, methylphenidate (Ritalin, NIDA Drug Supply, Rockville, MD), and other DAT blockers are not recognized as substrates even though they can access the primary substrate binding pocket. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

  16. 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

    2006-01-01

    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

  17. 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.

  18. Molecular transport through nanoporous silicon nitride membranes produced from self-assembling block copolymers.

    Science.gov (United States)

    Montagne, Franck; Blondiaux, Nicolas; Bojko, Alexandre; Pugin, Raphaël

    2012-09-28

    To achieve fast and selective molecular filtration, membrane materials must ideally exhibit a thin porous skin and a high density of pores with a narrow size distribution. Here, we report the fabrication of nanoporous silicon nitride membranes (NSiMs) at the full wafer scale using a versatile process combining block copolymer (BCP) self-assembly and conventional photolithography/etching techniques. In our method, self-assembled BCP micelles are used as templates for creating sub-100 nm nanopores in a thin low-stress silicon nitride layer, which is then released from the underlying silicon wafer by etching. The process yields 100 nm thick free-standing NSiMs of various lateral dimensions (up to a few mm(2)). We show that the membranes exhibit a high pore density, while still retaining excellent mechanical strength. Permeation experiments reveal that the molecular transport rate across NSiMs is up to 16-fold faster than that of commercial polymeric membranes. Moreover, using dextran molecules of various molecular weights, we also demonstrate that size-based separation can be achieved with a very good selectivity. These new silicon nanosieves offer a relevant technological alternative to commercially available ultra- and microfiltration membranes for conducting high resolution biomolecular separations at small scales.

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

    Science.gov (United States)

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

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

  20. 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.

  1. 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

  2. Orbital-free molecular dynamics simulations of transport properties in dense-plasma uranium

    Science.gov (United States)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-09-01

    We have calculated the self-diffusion coefficients and shear viscosity of dense-plasma uranium using orbital-free molecular dynamics (OFMD) at the Thomas-Fermi-Dirac level. The transport properties of uranium in this regime have not previously been investigated experimentally or theoretically. The OFMD calculations were performed for temperatures from 50 to 5000 eV and densities from ambient to 10 times compressed. The results are compared with the one-component-plasma (OCP) model, using effective charges given by the average-atom code INFERNO and by the regularization procedure from the OFMD method. The latter generally showed better agreement with the OFMD for viscosity and the former for diffusion. A Stokes-Einstein relationship of the OFMD viscosities and diffusion coefficients is found to hold fairly well with a constant of 0.075 ± 0.10, while the OCP/INFERNO model yields 0.13 ± 0.10.

  3. Analysis of persistence during intracellular actin-based transport mediated by molecular motors

    Energy Technology Data Exchange (ETDEWEB)

    Pallavicini, C; Levi, V; Bruno, L [Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Desposito, M A, E-mail: lbruno@df.uba.a

    2010-09-01

    The displacement of particles or probes in the cell cytoplasm as a function of time is characterized by different anomalous diffusion regimes. The transport of large cargoes, such as organelles, vesicles or large proteins, involves the action of ATP-consuming molecular motors. We investigate the motion of pigment organelles driven by myosin-V motors in Xenopus laevis melanocytes using a high spatio-temporal resolution tracking technique. By analyzing the turning angles ({phi}) of the obtained 2D trajectories as a function of the time lag, we determine the critical time of the transition between anticorrelated and directed motion as the time when the turning angles begin to concentrate around {phi} = 0. We relate this transition with the crossover from subdiffusive to superdiffusive behavior observed in a previous work [5]. We also assayed the properties of the trajectories in cells with inhibited myosin activity, and we can compare the results in the presence and absence of active motors.

  4. 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.

  5. Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms

    CERN Document Server

    Chowdhury, D; Nishinari, K; Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2005-01-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In particular, some of the methods of non-equilibrium statistical mechanics, pioneered almost a hundred years ago by Einstein, Langevin and others, turned out to be powerful theoretical tools for quantitaive analysis of model...

  6. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    Science.gov (United States)

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation.

  7. A logic-gated nanorobot for targeted transport of molecular payloads.

    Science.gov (United States)

    Douglas, Shawn M; Bachelet, Ido; Church, George M

    2012-02-17

    We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. The device can be loaded with a variety of materials in a highly organized fashion and is controlled by an aptamer-encoded logic gate, enabling it to respond to a wide array of cues. We implemented several different logical AND gates and demonstrate their efficacy in selective regulation of nanorobot function. As a proof of principle, nanorobots loaded with combinations of antibody fragments were used in two different types of cell-signaling stimulation in tissue culture. Our prototype could inspire new designs with different selectivities and biologically active payloads for cell-targeting tasks.

  8. Molecular mechanisms beyond glucose transport in diabetes-related male infertility.

    Science.gov (United States)

    Alves, M G; Martins, A D; Rato, L; Moreira, P I; Socorro, S; Oliveira, P F

    2013-05-01

    Diabetes mellitus (DM) is one of the greatest public health threats in modern societies. Although during a few years it was suggested that DM had no significant effect in male reproductive function, this view has been challenged in recent years. The increasing incidence of DM worldwide will inevitably result in a higher prevalence of this pathology in men of reproductive age and subfertility or infertility associated with DM is expected to dramatically rise in upcoming years. From a clinical perspective, the evaluation of semen parameters, as well as spermatozoa deoxyribonucleic acid (DNA) integrity, are often studied due to their direct implications in natural and assisted conception. Nevertheless, recent studies based on the molecular mechanisms beyond glucose transport in testicular cells provide new insights in DM-induced alterations in male reproductive health. Testicular cells have their own glucose sensing machinery that react to hormonal fluctuations and have several mechanisms to counteract hyper- and hypoglycemic events. Moreover, the metabolic cooperation between testicular cells is crucial for normal spermatogenesis. Sertoli cells (SCs), which are the main components of blood-testis barrier, are not only responsible for the physical support of germ cells but also for lactate production that is then metabolized by the developing germ cells. Any alteration in this tied metabolic cooperation may have a dramatic consequence in male fertility potential. Therefore, we present an overview of the clinical significance of DM in the male reproductive health with emphasis on the molecular mechanisms beyond glucose fluctuation and transport in testicular cells. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Orozco Gustavo A.

    2014-09-01

    Full Text Available 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 (N2O and nitrogen (N2 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.

  10. 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.

  11. Water transport in bentonite: evaluation by molecular dynamics, homogenization analysis and similitude law

    Energy Technology Data Exchange (ETDEWEB)

    Yasuaki, Ichikawa; Somehai, Prayongphan [Nagoya Univ., Dpt. of Environmental Engineering and Architecture, Chikusa, Nagoya (Japan); Kazumi, Kitayama [NUMO, Minato, Tokyo (Japan); Katsuyuki, Kawamura [Tokyo Institute of Technology, Tokyo (Japan)

    2005-07-01

    The major scenario of transport of radioactive nuclides is due to groundwater flow in most HLW projects. The phenomena of water flow and diffusion of chemical species in a bentonite buffer and surrounding rock mass have been treated mainly based on the classical porous media theories under the Darcy law and Fick law. The classical theories involve the following difficulties: 1) True velocity field is hard to be identified, especially in microscale sense. Note that it essentially affects the transport of chemical species. 2) The classical theories are not applicable to the problems in which experimental data are not available. Thus, the very long time behavior cannot be proven. We commonly recognize that the water flow in bentonite and mud-stone is strongly retarded. It is highly doubtful whether the above classical theories are applicable for such very low permeable materials. In this work we first show that the velocity and diffusion fields in pure smectite bentonite can be calculated by a coupled molecular dynamics (MD) simulation and the homogenization analysis (HA). The true velocity field can be calculated by applying HA to the Navier-Stokes equation, and the local distribution of viscosity used in this HA is obtained by MD. The diffusion field is also calculated under the same procedure of MD/HA by using the local diffusion equation with diffusivity calculated by MD. (authors)

  12. 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.

  13. Magnetic, transport and structural properties of Co/Ir multilayers grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Colis, S.; Dinia, A.; Ulhaq-Bouillet, C.; Panissod, P.; Meny, C.; Schmerber, G.; Arabski, J. [IPCMS-GEMME (UMR 7504 du CNRS), 23 rue du Loess, BP 34, F-67034 Strasbourg Cedex 2 (France)

    2003-09-01

    We report on the structural properties of a [Co{sub 30}/Ir{sub 10}]{sub 10} {sub x} (A) superlattice, as well as on the magnetic and transport properties of a Co{sub 15}/Ir{sub 5}/Co{sub 30} (A) artificial ferrimagnetic system. The samples were grown by molecular beam epitaxy (MBE) on MgO(001) substrates covered with a Ir{sub 130} (A) buffer layer. High resolution cross section and plan view transmission electron microscopy (TEM) images present a high quality epitaxial stack [100]MgO(001) parallel [100]Ir(001) parallel [100]Co(001), with a tetragonalization of the Co fcc structure, due to strains induced by the Ir buffer. TEM images also show that the Co/Ir interfaces are flat, while the layers are continuous and free of bridges. These observations are consistent with zero field nuclear magnetic resonance measurements which indicate an fcc structure of the Co layers, and an interface mixing between Co and Ir limited to one atomic layer. As a consequence the antiferromagnetically coupled Co/Ir/Co sandwich presents large saturation and coercive fields which exceed 20 kOe and 220 Oe, respectively. Annealing made on the same sandwich indicate that the magnetic and transport properties are stable up to 300 C. (copyright 2003 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. Molecular Dynamics Simulation of the Transport Properties of Molten Transuranic Salt Mixtures

    Science.gov (United States)

    Baty, Austin; McIntyre, Peter; Sattarov, Akhdiyor; Sooby, Elizabeth

    2012-10-01

    The Accelerator Research Laboratory at Texas A&M is proposing a revolutionary design for accelerator-driven subcritical fission in molten salt (ADSMS), a system that destroys the transuranic elements in spent nuclear fuel. The transuranics are the most enduring hazard of nuclear power, since they contain high radiotoxicity and have half-lives of a thousand to a million years. The ADSMS core is fueled by a homogeneous chloride-based molten salt mixture containing the chlorides of the transuranics and NaCl. Knowledge of the density, heat capacity, thermal conductivity, etc. of the salt mixtures is needed to accurately model the complex ADSMS system. There is a lack of experimental data on the density and transport properties of such mixtures. Molecular dynamics simulations using polarizable ion potentials are used to determine the density and heat capacity of these melts as a function of temperature. Green-Kubo methods are employed to calculate the electrical conductivity, thermal conductivity, and viscosity of the salt using the outputs of the model. Results for pure molten salt systems are compared to experimental data when possible to validate the potentials used. Here we discuss potential salt systems, their neutronic behavior, and the calculated transport properties.

  15. 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.

  16. 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.

  17. Transport properties of liquid para-hydrogen: The path integral centroid molecular dynamics approach

    Science.gov (United States)

    Yonetani, Yoshiteru; Kinugawa, Kenichi

    2003-11-01

    Several fundamental transport properties of a quantum liquid para-hydrogen (p-H2) at 17 K have been numerically evaluated by means of the quantum dynamics simulation called the path integral centroid molecular dynamics (CMD). For comparison, classical molecular dynamics (MD) simulations have also been performed under the same condition. In accordance with the previous path integral simulations, the calculated static properties of the liquid agree well with the experimental results. For the diffusion coefficient, thermal conductivity, and shear viscosity, the CMD predicts the values closer to the experimental ones though the classical MD results are far from the reality. The agreement of the CMD result with the experimental one is especially good for the shear viscosity with the difference less than 5%. The calculated diffusion coefficient and the thermal conductivity agree with the experimental values at least in the same order. We predict that the ratio of bulk viscosity to shear viscosity for liquid p-H2 is much larger than classical van der Waals simple liquids such as rare gas liquids.

  18. Hydroxylation of phenol over MeAPO molecular sieves synthesized by vapor phase transport

    Science.gov (United States)

    Shao, Hui; Chen, Jingjing; Chen, Xia; Leng, Yixin; Zhong, Jing

    2016-07-01

    In this study, MeAPO-25 (Me = Fe, Cu, Mn) molecular sieves were first synthesized by a vapor phase transport method using tetramethyl guanidine as the template and applied to hydroxylation of phenol. The zeolites were characterized by XRD, SEM, FT-IR, and DR UV-Vis. As a result, MeAPO-21 and MeAPO-15 were synthesized by changing the Me/Al ratio. UV-Visible diffuse reflectance study suggested incorporation of heteroatoms into the framework and FT-IR study also supported these data. Effects of heteroatoms, contents of Me in MeAPO-25, reaction temperature, phenol/H2O2 mole ratios, reaction time and concentration of catalyst on the conversion of phenol, as well as on the selectivity were studied. FeAPO-25 exhibited a high catalytic activity at the mole ratio of FeO and Al2O3 equal to 0.1 in the synthesis gel, giving the phenol conversion of 88.75% and diphenols selectivity of 66.23% at 60°C within 3 h [ n(phenol)/ n(H2O2) = 0.75, m(FeAPO-25)/ m(phenol) = 7.5%]. Experimental results indicated that the FeAPO-25 molecular sieve was a fairly promising candidate for the application in hydroxylation of phenol.

  19. Understanding the reaction of nuclear graphite with molecular oxygen: Kinetics, transport, and structural evolution

    Science.gov (United States)

    Kane, Joshua J.; Contescu, Cristian I.; Smith, Rebecca E.; Strydom, Gerhard; Windes, William E.

    2017-09-01

    For the next generation of nuclear reactors, HTGRs specifically, an unlikely air ingress warrants inclusion in the license applications of many international regulators. Much research on oxidation rates of various graphite grades under a number of conditions has been undertaken to address such an event. However, consequences to the reactor result from the microstructural changes to the graphite rather than directly from oxidation. The microstructure is inherent to a graphite's properties and ultimately degradation to the graphite's performance must be determined to establish the safety of reactor design. To understand the oxidation induced microstructural change and its corresponding impact on performance, a thorough understanding of the reaction system is needed. This article provides a thorough review of the graphite-molecular oxygen reaction in terms of kinetics, mass and energy transport, and structural evolution: all three play a significant role in the observed rate of graphite oxidation. These provide the foundations of a microstructurally informed model for the graphite-molecular oxygen reaction system, a model kinetically independent of graphite grade, and capable of describing both the observed and local oxidation rates under a wide range of conditions applicable to air-ingress.

  20. Scaling theory for percolative charge transport in molecular semiconductors: Correlated versus uncorrelated energetic disorder

    Science.gov (United States)

    Cottaar, J.; Coehoorn, R.; Bobbert, P. A.

    2012-06-01

    We recently introduced a scaling theory for charge transport in molecular semiconductors with uncorrelated Gaussian energetic disorder, considering Miller-Abrahams as well as Marcus hopping and different lattice structures [Cottaar , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.136601 107, 136601 (2011)]. A compact expression was derived for the dependence of the charge-carrier mobility on temperature and carrier concentration. We show here that for Miller-Abrahams hopping the theory can also be applied to non-Gaussian energetic disorder, without parameter changes. Moreover, we show how it can be applied to correlated energetic disorder as obtained from randomly oriented molecular dipoles, which experiments suggest to be often more suitable. The same compact expression still describes the charge-carrier mobility, with new parameter values as determined from numerically exact results. The critical scaling exponent for correlated disorder is about twice as large as for uncorrelated disorder, which is caused by a different topology of the percolating network. The temperature dependence of the mobility for correlated disorder is significantly weaker than for uncorrelated disorder, while the carrier-concentration dependence is slightly weaker, due to small deviations of the density of states from a Gaussian. We indicate how comparison with experiments could distinguish between the different models.

  1. 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

  2. Molecular cloning of mouse amino acid transport system B0, a neutral amino acid transporter related to Hartnup disorder.

    Science.gov (United States)

    Bröer, Angelika; Klingel, Karin; Kowalczuk, Sonja; Rasko, John E J; Cavanaugh, Juleen; Bröer, Stefan

    2004-06-04

    Resorption of amino acids in kidney and intestine is mediated by transporters, which prefer groups of amino acids with similar physico-chemical properties. It is generally assumed that most neutral amino acids are transported across the apical membrane of epithelial cells by system B(0). Here we have characterized a novel member of the Na(+)-dependent neurotransmitter transporter family (B(0)AT1) isolated from mouse kidney, which shows all properties of system B(0). Flux experiments showed that the transporter is Na(+)-dependent, electrogenic, and actively transports most neutral amino acids but not anionic or cationic amino acids. Superfusion of mB(0)AT1-expressing oocytes with neutral amino acids generated inward currents, which were proportional to the fluxes observed with labeled amino acids. In situ hybridization showed strong expression in intestinal microvilli and in the proximal tubule of the kidney. Expression of mouse B(0)AT1 was restricted to kidney, intestine, and skin. It is generally assumed that mutations of the system B(0) transporter underlie autosomal recessive Hartnup disorder. In support of this notion mB(0)AT1 is located on mouse chromosome 13 in a region syntenic to human chromosome 5p15, the locus of Hartnup disorder. Thus, the human homologue of this transporter is an excellent functional and positional candidate for Hartnup disorder.

  3. Role of zinc and zinc transporters in the molecular pathogenesis of diabetes mellitus.

    Science.gov (United States)

    Quraishi, Iram; Collins, Sibrina; Pestaner, Joseph P; Harris, Twaina; Bagasra, Omar

    2005-01-01

    . Understanding the molecular events in the pathogenesis of DM with regards to regulation of zinc uptake would be critical to the evaluation of the natural history of diabetes in humans and especially in various racial groups. If a direct link between zinc transport and diabetes can be established, then a special nutritional formula, medication or other intervention might be especially designed to test the ability to decrease the incidence of this disease in DM susceptible groups, particularly in AAs.

  4. 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.

  5. 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.; Berg, van den D.J.; Groenink, W.H.H.; Verpoorten, H.; Luttge, R.; 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 stai

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

    Science.gov (United States)

    Erickson, Robert P; Jia, Zhiyuan; Gross, Steven P; Yu, Clare C

    2011-05-01

    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.

  7. 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.

  8. Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.; Cheng, Yuhui; Dupuis, Michel; Raugei, Simone; Shaw, Wendy J.

    2014-01-15

    Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistent hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of

  9. Proton transport in triflic acid pentahydrate studied via ab initio path integral molecular dynamics.

    Science.gov (United States)

    Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E

    2011-06-16

    Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the

  10. Proton transport in triflic acid hydrates studied via path integral car-parrinello molecular dynamics.

    Science.gov (United States)

    Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E

    2009-12-31

    The mono-, di-, and tetrahydrates of trifluoromethanesulfonic acid, which contain characteristic H(3)O(+), H(5)O(2)(+), and H(9)O(4)(+) structures, provide model systems for understanding proton transport in materials with high perfluorosulfonic acid density such as perfluorosulfonic acid membranes commonly employed in hydrogen fuel cells. Ab initio molecular dynamics simulations indicate that protons in these solids are predisposed to transfer to the water most strongly bound to sulfonate groups via a Grotthuss-type mechanism, but quickly return to the most solvated defect structure either due to the lack of a nearby species to stabilize the new defect or a preference for the proton to be maximally hydrated. Path integral molecular dynamics of the mono- and dihydrate reveal significant quantum effects that facilitate proton transfer to the "presolvated" water or SO(3)(-) in the first solvation shell and increase the Zundel character of all the defects. These trends are quantified in free energy profiles for each bonding environment. Hydrogen bonding criteria for HOH-OH(2) and HOH-O(3)S are extracted from the two-dimensional potential of mean force. The quantum radial distribution function, radius of gyration, and root-mean-square displacement position correlation function show that the protonic charge is distributed over two or more water molecules. Metastable structural defects with one excess proton shared between two sulfonate groups and another Zundel or Eigen type cation defect are found for the mono- and dihydrate but not for the tetrahydrate crystal. Results for the tetrahydrate native crystal exhibit minor differences at 210 and 250 K. IR spectra are calculated for all native and stable defect structures. Graph theory techniques are used to characterize the chain lengths and ring sizes in the hydrogen bond network. Low conductivities when limited water is present may be attributable to trapping of protons between SO(3)(-) groups and the increased

  11. Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

    Science.gov (United States)

    Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

    2015-01-01

    Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.

  12. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  13. 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.

  14. Physics of transport and traffic phenomena in biology: from molecular motors and cells to organisms

    Science.gov (United States)

    Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2005-12-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukaryotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Novel efforts have been made to utilize some uni-cellular organisms as “micro-transporters”. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In this review we critically examine the current status of our understanding, expose the limitations of the existing methods, mention open challenging questions and speculate on the possible future directions of research in this interdisciplinary area where physics meets not only chemistry and biology but also (nano-)technology.

  15. Morphological and transport characteristics of swollen chitosan-based proton exchange membranes studied by molecular modeling.

    Science.gov (United States)

    Bahlakeh, Ghasem; Mahdi Hasani-Sadrabadi, Mohammad; Jacob, Karl I

    2017-01-01

    Chitosan biopolymer has been extensively applied in direct methanol fuel cells (DMFCs) as a potential replacement to conventional Nafion membrane for its considerably reduced methanol crossover. Here, we computationally explored the influences of methanol concentration, temperature, and pH parameters upon the nanostructure and dynamics, particularly the methanol crossover, in chitosan proton-exchange membrane (PEM) through molecular dynamics simulations. Theoretical results demonstrated the increased swelling and radius of gyration of chitosan chains at higher concentrations. Structural examinations further revealed that an increase in methanol loading weakened the water interactions with chitosan functionalities (amineNH2 , hydroxylOH, and methoxyCH2 OH) whereas improved the methanol affinities toward chitosan, reflecting higher methanol sorption capability of chitosan at enhanced concentrations. Additionally, it was found that interactions between solvents and chitosan strengthened under acidic pH conditions on account of amine protonation. The water diffusivity inside the swollen chitosan diminished by increasing CH3 OH uptake, and in contrast diffusivity of methanol was noted to enhance. Furthermore, it was observed that an enhancement in temperature or a decrease in pH intensified solvent mobility. These insights imply that supplying methanol-concentrated and/or acidic feed solutions into DMFCs based on chitosan PEMs could lower membrane performance due to the significant methanol transport dynamics. © 2016 Wiley Periodicals, Inc.

  16. Phonon thermal transport in silicene-germanene superlattice: a molecular dynamics study

    Science.gov (United States)

    Wang, Xinyu; Hong, Yang; Chan, Paddy K. L.; Zhang, Jingchao

    2017-06-01

    Two-dimensional (2D) hybrid materials have drawn enormous attention in thermoelectric applications. In this work, we apply a molecular dynamics (MD) simulation to investigate the phonon thermal transport in silicene-germanene superlattice. A non-monotonic thermal conductivity of silicene-germanene superlattice with period length is revealed, which is due to the coherent-incoherent phonon conversion and phonon confinement mechanisms. We also calculate the thermal conductivity of a Si-Ge random mixing monolayer, showing a U-shaped trend. Because of the phonon mode localizations at Ge concentration of 80%, thermal conductivity varies dramatically at low doping regions. By changing the total length (L total), the infinite-length thermal conductivities of pure silicene, pure germanene, silicene-germanene superlattice, and Si-Ge random mixing monolayer are extracted as 16.08, 15.95, 5.60 and 4.47 W/m-K, respectively. The thermal boundary conductance (TBC) of the silicene-germanene is also evaluated, showing a small thermal rectification. At L total = 274.7 nm, the TBC of silicene to germanene is 620.49 MW/m2-K, while that of germanene to silicene is 528.76 MW/m2-K.

  17. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol.

    Science.gov (United States)

    Gabrielsen, Mari; Kurczab, Rafał; Ravna, Aina W; Kufareva, Irina; Abagyan, Ruben; Chilmonczyk, Zdzisław; Bojarski, Andrzej J; Sylte, Ingebrigt

    2012-01-01

    The two main groups of antidepressant drugs, the tricyclic antidepressants (TCAs) and the selective serotonin reuptake inhibitors (SSRIs), as well as several other compounds, act by inhibiting the serotonin transporter (SERT). However, the binding mode and molecular mechanism of inhibition in SERT are not fully understood. In this study, five classes of SERT inhibitors were docked into an outward-facing SERT homology model using a new 4D ensemble docking protocol. Unlike other docking protocols, where protein flexibility is not considered or is highly dependent on the ligand structure, flexibility was here obtained by side chain sampling of the amino acids of the binding pocket using biased probability Monte Carlo (BPMC) prior to docking. This resulted in the generation of multiple binding pocket conformations that the ligands were docked into. The docking results showed that the inhibitors were stacked between the aromatic amino acids of the extracellular gate (Y176, F335) presumably preventing its closure. The inhibitors interacted with amino acids in both the putative substrate binding site and more extracellular regions of the protein. A general structure-docking-based pharmacophore model was generated to explain binding of all studied classes of SERT inhibitors. Docking of a test set of actives and decoys furthermore showed that the outward-facing ensemble SERT homology model consistently and selectively scored the majority of active compounds above decoys, which indicates its usefulness in virtual screening.

  18. Coarse-grain molecular dynamics study of fullerene transport across a cell membrane

    Science.gov (United States)

    Sridhar, Akshay; Srikanth, Bharath; Kumar, Amit; Dasmahapatra, Ashok Kumar

    2015-07-01

    The study of the ability of drug molecules to enter cells through the membrane is of vital importance in the field of drug delivery. In cases where the transport of the drug molecules through the membrane is not easily accomplishable, other carrier molecules are used. Spherical fullerene molecules have been postulated as potential carriers of highly hydrophilic drugs across the plasma membrane. Here, we report the coarse-grain molecular dynamics study of the translocation of C60 fullerene and its derivatives across a cell membrane modeled as a 1,2-distearoyl-sn-glycero-3-phosphocholine bilayer. Simulation results indicate that pristine fullerene molecules enter the bilayer quickly and reside within it. The addition of polar functionalized groups makes the fullerenes less likely to reside within the bilayer but increases their residence time in bulk water. Addition of polar functional groups to one half of the fullerene surface, in effect creating a Janus particle, offers the most promise in developing fullerene models that can achieve complete translocation through the membrane bilayer.

  19. Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

    Science.gov (United States)

    Mogurampelly, Santosh; Ganesan, Venkat

    2015-03-01

    Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

  20. Equations of state and transport properties of warm dense beryllium: a quantum molecular dynamics study.

    Science.gov (United States)

    Wang, Cong; Long, Yao; Tian, Ming-Feng; He, Xian-Tu; Zhang, Ping

    2013-04-01

    We have calculated the equations of state, the viscosity and self-diffusion coefficients, and electronic transport coefficients of beryllium in the warm dense regime for densities from 4.0 to 6.0 g/cm(3) and temperatures from 1.0 to 10.0 eV by using quantum molecular dynamics simulations. The principal Hugoniot curve is in agreement with underground nuclear explosive and high-power laser experimental results up to ~20 Mbar. The calculated viscosity and self-diffusion coefficients are compared with the one-component plasma model, using effective charges given by the average-atom model. The Stokes-Einstein relationship, which connects viscosity and self-diffusion coefficients, is found to hold fairly well in the strong coupling regime. The Lorenz number, which is the ratio between thermal and electrical conductivities, is computed via Kubo-Greenwood formula and compared to the well-known Wiedemann-Franz law in the warm dense region.

  1. Characteristic electron transport on pyridine-linked molecular devices with graphene nanoribbons electrodes and gold electrodes

    Science.gov (United States)

    Li, Jie; Zhou, Yi; Zhang, Leining; Li, Hui

    2016-09-01

    The electrodes in the molecular devices play a crucial role in creating functional organic electronic devices. We employed the first-principles calculations to investigate the conjugated pyridine-terminated molecule-4, 4‧-vinylenedipyridine attached to monolayer zigzag graphene nanoribbons (ZGNRs) and Au electrodes. Results show that the ZGNRs-based device exhibits excellent electrical properties. It has larger equilibrium conductance or stronger transmission capacity due to higher strength of individual channel and stronger delocalization of electronic states at the Fermi level. The transmission of two devices near the Fermi level is influenced by resonant electron transport through the discrete energy and the edge states. Comparatively, different from the rising trend of gold-based device with the increasing voltage, the current of the device with ZGNRs electrodes changes in a completely different way with the augment of the applied voltage, exhibiting a negative differential resistance effect unexpectedly. The changing trends of the current through two devices are elucidated by the evolution of the transmission peak nearest to the Fermi level.

  2. Molecular mechanism: the human dopamine transporter histidine 547 regulates basal and HIV-1 Tat protein-inhibited dopamine transport.

    Science.gov (United States)

    Quizon, Pamela M; Sun, Wei-Lun; Yuan, Yaxia; Midde, Narasimha M; Zhan, Chang-Guo; Zhu, Jun

    2016-12-14

    Abnormal dopaminergic transmission has been implicated as a risk determinant of HIV-1-associated neurocognitive disorders. HIV-1 Tat protein increases synaptic dopamine (DA) levels by directly inhibiting DA transporter (DAT) activity, ultimately leading to dopaminergic neuron damage. Through integrated computational modeling prediction and experimental validation, we identified that histidine547 on human DAT (hDAT) is critical for regulation of basal DA uptake and Tat-induced inhibition of DA transport. Compared to wild type hDAT (WT hDAT), mutation of histidine547 (H547A) displayed a 196% increase in DA uptake. Other substitutions of histidine547 showed that DA uptake was not altered in H547R but decreased by 99% in H547P and 60% in H547D, respectively. These mutants did not alter DAT surface expression or surface DAT binding sites. H547 mutants attenuated Tat-induced inhibition of DA transport observed in WT hDAT. H547A displays a differential sensitivity to PMA- or BIM-induced activation or inhibition of DAT function relative to WT hDAT, indicating a change in basal PKC activity in H547A. These findings demonstrate that histidine547 on hDAT plays a crucial role in stabilizing basal DA transport and Tat-DAT interaction. This study provides mechanistic insights into identifying targets on DAT for Tat binding and improving DAT-mediated dysfunction of DA transmission.

  3. Modeling of molecular and particulate transport in dry spent nuclear fuel canisters

    Science.gov (United States)

    Casella, Andrew M.

    2007-09-01

    these particles are transported with the fill gas into the breach, they may be deposited, leading to a restriction of flow and eventually to the plugging of the breach. This model uses an analytical solution to the problem of particle deposition in convective-diffusive fully-developed laminar flow through a straight cylindrical tube. Since the cylindrical flow geometry is a requirement for the use of this equation, it is assumed that all deposited particles are distributed uniformly both axially and circumferentially along the breach. The model is capable of monitoring the pressure, temperature, quantity of fill gas, breach radius, particle transmission fraction, and flow velocity through the breach as functions of time. The depressurization time can be significantly affected by the release of fission gases or helium generated from alpha decay if the cladding of a fuel rod within the canister is breached. To better quantify this phenomenon, a Monte Carlo model of molecular transport through nano-scale flow pathways in the spent fuel is developed in this thesis. This model is applied to cylindrical, conical, elliptical, and helical pathways. Finally, in order to remove some of the restrictions of the model of canister depressurization accounting for suspended particles, a Monte Carlo program was written to model the movement of particles through the breach. This program is capable of accounting for any transport mechanism specified but is focused in this work on laminar convective-diffusive flow. Each test particle is tracked as it is carried through the breach and if it impacts the breach wall, the three-dimensional location of the impact is recorded. In this way, the axial and circumferential deposition patterns can be recorded. This program can model any flow geometry as long as a velocity profile can be provided. In this thesis, the program is expanded to account for flow through straight and torroidal cylindrical tubes.

  4. Coleta, transporte e armazenamento de amostras para diagnóstico molecular Collection, transport and storage of samples for molecular diagnosis

    Directory of Open Access Journals (Sweden)

    Murilo Rezende Melo

    2010-10-01

    Full Text Available A Sociedade Brasileira de Patologia Clínica/Medicina Laboratorial (SBPC/ML lançou, em seu 44º Congresso Brasileiro de Patologia Clínica e Medicina Laboratorial, uma série de recomendações para minimizar os erros na fase pré-analítica, sendo este texto uma delas. Além do crescimento do mercado de testes moleculares, é frequente a percepção errônea de que esses testes são menos sujeitos a erros. Enfatizamos, neste documento, que certos cuidados na fase pré-analítica são extremamente importantes para garantir a confiabilidade de testes moleculares.The Brazilian Society of Clinical Pathology/Laboratory Medicine (SBPC/ML launched a series of recommendations on how to minimize errors on the pre-analytical testing phase during the 44th Brazilian Congress of Clinical Pathology and Laboratory Medicine. This is one of them. The molecular diagnostics market is growing fast and many people believe these tests are less error-prone. In this study we highlight that proper care during the pre-analytical phase is extremely important in order to ensure the reliability of molecular diagnostic tests.

  5. Molecular analysis of the human SLC13A4 sulfate transporter gene promoter

    Energy Technology Data Exchange (ETDEWEB)

    Jefferis, J. [Mater Medical Research Institute, South Brisbane, Queensland (Australia); Rakoczy, J. [Mater Medical Research Institute, South Brisbane, Queensland (Australia); School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland (Australia); Translational Research Institute, Woolloongabba, Queensland (Australia); Simmons, D.G. [School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland (Australia); Dawson, P.A., E-mail: paul.dawson@mmri.mater.org.au [Mater Medical Research Institute, South Brisbane, Queensland (Australia); Translational Research Institute, Woolloongabba, Queensland (Australia)

    2013-03-29

    Highlights: ► Basal promoter activity of SLC13A4 −57 to −192 nt upstream of transcription initiation site. ► Human SLC13A4 5′-flanking region has conserved motifs with other placental species. ► Putative NFY, SP1 and KLF7 motifs in SLC13A4 5′-flanking region enhance transcription. -- Abstract: The human solute linked carrier (SLC) 13A4 gene is primarily expressed in the placenta where it is proposed to mediate the transport of nutrient sulfate from mother to fetus. The molecular mechanisms involved in the regulation of SLC13A4 expression remain unknown. To investigate the regulation of SLC13A4 gene expression, we analysed the transcriptional activity of the human SLC13A4 5′-flanking region in the JEG-3 placental cell line using luciferase reporter assays. Basal transcriptional activity was identified in the region −57 to −192 nucleotides upstream of the SLC13A4 transcription initiation site. Mutational analysis of the minimal promoter region identified Nuclear factor Y (NFY), Specificity protein 1 (SP1) and Krüppel like factor 7 (KLF7) motifs which conferred positive transcriptional activity, as well as Zinc finger protein of the cerebellum 2 (ZIC2) and helix–loop–helix protein 1 (HEN1) motifs that repressed transcription. The conserved NFY, SP1, KLF7, ZIC2 and HEN1 motifs in the SLC13A4 promoter of placental species but not in non-placental species, suggests a potential role for these putative transcriptional factor binding motifs in the physiological control of SLC13A4 mRNA expression.

  6. Coordination compounds for molecular electronics: Synthesis, characterization and electronic transport properties of copper rotaxanes and molecular complexes

    OpenAIRE

    Ponce González, Julia

    2014-01-01

    Esta tesis se centra en el estudio de compuestos de coordinación de interés en el campo de la electrónica molecular. Este campo tiene como objetivo la utilización de unidades moleculares como componentes activos en circuitos electrónicos. Los dispositivos unimoleculares presentan cualidades únicas, inherentes a la nanoescala, que no poseen equivalencia en los componentes convencionales, actualmente basados en el silicio. Además, la síntesis de moléculas dispone de un altísimo grado de control...

  7. Surface-modified silica colloidal crystals: nanoporous films and membranes with controlled ionic and molecular transport.

    Science.gov (United States)

    Zharov, Ilya; Khabibullin, Amir

    2014-02-18

    Nanoporous membranes are important for the study of the transport of small molecules and macromolecules through confined spaces and in applications ranging from separation of biomacromolecules and pharmaceuticals to sensing and controlled release of drugs. For many of these applications, chemists need to gate the ionic and molecular flux through the nanopores, which in turn depends on the ability to control the nanopore geometry and surface chemistry. Most commonly used nanoporous membrane materials are based on polymers. However, the nanostructure of polymeric membranes is not well-defined, and their surface is hard to modify. Inorganic nanoporous materials are attractive alternatives for polymers in the preparation of nanoporous membranes. In this Account, we describe the preparation and surface modification of inorganic nanoporous films and membranes self-assembled from silica colloidal spheres. These spheres form colloidal crystals with close-packed face centered cubic lattices upon vertical deposition from colloidal solutions. Silica colloidal crystals contain ordered arrays of interconnected three dimensional voids, which function as nanopores. We can prepare silica colloidal crystals as supported thin films on various flat solid surfaces or obtain free-standing silica colloidal membranes by sintering the colloidal crystals above 1000 °C. Unmodified silica colloidal membranes are capable of size-selective separation of macromolecules, and we can surface-modify them in a well-defined and controlled manner with small molecules and polymers. For the surface modification with small molecules, we use silanol chemistry. We grow polymer brushes with narrow molecular weight distribution and controlled length on the colloidal nanopore surface using atom transfer radical polymerization or ring-opening polymerization. We can control the flux in the resulting surface-modified nanoporous films and membranes by pH and ionic strength, temperature, light, and small molecule

  8. 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.

  9. Molecular characterization of a membrane transporter for lactate, pyruvate, and other monocarboxylates: implications for the Cori cycle.

    Science.gov (United States)

    Garcia, C K; Goldstein, J L; Pathak, R K; Anderson, R G; Brown, M S

    1994-03-11

    Lactate and pyruvate cross cell membranes via a monocarboxylate transporter (MCT) with well-defined properties but undefined molecular structure. We report the cloning of a cDNA encoding MCT1, a monocarboxylate transporter whose properties resemble those of the erythrocyte MCT, including proton symport, trans acceleration, and sensitivity to alpha-cyanocinnammates. A Phe to Cys substitution in MCT1 converts it to Mev, a mevalonate transporter. MCT1 is abundant in erythrocytes, cardiac muscle, and basolateral intestinal epithelium. In skeletal muscle it is restricted to mitochondria-rich myocytes. As sperm traverse the epididymis, MCT1 switches from sperm to epithelial cells. MCT1 is present at low levels in liver, suggesting another MCT in this tissue. By exporting lactate from intestine and erythrocytes, MCT1 participates in the Cori cycle. It also participates in novel pathways of monocarboxylate metabolism in muscle and sperm.

  10. Delineation on Therapeutic Significance of Transporters as Molecular Targets of Drugs

    Institute of Scientific and Technical Information of China (English)

    KANAI Yoshikat; HE Xin; LIU Chang-xiao

    2011-01-01

    Transporters are membrane proteins mediating permeation of organic and inorganic solutes through the plasma membrane and membranes of intracellular organella.They play essential roles in the epithelial absorption and cellular uptake of nutrients as well as absorption,distribution,metabolism,and excretion of drugs.Because transporters contribute to determining the distribution of compounds in the body in concert with metabolic/synthetic enzymes,the drugs that affect the functions of transporters are expected to alter the distribution of compounds in the body and to ameliorate disrupted homeostasis.In this context,drugs targeting transporters have been used clinically.Such drugs include antidepressants targeting monoamine transporters,diuretics targeting inorganic ion transporters of renal tubules,and uricosuric agents targeting renal urate transporters.Now new transporter-targeting drugs designed based on post-genome drug development strategy have been in the process of clinical trials or basic/clinical researches.For example,the inhibitors of renal Na/glucose cotransporter SGLT2 have been proved for their efficacy in the treatment of diabetes mellitus.The cancer L-type amino acid transporter 1(LAT1)has been considered as a target of cancer diagnosis and therapeutics.The transporter-targeting drugs are expected to provide new rationale in the therapeutics of various diseases.

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Chao Zhang

    2016-11-01

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

  13. Ab initio study of transport properties of an all-carbon molecular switch based on C20 molecule

    Institute of Scientific and Technical Information of China (English)

    OUYANG Fang-ping; XU Hui

    2007-01-01

    Choosing closed-ended armchair (5, 5) singlewall carbon nanotubes (CCNTs) as electrodes, we have investigated the electron transport properties across a carbon molecular junction consisting of a C20 molecule sandwiched between two semi-infinite carbon nanotubes. It is shown that the Landauer conductance of this carbon hybrid system can be tuned within several orders of magnitude not only by varying the tube-C20 distance, but more importantly by changing the orientation of the C20 molecule and rotating the C20 molecule or one of the tubes around the symmetry axis of the system at fixed distances. This fact could make this all-carbon molecular system a possible candidate for a nanoelectronic switching device. Moreover, our study also reveals that molecular configuration selection and structural relaxation would play an important role in the design of such devices.

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

    Science.gov (United States)

    Owens, Jonathan R.

    In this work, we first present two powerful methods for understanding the electronic, structural, conducting, and energetic properties of nano-materials: density functional theory (DFT) and quantum transport. The basics of the theory and background of both methods are discussed thoroughly. After establishing a firm foundation, we turn our attention to using these tools to solve practical problems, often in collaboration with experimental colleagues. The first two projects pertain to nitrogen doping in graphene nanoribbons (GNRs). We study nitrogen doping in two different schema: concentration-based (N_x-doped) and structural based (N_2. {AA}-doped). Concentration based doping is explored in the context of experimental measurements of IV curves on GNRs with differing dopant concentrations. These results show a shift towards semi-conducting behavior with an increase in dopant concentration. We combine first principles calculations (DFT) and transport calculations in the Landauer formalism to compute the density-of-states (DOS) and transport curves for various dopant concentrations (0.46%, 1.39%, 1.89%, and 2.31%), which corroborate the experimental observations. The N_2. {AA}-doped GNR study was inspired by experimental observation of an atomically precise nitrogen doping scheme in bulk graphene. Experimental STM images, combined with simulated STM images, revealed that the majority (80%) of doping sites consist of nitrogen atoms on neighboring sites of the same sublattice (A) in graphene, hence N_2. {AA} doping. We examine this doping scheme applied to zigzag and armchair GNRs under different orientations of the dopants. We present spin-resolved charge densities, energetics, transport, DOS, and simulated STM images for all four systems studied. Our results show the possibility of spin-filtered devices and the STM images provide an aid in helping experimentalist identify the dopant patterns, if these GNRs are fabricated. We next venture to explain different observed

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

    Science.gov (United States)

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

    2017-06-01

    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.

  16. Molecular characterisation of transport mechanisms at the developing mouse blood-CSF interface

    DEFF Research Database (Denmark)

    Liddelow, Shane A; Temple, Sally; Møllgård, Kjeld

    2012-01-01

    -immunopositive. Results showed a significant degree of concordance between plasma protein/albumin immunoreactivity and expression of the putative transporters. Immunohistochemistry identified SPARC and GYPA in choroid plexus epithelial cells in the embryo with a subcellular distribution that was consistent with transport...

  17. 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...

  18. Proton transport in a binary biomimetic solution revealed by molecular dynamics simulation

    NARCIS (Netherlands)

    Liang, C.; Jansen, T.L.Th.A.

    2011-01-01

    We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration. The

  19. Molecular basis of transport and regulation in the Na+/betaine symporter BetP

    NARCIS (Netherlands)

    Ressl, Susanne; Terwisscha van Scheltinga, Anke C.; Vonrhein, Clemens; Ott, Vera; Ziegler, Christine

    2009-01-01

    Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by accumulation of osmolytes to restore normal hydration levels. Here we report the determination of the X-ray structure of a member of the family of betaine/choline/carnitine transporters, the Na+-cou

  20. Molecular basis of transport and regulation in the Na+/betaine symporter BetP

    NARCIS (Netherlands)

    Ressl, Susanne; Terwisscha van Scheltinga, Anke C.; Vonrhein, Clemens; Ott, Vera; Ziegler, Christine

    2009-01-01

    Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by accumulation of osmolytes to restore normal hydration levels. Here we report the determination of the X-ray structure of a member of the family of betaine/choline/carnitine transporters, the

  1. Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter

    DEFF Research Database (Denmark)

    Weyand, Simone; Shimamura, Tatsuro; Yajima, Shunsuke

    2008-01-01

    The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 trans...

  2. 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.

  3. Anion channels/transporters in plants: from molecular bases to regulatory networks.

    Science.gov (United States)

    Barbier-Brygoo, Hélène; De Angeli, Alexis; Filleur, Sophie; Frachisse, Jean-Marie; Gambale, Franco; Thomine, Sébastien; Wege, Stefanie

    2011-01-01

    Anion channels/transporters are key to a wide spectrum of physiological functions in plants, such as osmoregulation, cell signaling, plant nutrition and compartmentalization of metabolites, and metal tolerance. The recent identification of gene families encoding some of these transport systems opened the way for gene expression studies, structure-function analyses of the corresponding proteins, and functional genomics approaches toward further understanding of their integrated roles in planta. This review, based on a few selected examples, illustrates that the members of a given gene family exhibit a diversity of substrate specificity, regulation, and intracellular localization, and are involved in a wide range of physiological functions. It also shows that post-translational modifications of transport proteins play a key role in the regulation of anion transport activity. Key questions arising from the increasing complexity of networks controlling anion transport in plant cells (the existence of redundancy, cross talk, and coordination between various pathways and compartments) are also addressed.

  4. Impact of redox-active polymer molecular weight on the electrochemical properties and transport across porous separators in nonaqueous solvents.

    Science.gov (United States)

    Nagarjuna, Gavvalapalli; Hui, Jingshu; Cheng, Kevin J; Lichtenstein, Timothy; Shen, Mei; Moore, Jeffrey S; Rodríguez-López, Joaquín

    2014-11-19

    Enhancing the ionic conductivity across the electrolyte separator in nonaqueous redox flow batteries (NRFBs) is essential for improving their performance and enabling their widespread utilization. Separating redox-active species by size exclusion without greatly impeding the transport of supporting electrolyte is a potentially powerful alternative to the use of poorly performing ion-exchange membranes. However, this strategy has not been explored possibly due to the lack of suitable redox-active species that are easily varied in size, remain highly soluble, and exhibit good electrochemical properties. Here we report the synthesis, electrochemical characterization, and transport properties of redox-active poly(vinylbenzyl ethylviologen) (RAPs) with molecular weights between 21 and 318 kDa. The RAPs reported here show very good solubility (up to at least 2.0 M) in acetonitrile and propylene carbonate. Ultramicroelectrode voltammetry reveals facile electron transfer with E1/2 ∼ -0.7 V vs Ag/Ag(+)(0.1 M) for the viologen 2+/+ reduction at concentrations as high as 1.0 M in acetonitrile. Controlled potential bulk electrolysis indicates that 94-99% of the nominal charge on different RAPs is accessible and that the electrolysis products are stable upon cycling. The dependence of the diffusion coefficient on molecular weight suggests the adequacy of the Stokes-Einstein formalism to describe RAPs. The size-selective transport properties of LiBF4 and RAPs across commercial off-the-shelf (COTS) separators such as Celgard 2400 and Celgard 2325 were tested. COTS porous separators show ca. 70 times higher selectivity for charge balancing ions (Li(+)BF4(-)) compared to high molecular weight RAPs. RAPs rejection across these separators showed a strong dependence on polymer molecular weight as well as the pore size; the rejection increased with both increasing polymer molecular weight and reduction in pore size. Significant rejection was observed even for rpoly/rpore (polymer

  5. 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.

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

    DEFF Research Database (Denmark)

    Sinning, Steffen; Said, Saida; Malinauskaite, Lina

    as an endogenous substrate mimic in the empty transporter in order for it to overcome the transition from the inward-facing to the outward-facing conformation. We also show that the local conformational changes associated with the rotation of this conserved leucine explains how cation sites are perturbed...... and are targets for drugs of abuse such as cocaine, amphetamine and ecstasy as well as anxiolytics and antidepressants. The transporters undergo a series of concerted conformational changes in order to harness the driving force of co-transported cations to translocate the neurotransmitter across the neuronal...

  7. 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.

  8. 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

    2017-09-01

    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.

  9. 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

  10. Studies on Molecular and Ion Transport in Silicalite Membranes and Applications as Ion Separator for Redox Flow Battery

    Science.gov (United States)

    Yang, Ruidong

    Microporous zeolite membranes have been widely studied for molecular separations based on size exclusion or preferential adsorption-diffusion mechanisms. The MFI-type zeolite membranes were also demonstrated for brine water desalination by molecular sieving effect. In this research, the pure silica MFI-type zeolite (i.e. silicalite) membrane has been for the first time demonstrated for selective permeation of hydrated proton (i.e. H3O+) in acidic electrolyte solutions. The silicalite membrane allows for permeation of H 3O+ ions, but is inaccessible to the large hydrated multivalent vanadium ions due to steric effect. The silicalite membrane has been further demonstrated as an effective ion separator in the all-vanadium redox flow battery (RFB).The silicalite is nonionic and its proton conductivity relies on the electric field-driven H3O+ transport through the sub nanometer-sized pores under the RFB operation conditions. The silicalite membrane displayed a significantly reduced self-discharge rate because of its high proton-to-vanadium ion transport selectivity. However, the nonionic nature of the silicalite membrane and very small diffusion channel size render low proton conductivity and is therefore inefficient as ion exchange membranes (IEMs) for practical applications. The proton transport efficiency may be improved by reducing the membrane thickness. However, the zeolite thin films are extremely fragile and must be supported on mechanically strong and rigid porous substrates. In this work, silicalite-Nafion composite membranes were synthesized to achieve a colloidal silicalite skin on the Nafion thin film base. The "colloidal zeolite-ionic polymer" layered composite membrane combines the advantages of high proton-selectivity of the zeolite layer and the mechanical flexibility and low proton transport resistance of the ionic polymer membrane. The composite membrane exhibited higher proton/vanadium ion separation selectivity and lower electrical resistance than

  11. Molecular simulations for determination of transport properties of nano-composites

    Science.gov (United States)

    Mahajan, Sanket S.

    In several recent applications, including those aimed at developing novel thermal interface materials, nano-particulate systems have been proposed to improve the effective behavior of the system. One critical challenge in using nano-particulate systems is the lack of knowledge regarding their thermal conductivity. In this thesis, techniques based on Molecular Dynamics (MD) simulations are developed to determine transport properties of various types of homogeneous and inhomogeneous systems. In particular, the thermal conductivity values of bulk silica, silica nano-wire and nano-particle are determined using MD simulations. The equilibrium MD simulations of nano-particles using Green-Kubo relations are demonstrated to be computationally very expensive and unsuitable for nano-scale systems. The reverse non-equilibrium MD method of imposing heat flux is shown to be efficient and more accurate. The method is first demonstrated on bulk amorphous silica and silica nano-wires. The mean thermal conductivity values for bulk silica and silica nano-wire are estimated to be 1.221 W/mK and 1.430 W/mK, respectively. To model nano-particles, a novel methodology inspired by the imposition of heat flux technique, is developed by dividing the nano-particle into concentric shells so as to capture the naturally radial mode of heat transfer. The mean thermal conductivity value of a 600-atom silica nano-particle obtained using this approach is 0.589 W/mK. This value is ˜50-60% lower than those of bulk silica and silica nano-wire. The above developed technique for estimating the thermal conductivity of nano-structured homogeneous systems is naturally extended to determine the Kapitza resistance between solid-solid interfaces. The systems considered are interfaces between Si-SiO2 and Si-HfO2 thin films. For the Si-SiO2 interface, the average Kapitza resistance for ˜8 A thick oxide layer system is 0.503 x 10-9 m2K/W and for the ˜11.5 A thick oxide layer system is 0.518 x 10-9 m 2K/W. For

  12. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    CERN Document Server

    Zhang, Zhedong

    2015-01-01

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in th...

  13. Molecular reorganization in organic field-effect transistors and its effect on two-dimensional charge transport pathways.

    Science.gov (United States)

    Liscio, Fabiola; Albonetti, Cristiano; Broch, Katharina; Shehu, Arian; Quiroga, Santiago David; Ferlauto, Laura; Frank, Christian; Kowarik, Stefan; Nervo, Roberto; Gerlach, Alexander; Milita, Silvia; Schreiber, Frank; Biscarini, Fabio

    2013-02-26

    Charge transport in organic thin film transistors takes place in the first few molecular layers in contact with the gate dielectric. Here we demonstrate that the charge transport pathways in these devices are extremely sensitive to the orientational defects of the first monolayers, which arise from specific growth conditions. Although these defects partially heal during the growth, they cause depletion of charge carriers in the first monolayer, and drive the current to flow in the monolayers above the first one. Moreover, the residual defects induce lower crystalline order and charge mobility. These results, which are not intuitively explained by electrostatics arguments, have been obtained by combining in situ real time structural and electrical characterization together with ex situ AFM measurements, on thin films of a relevant n-type organic semiconductor, N,N'-bis(n-octyl)-dicyanoperylene-3,4:9,10-bis dicarboximide grown by sublimation in a quasi-layer-by-layer mode at different substrate temperatures.

  14. Molecular cloning and expression analysis of a gene for sucrose transporter from pear (Pyrus bretschneideri Rehd.) fruit.

    Science.gov (United States)

    Zhang, Huping; Zhang, Shujun; Qin, Gaihua; Wang, Lifen; Wu, Tao; Qi, Kaijie; Zhang, Shaoling

    2013-12-01

    Here we report the cloning of a sucrose transporter cDNA from pear (Pyrus bretschneideri Rehd. cv 'Yali') fruit and an analysis of the expression of the gene. A cDNA clone, designated PbSUT1 was identified as a sucrose transporter cDNA from its sequence homology at the amino acid level to sucrose transporters that have been cloned from other higher plant species. PbSUT1 potentially encoded a protein of 499 amino acid residues with a predicted molecular mass of 53.4 kDa and an isoelectric point (pI) of 9.21. Phylogenetic analysis revealed that the PbSUT1 belonged to type III SUTs and was more closely related to the MdSUT1 from apple fruit. Some major facilitator superfamily (MFS)-specific sequence motifs were found in the predicted PbSUT1 peptides, and an MFS_1 domain was located at the amino acid positions of 29-447 of the sequence. A study of gene expression along fruit development showed that PbSUT1 transcripts are present at all stages but significantly increase before fruit enlargement and during the ripening process with increasing sucrose levels. In contrast, the expression levels don't change much during the period of rapid fruit growth. This work shows that sucrose transporter may play a role in the accumulation of sugars during maturation and in maintaining the internal cellular distribution.

  15. Molecular Mechanism of Ion-Ion and Ion-Substrate Coupling in the Na+-Dependent Leucine Transporter LeuT

    OpenAIRE

    Caplan, David A.; Subbotina, Julia O.; Noskov, Sergei Yu.

    2008-01-01

    Ion-coupled transport of neurotransmitter molecules by neurotransmitter:sodium symporters (NSS) play an important role in the regulation of neuronal signaling. One of the major events in the transport cycle is ion-substrate coupling and formation of the high-affinity occluded state with bound ions and substrate. Molecular mechanisms of ion-substrate coupling and the corresponding ion-substrate stoichiometry in NSS transporters has yet to be understood. The recent determination of a high-resol...

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

    Science.gov (United States)

    Song, Linze; Shi, Qiang

    2015-05-07

    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.

  17. 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.

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

    Science.gov (United States)

    Pal, Partha Pratim; Pati, Ranjit

    2010-07-01

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

  19. Runoff- and erosion-driven transport of cattle slurry: linking molecular tracers to hydrological processes

    Directory of Open Access Journals (Sweden)

    C. E. M. Lloyd

    2015-10-01

    Full Text Available The addition of cattle slurry to agricultural land is a widespread practise, but if not correctly managed it can pose a contamination risk to aquatic ecosystems. The transport of inorganic and organic components of cattle slurry to watercourses is a major concern, yet little is known about the physical transport mechanisms and associated fluxes and timings of contamination threats. Therefore, the aim of the study was to ascertain the importance of flow pathway partitioning in the transport (fluxes and timing of dissolved and particulate slurry-derived compounds with implications for off-site contamination. A series of rainfall–runoff and erosion experiments were carried out using the TRACE (Test Rig for Advancing Connectivity Experiments experimental hillslope facility. The experiments allowed the quantification of the impact of changing slope gradient and rainfall intensity on nutrient transport from cattle slurry applied to the hillslope, via surface, subsurface and vertical percolated flow pathways, as well as particulate transport from erosion. The dissolved components were traced using a combination of ammonium (NH4+ and fluorescence analysis, while the particulate fraction was traced using organic biomarkers, 5β-stanols. Results showed that rainfall events which produced flashy hydrological responses, resulting in large quantities of surface runoff, were likely to move sediment and also flush dissolved components of slurry-derived material from the slope, increasing the contamination risk. Rainfall events which produced slower hydrological responses were dominated by vertical percolated flows removing less sediment-associated material, but produced leachate which could contaminate deeper soil layers, and potentially groundwater, over a more prolonged period. Overall, this research provides new insights into the partitioning of slurry-derived material when applied to an unvegetated slope and the transport mechanisms by which

  20. Runoff- and erosion-driven transport of cattle slurry: linking molecular tracers to hydrological processes

    Science.gov (United States)

    Lloyd, C. E. M.; Michaelides, K.; Chadwick, D. R.; Dungait, J. A. J.; Evershed, R. P.

    2016-02-01

    The addition of cattle slurry to agricultural land is a widespread practise, but if not correctly managed it can pose a contamination risk to aquatic ecosystems. The transport of inorganic and organic components of cattle slurry to watercourses is a major concern, yet little is known about the physical transport mechanisms and associated fluxes and timings of contamination threats. Therefore, the aim of the study was to ascertain the importance of flow pathway partitioning in the transport (fluxes and timing) of dissolved and particulate slurry-derived compounds with implications for off-site contamination. A series of rainfall-runoff and erosion experiments were carried out using the TRACE (Test Rig for Advancing Connectivity Experiments) experimental hillslope facility. The experiments allowed the quantification of the impact of changing slope gradient and rainfall intensity on nutrient transport from cattle slurry applied to the hillslope, via surface, subsurface, and vertical percolated flow pathways, as well as particulate transport from erosion. The dissolved components were traced using a combination of ammonium (NH4+) and fluorescence analysis, while the particulate fraction was traced using organic biomarkers, 5β-stanols. Results showed that rainfall events which produced flashy hydrological responses, resulting in large quantities of surface runoff, were likely to move sediment and also flush dissolved components of slurry-derived material from the slope, increasing the contamination risk. Rainfall events which produced slower hydrological responses were dominated by vertical percolated flows removing less sediment-associated material, but produced leachate which could contaminate deeper soil layers, and potentially groundwater, over a more prolonged period. Overall, this research provides new insights into the partitioning of slurry-derived material when applied to an unvegetated slope and the transport mechanisms by which contamination risks are

  1. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations

    Science.gov (United States)

    La Rosa, Carmelo; Scalisi, Silvia; Lolicato, Fabio; Pannuzzo, Martina; Raudino, Antonio

    2016-05-01

    The protein transport inside a cell is a complex phenomenon that goes through several difficult steps. The facilitated transport requires sophisticated machineries involving protein assemblies. In this work, we developed a diffusion-reaction model to simulate co-transport kinetics of proteins and lipids. We assume the following: (a) there is always a small lipid concentration of order of the Critical Micellar Concentration (CMC) in equilibrium with the membrane; (b) the binding of lipids to proteins modulates the hydrophobicity of the complexes and, therefore, their ability to interact and merge with the bilayer; and (c) some lipids leave the bilayer to replenish those bound to proteins. The model leads to a pair of integral equations for the time-evolution of the adsorbed proteins in the lipid bilayer. Relationships between transport kinetics, CMC, and lipid-protein binding constants were found. Under particular conditions, a perturbation analysis suggests the onset of kinks in the protein adsorption kinetics. To validate our model, we performed leakage measurements of vesicles composed by either high or low CMC lipids interacting with Islet Amyloid PolyPeptide (IAPP) and Aβ (1-40) used as sample proteins. Since the lipid-protein complex stoichiometry is not easily accessible, molecular dynamics simulations were performed using monomeric IAPP interacting with an increasing number of phospholipids. Main results are the following: (a) 1:1 lipid-protein complexes generally show a faster insertion rate proportional to the complex hydrophobicity and inversely related to lipid CMC; (b) on increasing the number of bound lipids, the protein insertion rate decreases; and (c) at slow lipids desorption rate, the lipid-assisted proteins transport might exhibit a discontinuous behavior and does non-linearly depend on protein concentration.

  2. 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....

  3. 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.

  4. 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

    there are at least two phonon degrees of freedom. After deriving expressions for the linear drag coefficients, obeying the Onsager relation, we further investigate their effect on nonequilibrium transport. We show that the drag effect is closely related to two other phenomena: (1) adiabatic charge pumping through...

  5. 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.

  6. Molecular transport behaviour of organic solvents through halloysite nanotubes filled ethylene–vinyl acetate copolymer

    Indian Academy of Sciences (India)

    Suvendu Padhi; P Ganga Raju Achary; Nimai C Nayak

    2015-08-01

    The transport behaviour of three organic solvents (benzene, toluene and xylene) through halloysite nanotubes (HNTs) filled ethylene–vinyl acetate (EVA) copolymer composites have been investigated in the temperature range 303–323 K. The effects of HNTs loading, nature of solvent and temperature on the transport behaviour of solvents through composites were studied. It has been observed that all the systems follow a Fickian mode of transport on increasing temperature. The solvent uptake and sorption coefficient decreases with the increase in halloysite loading while diffusion coefficients and permeation coefficients were found to be dependent on the concentration of filler. The percentage of bounds rubber content and swelling ratio decreases up to 7.5 phr filler content, whereas above 7.5 phr filler loading were found to be increased due to poor dispersion of halloysite in EVA copolymer matrix. The transport behaviour of three organic solvents was further validated by their crosslink density values. The thermodynamic parameters such as enthalpy, entropy and free energy of sorption were evaluated. The positive values of free energy indicate the non-spontaneity of the sorption of HNTs filled EVA in aromatic solvents at 303 K.

  7. Apparatus and process for atomic or molecular layer deposition onto particles during pneumatic transport

    NARCIS (Netherlands)

    Van Ommen, J.R.

    2010-01-01

    The invention provides a process for depositing a coating onto particles being pneumatically transported in a tube. The process comprising the steps of providing a tube having an inlet opening and an outlet opening; feeding a carrier gas entraining particles into the tube at or near the inlet openin

  8. Electrical transport properties of oligothiophene based molecular films studied by current sensing Atomic Force Microscopy

    NARCIS (Netherlands)

    Hendriksen, Bas L.M.; Martin, Florent; Qi, Yabing; Qi, Y.; Mauldin, Clayton; Vukmirovic, Nenad; Ren, JunFeng; Wormeester, Herbert; Katan, Allard J.; Altoe, Virginia; Aloni, Shaul; Frechet, Jean M.J.; Wang, Lin-Wang; Salmeron, Miquel

    2011-01-01

    Using conducting probe atomic force microscopy (CAFM) we have investigated the electrical conduction properties of monolayer films of a pentathiophene derivative on a SiO2/Si-p+ substrate. By a combination of current–voltage spectroscopy and current imaging we show that lateral charge transport

  9. 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

  10. Biochemical and molecular characterization of the gentisate transporter GenK in Corynebacterium glutamicum.

    Directory of Open Access Journals (Sweden)

    Ying Xu

    Full Text Available BACKGROUND: Gentisate (2,5-dihydroxybenzoate is a key ring-cleavage substrate involved in various aromatic compounds degradation. Corynebacterium glutamicum ATCC13032 is capable of growing on gentisate and genK was proposed to encode a transporter involved in this utilization by its disruption in the restriction-deficient mutant RES167. Its biochemical characterization by uptake assay using [(14C]-labeled gentisate has not been previously reported. METHODOLOGY/PRINCIPAL FINDINGS: In this study, biochemical characterization of GenK by uptake assays with [(14C]-labeled substrates demonstrated that it specifically transported gentisate into the cells with V(max and K(m of 3.06 ± 0.16 nmol/min/mg of dry weight and 10.71 ± 0.11 µM respectively, and no activity was detected for either benzoate or 3-hydoxybenzoate. When GenK was absent in strain RES167 ΔgenK, it retained 85% of its original transport activity at pH 6.5 compared to that of strain RES167. However, it lost 79% and 88% activity at pH 7.5 and 8.0, respectively. A number of competing substrates, including 3-hydroxybenzoate, benzoate, protocatechuate and catechol, significantly inhibited gentisate uptake by more than 40%. Through site-directed mutagenesis, eight amino acid residues of GenK, Asp-54, Asp-57 and Arg-386 in the hydrophobic transmembrane regions and Arg-103, Trp-309, Asp-312, Arg-313 and Ile-317 in the hydrophilic cytoplasmic loops were shown to be important for gentisate transport. When conserved residues Asp-54 and Asp-57 respectively were changed to glutamate, both mutants retained approximately 50% activity and were able to partially complement the ability of strain RES167 ΔgenK to grow on gentisate. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that GenK is an active gentisate transporter in Corynebacterium glutamicum ATCC13032. The GenK-mediated gentisate transport was also shown to be a limiting step for the gentisate utilization by this strain. This enhances our

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

    Science.gov (United States)

    Zhao, Chunfeng; Noskov, Sergei Yu

    2013-10-01

    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 than that to the

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

    Science.gov (United States)

    Jee, Sang Eun; Sholl, David

    2009-03-01

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

  13. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)

    Science.gov (United States)

    Lill, Markus A.; Helms, Volkhard

    2001-11-01

    A very efficient scheme is presented to simulate proton transport by classical molecular dynamics simulation coupled with quantum mechanically derived proton hopping. Simulated proton transfer rates and proton diffusion constants for an excess proton in a box of water molecules are in good agreement with experimental data and with previous simulations that employed empirical valence bond (EVB) theory. For the first time, the proton occupancy of an aspartic acid residue in water was computed directly by MD simulations. Locally enhanced sampling or multi copy techniques were used to facilitate proton release in simulations of an imidazole ring in a solvent box. Summarizing, a quasiclassical description of proton transfer dynamics has been able to capture important kinetic and thermodynamic features of these systems at less than 50% computational overhead compared to standard molecular dynamics simulations. The method can be easily generalized to simulate the protonation equilibria of a large number of titratable sites. This should make it an attractive method to study proton transport in large biological systems.

  14. 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.

  15. [Conformation motion equation and primitive molecular machines for electron (ion) transport in biological systems].

    Science.gov (United States)

    Shaĭtan, K V; Rubin, A B

    1982-01-01

    A general theory of electron-conformation interactions and correlation between electron transfer rates and conformational mobility are discussed on the basis of a stochastic model of protein dynamics. A set of equations is developed and solved for primitive molecular "machines". Estimation of structural parameters for the reduction of the secondary acceptor in bacterial photosynthesis is given.

  16. 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.

  17. A switchable DNA origami nanochannel for regulating molecular transport at the nanometer scale

    Science.gov (United States)

    Wang, Dianming; Zhang, Yiyang; Wang, Miao; Dong, Yuanchen; Zhou, Chao; Isbell, Mark Antonin; Yang, Zhongqiang; Liu, Huajie; Liu, Dongsheng

    2016-02-01

    A nanochannel with a shutter at one end was built by DNA nanotechnology. Using DNA hybridization the shutter could be opened or closed, influencing the transport of materials through the channel. This process was visualized by an enzyme cascade reaction occurring in the structure.A nanochannel with a shutter at one end was built by DNA nanotechnology. Using DNA hybridization the shutter could be opened or closed, influencing the transport of materials through the channel. This process was visualized by an enzyme cascade reaction occurring in the structure. Electronic supplementary information (ESI) available: Experimental details including methods, materials, ESI figures and DNA sequences. See DOI: 10.1039/c5nr08206d

  18. Molecular cloning and ontogenesis expression of fatty acid transport protein-1 in yellow-feathered broilers.

    Science.gov (United States)

    Song, Yuzhen; Feng, Jiaying; Zhou, Lihua; Shu, Gang; Zhu, Xiaotong; Gao, Ping; Zhang, Yongliang; Jiang, Qingyan

    2008-06-01

    Fatty acid transport protein-1 (FATP-1) is one of the important transporter proteins involved in fatty acid transmembrane transport and fat deposition. To study the relationship between FATP-1 mRNA expression and fat deposition, chicken (Gallus gallus) FATP-1 sequence was first cloned by rapid amplification of cDNA ends (RACE). Tissue samples of chest muscle, leg muscle, subcutaneous fat, and abdominal fat were collected from six male and six female broilers each, at 22 days, 29 days, and 42 days, respectively. The tissue specificity and ontogenesis expression pattern of the FATP-1 mRNA of yellow-feathered broilers was studied by real-time reverse transcription polymerase chain reaction (RT-PCR), and the fat deposition laws in different tissues were also compared. A 2,488 bp cDNA sequence of chicken FATP-1 was cloned by RACE (GenBank accession no. DQ352834), including 547 bp 3' end untranslated region (URT) and 1,941 bp open reading frame (ORF). Chicken FATP-1 encoded 646 amino acid residues, which shared 83.9% and 83.0% identity with those of human and rat, respectively. The results of quantitative PCR demonstrated a constant FATP-1 mRNA expression level in the chest muscle and subcutaneous fat of both male and female broilers at three stages, whereas the expression level of the FATP-1 mRNA in the leg muscle at 42 days was significantly higher than that at 22 days or 29 days. In the abdominal fat of male broilers, the gene expression significantly increased with age, whereas the female broilers showed a dramatic downregulation of FATP-1 expression in abdominal fat at 42 days. This suggested a typical tissue- and gender-specific expression pattern of chicken FATP-1, mediating the specific process of fatty acid transport or utilization in muscle and adipose tissues.

  19. Molecular cloning and ontogenesis expression of fatty acid transport protein-1 in yellow-feathered broilers

    Institute of Scientific and Technical Information of China (English)

    Yuzhen Song; Jiaying Feng; Lihua Zhou; Gang Shu; Xiaotong Zhu; Ping Gao; Yongliang Zhang; Qingyan Jiang

    2008-01-01

    Fatty acid transport protein-1 (FATP-1) is one of the important transporter proteins involved in fatty acid transmembrane transport and fat deposition. To study the relationship between FATP-1 mRNA expression and fat deposition, chicken (Gallus gallus) FATP-1 sequence was first cloned by rapid amplification of cDNA ends (RACE). Tissue samples of chest muscle, leg muscle, subcutaneous fat, and abdominal fat were collected from six male and six female broilers each, at 22 days, 29 days, and 42 days, respectively. The tissue specificity and ontogenesis expression pattern of the FATP-1 mRNA of yellow-feathered broilers was studied by real-time reverse transcription polymerase chain reaction (RT-PCR), and the fat deposition laws in different tissues were also compared. A 2,488 bp cDNA sequence of chicken FATP-1 was cloned by RACE (GenBank accession no. DQ352834), including 547 bp 3' end untranslated region (URT) and 1,941 bp open reading frame (ORF). Chicken FATP-1 encoded 646 amino acid residues, which shared 83.9% and 83.0% identity with those of human and rat, respectively. The results of quantitative PCR demonstrated a constant FATP-1 mRNA expression level in the chest muscle and subcutaneous fat of both male and female broilers at three stages, whereas the expression level of the FATP-1 mRNA in the leg muscle at 42 days was significantly higher than that at 22 days or 29 days. In the abdominal fat of male broilers, the gene expression significantly increased with age, whereas the female broilers showed a dramatic downregulation of FATP-1 expression in abdominal fat at 42 days. This suggested a typical tissue-and gender-specific expression pattern of chicken FATP-1, mediating the specific process of fatty acid transport or utilization in muscle and adipose tissues.

  20. Self-assembly, redox activity, and charge transport of functional surface nano-architectures by molecular design

    Science.gov (United States)

    Skomski, Daniel

    Surface-assisted molecular self-assembly is a promising strategy to program the structure and chemical state of atoms and molecules in nano-architectures to achieve a specific function. The experiments described in this thesis demonstrate that the design and programming of basic organic components leads to desired characteristics by self-assembly. The fabrication of uniform single-site metal centers at surfaces, important for high selectivity in next-generation catalysts, was accomplished by coordination to redox non-innocent phenanthroline and tetrazine-based ligands. These examples were the first demonstrating tuning of the metal oxidation state in surface coordination architectures through rational ligand design. The molecular-scale coordination architectures were the first formed from chromium and vanadium, and the first from platinum in a non-porphyrin system. The first mixed valence metal-ligand surface structure was fabricated that attained the same ligand coordination number for all metal sites. A new surface reaction method was demonstrated between an inexpensive sodium chloride reagent and carboxylate ligands. High-temperature, molecular-resolution microscopy and spectroscopy of the ordered metal-organic structures demonstrated thermal stability up to 300 °C, the highest molecular-level thermal stability in organic surface nanostructures yet achieved, making such systems potential candidates for moderate-temperature catalytic reactions. Molecular self-assembly was expanded into organic semiconductor thin films. In a two-component, bi-layered system, hydrogen bonding between carboxylates and carboxylic acid-substituted thiophenes was utilized, yielding the first real-space images of phenyl-thiophene stacking. In a one-component system, multiple donor-acceptor pi-pi contacts between phenyltriazole building blocks accomplished assembly of flat-lying molecules from a surface with molecular-scale precision through more than twenty molecular layers. Sufficient

  1. Collective effects in intra-cellular molecular motor transport: coordination, cooperation and competetion

    CERN Document Server

    Chowdhury, D

    2006-01-01

    Molecular motors do not work in isolation {\\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like movement of motors on a track, we emphasize the importance of single-motor bio-chemical cycle and enzymatic activity on their collective spatio-temporal organisation. Our modelling strategy is based on a synthesis- the same model describes the single-motor mechano-chemistry at sufficiently low densities whereas at higher densities it accounts for the collective flow properties and the density profiles of the motors. We consider two specific examples, namely, traffic of single-headed kinesin motors KIF1A on a microtubule track and ribosome traffic on a messenger RNA track.

  2. 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.

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

    OpenAIRE

    Pshenichnyuk, Ivan A.; Čížek, Martin

    2010-01-01

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

  4. The synthesis and molecular recognization of the polyamine transporter of hydrazine-modified diamine conjugates

    Institute of Scientific and Technical Information of China (English)

    Jun Jun Zhou; Hao Huang; Song Qiang Xie; Yu Xia Wang; Jin Zhao; Chao Jie Wang

    2008-01-01

    A series of four novel hydrazine-modified diamine conjugates (7a-b, 8a-b) were synthesized and evaluated for cytotoxicityagainst Melanoma B 16, α-difluoromethylornithine (DFMO)-treated B 16, spermidine (SPD)-treated B 16, Mouse leukemia L 1210and Hela cell lines. Both the DFMO-B 16 and SPD-B 16 experiments indicated that conjugates 7a-b and 8a-b could recognize thepolyamine transporter (PAT) and enter the cells in part or in whole via PAT, although they were not as efficient as the reference, 9-anthracenemethyl homospermidine (1).

  5. Effect of the molecular chain orientation on carrier transport and optical properties of polymer blends

    Science.gov (United States)

    Kažukauskas, V.; Čyras, V.; Pranaitis, M.; Apostoluk, A.; Rocha, L.; Sicot, L.; Raimond, P.; Sentein, C.

    2007-03-01

    We have investigated properties of poly(9-vinylcarbazole) (PVK) doped with 30% wt 4-dibutylamino-4'-nitrostilbene (DBANS), depending on the orientation of the polar DBANS molecules. Appearance of the orientation-induced built-in electrical field was proven optically by the Solid Electric Field Induced Second Harmonic Generation and electrically by Current-Voltage characterization. Modification of optical properties was evidenced by the spectral dependencies of absorption coefficient. The Thermally Stimulated Currents spectra demonstrated that carrier transport and trapping are affected, too. This paper has been presented at “ECHOS06”, Paris, 28 30 juin 2006.

  6. 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.

  7. Non-equilibrium molecular simulations of simple fluid transport at fluid-solid interfaces and fluidic behaviors at nanoscale

    Science.gov (United States)

    Yong, Xin

    Nano fluidics has shown promising potential for applications that could significantly impact our daily life, such as energy harvest, lab on a chip, desalination, etc. Current techniques to realize nano fluidic ideas are still very limited due to manufacturing technology. Although sub-micron fabrication techniques are undergoing rapid development recently, scientists and engineers are still not able to access actual nanometric systems. This reason prompts the development of computational tools to reveal physical principles underlying nano fluidic phenomena. Among various numerical approaches ranging from macroscopic to microscopic, molecular dynamics stands out because of its ability to faithfully model both equilibrium and non-equilibrium nanosystems by involving an appropriate amount of molecular details. The results from molecular dynamics simulations could elucidate essential physics and benefit designs of practical nano fluidic systems. This thesis attempts to provide the theoretical foundation for modeling nano fluidic systems, by investigating nanoscale fluid behaviors and nanoscale fluid-solid interfacial physics and transport for simple fluids via molecular dynamics simulations. Boundary-driven-shear, homogeneous-shear and reverse non-equilibrium molecular dynamics methods are implemented to generate non-equilibrium systems. The fundamental fluid behaviors such as velocity profile, temperature distribution and rheological material functions under steady planar shear are explored comprehensively by each method corresponding to different perspectives. The influences of nanoscale confinement are analyzed from the comparison among these methods. The advantages and disadvantages of each method are clarified, which provide guidance to conduct appropriate molecular dynamics simulations for nano fluidics. Further studies on the intrinsic slip of smooth solid surfaces is realized by the boundary-driven-shear method. Inspired by previous hypothesis of momentum

  8. Unravelling Doping Effects on PEDOT at the Molecular Level: From Geometry to Thermoelectric Transport Properties.

    Science.gov (United States)

    Shi, Wen; Zhao, Tianqi; Xi, Jinyang; Wang, Dong; Shuai, Zhigang

    2015-10-14

    Tuning carrier concentration via chemical doping is the most successful strategy to optimize the thermoelectric figure of merit. Nevertheless, how the dopants affect charge transport is not completely understood. Here we unravel the doping effects by explicitly including the scattering of charge carriers with dopants on thermoelectric properties of poly(3,4-ethylenedioxythiophene), PEDOT, which is a p-type thermoelectric material with the highest figure of merit reported. We corroborate that the PEDOT exhibits a distinct transition from the aromatic to quinoid-like structure of backbone, and a semiconductor-to-metal transition with an increase in the level of doping. We identify a close-to-unity charge transfer from PEDOT to the dopant, and find that the ionized impurity scattering dominates over the acoustic phonon scattering in the doped PEDOT. By incorporating both scattering mechanisms, the doped PEDOT exhibits mobility, Seebeck coefficient and power factors in very good agreement with the experimental data, and the lightly doped PEDOT exhibits thermoelectric properties superior to the heavily doped one. We reveal that the thermoelectric transport is highly anisotropic in ordered crystals, and suggest to utilize large power factors in the direction of polymer backbone and low lattice thermal conductivity in the stacking and lamellar directions, which is viable in chain-oriented amorphous nanofibers.

  9. Molecular evolutionary analysis of the high-affinity K+ transporter gene family in angiosperms.

    Science.gov (United States)

    Yang, P; Hua, C; Zhou, F; Zhang, B-J; Cai, X-N; Chen, Q-Z; Wang, R-L

    2016-07-15

    The high-affinity K(+) transporter (HKT) family comprises a group of multifunctional cation transporters widely distributed in organisms ranging from Bacteria to Eukarya. In angiosperms, the HKT family consists primarily of nine types, whose evolutionary relationships are not fully understood. The available sequences from 31 plant species were used to perform a comprehensive evolutionary analysis, including an examination of selection pressure and estimating phylogenetic tree and gene duplication events. Our results show that a gene duplication in the HKT1;5/HKT1;4 cluster might have led to the divergence of the HKT1;5 and HKT1;4 subfamilies. Additionally, maximum likelihood analysis revealed that the HKT family has undergone a strong purifying selection. An analysis of the amino acids provided strong statistical evidence for a functional divergence between subfamilies 1 and 2. Our study was the first to provide evidence of this functional divergence between these two subfamilies. Analysis of co-evolution in HKT identified 25 co-evolved groups. These findings expanded our understanding of the evolutionary mechanisms driving functional diversification of HKT proteins.

  10. Molecular cloning and structural analysis of human norepinephrine transporter gene(NETHG)

    Institute of Scientific and Technical Information of China (English)

    GUOLIHE; LIHUAZHU; 等

    1995-01-01

    A cDNA molecule encoding a major part of the human Norepinephrine transporter(hNET) was synthesized by means of Polymerase Chain Reaction(PCR) technique and used as a probe for selecting the human genomic NET gene.A positive clone harbouring the whole gene was obtained from a human lymphocyte genomic library through utilizing the “genomic walking” technique.The clone,designated as phNET,harbours a DNA fragment of about 59 kd in length inserted into BamH I site in cosmid pWE15.The genomic clone contains 14 exons encoding all amino acid residues in the protein.A single exon encodes a distinct transmembrane domain,except for transmembrane domain 10 and 11,which are encoded by part of two exons respectively,and exon 12,which encodes part of domain 11 and all of domain 12.These results imply that there is a close relationship between exon splicing of a gene and structureal domains of the protein,as is the case for the human γ-aminobutyric acid transporter(hGAT) and a number of other membrane proteins.

  11. Transport coefficients of normal liquid helium-4 calculated by path integral centroid molecular dynamics simulation

    Science.gov (United States)

    Imaoka, Haruna; Kinugawa, Kenichi

    2017-03-01

    Thermal conductivity, shear viscosity, and bulk viscosity of normal liquid 4He at 1.7-4.0 K are calculated using path integral centroid molecular dynamics (CMD) simulations. The calculated thermal conductivity and shear viscosity above lambda transition temperature are on the same order of magnitude as experimental values, while the agreement of shear viscosity is better. Above 2.3 K the CMD well reproduces the temperature dependences of isochoric shear viscosity and of the time integral of the energy current and off-diagonal stress tensor correlation functions. The calculated bulk viscosity, not known in experiments, is several times larger than shear viscosity.

  12. Effect of molecular diameters on state-to-state transport properties: The shear viscosity coefficient

    Science.gov (United States)

    Kustova, Elena V.; Kremer, Gilberto M.

    2015-09-01

    Shear viscosity coefficient is calculated for both equilibrium and strongly non-equilibrium state-to-state vibrational distributions taking into account increasing diameters of vibrationally excited molecules. Under conditions of local thermal equilibrium, the effect of vibrational excitation on the shear viscosity coefficient is found to be negligible for temperatures below 5000 K. For T > 10 000 K, the contribution of excited states becomes important. Under non-equilibrium conditions characteristic for shock heated and supersonic expanding flows vibrational level populations deviate strongly from the Boltzmann distribution. Nevertheless, estimated coupled effect of molecular size and non-Boltzmann distributions on the shear viscosity coefficient is negligible.

  13. Photoinduced interfacial electron transfer and lateral charge transport in molecular donor-acceptor photovoltaic systems.

    Science.gov (United States)

    Punzi, Angela; Brauer, Jan C; Marchioro, Arianna; Ghadiri, Elham; de Jonghe, Jelissa; Moser, Jacques E

    2011-01-01

    Nanostructured liquid/solid and solid/solid bulk heterojunctions designed for the conversion of solar energy offer ideal models for the investigation of light-induced ET dynamics at surfaces. Despite significant study of processes leading to charge generation in third-generation solar cells, a conclusive picture of the photophysics of these photovoltaic converters is still missing. More specifically searched is the link between the molecular structure of the interface and the kinetics of surface photoredox reactions. Fundamental scientific issues in this field are addressed by the research project undertaken in the frame of the NCCR MUST endeavor, an outline of which is given here.

  14. Molecular dynamics study on mechanism of preformed particle gel transporting through nanopores: Surface chemistry and heterogeneity

    Science.gov (United States)

    Cui, Peng; Zhang, Heng; Ma, Ying; Hao, Qingquan; Liu, Gang; Sun, Jichao; Yuan, Shiling

    2017-10-01

    The translocation behavior of preformed particle gel (PPG) in porous media is crucial for its application in enhanced oil recovery. By means of non-equilibrium molecular dynamics simulation, the translocation mechanism of PPG confined in different silica nanopores were investigated. The influence of surface chemistry and chemical heterogeneity of silica nanopore on the translocation process was revealed. As the degree of surface hydroxylation increases and the heterogeneity decreases, the pulling force needed to drive PPG decreases. We infer that the nanopore's surface (i.e. surface chemistry and heterogeneity) affects the translocation of PPG indirectly by forming different hydration layers.

  15. First-Principles Molecular Dynamics Investigation of the Atomic-Scale Energy Transport: From Heat Conduction to Thermal Radiation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing thermostats to keep constant temperatures of the nanoscale thin layers, initial thermal non-equilibrium between the neighboring layers is established under the vacuum condition. Models with variable gap distances with an interval of lattice constant increment of the simulated materials are set up and statistical comparisons of temperature evolution curves are made. Moreover, the equilibration time from non-equilibrium state to thermal equilibrium state of different silicon or/and germanium layers combinations are calculated. The results show significant distinctions of heat transfer under different materials and temperatures combinations. Further discussions on the equilibrium time are made to explain the simulation results. As the first work of the atomic scale energy tra...

  16. 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.

  17. Anchor position and donor/acceptor effects on transport properties in fused benzene-substituted oligothiophene molecular device

    Science.gov (United States)

    Gathitu, Nahashon Ndegwa; Chang, Yingfei; Zhang, Jingping

    2013-12-01

    Utilizing non-equilibrium Green's functions in combination with density-functional theory, the transport properties of molecular devices based on fused benzene-substituted oligothiophenes were explored theoretically. The results show that the positions of anchor group and push-pull substituent groups can affect the conduction properties significantly, and the favorite current direction of the investigated devices can be tuned by applied bias. The first-principle calculations demonstrate that the forward current is favorable under low bias due to the asymmetric shift of transmission peaks of those that are derived from the resonant tunneling through HOMO state, while the asymmetric localization of HOMO states under high bias is beneficial to the reverse current.

  18. Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium

    Science.gov (United States)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-02-01

    We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code inferno. The inferno-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.

  19. Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium.

    Science.gov (United States)

    Kress, J D; Cohen, James S; Kilcrease, D P; Horner, D A; Collins, L A

    2011-02-01

    We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code INFERNO. The INFERNO-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.

  20. Charge Density Analysis and Transport Properties of TTF Based Molecular Nanowires: A DFT Approach

    Directory of Open Access Journals (Sweden)

    Karuppannan Selvaraju

    2015-01-01

    Full Text Available The present study has been performed to understand the charge density distribution and the electrical characteristics of Au and thiol substituted tetrathiafulvalene (TTF based molecular nanowire. A quantum chemical calculation has been carried out using DFT method (B3LYP with the LANL2DZ basis set under various applied electric fields (EFs. The bond topological analysis characterizes the terminal Au–S and S–C bonds as well as all the bonds of central TTF unit of the molecule. The variation of electron density and Laplacian of electron density at the bond critical point of bonds for zero and different applied fields reveal the electron density distribution of the molecule. The molecular conformation, the variation of atomic charges and energy density distribution of the molecule have been analyzed for the various levels of applied EFs. The HOMO-LUMO gap calculated from quantum chemical calculations has been compared with the value calculated from the density of states. The variation of dipole moment due to the polarization effect and the I-V characteristics of the molecule for the various applied EFs have been well discussed.

  1. 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.

  2. 分子马达的输运方式研究进展%Research Progress on Transport Ways of the Molecular Motors

    Institute of Scientific and Technical Information of China (English)

    吴魏霞

    2012-01-01

    分子马达(molecularmotor)是生物体细胞内一类具有马达功能的蛋白质大分子,几乎执行了生物体的所有生命活动,其中物质的输运是分子马达的一项重要功能。以往人们一直认为分子马达都是沿着单一轨道单独来输运物质,但随着实验的发展,研究发现分子马达的输运方式多种多样,并且输运过程与多种疾病有关。就分子马达的输运方式最新进展进行综述,阐述分子马达在体内可能的输运方式及与输运过程相关的疾病,最后总结并展望未来。%Molecular motors are protein that perform all tasks vital to the life. Intracellular transport is a very important task. In the past years, people insisted that individual molecular motor transported 'cargo' along single track. But in recent years, various transport ways of molecular motors have been observed from experiments. In addition, research results show that many diseases associate with transport of molecular motors. The new process about transport ways of molecular motors is summarized, including the possible transport behavior patterns of molecular motors and the related diseases. A summary is given and possible future directions are discussed.

  3. Flow and transport in brush-coated capillaries: A molecular dynamics simulation

    Science.gov (United States)

    Dimitrov, D. I.; Klushin, L. I.; Milchev, A.; Binder, K.

    2008-09-01

    We apply an efficient method of forced imbibition to (nano-)capillaries, coated internally with a polymer brush, to derive the change in permeability and suction force, corresponding to different grafting densities and lengths of the polymer chains. While the fluid is modeled by simple point particles interacting with Lennard-Jones forces, the (end-grafted, fully flexible) polymers, which form the brush coating, are described by a standard bead-spring model. Our computer experiments reveal a significant increase in the suction force (by a factor of 4, as compared to the case of a capillary with bare walls) when the brush width approaches the tube radius. A similar growth in the suction force is found when the grafting density of the brush is systematically increased. Even though the permeability of the tube is found to decline with both growing brush width and grafting density, the combined effect on the overall fluid influx into the capillary turns out to be weak, i.e., the total fluid uptake under spontaneous imbibition decreases only moderately. Thus we demonstrate that one may transport the fluid in vertical brush-coated capillaries to a much larger height than in an equivalent capillary with bare walls. Eventually, we also study the spreading of tracer particles transported by the uptaking fluid in brush-coated capillaries with regard to the grafting density of the brush and the length of the polymers. The observed characteristic asymmetric concentration profiles of the tracers and their evolution with elapsed time are interpreted in terms of a drift-diffusion equation with a reflecting boundary that moves with the fluid front. The resulting theoretical density profiles of the tracer particles are found to be in good agreement with those observed in the computer experiment.

  4. 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.

  5. Charge transport across insulating self-assembled monolayers: non-equilibrium approaches and modeling to relate current and molecular structure.

    Science.gov (United States)

    Mirjani, Fatemeh; Thijssen, Joseph M; Whitesides, George M; Ratner, Mark A

    2014-12-23

    This paper examines charge transport by tunneling across a series of electrically insulating molecules with the structure HS(CH2)4CONH(CH2)2R) in the form of self-assembled monolayers (SAMs), supported on silver. The molecules examined were studied experimentally by Yoon et al. (Angew. Chem. Int. Ed. 2012, 51, 4658-4661), using junctions of the structure AgS(CH2)4CONH(CH2)2R//Ga2O3/EGaIn. The tail group R had approximately the same length for all molecules, but a range of different structures. Changing the R entity over the range of different structures (aliphatic to aromatic) does not influence the conductance significantly. To rationalize this surprising result, we investigate transport through these SAMs theoretically, using both full quantum methods and a generic, independent-electron tight-binding toy model. We find that the highest occupied molecular orbital, which is largely responsible for the transport in these molecules, is always strongly localized on the thiol group. The relative insensitivity of the current density to the structure of the R group is due to a combination of the couplings between the carbon chains and the transmission inside the tail. Changing from saturated to conjugated tail groups increases the latter but decreases the former. This work indicates that significant control over SAMs largely composed of nominally insulating groups may be possible when tail groups are used that are significantly larger than those used in the experiments of Yoon et al.1.

  6. 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.

  7. 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......, and hibernating mammals, as an example of closely balanced internal low O2. Studies have had two main focus points. Firstly, I have investigated variations in hemolysate and hemoglobin (Hb) O2 affinity, working to pinpoint whether and how functional changes in intrinsic affinity or cofactor sensitivity of the Hb...... molecule compares to amino acid substitutions in the molecule, i.e., can be characterized as evolved genetic adaptation. Phenotypic acclimatization in Hb- O2 affinity responses involves changes in cofactor to Hb tetramer ratio. Secondly, I have worked with (in a cardiovascular perspective) fine...

  8. Field-enhanced ion transport in solids: Reexamination with molecular dynamics simulations

    Science.gov (United States)

    Genreith-Schriever, A. R.; De Souza, R. A.

    2016-12-01

    Classical molecular-dynamics simulations were used to examine the effect of an electric field on the mobility of oxygen ions in the model crystalline oxide CeO2. Simulation cells containing oxygen vacancies were subjected at temperatures 1000 ≤T /K ≤1600 to electric field strengths 0.1 ≤E /MV cm-1≤40 to obtain the oxygen-ion mobility ui(E ,T ) . In addition, static nudged-elastic-band calculations were performed to obtain directly the forward/reverse barriers for oxygen-ion migration, Δ Hmigf /r . Qualitatively, ui behaves as expected: independent of E at low values of E and exponentially dependent on E at high values. The quantitative (standard) Mott-Gurney treatment, however, underestimates Δ Hmigf at high E and thus overestimates ui. A new, superior analytical expression for ui(E ,T ) is consequently derived.

  9. Molecular Dynamics Simulations Illuminate the Role of Counterion Condensation in the Electrophoretic Transport of Homogalacturonans.

    Science.gov (United States)

    Irani, Amir H; Owen, Jessie L; Mercadante, Davide; Williams, Martin A K

    2017-02-13

    Homogalacturonans (HGs) are polysaccharide copolymers of galacturonic acid and its methylesterified counterpart. The inter- and intramolecular distributions of the methylesterifed residues are vital behavior-determining characteristics of a sample's structure, and much experimental effort has been directed to their measurement. While many techniques are able to measure the sample-averaged degree of methylesterification (DM), the measurement of inter- and intramolecular charge distributions are challenging. Here, molecular dynamics (MD) simulations are used to calculate the electrophoretic mobilities of HGs that have different amounts and distributions of charges placed along the backbone. The simulations are shown to capture experimental results well, even for low-DM samples that possess high charge densities. In addition, they illuminate the role that local counterion condensation can play in the determination of the electrophoretic mobility of heterogeneous blocky polyelectrolytes that cannot be adequately described by a single chain-averaged charge spacing.

  10. Anisotropy effects in phonon-assisted charge-carrier transport in organic molecular crystals

    Science.gov (United States)

    Hannewald, K.; Bobbert, P. A.

    2004-02-01

    We present a theoretical description of polaron dc conductivities in organic molecular crystals. Our approach is based on a rigorous evaluation of the Kubo formula for electrical conductivity within a mixed Holstein-Peierls model. It generalizes the result of Holstein’s local-coupling theory by treating both local and nonlocal electron-phonon interactions nonperturbatively. The general theory is supplemented by an application to a simplified model crystal in order to emphasize the essential physics. Accompanied by an illustrative numerical example, special emphasis is put on the emergence of anisotropy effects in the temperature dependence of the conductivity tensor. These anisotropy effects are shown to originate from phonon-assisted currents due to the nonlocal electron-lattice interaction which demonstrates the importance to go beyond local-coupling theories in order to describe the experimental observations.

  11. 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.

  12. A molecular network for the transport of the TI-VAMP/VAMP7 vesicles from cell center to periphery.

    Science.gov (United States)

    Burgo, Andrea; Proux-Gillardeaux, Véronique; Sotirakis, Emmanuel; Bun, Philippe; Casano, Alessandra; Verraes, Agathe; Liem, Ronald K H; Formstecher, Etienne; Coppey-Moisan, Maïté; Galli, Thierry

    2012-07-17

    The compartmental organization of eukaryotic cells is maintained dynamically by vesicular trafficking. SNARE proteins play a crucial role in intracellular membrane fusion and need to be targeted to their proper donor or acceptor membrane. The molecular mechanisms that allow for the secretory vesicles carrying the v-SNARE TI-VAMP/VAMP7 to leave the cell center, load onto microtubules, and reach the periphery to mediate exocytosis are largely unknown. Here, we show that the TI-VAMP/VAMP7 partner Varp, a Rab21 guanine nucleotide exchange factor, interacts with GolginA4 and the kinesin 1 Kif5A. Activated Rab21-GTP in turn binds to MACF1, an actin and microtubule regulator, which is itself a partner of GolginA4. These components are required for directed movement of TI-VAMP/VAMP7 vesicles from the cell center to the cell periphery. The molecular mechanisms uncovered here suggest an integrated view of the transport of vesicles carrying a specific v-SNARE toward the cell surface.

  13. Molecular structure of the discotic liquid crystalline phase of hexa-peri-hexabenzocoronene/oligothiophene hybrid and their charge transport properties

    Energy Technology Data Exchange (ETDEWEB)

    Bag, Saientan; Maingi, Vishal; Maiti, Prabal K., E-mail: maiti@physics.iisc.ernet.in [Department of Physics, Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012 (India); Yelk, Joe; Glaser, Matthew A.; Clark, Noel A. [Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States); Walba, David M. [Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 (United States)

    2015-10-14

    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.

  14. Understanding the relationship between molecular order and charge transport properties in conjugated polymer based organic blend photovoltaic devices.

    Science.gov (United States)

    Wood, Sebastian; Kim, Jong Soo; James, David T; Tsoi, Wing C; Murphy, Craig E; Kim, Ji-Seon

    2013-08-14

    We report a detailed characterization of the thin film morphology of all-polymer blend devices by applying a combined analysis of physical, chemical, optical, and charge transport properties. This is exemplified by considering a model system comprising poly(3-hexylthiophene) (P3HT) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT). We show that the interactions between the two conjugated polymer components can be controlled by pre-forming the P3HT into highly ordered nanowire structures prior to blending with F8BT, and by varying the molecular weight of the F8BT. As a result, it is possible to produce films containing highly ordered P3HT with hole mobilities enhanced by three orders of magnitude over the pristine blends. Raman spectroscopy under resonant excitation conditions is used to probe the molecular order of both P3HT and F8BT phases within the blend films and these morphological studies are complemented by measurements of photocurrent generation. The resultant increase in photocurrent is associated with the enhanced charge carrier mobilities. The complementary analytical method demonstrated here is applicable to a wide range of polymer blend systems for all applications where the relationships between morphology and device performance are of interest.

  15. Effect of metallation, substituents and inter/intra-molecular polarization on electronic couplings for hole transport in stacked porphyrin dyads.

    Science.gov (United States)

    Hernández-Fernández, F; Pavanello, M; Visscher, L

    2016-08-03

    We carried out a systematic study of the hole transport properties for a series of symmetrically stacked porphyrin dimers. In the first part of this study, we evaluated the sensitivity of electronic couplings to orbital relaxation due to molecular ionization and intermolecular interactions for a series of halogenated porphyrins. The effect of polarization was estimated by comparing electronic couplings from fragment orbital density functional theory (FODFT) and frozen density embedding electron transfer (FDE-CT). For the dimers considered, the effect of polarization was estimated to be less than 20%, in line with previous studies on different molecular dimers. Thus, we decided to employ a computationally cheaper FODFT method to continue our study of the effect of metals and substituents on the electronic couplings for hole transfer. We find that, compared to the non-metallated porphyrins, Ni, Fe and Pt significantly reduce the coupling, while Zn, Ti, Cd and Pd increase it. The effect of substituents was studied on a series of meso-substituted porphyrins (meso-tetrapyridineporphyrin, meso-tetraphenylporphyrin and derivatives) for which we could relate a reduction of the coupling to steric effects that reduce the overlap between the frontier orbitals of the monomers.

  16. Effects of energy correlations and superexchange on charge transport and exciton formation in amorphous molecular semiconductors: An ab initio study

    Science.gov (United States)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Meded, Velimir; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2017-03-01

    In this study, we investigate on the basis of ab initio calculations how the morphology, molecular on-site energies, reorganization energies, and charge transfer integral distribution affect the hopping charge transport and the exciton formation process in disordered organic semiconductors. We focus on three materials applied frequently in organic light-emitting diodes: α -NPD , TCTA, and Spiro-DPVBi. Spatially correlated disorder and, more importantly, superexchange contributions to the transfer integrals, are found to give rise to a significant increase of the electric field dependence of the electron and hole mobility. Furthermore, a material-specific correlation is found between the HOMO and LUMO energy on each specific molecular site. For α -NPD and TCTA, we find a positive correlation between the HOMO and LUMO energies, dominated by a Coulombic contribution to the energies. In contrast, Spiro-DPVBi shows a negative correlation, dominated by a conformational contribution. The size and sign of this correlation have a strong influence on the exciton formation rate.

  17. 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

  18. Crucial role of decoherence for electronic transport in molecular wires: Polyaniline as a case study

    Science.gov (United States)

    Cattena, Carlos J.; Bustos-Marún, Raúl A.; Pastawski, Horacio M.

    2010-10-01

    In this work we attempt to elucidate the nature of conductivity in polymers by taking the acid-base doped polyaniline (PAni) polymer. We evaluate the PAni conductance by using realistic ab initio parameters and including decoherent processes within the minimal parametrization model of D’Amato-Pastawski. In contrast to general wisdom, which associates the conducting state with coherent propagation in a periodic polaronic lattice, we show that decoherence can account for high conductance in the strongly disordered bipolaronic lattice. Hence, according to our results, there is no need of considering a mix model of “conducting” polaronic lattice islands separated by “insulating” bipolaronic lattice strands as is usually assumed for PAni. We find that without dephasing events, even very short strands of bipolaronic lattices are not able to sustain electronic transport. We also include a discussion of specific mechanisms that should be involved in decoherence rates of PAni and relate them with Marcus-Hush theory of electron transfer.

  19. Transport phenomena of electrons at the carbon nanotube interface with molecular adsorption

    Science.gov (United States)

    Kokabu, Takuya; Takashima, Kengo; Inoue, Shuhei; Matsumura, Yukihiko; Yamamoto, Takahiro

    2017-07-01

    The electric conductance of carbon-nanotube (CNT) films is affected by gas adsorption. Previous studies have shown that the adsorption of gas molecules on the CNT/CNT interface is the key to the changing CNT-film conductance. However, it is still unclear how the gas molecules affect the electric conduction of the CNT/CNT interface or its electron transport properties. We present here a study on the effects of gas-molecule adsorption on the CNT/CNT interface using a fluctuation-induced tunneling (FIT) model of the CNT-film electrical conduction. We demonstrated that the CNT-film conduction follows the FIT model, and the subsequently estimated electrostatic potential between the CNT/CNT interfaces was in good agreement with estimates from density functional theory simulations. Since the FIT model treats the CNT/CNT interface as a parallel-plate capacitor, we propose a modified FIT model that accounts for the change in the dielectric constant at the CNT/CNT interface due to the adsorption of gas molecules. This model well explained the electric-conductance change of the CNT film with respect to the gas pressure. Finally, we found that the adsorbed gas molecules affected the local dielectric constant at the CNT/CNT interface.

  20. 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.

  1. 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.

  2. An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

    Science.gov (United States)

    Rognlien, Thomas; Rensink, Marvin

    2016-10-01

    Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

  3. Transport and morphological characteristics of polyetherimide-based carbon molecular sieve membranes

    Energy Technology Data Exchange (ETDEWEB)

    Sedigh, M.G.; Xu, L.; Tsotsis, T.T.; Sahimi, M. [Univ. of Southern California, Los Angeles, CA (United States). Dept. of Chemical Engineering

    1999-09-01

    A new class of carbon molecular sieve membranes (CMSMs) has been prepared by carbonization of polyetherimide-coated mesoporous tubular supports. The membranes show higher permeance and better separation factors than other supported CMSMs reported in the literature for the CO{sub 2}/CH{sub 4} and H{sub 2}/CH{sub 4} binary mixtures as well as for the CO{sub 2}H{sub 2}/CH{sub 4} ternary mixture. CO{sub 2}/CH{sub 4} separation factors as high as 145 for the equimolar binary and 155 for the ternary mixture were obtained with a CO{sub 2} permeance about 0.15 (cm{sup 3}/cm{sup 2}{center_dot}psi{center_dot}min). The corresponding H{sub 2}/CH{sub 4} separation factors for the equimolar binary and ternary mixtures were 68 and 50, respectively, with a H{sub 2} permeance of 0.13 (cm{sup 3}/cm{sup 2}{center_dot}psi{center_dot}min). The membrane also shows good stability when tested with CO{sub 2} and Ar single gases, as well as with an equimolar mixture of CO{sub 2}/CH{sub 4}. To study the mechanism of permeation and separation in CMSMs, tests with single gases as well as with binary and ternary mixtures were performed at different temperatures, transmembrane pressure differences, and feed compositions. Elemental analysis, scanning electron microscopy, and gas adsorption were also employed to study the morphology of the resulting membranes. Elemental analysis shows that although the structure consists mostly of carbon, it also still contains oxygen, nitrogen and hydrogen. Scanning electron microscopy of the cross section of the carbonized membrane shows that the carbonized layer lies essentially within the mesoporous {gamma}-alumina layer, a result also verified by N{sub 2} adsorption analysis at 77 K. The experimental data were compared with simulation results with the same mixtures using a nonequilibrium molecular dynamics method.

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

    KAUST Repository

    French, William R.

    2013-01-01

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

  5. 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.

  6. Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations

    Science.gov (United States)

    Li, Zhi-Guo; Cheng, Yan; Chen, Qi-Feng; Chen, Xiang-Rong

    2016-05-01

    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/cm3 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. Path-integral Monte Carlo simulations for electronic dynamics on molecular chains. II. Transport across impurities

    Science.gov (United States)

    Mühlbacher, Lothar; Ankerhold, Joachim

    2005-05-01

    Electron transfer (ET) across molecular chains including an impurity is studied based on a recently improved real-time path-integral Monte Carlo (PIMC) approach [L. Mühlbacher, J. Ankerhold, and C. Escher, J. Chem. Phys. 121 12696 (2004)]. The reduced electronic dynamics is studied for various bridge lengths and defect site energies. By determining intersite hopping rates from PIMC simulations up to moderate times, the relaxation process in the extreme long-time limit is captured within a sequential transfer model. The total transfer rate is extracted and shown to be enhanced for certain defect site energies. Superexchange turns out to be relevant for extreme gap energies only and then gives rise to different dynamical signatures for high- and low-lying defects. Further, it is revealed that the entire bridge compound approaches a steady state on a much shorter time scale than that related to the total transfer. This allows for a simplified description of ET along donor-bridge-acceptor systems in the long-time range.

  8. A hopping mechanism for cargo transport by molecular motors in crowded microtubules

    CERN Document Server

    Goldman, Carla

    2010-01-01

    Most models designed to study the bidirectional movement of cargos as they are driven by molecular motors rely on the idea that motors of different polarities can be coordinated by external agents if arranged into a motor-cargo complex to perform the necessary work [gross04]. Although these models have provided us with important insights into these phenomena, there are still many unanswered questions regarding the mechanisms through which the movement of the complex takes place on crowded microtubules. For example (i) how does cargo-binding affect motor motility? and in connection with that - (ii) how does the presence of other motors (and also other cargos) on the microtubule affect the motility of the motor-cargo complex? We discuss these questions from a different perspective. The movement of a cargo is conceived here as a hopping process resulting from the transference of cargo between neighboring motors. In the light of this, we examine the conditions under which cargo might display bidirectional movemen...

  9. Transport, resealing, and re-poration dynamics of two-pulse electroporation-mediated molecular delivery.

    Science.gov (United States)

    Demiryurek, Yasir; Nickaeen, Masoud; Zheng, Mingde; Yu, Miao; Zahn, Jeffrey D; Shreiber, David I; Lin, Hao; Shan, Jerry W

    2015-08-01

    Electroporation is of interest for many drug-delivery and gene-therapy applications. Prior studies have shown that a two-pulse-electroporation protocol consisting of a short-duration, high-voltage first pulse followed by a longer, low-voltage second pulse can increase delivery efficiency and preserve viability. In this work the effects of the field strength of the first and second pulses and the inter-pulse delay time on the delivery of two different-sized Fluorescein-Dextran (FD) conjugates are investigated. A series of two-pulse-electroporation experiments were performed on 3T3-mouse fibroblast cells, with an alternating-current first pulse to permeabilize the cell, followed by a direct-current second pulse. The protocols were rationally designed to best separate the mechanisms of permeabilization and electrophoretic transport. The results showed that the delivery of FD varied strongly with the strength of the first pulse and the size of the target molecule. The delivered FD concentration also decreased linearly with the logarithm of the inter-pulse delay. The data indicate that membrane resealing after electropermeabilization occurs rapidly, but that a non-negligible fraction of the pores can be reopened by the second pulse for delay times on the order of hundreds of seconds. The role of the second pulse is hypothesized to be more than just electrophoresis, with a minimum threshold field strength required to reopen nano-sized pores or defects remaining from the first pulse. These results suggest that membrane electroporation, sealing, and re-poration is a complex process that has both short-term and long-term components, which may in part explain the wide variation in membrane-resealing times reported in the literature.

  10. 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

  11. A test of systematic coarse-graining of molecular dynamics simulations: Transport properties.

    Science.gov (United States)

    Fu, Chia-Chun; Kulkarni, Pandurang M; Shell, M Scott; Leal, L Gary

    2013-09-07

    To what extent can a "bottom-up" mesoscale fluid model developed through systematic coarse-graining techniques recover the physical properties of a molecular scale system? In a previous paper [C.-C. Fu, P. M. Kulkarni, M. S. Shell, and L. G. Leal, J. Chem. Phys. 137, 164106 (2012)], we addressed this question for thermodynamic properties through the development of coarse-grained (CG) fluid models using modified iterative Boltzmann inversion methods that reproduce correct pair structure and pressure. In the present work we focus on the dynamic behavior. Unlike the radial distribution function and the pressure, dynamical properties such as the self-diffusion coefficient and viscosity in a CG model cannot be matched during coarse-graining by modifying the pair interaction. Instead, removed degrees of freedom require a modification of the equations of motion to simulate their implicit effects on dynamics. A simple but approximate approach is to introduce a friction coefficient, γ, and random forces for the remaining degrees of freedom, in which case γ becomes an additional parameter in the coarse-grained model that can be tuned. We consider the non-Galilean-invariant Langevin and the Galilean-invariant dissipative particle dynamics (DPD) thermostats with CG systems in which we can systematically tune the fraction φ of removed degrees of freedom. Between these two choices, only DPD allows both the viscosity and diffusivity to match a reference Lennard-Jones liquid with a single value of γ for each degree of coarse-graining φ. This friction constant is robust to the pressure correction imposed on the effective CG potential, increases approximately linearly with φ, and also depends on the interaction cutoff length, rcut, of the pair interaction potential. Importantly, we show that the diffusion constant and viscosity are constrained by a simple scaling law that leads to a specific choice of DPD friction coefficient for a given degree of coarse-graining. Moreover, we

  12. The molecular transport and intercalation of guest molecules into hydrogen-bonded metal-organic frameworks (HMOFs)

    Science.gov (United States)

    Hogan, Greg Anthony

    The process of molecular transport and intercalation has been widely studied for many years, resulting in the discovery of molecular frameworks that are capable of hosting guest molecules or ions. Layered and porous metal-organic frameworks (MOFs) have been found to have applications in the field of catalysis, storage, separations, and ion-exchange. More recently, molecular components with peripheral hydrogen-bonding moieties have been used to affect the synthesis of hydrogen-bonded metal-organic frameworks (HMOFs) as an alternative to MOFs, which are interconnected via coordinate-covalent bonds. While MOFs are perhaps stronger materials, HMOFs have the advantage of being easily modifiable and more flexible. Because HMOFs have not been extensively studied for their ability to host molecules, and because their ability to withstand guest loss and guest exchange is essentially unknown, here we report the synthesis and molecular transport properties of both close-packed and porous HMOFs. Layered materials can mimic the behavior of naturally occurring clays, where guest molecules are absorbed and the layer will expand to accommodate the entering guest molecule. We have created a clay mimic composed of a metal pyridine-dicarboxylates and ammonium counterions (a layered HMOF), which is suitable for studying the ability of such materials to absorb guest molecules. We can control the distance of the interlayer region, as well as the chemical nature (hydrophobic or hydrophilic) by varying the organic amine. The metal complex contains axial water ligands that are replaceable, and such ligand exchange has precedence in coordination polymer (MOF) systems, and has been termed "coordinative intercalation". Using the synthesized layered material we examined the process of intercalation, having chosen a variety of guest molecules ranging from alkyl to aryl molecules, each of which have substituents varying in size, shape and electronics. The first set of guest molecules are non

  13. Molecular mechanics investigation of the transport mechanisms in the CIC-ec1 H+/CI⁻ exchanger and P-glycoprotein/Sav1866 ABC transporter

    OpenAIRE

    Xu, Yanyan

    2014-01-01

    Although channels and transporters were thought to display completely different transport mechanisms, new findings have revealed that the boundaries between them might be more blurred. ABC family, which includes thousands of transporters, holds a channel member, CFTR (cystic fibrosis transmembrane conductance regulator). ClC-ec1, which was considered as a chloride ion channel as other members of the ClC family, was found to function as a Cl-/H+ exchanger. Since the proteins within the family ...

  14. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Z. D. [Department of Physics and Astronomy, SUNY Stony Brook, New York 11794 (United States); Wang, J. [Department of Physics and Astronomy, SUNY Stony Brook, New York 11794 (United States); Department of Chemistry, SUNY Stony Brook, New York 11794 (United States); State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (China)

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  15. 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.

  16. Molecular Evolutionary Analysis of ABCB5: The Ancestral Gene Is a Full Transporter with Potentially Deleterious Single Nucleotide Polymorphisms

    OpenAIRE

    Karobi Moitra; Mark Scally; Kate McGee; Germaine Lancaster; Bert Gold; Michael Dean

    2011-01-01

    BACKGROUND: ABCB5 is a member of the ABC protein superfamily, which includes the transporters ABCB1, ABCC1 and ABCG2 responsible for causing drug resistance in cancer patients and also several other transporters that have been linked to human disease. The ABCB5 full transporter (ABCB5.ts) is expressed in human testis and its functional significance is presently unknown. Another variant of this transporter, ABCB5 beta possess a "half-transporter-like" structure and is expressed in melanoma ste...

  17. From linked open data to molecular interaction: studying selectivity trends for ligands of the human serotonin and dopamine transporter.

    Science.gov (United States)

    Zdrazil, Barbara; Hellsberg, Eva; Viereck, Michael; Ecker, Gerhard F

    2016-09-14

    Retrieval of congeneric and consistent SAR data sets for protein targets of interest is still a laborious task to do if no appropriate in-house data set is available. However, combining integrated open data sources (such as the Open PHACTS Discovery Platform) with workflow tools now offers the possibility of querying across multiple domains and tailoring the search to the given research question. Starting from two phylogenetically related protein targets of interest (the human serotonin and dopamine transporters), the whole chemical compound space was explored by implementing a scaffold-based clustering of compounds possessing biological measurements for both targets. In addition, potential hERG blocking liabilities were included. The workflow allowed studying the selectivity trends of scaffold series, identifying potentially harmful compound series, and performing SAR, docking studies and molecular dynamics (MD) simulations for a consistent data set of 56 cathinones. This delivered useful insights into driving determinants for hDAT selectivity over hSERT. With respect to the scaffold-based analyses it should be noted that the cathinone data set could be retrieved only when Murcko scaffold analyses were combined with similarity searches such as a common substructure search.

  18. 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.

  19. 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) < 102 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 Ecoop(T) ≡ E(T)-E∞ increases exponentially while cooling. A scaling is introduced, specifically Ecoop(T)/E∞ ∝ exp[-λ(T/TA-1)], where λ is a fragility parameter and TA 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.

  20. Vertical transport through AlGaN barriers in heterostructures grown by ammonia molecular beam epitaxy and metalorganic chemical vapor deposition

    Science.gov (United States)

    Browne, David A.; Fireman, Micha N.; Mazumder, Baishakhi; Kuritzky, Leah Y.; Wu, Yuh-Renn; Speck, James S.

    2017-02-01

    The results of vertical transport through AlGaN heterobarriers are presented for ammonia molecular beam epitaxy (NH3-MBE) on c-plane GaN on sapphire templates and on m-plane bulk GaN substrates, as well as by metalorganic chemical vapor deposition (MOCVD) on m-plane bulk GaN substrates. Experiments were performed to determine the role of the AlGaN alloy as an effective barrier to vertical transport, which is an essential component of both optoelectronic and power electronic devices. The alloy composition, thickness, and doping levels of the AlGaN layers, as well as substrate orientation, were systematically varied to examine their influence on electron transport. Atom probe tomography (APT) was used to directly determine the alloy composition at the atomic scale to reveal the presence of random alloy fluctuations which provides insight into the nature of the observed transport.

  1. Effect of molecular weight on the transepithelial transport and peptidase degradation of casein-derived peptides by using Caco-2 cell model.

    Science.gov (United States)

    Wang, Bo; Li, Bo

    2017-03-01

    The transepithelial transport routes of casein-derived peptides with different molecular weights (MWs) were investigated using a Caco-2 cell monolayer. The peptidase hydrolysis during transport was also studied. The results indicate that the paracellular route was the main pathway for F1 (1600-1300Da) and F2 (1000-500Da), and the bioavailabilities were 10.66% and 9.54%, respectively. Peptidase hydrolysis results reveal that brush-border peptidases (BBPs) as well as some other peptidases were responsible for peptide degradation in the paracellular route. The maximum hydrolysis rate of the former was 6.91 and 5.59μM Gly/min for the latter. However, PepT1 was involved in the transport of F3 (transport and the maximum hydrolysis rate was 11.4μM Gly/min. Furthermore, we found that the amino acid sequence of di- and tripeptides might affect their bioavailabilities significantly.

  2. Temperature Fluctuations driven by Magnetorotational Instability in Protoplanetary Disks

    CERN Document Server

    McNally, Colin P; Yang, Chao-Chin; Mac Low, Mordecai-Mark

    2014-01-01

    The magnetorotational instability (MRI) drives magnetized turbulence in sufficiently ionized regions of protoplanetary disks, leading to mass accretion. The dissipation of the potential energy associated with this accretion determines the thermal structure of accreting regions. Until recently, the heating from the turbulence has only been treated in an azimuthally averaged sense, neglecting local fluctuations. However, magnetized turbulence dissipates its energy intermittently in current sheet structures. We study this intermittent energy dissipation using high resolution numerical models including a treatment of radiative thermal diffusion in an optically thick regime. Our models predict that these turbulent current sheets drive order unity temperature variations even where the MRI is damped strongly by Ohmic resistivity. This implies that the current sheet structures where energy dissipation occurs must be well resolved to correctly capture the flow structure in numerical models. Higher resolutions are requ...

  3. Temperature fluctuations driven by magnetorotational instability in protoplanetary disks

    Energy Technology Data Exchange (ETDEWEB)

    McNally, Colin P. [Niels Bohr International Academy, Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen Ø (Denmark); Hubbard, Alexander; Low, Mordecai-Mark Mac [Department of Astrophysics, American Museum of Natural History, New York, NY 10024-5192 (United States); Yang, Chao-Chin, E-mail: cmcnally@nbi.dk, E-mail: ahubbard@amnh.org, E-mail: mordecai@amnh.org, E-mail: ccyang@astro.lu.se [Lund Observatory, Department of Astronomy and Theoretical Physics, Lund University, Box 43, SE-22100 Lund (Sweden)

    2014-08-10

    The magnetorotational instability (MRI) drives magnetized turbulence in sufficiently ionized regions of protoplanetary disks, leading to mass accretion. The dissipation of the potential energy associated with this accretion determines the thermal structure of accreting regions. Until recently, the heating from the turbulence has only been treated in an azimuthally averaged sense, neglecting local fluctuations. However, magnetized turbulence dissipates its energy intermittently in current sheet structures. We study this intermittent energy dissipation using high resolution numerical models including a treatment of radiative thermal diffusion in an optically thick regime. Our models predict that these turbulent current sheets drive order-unity temperature variations even where the MRI is damped strongly by Ohmic resistivity. This implies that the current sheet structures where energy dissipation occurs must be well-resolved to correctly capture the flow structure in numerical models. Higher resolutions are required to resolve energy dissipation than to resolve the magnetic field strength or accretion stresses. The temperature variations are large enough to have major consequences for mineral formation in disks, including melting chondrules, remelting calcium-aluminum-rich inclusions, and annealing silicates; and may drive hysteresis: current sheets in MRI active regions could be significantly more conductive than the remainder of the disk.

  4. Molecular characterization of LhpR in control of hydroxyproline catabolism and transport in Pseudomonas aeruginosa PAO1.

    Science.gov (United States)

    Li, Guoqing; Lu, Chung-Dar

    2016-07-01

    Utilization of hydroxy-l-proline (l-Hyp) in Pseudomonas aeruginosa requires conversion of l-Hyp to d-Hyp followed by the d-Hyp dehydrogenase pathway; however, the molecular mechanism in control of l-Hyp catabolism and transport was not clear. DNA microarray analysis revealed twelve genes in two adjacent loci that were induced by exogenous l-Hyp and d-Hyp. The first locus includes lhpABFE encoding a Hyp epimerase (LhpA) and d-Hyp dehydrogenase (LhpBEF), while the second locus codes for a putative ABC transporter (LhpPMNO), a protein of unknown function (LhpH), Hyp/Pro racemase (LhpK) and two enzymes in l-Hyp catabolism (LhpC and LhpG). Proximal to these two loci, lhpR encodes a transcriptional regulator of the AraC family. The importance of these genes on l-Hyp catabolism was supported by growth phenotype analysis on knockout mutants. Induction of the lhpA and lhpP promoters by exogenous l-Hyp and d-Hyp was demonstrated by the measurement of β-galactosidase activities from promoter-lacZ fusions in PAO1, and no induction could be detected in the ΔlhpR mutant. Induction of the lhpA promoter by d-Hyp was completely abolished in the lhpA lhpK double mutant devoid of two epimerases, while the induction effect of l-Hyp remained unchanged. The purified His-tagged LhpR binds specifically to the lhp promoter regions, and formation of nucleoprotein complexes is affected by the presence of l-Hyp but not d-Hyp. Putative LhpR binding sites were deduced from serial deletions and comparative genomic sequence analysis. In summary, expression of lhp genes for Hyp catabolism and uptake requires the transcriptional activator LhpR and l-Hyp as the signalling compound.

  5. Molecular cloning and expression analysis of a monosaccharide transporter gene OsMST4 from rice (Oryza sativa L.)

    NARCIS (Netherlands)

    Wang, Y.; Xu, H.; Wei, X.; Chai, C.; Xiao, Y.; Zhang, Y.; Chen, B.; Xiao, G.; Ouwerkerk, P.B.F.; Wang, M.; Zhu, Z.

    2007-01-01

    Monosaccharide transporters mediate the membrane transport of a variable range of monosaccharides, which plays a crucial role in sugar distribution throughout the plant. To investigate the significance of monosaccharide transporters for rice (Oryza sativa L.) seed development, cDNA of a new putative

  6. Quantum dissipative effects on non-equilibrium transport through a single-molecular transistor: The Anderson-Holstein-Caldeira-Leggett model

    Science.gov (United States)

    Raju, Ch. Narasimha; Chatterjee, Ashok

    2016-01-01

    The Anderson-Holstein model with Caldeira-Leggett coupling with environment is considered to describe the damping effect in a single molecular transistor (SMT) which comprises a molecular quantum dot (with electron-phonon interaction) mounted on a substrate (environment) and coupled to metallic electrodes. The electron-phonon interaction is first eliminated using the Lang-Firsov transformation and the spectral density function, charge current and differential conductance are then calculated using the non-equilibrium Keldysh Green function technique. The effects of damping rate, and electron-electron and electron-phonon interactions on the transport properties of SMT are studied at zero temperature.

  7. 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.

  8. (4,4')-Bipyridine in Vacuo and in Solvents: A Quantum Chemical Study of a Prototypical Floppy Molecule From a Molecular Transport Perspective

    CERN Document Server

    Bâldea, Ioan; Wenzel, Wonfgang

    2015-01-01

    We report results of quantum chemical calculations for the neutral and anionic species of (4,4{'})-bipyridine (44BPY), a prototypical molecule with a floppy degree of freedom, placed in vacuo and in solvents. In addition to equilibrium geometries and vibrational frequencies and spectra, we present adiabatic energy curves for the vibrational modes with significant intramolecular reorganization upon charge transfer. Special attention is paid to the floppy strongly anharmonic degree of freedom of 44BPY, which is related to the most salient structural feature, namely the twist angle $\\theta$ between the two pyridine rings. The relevance of the present results for molecular transport will be emphasized. We show that the solvent acts as an effective gate electrode and propose a scissor operator to account for solvent effects on molecular transport. Our result on the conductance $G$ vs. $\\cos^2\\theta$ is consistent with a significant transmission in perpendicular conformation indicated by previous microscopic analys...

  9. Molecular cloning, immunochemical localization to the vacuole, and expression in transgenic yeast and tobacco of a putative sugar transporter from sugar beet.

    Science.gov (United States)

    Chiou, T J; Bush, D R

    1996-02-01

    Several plant genes have been cloned that encode members of the sugar transporter subgroup of the major facilitator superfamily of transporters. Here we report the cloning, expression, and membrane localization of one of these porters found in sugar beet (Beta vulgaris L.). This clone, cDNA-1, codes for a protein with 490 amino acids and an estimated molecular mass of 54 kD. The predicted membrane topology and sequence homology suggest that cDNA-1 is a member of the sugar transporter family. RNA gel blot analysis revealed that this putative sugar transporter is expressed in all vegetative tissues and expression increases with development in leaves. DNA gel blot analysis indicated that multiple gene copies exist for this putative sugar transporter in the sugar beet genome. Antibodies directed against small peptides representing the N- and C-terminal domains of the cDNA1 protein identified a 40-kD polypeptide in microsomes isolated from cDNA-1-transformed yeast (Saccharomyces cerevisiae). Moreover, the same protein was identified in sugar beet and transgenic tobacco (Nicotaina tobacum L.) membrane fractions. Detailed analysis of the transporter's distribution across linear sucrose gradients and flotation centrifugations showed that it co-migrates with tonoplast membrane markers. We conclude that this carrier is located on the tonoplast membrane and that it may mediate sugar partitioning between the vacuole and cytoplasmic compartments.

  10. 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.

    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

  11. 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

  12. 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...

  13. 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....../or glial cells: the solute carrier (SLC)1 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of glutamate, and the SLC6 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of dopamine, 5-HT, norepinephrine, glycine and GABA....... 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...

  14. 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 ...... of EAATs and their intricate transport process, the novel approaches to pharmacological modulation of the transporters that have emerged, and interesting new perspectives in EAAT as drug targets proposed in recent years....

  15. Interactions of human P-glycoprotein transport substrates and inhibitors at the drug binding domain: Functional and molecular docking analyses.

    Science.gov (United States)

    Kadioglu, Onat; Saeed, Mohamed E M; Valoti, Massimo; Frosini, Maria; Sgaragli, Giampietro; Efferth, Thomas

    2016-03-15

    Rhodamine 123 (R123) transport substrate sensitizes P-glycoprotein (P-gp) to inhibition by compound 2c (cis-cis) N,N-bis(cyclohexanolamine)aryl ester isomer in a concentration-dependent manner in human MDR1-gene transfected mouse T-lymphoma L5178 cells as shown previously. By contrast, epirubicin (EPI) concentration changes left unaltered 2c IC50 values of EPI efflux. To clarify this discrepancy, defined molecular docking (DMD) analyses of 12 N,N-bis(cyclohexanolamine)aryl esters, the highly flexible aryl ester analog 4, and several P-gp substrate/non-substrate inhibitors were performed on human P-gp drug- or nucleotide-binding domains (DBD or NBD). DMD measurements yielded lowest binding energy (LBE, kcal/mol) values (mean ± SD) ranging from -11.8 ± 0.54 (valspodar) to -3.98 ± 0.01 (4). Lys234, Ser952 and Tyr953 residues formed H-bonds with most of the compounds. Only 2c docked also at ATP binding site (LBE value of -6.9 ± 0.30 kcal/mol). Inhibition of P-gp-mediated R123 efflux by 12 N,N-bis(cyclohexanolamine)aryl esters and 4 significantly correlated with LBE values. DMD analysis of EPI, (3)H-1EPI, (3)H-2EPI, (14)C-1EPI, (14)C-2EPI, R123 and 2c before and after previous docking of each of them indicated that pre-docking of either 2c or EPI significantly reduced LBE of both EPI and R123, and that of both (3)H-2EPI and (14)C-2EPI, respectively. Since the clusters of DBD amino acid residues interacting with EPI were different, if EPI docked alone or after pre-docking of EPI or 2c, the existence of alternative secondary binding site for EPI on P-gp is credible. In conclusion, 2c may allocate the drug-binding pocket and reduce strong binding of EPI and R123 in agreement with P-gp inhibition experiments, where 2c reduced efflux of EPI and R123.

  16. Direct Comparison of Manganese Detoxification/Efflux Proteins and Molecular Characterization of ZnT10 Protein as a Manganese Transporter.

    Science.gov (United States)

    Nishito, Yukina; Tsuji, Natsuko; Fujishiro, Hitomi; Takeda, Taka-Aki; Yamazaki, Tomohiro; Teranishi, Fumie; Okazaki, Fumiko; Matsunaga, Ayu; Tuschl, Karin; Rao, Rajini; Kono, Satoshi; Miyajima, Hiroaki; Narita, Hiroshi; Himeno, Seiichiro; Kambe, Taiho

    2016-07-08

    Manganese homeostasis involves coordinated regulation of specific proteins involved in manganese influx and efflux. However, the proteins that are involved in detoxification/efflux have not been completely resolved nor has the basis by which they select their metal substrate. Here, we compared six proteins, which were reported to be involved in manganese detoxification/efflux, by evaluating their ability to reduce manganese toxicity in chicken DT40 cells, finding that human ZnT10 (hZnT10) was the most significant contributor. A domain swapping and substitution analysis between hZnT10 and the zinc-specific transporter hZnT1 showed that residue Asn(43), which corresponds to the His residue constituting the potential intramembranous zinc coordination site in other ZnT transporters, is necessary to impart hZnT10's unique manganese mobilization activity; residues Cys(52) and Leu(242) in transmembrane domains II and V play a subtler role in controlling the metal specificity of hZnT10. Interestingly, the His → Asn reversion mutant in hZnT1 conferred manganese transport activity and loss of zinc transport activity. These results provide important information about manganese detoxification/efflux mechanisms in vertebrate cells as well as the molecular characterization of hZnT10 as a manganese transporter.

  17. Molecular cloning of two Arabidopsis UDP-galactose transporters by complementation of a deficient Chinese hamster ovary cell line

    NARCIS (Netherlands)

    Bakker, H.; Routier, F.; Oelmann, S.; Jordi, W.J.R.M.; Lommen, A.; Gerardy-Schahn, R.; Bosch, H.J.

    2005-01-01

    Nucleotide-sugar transporters (NSTs) form a family of structurally related transmembrane proteins that transport nucleotide-sugars from the cytoplasm to the endoplasmic reticulum and Golgi lumen. In these organelles, activated sugars are substrates for various glycosyltransferases involved in oligo-

  18. 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 synth

  19. 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 synth

  20. 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.

  1. Molecular features of the L-type amino acid transporter 2 determine different import and export profiles for thyroid hormones and amino acids.

    Science.gov (United States)

    Hinz, Katrin M; Neef, Dominik; Rutz, Claudia; Furkert, Jens; Köhrle, Josef; Schülein, Ralf; Krause, Gerd

    2017-03-05

    The L-type amino acid transporter 2 (LAT2) imports amino acids (AA) and also certain thyroid hormones (TH), e.g. 3,3'-T2 and T3, but not rT3 and T4. We utilized LAT2 mutations (Y130A, N133S, F242W) that increase 3,3'-T2 import and focus here on import and export capacity for AA, T4, T3, BCH and derivatives thereof to delineate molecular features. Transport studies and analysis of competitive inhibition of import by radiolabelled TH and AA were performed in Xenopus laevis oocytes. Only Y130A, a pocket widening mutation, enabled import for T4 and increased it for T3. Mutant F242W showed increased 3,3'-T2 import but no import rates for other TH derivatives. No export was detected for any TH by LAT2-wild type (WT). Mutations Y130A and N133S enabled only the export of 3,3'-T2, while N133S also increased AA export. Thus, distinct molecular LAT2-features determine bidirectional AA transport but only an unidirectional 3,3'-T2 and T3 import.

  2. The size effects of electrodes in molecular devices: an ab initio study on the transport properties of C{sub 60}

    Energy Technology Data Exchange (ETDEWEB)

    Zheng Xiaohong; Dai Zhenxiang; Zeng Zhi [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China)

    2009-04-08

    The role of electrodes in the transport properties of molecular devices is investigated by taking C{sub 60} as an example and using gold nanowire and a gold atomic chain as the electrodes. The calculations are done by an ab initio method combined with the non-equilibrium Green function technique. We find that devices in which a single C{sub 60} molecule is connected with different electrodes show completely different transport behavior. In the case of nanowire/C{sub 60}/nanowire the device shows a metallic behavior with a big equilibrium conductance (about 2.18G{sub 0}) and the current increases rapidly and almost linearly starting from zero. The transmission function shows wide peaks and platforms around the Fermi level. While in the atomic-chain/C{sub 60}/atomic-chain case, the device shows resonant tunneling behavior and the Fermi level lies between the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) transmission peaks. This results in a current that is one order of magnitude smaller than that in the nanowire/C{sub 60}/nanowire system and the current increases very slowly until the bias is big enough to include the LUMO peak in the bias window. The big difference in the conductance and the current arises from the different coupling between the electrodes and the C{sub 60} and the different number of channels in the electrodes.

  3. Experimental and Computational Studies of Temperature Gradient Driven Molecular Transport in Gas Flows through Nano/Micro-Scale Channels

    OpenAIRE

    Han, Yen-Lin; Alexeenko, Alina A.; Young, Marcus; Muntz, Eric Phillip

    2007-01-01

    Studies at the University of Southern California have shown that an unconventional solid-state device, the Knudsen Compressor, can be operated as a micro-scale pump or compressor. The critical components of Knudsen Compressors are gas transport membranes, which can be formed from porous materials or densely packed parallel arrays of channels. An applied temperature gradient across a transport membrane creates a thermal creep pumping action. Experimental and computational techniques that have ...

  4. Experimental and Computational Studies of Temperature Gradient Driven Molecular Transport in Gas Flows through Nano/Micro-Scale Channels

    OpenAIRE

    Han, Yen-Lin; Alexeenko, Alina A; Young, Marcus; Muntz, Eric Phillip

    2007-01-01

    Studies at the University of Southern California have shown that an unconventional solid-state device, the Knudsen Compressor, can be operated as a micro-scale pump or compressor. The critical components of Knudsen Compressors are gas transport membranes, which can be formed from porous materials or densely packed parallel arrays of channels. An applied temperature gradient across a transport membrane creates a thermal creep pumping action. Experimental and computational techniques that have ...

  5. Ambient air particle transport into the effluent of a cold atmospheric-pressure argon plasma jet investigated by molecular beam mass spectrometry

    Science.gov (United States)

    Dünnbier, M.; Schmidt-Bleker, A.; Winter, J.; Wolfram, M.; Hippler, R.; Weltmann, K.-D.; Reuter, S.

    2013-10-01

    Ambient air species, which are transported into the active effluent of an atmospheric-pressure plasma jet result in highly reactive oxygen and nitrogen species (RONS). Especially for the envisaged application field of plasma medicine, these RONS are responsible for strong biological responses. In this work, the effect of ambient air transport into the effluent of an atmospheric-pressure plasma argon jet on the on-axis densities of nitrogen, oxygen and argon was investigated by means of absolutely calibrated molecular beam mass spectrometry (MBMS). According to biomedical experiments a (bottomless) Petri dish was installed in front of the MBMS. In the following, the near flow field is referring to the region close to the nozzle exit and the far flow field is referring to the region beyond that. The absolute on-axis densities were obtained by three different methods, for the near flow field with VUV-absorption technique, for the far flow field with the MBMS and the total flow field was calculated with a computational fluid dynamics (CFD) simulation. The results of the ambient air particle densities of all independent methods were compared and showed an excellent agreement. Therefore the transport processes of ambient air species can be measured for the whole effluent of an atmospheric-pressure plasma jet. Additionally, with the validation of the simulation it is possible in future to calculate the ambient species transport for various gas fluxes in the same turbulent flow regime. Comparing the on-axis densities obtained with an ignited and with a non-ignited plasma jet shows that for the investigated parameters, the main influence on the ambient air species transport is due to the increased temperature in the case when the jet is switched on. Moreover, the presence of positive ions (e.g. ArN_{2}^{+} ) formed due to the interaction of plasma-produced particles and ambient air species, which are transported into the effluent, is shown.

  6. Transport properties of the two-dimensional electron gas in GaN/AlGaN heterostructures grown by ammonia molecular-beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Pogosov, A.G.; Budantsev, M.V.; Lavrov, R.A.; Mansurov, V.G.; Nikitin, A.Yu.; Preobrazhenskii, V.V.; Zhuravlev, K.S. [Institute of Semiconductor Physics, 13 Lavrentiev Avenue, 630090 Novosibirsk (Russian Federation)

    2006-07-15

    Transport properties of the two-dimensional electron gas in AlGaN/GaN heterostructures grown by ammonia molecular-beam epitaxy are experimentally investigated. Conventional Hall and Shubnikov-de Haas measurements as well as investigations of quantum transport phenomena are reported. It is found that negative magnetoresistance (NMR) caused by weak localization demonstrates an unusual behavior at low temperature (1.8 K). The observed NMR cannot be described by the ordinary theory of quantum corrections to conductivity based on a single phase breaking time {tau}{sub {phi}}. The anomalous NMR behavior can be explained by the presence of two occupied quantum subbands, characterized by their own phase breaking times {tau} {sub {phi}} {sub 1} and {tau} {sub {phi}} {sub 2}. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  7. The Chick Chorioallantoic Membrane: A Model of Molecular, Structural, and Functional Adaptation to Transepithelial Ion Transport and Barrier Function during Embryonic Development

    Directory of Open Access Journals (Sweden)

    Maria Gabriella Gabrielli

    2010-01-01

    Full Text Available The chick chorioallantoic membrane is a very simple extraembryonic membrane which serves multiple functions during embryo development; it is the site of exchange of respiratory gases, calcium transport from the eggshell, acid-base homeostasis in the embryo, and ion and H2O reabsorption from the allantoic fluid. All these functions are accomplished by its epithelia, the chorionic and the allantoic epithelium, by differentiation of a wide range of structural and molecular peculiarities which make them highly specialized, ion transporting epithelia. Studying the different aspects of such a developmental strategy emphasizes the functional potential of the epithelium and offers an excellent model system to gain insights into questions partly still unresolved.

  8. Gated supramolecular chemistry in hybrid mesoporous silica nanoarchitectures: controlled delivery and molecular transport in response to chemical, physical and biological stimuli.

    Science.gov (United States)

    Alberti, Sebastián; Soler-Illia, Galo J A A; Azzaroni, Omar

    2015-04-11

    This review presents and discusses recent advances in the emerging field of "gated nanochemistry", outlining the substantial progress made so far. The development of hybrid mesoporous silica with complex tailored pore nanoarchitectures bridges the gap between molecular materials and the requirements of nanodevices for controlled nanoscale chemistry. In the last decade, membranes, particles and thin film porous architectures have been designed, synthesized and selectively modified by molecular, polymeric, organometallic or biologically active groups. The exquisite manipulation of mesopore morphology and interconnection combined with molecular or supramolecular functionalities, and the intrinsic biological compatibility of silica have made these materials a potential platform for selective sensing and drug delivery. The wide répertoire of these hard-soft architectures permit us to envisage sophisticated intelligent nano-systems that respond to a variety of external stimuli such as pH, redox potential, molecule concentration, temperature, or light. Transduction of these stimuli into a predefined response implies exploiting spatial and physico-chemical effects such as charge distribution, steric constraints, equilibria displacements, or local changes in ionic concentration, just to name a few examples. As expected, this "positional mesochemistry" can be only attained through the concerted control of assembly, surface tailoring and, confinement conditions, thus giving birth to a new class of stimuli-responsive materials with modulable transport properties. As a guiding framework the emerging field of "gated nanochemistry" offers methodologies and tools for building up stimuli-sensitive porous architectures equipped with switchable entities whose transport properties can be triggered at will. The gated nanoscopic hybrid materials discussed here not only herald a new era in the integrative design of "smart" drug delivery systems, but also give the reader a perspective of

  9. Molecular evolutionary analysis of ABCB5: the ancestral gene is a full transporter with potentially deleterious single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Karobi Moitra

    Full Text Available BACKGROUND: ABCB5 is a member of the ABC protein superfamily, which includes the transporters ABCB1, ABCC1 and ABCG2 responsible for causing drug resistance in cancer patients and also several other transporters that have been linked to human disease. The ABCB5 full transporter (ABCB5.ts is expressed in human testis and its functional significance is presently unknown. Another variant of this transporter, ABCB5 beta possess a "half-transporter-like" structure and is expressed in melanoma stem cells, normal melanocytes, and other types of pigment cells. ABCB5 beta has important clinical implications, as it may be involved with multidrug resistance in melanoma stem cells, allowing these stem cells to survive chemotherapeutic regimes. METHODOLOGY/PRINCIPAL FINDINGS: We constructed and examined in detail topological structures of the human ABCB5 protein and determined in-silico the cSNPs (coding single nucleotide polymorphisms that may affect its function. Evolutionary analysis of ABCB5 indicated that ABCB5, ABCB1, ABCB4, and ABCB11 share a common ancestor, which began duplicating early in the evolutionary history of chordates. This suggests that ABCB5 has evolved as a full transporter throughout its evolutionary history. CONCLUSIONS/SIGNIFICANCE: From our in-silco analysis of cSNPs we found that a large number of non-synonymous cSNPs map to important functional regions of the protein suggesting that these SNPs if present in human populations may play a role in diseases associated with ABCB5. From phylogenetic analyses, we have shown that ABCB5 evolved as a full transporter throughout its evolutionary history with an absence of any major shifts in selection between the various lineages suggesting that the function of ABCB5 has been maintained during mammalian evolution. This finding would suggest that ABCB5 beta may have evolved to play a specific role in human pigment cells and/or melanoma cells where it is predominantly expressed.

  10. Molecular dynamics simulation of the thermodynamic and transport properties of the molten salt fast reactor fuel LiF–ThF{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Dewan, Leslie C., E-mail: ldewan@mit.edu [Massachusetts Institute of Technology, Department of Nuclear Science and Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Simon, Christian, E-mail: christian.simon@upmc.fr [UPMC Université Paris 06, CNRS, ESPCI, UMR 7195, PECSA, 75005 Paris (France); Madden, Paul A., E-mail: paul.madden@queens.ox.ac.uk [University of Oxford, Department of Materials, Parks Road, Oxford OX1 3PH (United Kingdom); Hobbs, Linn W., E-mail: hobbs@mit.edu [Massachusetts Institute of Technology, Department of Nuclear Science and Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Salanne, Mathieu, E-mail: mathieu.salanne@upmc.fr [UPMC Université Paris 06, CNRS, ESPCI, UMR 7195, PECSA, 75005 Paris (France)

    2013-03-15

    The local structure and transport properties of molten LiF–ThF{sub 4} at the eutectic composition have been studied at a range of temperatures, using molecular dynamics simulations that incorporate dipole polarization effects. This polarizable interaction potential was parameterized from first-principles calculations. We have calculated the density, self-diffusion coefficients, electrical conductivity, viscosity, and heat capacity at a range of temperatures from 850 K to 1273 K. We have also examined the changes in coordination number as a function of temperature. The simulation results were in good agreement with available experimental data, indicating that such simulations can fulfill a valuable role in augmenting existing experimental work.

  11. Molecular dynamics simulation of the thermodynamic and transport properties of the molten salt fast reactor fuel LiF-ThF4

    Science.gov (United States)

    Dewan, Leslie C.; Simon, Christian; Madden, Paul A.; Hobbs, Linn W.; Salanne, Mathieu

    2013-03-01

    The local structure and transport properties of molten LiF-ThF4 at the eutectic composition have been studied at a range of temperatures, using molecular dynamics simulations that incorporate dipole polarization effects. This polarizable interaction potential was parameterized from first-principles calculations. We have calculated the density, self-diffusion coefficients, electrical conductivity, viscosity, and heat capacity at a range of temperatures from 850 K to 1273 K. We have also examined the changes in coordination number as a function of temperature. The simulation results were in good agreement with available experimental data, indicating that such simulations can fulfill a valuable role in augmenting existing experimental work.

  12. 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; Sherman, Benjamin D.; Klug, Christina; Nayak, Animesh; Marquard, Seth; Liu, Qing; Bullock, Ronald M.; Meyer, Thomas J.

    2017-08-30

    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%.

  13. Molecular mechanisms of the epithelial transport of toxic metal ions. Final report, September 1, 1975-December 31, 1985

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. DFT study of the conductance of molecular wire: The effect of coupling geometry and intermolecular interaction on the transport properties

    Institute of Scientific and Technical Information of China (English)

    QI; Yuanhua; GUAN; Daren; LIU; Chengbu

    2006-01-01

    The density functional theory (DFT) combining with the non-equilibrium Green functions (NEGF) method is applied to the study of the electronic transport properties for a Di-thiol-benzene (DTB) molecule coupled to two Au(111) surfaces. The dependence of the transport properties on the bias, the coupling geometry of the molecule-electrode interface, and the intermolecular interaction are examined in detail. The results show that the existence of the hydrogen atom at the end of the DTB molecule would significantly decrease the transmission coefficients, and then the differential conductance (dI/dV). By changing the position of the DTB molecule located between two electrodes a maximum value of calculated current is observed. It is also found that the intermolecular interaction will strongly influence the transport properties of the system studied.

  15. Covariance structure of neuroticism and agreeableness: a twin and molecular genetic analysis of the role of the serotonin transporter gene.

    Science.gov (United States)

    Jang, K L; Hu, S; Livesley, W J; Angleitner, A; Riemann, R; Ando, J; Ono, Y; Vernon, P A; Hamer, D H

    2001-08-01

    The Revised NEO Personality Inventory domains of Neuroticism and Agreeableness are considered factorially distinct despite several intercorrelations between these domains. The genetic correlation, an index of the degree to which these intercorrelations are caused by genetic influences, was estimated using data from 913 monozygotic and 562 dizygotic volunteer twin pairs from Canada, Germany, and Japan. The serotonin transporter gene, 5-HTTLPR, was assayed in a sample of 388 nontwin sibling pairs from the United States to determine the contribution of the serotonin transporter locus to the covariation between the Neuroticism and Agreeableness scales. In all four samples, genetic influences contributed to the covariance of Neuroticism and Agreeableness, with the serotonin transporter gene accounting for 10% of the relationship between these domains.

  16. Molecular identification and cellular localization of a potential transport system involved in cystine/cysteine uptake in human lenses.

    Science.gov (United States)

    Lim, Julie C; Lam, Leo; Li, Bo; Donaldson, Paul J

    2013-11-01

    In this study we have sought to identify whether cystine uptake mechanisms previously identified in the rat lens are also found in the human lens. Using a combination of reverse transcriptase PCR, Western blotting and immunohistochemistry, we show that the light chain subunit of the cystine/glutamate exchanger (XC-), xCT, and members of the glutamate transporter family (XAG) which include the Excitatory Amino Acid Transporter 4 (EAAT4) and the Alanine Serine Cysteine Transporter 2 (ASCT2) are all present at the transcript and protein level in human lenses. We demonstrate that in young lenses xCT, EAAT4 and ASCT2 are expressed in all regions indicating that a potential cystine uptake pathway similar to that found in the rat might also exist in human lenses. However, with increasing age, the immunolabeling for all transporters decreases, with no xCT labelling detected in the centre of old donor lenses. Our results show that XC- and EAAT4/ASCT2 may work together to mediate cystine uptake in the lens core of young human lenses. This suggests that the lens contains uptake mechanisms that are capable of accumulating cystine/cysteine in the lens centre where cysteine can be used as an antioxidant or cystine utilised as a source for protein-S-S-cysteine (PSSC) formation to buffer against oxidative stress. With increasing age, transporters in the lens core undergo age dependent post translational modifications. However, despite processing of these transporters with age, our results indicate that this cystine uptake pathway could account for the increased PSSC levels previously observed in the nucleus of older human lenses.

  17. Molecular self ordering and charge transport in layer by layer deposited poly (3,3‴-dialkylquarterthiophene) films formed by Langmuir-Schaefer technique

    Energy Technology Data Exchange (ETDEWEB)

    Pandey, Rajiv K.; Singh, Arun Kumar; Upadhyay, C.; Prakash, Rajiv, E-mail: rprakash.mst@itbhu.ac.in [School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005 (India)

    2014-09-07

    The performance of π-conjugated polymer based electronic devices is directly governed by the molecular morphology of polymer aggregation, the extent to which a molecule is electronically coupled (self ordered and interacted) to neighboring molecules, and orientation. The well electronic coupled and crystalline/ordered polymer films have the potential to enhance the charge transport properties up to a benchmark. However, there is insufficient knowledge about the direct formation of large area, oriented, crystalline, and smooth films. In this study, we have presented Langmuir Schaefer technique to obtain the large area, oriented, crystalline, and smooth film of Poly (3,3‴-dialkylquarterthiophene) (PQT-12) polymer. The effect of self ordering and orientation of PQT-12 polymer on optical, morphological, and charge transport properties has been investigated. The prepared films have been characterized by UV-vis spectroscopy, Raman spectroscopy, transmission electron microscopy (TEM), selected area diffractions pattern (SAED), and atomic force microscopy (AFM) techniques. UV-vis spectra, TEM, SAED, and AFM images of monolayer films reveal the formation of well ordered and electronically coupled polymer domains. Layer by layer deposited films reveal the change in the orientation, which is confirmed by Raman spectra. Electronic properties and layer dependent charge transport properties are investigated using sandwiched structure Al/PQT-12/ITO Schottky configuration with perpendicular to the deposited films. It is observed that the charge transport properties and device electronic parameters (ideality factor and turn on voltage) are significantly changing with increasing the number of PQT-12 layers. Our study also demonstrates the charge transport between polymer crystallites and cause of deviation of ideal behavior of organic Schottky diodes. It may be further explored for improving the performance of other organic and optoelectronic devices.

  18. Multiscale Gyrokinetics for Rotating Tokamak Plasmas: Fluctuations, Transport and Energy Flows

    CERN Document Server

    Abel, I G; Wang, E; Barnes, M; Cowley, S C; Dorland, W; Schekochihin, A A

    2012-01-01

    This paper presents a complete theoretical framework for plasma turbulence and transport in tokamak plasmas. The fundamental scale separations present in plasma turbulence are codified as an asymptotic expansion in the ratio of the gyroradius to the equilibrium scale length. Proceeding order-by-order in this expansion, a framework for plasma turbulence is developed. It comprises an instantaneous equilibrium, the fluctuations driven by gradients in the equilibrium quantities, and the transport-timescale evolution of mean profiles of these quantities driven by the fluctuations. The equilibrium distribution functions are local Maxwellians with each flux surface rotating toroidally as a rigid body. The magnetic equillibrium is obtained from the Grad-Shafranov equation for a rotating plasma and the slow (resistive) evolution of the magnetic field is given by an evolution equation for the safety factor q. Large-scale deviations of the distribution function from a Maxwellian are given by neoclassical theory. The flu...

  19. Charge Transport Across Insulating Self-Assembled Monolayers: Non-equilibrium Approaches and Modeling To Relate Current and Molecular Structure

    NARCIS (Netherlands)

    Mirjani, F.; Thijssen, J.M.; Whitesides, G.M.; Ratner, M.A.

    2014-01-01

    This paper examines charge transport by tunneling across a series of electrically insulating molecules with the structure HS(CH2)4CONH(CH2)2R) in the form of self-assembled monolayers (SAMs), supported on silver. The molecules examined were studied experimentally by Yoon et al. (Angew. Chem. Int. Ed

  20. Creatine transporter deficiency: molecular and functional tools for diagnosis, and prevalence of this X-linked mental retardation syndrome

    NARCIS (Netherlands)

    Rosenberg, E.H.

    2006-01-01

    Van de verstandelijk gehandicapten is tweederde man. Lang niet altijd wordt voor de handicap een oorzaak gevonden. Uit het promotieonderzoek van Efraim Rosenberg blijkt in één procent van de gevallen een fout in het creatine transporter gen (SLC6A8) hiervoor verantwoordelijk. Patiënten met

  1. Creatine transporter deficiency: molecular and functional tools for diagnosis, and prevalence of this X-linked mental retardation syndrome

    NARCIS (Netherlands)

    Rosenberg, E.H.

    2006-01-01

    Van de verstandelijk gehandicapten is tweederde man. Lang niet altijd wordt voor de handicap een oorzaak gevonden. Uit het promotieonderzoek van Efraim Rosenberg blijkt in één procent van de gevallen een fout in het creatine transporter gen (SLC6A8) hiervoor verantwoordelijk. Patiënten met creatin

  2. Molecular characterization of zebrafish Oatp1d1 (Slco1d1), a novel organic anion-transporting polypeptide.

    Science.gov (United States)

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

    2013-11-22

    The organic anion-transporting polypeptide (OATP/Oatp) superfamily includes a group of polyspecific transporters that mediate transport of large amphipathic, mostly anionic molecules across cell membranes of eukaryotes. OATPs/Oatps are involved in the disposition and elimination of numerous physiological and foreign compounds. However, in non-mammalian species, the functional properties of Oatps remain unknown. We aimed to elucidate the role of Oatp1d1 in zebrafish to gain insights into the functional and structural evolution of the OATP1/Oatp1 superfamily. We show that diversification of the OATP1/Oatp1 family occurs after the emergence of jawed fish and that the OATP1A/Oatp1a and OATP1B/Oatp1b subfamilies appeared at the root of tetrapods. The Oatp1d subfamily emerged in teleosts and is absent in tetrapods. The zebrafish Oatp1d1 is similar to mammalian OATP1A/Oatp1a and OATP1B/Oatp1b members, with the main physiological role in transport and balance of steroid hormones. Oatp1d1 activity is dependent upon pH gradient, which could indicate bicarbonate exchange as a mode of transport. Our analysis of evolutionary conservation and structural properties revealed that (i) His-79 in intracellular loop 3 is conserved within OATP1/Oatp1 family and is crucial for the transport activity; (ii) N-glycosylation impacts membrane targeting and is conserved within the OATP1/Oatp1 family with Asn-122, Asn-133, Asn-499, and Asn-512 residues involved; (iii) the evolutionarily conserved cholesterol recognition interaction amino acid consensus motif is important for membrane localization; and (iv) Oatp1d1 is present in dimeric and possibly oligomeric form in the cell membrane. In conclusion, we describe the first detailed characterization of a new Oatp transporter in zebrafish, offering important insights into the functional evolution of the OATP1/Oatp1 family and the physiological role of Oatp1d1.

  3. 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.

  4. 分数阶双头分子马达的欠扩散输运现象%Subdiffusive transport of fractional two-headed molecular motor

    Institute of Scientific and Technical Information of China (English)

    林丽烽; 周兴旺; 马洪

    2013-01-01

    Focusing on the directed transport phenomena of the two-headed molecular motor, we adopt power function as the damping kernel function of general Langevin equation due to the power-law memory characteristics of cytosol in biological cells and present the model of fractional coupling Brownian motor in overdamped condition in this paper. We also discuss the influences of fractional order and coupling factor on the transport speed. From the simulation results there are found the directed transport phenomena and the inverse transport which is not seen in the conventional Brownian motor, in the overdamped fractional coupling Brownian motor. When the noise density is fixed, the generalized stochastic resonance appears when transport speed varies with the fractional order and coupling factor. In particular, the results reveal that the magnitude and direction of the directional flow are controlled by coupling the noise with the interaction force between the two heads, which is the movement characteristic of the two-headed molecular motor in the memory ratchet, rather than of the single-headed motor.%研究具有幂律记忆性的细胞液中双头分子马达的定向输运现象,选取幂函数作为广义Langevin方程的阻尼核函数,建立了分数阶过阻尼耦合Brown马达模型,讨论了阶数及耦合系数对双头分子马达定向输运速度的影响。仿真结果表明,分数阶过阻尼双头分子马达也会产生定向输运现象,并且在某些阶数下会产生整数阶情形所不具有的反向定向流。当噪声强度固定时,输运速度随着阶数以及耦合系数的变化均会出现广义随机共振现象。特别地,研究发现双头分子马达在记忆闪烁棘轮势中具有某些单头分子马达所不具备的运动特性,定向流的大小和方向由噪声与双头间作用力相互耦合控制。

  5. 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

    2016-03-01

    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.

  6. 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.

  7. A combined experimental and theoretical approach towards the understanding of transport in one-dimensional molecular nanostructures

    OpenAIRE

    Grimm, Daniel

    2008-01-01

    This thesis comprises detailed experimental and theoretical investigations of the transport properties of one-dimensional nanostructures. Most of the work is dedicated to the exploration of the fascinating effects occurring in single wall carbon nanotubes (SWCNT). These particular nanostructures gained an overwhelming interest in the past two decades due to its outstanding electronic and mechanical features. We have investigated the properties of a novel family of carbon nanostructures, named...

  8. Quantitative visualization of molecular transport through porous membranes: enhanced resolution and contrast using intermittent contact-scanning electrochemical microscopy.

    Science.gov (United States)

    McKelvey, Kim; Snowden, Michael E; Peruffo, Massimo; Unwin, Patrick R

    2011-09-01

    The use of intermittent contact-scanning electrochemical microscopy (IC-SECM) in diffusion-limited amperometric mode to visualize and quantify mass transport through multiporous membranes is described using dentin as a model example. The IC mode of SECM employs the damping of a vertically modulated ultramicroelectrode (UME) to achieve positioning close to the receptor side of a membrane. In this way the UME can detect electroactive species close to the pore exit. A key aspect of IC-SECM is that in addition to the direct current (dc) from the diffusion-limited detection of the analyte, an alternating current (ac) also develops due to the motion of the probe. It demonstrates that this ac signal enhances the spatial resolution of SECM detection and allows the hydrodynamic flow of species to be detected from individual closely spaced pores. The experimental deductions are supported by three-dimensional finite element modeling which allows IC-SECM current maps to be analyzed to reveal transport rates through individual pores. The method described should be widely applicable to multiporous membrane transport.

  9. First-principles and molecular dynamics study of thermoelectric transport properties of N-type silicon-based superlattice-nanocrystalline heterostructures

    Science.gov (United States)

    Zhou, Yanguang; Gong, Xiaojing; Xu, Ben; Hu, Ming

    2017-08-01

    Electrical and thermal transport in silicon germanium superlattice nanostructures has received extensive attention from scientists for understanding carrier properties at the nanoscale, and the figure-of-merit (ZT) reported in such structures has inspired engineers to develop cost-effective waste heat recovery systems. In this paper, the thermoelectric transport properties of the silicon-based superlattice- and anti-superlattice-nanocrystalline heterostructures are systematically studied by first-principles and molecular dynamics simulations combined with the Boltzmann transport theory. The thermal conductivity, which is thought to be the essential bottleneck for bulk crystalline Si to gain a high ZT value, of such structures is found to be reduced by two orders of magnitude and reaches a level far below the amorphous limit of Si. This is achieved due to the extremely strong phonon-boundary scattering at both grain boundaries and Si-Ge interfaces, which will lead to the phonon mean free path being much smaller than the grain size (Casmir limit): for instance, the dominant phonons are in range of 0.5 to 3 nm for the heterostructures with a grain size of around 8 nm. Meanwhile, the power factor can be preserved at the level comparable to bulk crystalline because of the quantum confinement effect, which resulted from the conduction band minima converge, reduction of band gap, and the short mean free path of carriers. As a result, the ZT of such superlattice based nanomembranes can reach around 0.3 at room temperature, which is two orders of magnitude higher than the bulk crystalline case. The corresponding bulk superlattice-nanocrystalline heterostructures possess a ZT value of 0.5 at room temperature, which is superior to all other bulk silicon-based thermoelectrics. Our results here show that nanostructuring the superlattice structure can further decrease the thermal conductivity while keeping the electrical transport properties at the bulk comparable level, and

  10. 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.

  11. Molecular Characterization of an Ice Nucleation Protein Variant (InaQ from Pseudomonas syringae and the Analysis of Its Transmembrane Transport Activity in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Qianqian Li, Qi Yan, Jinsi Chen, Yan He, Jing Wang, Hongxing Zhang, Ziniu Yu, Lin Li

    2012-01-01

    Full Text Available The ice nucleation protein (INP of Pseudomonas syringae has gained scientific interest not only because of its pathogenicity of foliar necroses but also for its wide range of potential applications, such as in snow making, frozen food preparation, and surface-display system development. However, studies on the transport activity of INP remain lacking. In the present study, a newly identified INP-gene variant, inaQ, from a P. syringae MB03 strain was cloned. Its structural domains, signal sequences, and the hydrophilicity or hydrophobicity of each domain, were then characterized. The deduced amino acid sequence of InaQ shares similar protein domains with three P. syringae INPs, namely, InaK, InaZ, and InaV, which were identified as an N-terminal domain, a central repeating domain, and a C-terminal domain. The expression of the full-length InaQ and of various truncated variants was induced in Escherichia coli to analyze their transmembrane transport and surface-binding activities, while using the green fluorescence protein (GFP as the fusion partner. With two transmembrane segments and a weak secretion signal, the N-terminal domain (InaQ-N alone was found to be responsible for the transport process as well as for the binding to the outer membrane, whereas the C-terminal region was nonfunctional in protein transport. Increased membrane transport and surface-binding capacities were induced by a low isopropyl-β-D-thiogalactoside concentration (0.1 mmol/l but not by culture temperatures (15 ºC to 37 ºC. Furthermore, by constructing the GFP-fused proteins with a single InaQ-N, as well as two and three tandemly aligned InaQ-N molecules, the transport and membrane-binding activities of these proteins were compared using Western blot analysis, immmunofluorescence microscopy, and assays of the GFP specific fluorescence intensity of subcellular fractions and flow cytometry, which showed that the increase of InaQ-N repeats resulted in a coordinated

  12. Molecular characterization of an ice nucleation protein variant (inaQ) from Pseudomonas syringae and the analysis of its transmembrane transport activity in Escherichia coli.

    Science.gov (United States)

    Li, Qianqian; Yan, Qi; Chen, Jinsi; He, Yan; Wang, Jing; Zhang, Hongxing; Yu, Ziniu; Li, Lin

    2012-01-01

    The ice nucleation protein (INP) of Pseudomonas syringae has gained scientific interest not only because of its pathogenicity of foliar necroses but also for its wide range of potential applications, such as in snow making, frozen food preparation, and surface-display system development. However, studies on the transport activity of INP remain lacking. In the present study, a newly identified INP-gene variant, inaQ, from a P. syringae MB03 strain was cloned. Its structural domains, signal sequences, and the hydrophilicity or hydrophobicity of each domain, were then characterized. The deduced amino acid sequence of InaQ shares similar protein domains with three P. syringae INPs, namely, InaK, InaZ, and InaV, which were identified as an N-terminal domain, a central repeating domain, and a C-terminal domain. The expression of the full-length InaQ and of various truncated variants was induced in Escherichia coli to analyze their transmembrane transport and surface-binding activities, while using the green fluorescence protein (GFP) as the fusion partner. With two transmembrane segments and a weak secretion signal, the N-terminal domain (InaQ-N) alone was found to be responsible for the transport process as well as for the binding to the outer membrane, whereas the C-terminal region was nonfunctional in protein transport. Increased membrane transport and surface-binding capacities were induced by a low isopropyl-β-D-thiogalactoside concentration (0.1 mmol/l) but not by culture temperatures (15 ºC to 37 ºC). Furthermore, by constructing the GFP-fused proteins with a single InaQ-N, as well as two and three tandemly aligned InaQ-N molecules, the transport and membrane-binding activities of these proteins were compared using Western blot analysis, immmunofluorescence microscopy, and assays of the GFP specific fluorescence intensity of subcellular fractions and flow cytometry, which showed that the increase of InaQ-N repeats resulted in a coordinated increase of the

  13. 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.

  14. Molecular modulation of the copper and cisplatin transport function of CTR1 and its interaction with IRS-4

    Science.gov (United States)

    Tsai, Cheng-Yu; Larson, Christopher A.; Safaei, Roohangiz

    2015-01-01

    The copper influx transporter CTR1 is also a major influx transporter for cisplatin (cDDP) in tumor cells. It influences the cytotoxicity of cDDP both in vivo and in vitro. Whereas Cu triggers internalization of CTR1 from the plasma membrane, cDDP does not. To investigate the mechanisms of these effects, myc-tagged forms of wild type hCTR1 and variants in which Y103 was converted to alanine, C189 was converted to serine, or the K178/K179 dilysine motif was converted to alanines were re-expressed in mouse embryo cells in which both alleles of CTR1 had been knocked out and also in HEK293T cells. The Y103A mutation and to a lesser extent the C189S mutation reduced internalization of CTR1 induced by Cu while the K178A/K179A had little effect. Both Y103 and C189 were required for Cu and cDDP transport whereas the K178/K179 motif was not. While Y103 lies in an YXXM motif that, when phosphorylated, is a potential docking site for phosphatidylinositol 3-kinase and other proteins involved in endocytosis, Western blot analysis of immunoprecipitated myc-CTR1, and proteomic analysis of peptides derived from CTR1, failed to identify any basal or Cu-induced phosphorylation. However, proteomic analysis did identify an interaction of CTR1 with IRS-4 and this was confirmed by co-immunoprecipitation from HEK cells expressing either FLAG-CTR1 or myc-CTR1. The interaction was greater in the Y103A-expressing cells. We conclude that Y103 is required for the internalization of hCTR1 in response to Cu, that this occurs by a mechanism other than phosphorylation and that mutation of Y103 modulates the interaction with IRS-4. PMID:24967972

  15. Molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  16. 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.

  17. 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.

  18. 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}.

  19. 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 (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.

  20. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.

    Science.gov (United States)

    Edelmann, Franziska Theresia; Schlundt, Andreas; Heym, Roland Gerhard; Jenner, Andreas; Niedner-Boblenz, Annika; Syed, Muhammad Ibrahim; Paillart, Jean-Christophe; Stehle, Ralf; Janowski, Robert; Sattler, Michael; Jansen, Ralf-Peter; Niessing, Dierk

    2017-02-01

    mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p. Although the RNA alone formed a flexible stem loop, She2p binding induced marked conformational changes. However, only joining by the unstructured She3p resulted in specific RNA recognition. The notable RNA rearrangements and joint action of a globular and an unfolded RNA-binding protein offer unprecedented insights into the step-wise maturation of an mRNA-transport complex.

  1. Impurity effects on toroidal ITG-modes and transport in tokamaks

    Energy Technology Data Exchange (ETDEWEB)

    Froejdh, M.

    1993-04-01

    The presence of impurities in tokamak plasmas has until recently been ignored in several fluctuation driven transport models. In this thesis some of the consequences of including an ion impurity species into a model for low frequency electrostatic modes and fluctuation driven transport are discussed. The direction of the particle flows in a two-ion-component plasma is studied for the outer part of the good confinement region. When the two ion species, main and impurity ions, have similar inwardly peaked density profiles the latter tends to determine the flow directions for typical tokamak plasma conditions. Hence, the impurities flow outwards and the main ions inwards, leading to so called plasma decontamination. The stability of the toroidal main and impurity ion temperature gradient modes (ITG-modes) is determined by using an advanced fluid model. The impurity effect on the background mode is found to be stabilizing for a large domain of parameters. However, a destabilization is also possible. An impurity mode driven by toroidicity is found and shown to be unstable in a new parameter region. The particle and thermal diffusivities are estimated and the scaling properties are studied. The magnitude of the ion thermal conductivity is shown to decrease due to the stabilizing influence of impurities. The radial variation of the transport coefficients are considered for some experimental equilibrium profiles. The stability properties of a contaminated tokamak plasma with dissipative trapped electrons are investigated. The dissipation is found to change the instability thresholds. The relation between wave energy, electron dissipation and instability is discussed. (35 refs.).

  2. Magnetic and transport properties of epitaxial thin film MgFe2O4 grown on MgO (100) by molecular beam epitaxy.

    Science.gov (United States)

    Wu, Han-Chun; Mauit, Ozhet; Coileáin, Cormac Ó; Syrlybekov, Askar; Khalid, Abbas; Mouti, Anas; Abid, Mourad; Zhang, Hong-Zhou; Abid, Mohamed; Shvets, Igor V

    2014-11-12

    Magnesium ferrite is a very important magnetic material due to its interesting magnetic and electrical properties and its chemical and thermal stability. Here we report on the magnetic and transport properties of epitaxial MgFe2O4 thin films grown on MgO (001) by molecular beam epitaxy. The structural properties and chemical composition of the MgFe2O4 films were characterized by X-Ray diffraction and X-Ray photoelectron spectroscopy, respectively. The nonsaturation of the magnetization in high magnetic fields observed for M (H) measurements and the linear negative magnetoresistance (MR) curves indicate the presence of anti-phase boundaries (APBs) in MgFe2O4. The presence of APBs was confirmed by transmission electron microscopy. Moreover, post annealing decreases the resistance and enhances the MR of the film, suggesting migration of the APBs. Our results may be valuable for the application of MgFe2O4 in spintronics.

  3. Thermodynamic, Structural and Transport Properties of Lennard-Jones Liquid Systems. A Molecular Dynamics Simulations of Liquid Helium, Neon, Methane and Nitrogen

    Directory of Open Access Journals (Sweden)

    F. Ould Kadour

    2003-12-01

    Full Text Available Abstract: Molecular dynamics calculations are carried out in order to find the properties of Lennard Jones liquids in different state points of their phase diagram. The spherical shape and the stability of the helium, neon, methane and nitrogen make the liquids easily accessible to numerical simulation. Thermodynamic, structural, and transport properties are studied and compared with both experimental data and recent theoretical investigations. In the present work, up to 22 state points are covered, some of which are near or at the triple point. It will be shown that the classical approach leads to data that are in very good agreement with experiments and other types of calculations. At high temperatures and low densities, we observe a decrease in the uncertainties in the stress autocorrelation function by increasing the number of iterations.

  4. A Quasi-Solid State DSSC with 10.1% Efficiency through Molecular Design of the Charge-Separation and -Transport

    Science.gov (United States)

    Suzuka, Michio; Hayashi, Naoki; Sekiguchi, Takashi; Sumioka, Kouichi; Takata, Masakazu; Hayo, Noriko; Ikeda, Hiroki; Oyaizu, Kenichi; Nishide, Hiroyuki

    2016-06-01

    Organic-based solar cells potentially offer a photovoltaic module with low production costs and low hazard risk of the components. We report organic dye-sensitized solar cells, fabricated with molecular designed indoline dyes in conjunction with highly reactive but robust nitroxide radical molecules as redox mediator in a quasi-solid gel form of the electrolyte. The cells achieve conversion efficiencies of 10.1% at 1 sun, and maintain the output performance even under interior lighting. The indoline dyes, customized by introducing long alkyl chains, specifically interact with the radical mediator to suppress a charge-recombination process at the dye interface. The radical mediator also facilitates the charge-transport with remarkably high electron self-exchange rate even in the quasi-solid state electrolyte to lead to a high fill factor.

  5. Some methods to regulate low-bias negative differential resistance in σ barrier separating nanoscale molecular transport systems

    Science.gov (United States)

    Shen, Ji-Mei; Liu, Jing; Min, Yi; Zhou, Li-Ping

    2016-12-01

    Using the first-principles method which combines the nonequilibrium Green’s function (NEGF) with density functional theory (DFT), the role of defect, dopant, barrier length and geometric deformation for low-bias negative differential resistance (NDR) in two capped armchair carbon nanotubes (CNTs) sandwiching σ barrier are systematically analyzed. We found that this method can regulate the negative differential resistance (NDR) effects such as current peak and peak position. The adjusting mechanism may originate from orbital interaction and orbital reconstruction. Our calculations try to manipulate the transport characteristics in energy space by simply manipulating the structure in real space, which may promise the potential applications in nanomolecular-electronics in the future.

  6. Molecular basis for interaction of Na+/K+-ATPase with other transporters in membrane microdomains of vascular smooth muscle cells

    DEFF Research Database (Denmark)

    Hansen, Anne Kirstine; Matchkov, Vladimir; Bouzinova, Elena

    2008-01-01

    an interaction between the Na+/K+-pump and the Na+/Ca2+-exchanger leading to an increase in the intracellular calcium concentration in discrete areas near the plasma membrane. This regulation suggests a close association of the proteins in microdomains. We have also suggested that this Na......+/K+-pump-containing microdomain is functionally linked to KATP channels via the local ion homeostasis and that this interaction can be bidirectional (1;2). Using PCR, Western blotting and immunohistochemistry we aimed to identify the isoforms of membrane transporters involved in the suggested interaction in SMCs from mesenteric...... small arteries and in the SMC cell line A7r5. Confocal microscopy and conventional patch clamp were used in functional studies. The Na+/K+-ATPase subunits in SMCs were found to be α1 and α2. As indicated by loss of mechanical synchronization and synchronization of Ca2+ transients between SMCs...

  7. Molecular modeling of the morphology and transport properties of two direct methanol fuel cell membranes: phenylated sulfonated poly(ether ether ketone ketone) versus Nafion

    Energy Technology Data Exchange (ETDEWEB)

    Devanathan, Ramaswami; Idupulapati, Nagesh B.; Dupuis, Michel

    2012-08-14

    We have used molecular dynamics simulations to examine membrane morphology and the transport of water, methanol and hydronium in phenylated sulfonated poly ether ether ketone ketone (Ph-SPEEKK) and Nafion membranes at 360 K for a range of hydration levels. At comparable hydration levels, the pore diameter is smaller, the sulfonate groups are more closely packed, the hydronium ions are more strongly bound to sulfonate groups, and the diffusion of water and hydronium is slower in Ph-SPEEKK relative to the corresponding properties in Nafion. The aromatic carbon backbone of Ph-SPEEKK is less hydrophobic than the fluorocarbon backbone of Nafion. Water network percolation occurs at a hydration level ({lambda}) of {approx}8 H{sub 2}O/SO{sub 3}{sup -}. At {lambda} = 20, water, methanol and hydronium diffusion coefficients were 1.4 x 10{sup -5}, 0.6 x 10{sup -5} and 0.2 x 10{sup -5} cm{sup 2}/s, respectively. The pore network in Ph-SPEEKK evolves dynamically and develops wide pores for {lambda} > 20, which leads to a jump in methanol crossover and ion transport. This study demonstrates the potential of aromatic membranes as low-cost challengers to Nafion for direct methanol fuel cell applications and the need to develop innovative strategies to combat methanol crossover at high hydration levels.

  8. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    Full Text Available Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III Hexamine ions or Mg(2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III Hexamine ions were found to bind stronger with the loop than Mg(2+ ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III Hexamine ions on CorA ions transportation.

  9. 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.

  10. Generation of a 3D model for human GABA transporter hGAT-1 using molecular modeling and investigation of the binding of GABA.

    Science.gov (United States)

    Wein, Thomas; Wanner, Klaus T

    2010-01-01

    A three-dimensional model of the human Na(+)/Cl(-)-dependent gamma-aminobutyric acid (GABA) transporter hGAT-1 was developed by homology modeling and refined by subsequent molecular modeling using the crystal structure of a bacterial homologue leucine transporter from Aquifex aeolicus (LeuT(Aa)) as the template. Protein structure quality checks show that the resulting structure is particularly suited for the analysis of the substrate binding pocket and virtual screening experiments. Interactions of GABA and the substrate binding pocket were investigated using docking studies. The difference of 6 out of 13 substrate interacting side chains between hGAT-1 and LeuT(Aa) lead to the different substrate preference which can be explained using our three-dimensional model of hGAT-1. In particular the replacement of serine 256 and isoleucine 359 in LeuT(Aa) with glycine and threonine in hGAT-1 seems to facilitate the selection of GABA as the main substrate by changing the hydrogen bonding pattern in the active site to the amino group of the substrate. For a set of 12 compounds flexible docking experiments were performed using LigandFit in combination with the Jain scoring function. With few exceptions the obtained rank order of potency was in line with experimental data. Thus, the method can be assumed to give at least a rough estimate of the potency of the potential of GABA uptake inhibitors.

  11. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  12. Molecular characterization of the citrate transporter gene TaMATE1 and expression analysis of upstream genes involved in organic acid transport under Al stress in bread wheat (Triticum aestivum).

    Science.gov (United States)

    Garcia-Oliveira, Ana Luísa; Martins-Lopes, Paula; Tolrá, Roser; Poschenrieder, Charlotte; Tarquis, Marta; Guedes-Pinto, Henrique; Benito, César

    2014-11-01

    In bread wheat, besides malate, the importance of citrate efflux for Al tolerance has also been reported. For better understanding the Al tolerance mechanism in bread wheat, here, we performed both a molecular characterization of the citrate transporter gene TaMATE1 and an investigation on the upstream variations in citrate and malate transporter genes. TaMATE1 belong to multidrug transporter protein family, which are located on the long arm of homoeologous group 4 chromosomes (TaMATE1-4A, TaMATE1-4B TaMATE1-4D). TaMATE1 homoeologues transcript expression study exhibited the preponderance of homoeologue TaMATE1-4B followed by TaMATE1-4D whereas homoeologue TaMATE1-4A seemed to be silenced. TaMATE1, particularly homoeologue TaMATE1-4B and TaALMT1 transcripts were much more expressed in the root apices than in shoots of Al tolerant genotype Barbela 7/72/92 under both control and Al stress conditions. In addition, in both tissues of Barbela 7/72/92, higher basal levels of these gene transcripts were observed than in Anahuac (Al sensitive). Noticeably, the presence of a transposon in the upstream of TaMATE1-4B in Barbela 7/72/92 seems to be responsible for its higher transcript expression where it may confer citrate efflux. Thus, promoter variations (transposon in TaMATE1-4B upstream and type VI promoter in TaALMT1) associated with higher basal transcript expression of TaMATE1-4B and TaALMT1 clearly show how different mechanisms for Al tolerance operate simultaneously in a single genotype. In conclusion, our results demonstrate that Barbela 7/72/92 has favorable alleles for these organic acids transporter genes which could be utilized through genomic assisted selection to develop improved cultivars for acidic soils.

  13. Comparative molecular field analysis using selectivity fields reveals residues in the third transmembrane helix of the serotonin transporter associated with substrate and antagonist recognition.

    Science.gov (United States)

    Walline, Crystal C; Nichols, David E; Carroll, F Ivy; Barker, Eric L

    2008-06-01

    The human serotonin transporter (hSERT) regulates the spatial and temporal actions of serotonin (5-HT) neurotransmission by removing 5-HT from the synapse. Previous studies have identified residues in the third transmembrane helix (TMH) that may be important for substrate translocation or antagonist recognition. We identified hSERT residues in TMH III that are divergent from Drosophila SERT and used species-scanning mutagenesis to generate reciprocal mutants. Transport inhibition assays suggest that the potency of substituted amphetamines was decreased for the hSERT mutants A169D, I172M, and S174M. In addition, there was a loss of potency for several antidepressants and 3-phenyltropane analogs for the I172M mutant. These results suggest that residues in TMH III may contribute to antagonist recognition. We carried out comparative molecular field analyses using selectivity fields to directly visualize the mutation-induced effects of antagonist potency for antidepressants, 3-phenyltropane analogs, and amphetamines. The hSERT I172M selectivity field analysis for the 3-phenyltropane analogs revealed that electrostatic interactions resulted in decreased potency. The amphetamine and antidepressant selectivity field analyses reveal the observed decreases in potencies for the hSERT I172M mutant are due to a change in tertiary structure of the hSERT protein and are not due to disruption of a direct binding site. Finally, the hSERT mutant A169D displayed altered kinetics for sodium binding, indicating that this residue may lie near the putative sodium binding site. A SERT homology model developed from the Aquifex aeolicus leucine transporter structure provides a structural context for further interpreting the results of the TMH III mutations.

  14. Tailoring the highest occupied molecular orbital level of poly(N-vinylcarbazole) hole transport layers in organic multilayer heterojunctions

    Energy Technology Data Exchange (ETDEWEB)

    Park, Young Ran [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Kim, Hyeong Jin; Hong, Young Joon, E-mail: shink@sejong.ac.kr, E-mail: yjhong@sejong.ac.kr [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Faculty of Nanotechnology and Advanced Materials Engineering, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Hybrid Materials Research Center, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Im, Sungjin; Shin, Koo, E-mail: shink@sejong.ac.kr, E-mail: yjhong@sejong.ac.kr [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Department of Chemistry, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Seo, Sunae [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Department of Physics, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Choi, Won Kook [Materials and Life Science Research Division, Korea Institute of Science and Technology, Hwarang-ro 14-gil, Seoul 136-791 (Korea, Republic of)

    2016-01-11

    We report the tailoring of the electronic structure of poly(N-vinylcarbazole) (PVK) using a mixture layer of polyaniline:poly(p-styrenesulfonic acid) (PANI:PSS) in organic multilayer PVK/PANI:PSS/poly(3,4-ethylenedioxythiophene):PSS heterojunctions. The overall electronic structure of the PVK overlayer was systematically down-shifted while the work function of PANI:PSS increased as a function of the PSS-to-PANI weight ratio for the ratio range from 1 to 11 in the PANI:PSS film. The down-shift in the highest occupied molecular orbital of PVK markedly reduced the hole injection barrier from PVK to quantum-dot (QD) layers in QD-light emitting diode (QD-LED) structures, resulting in superior electrical and electroluminescent characteristics for QD-LEDs. The influences of PANI:PSS thickness on the electronic structure of PVK and the performance of QD-LEDs are also discussed.

  15. Effect of the orientation of doped nanoparticles on thermal transportation of a solid: A molecular dynamics study

    Science.gov (United States)

    Shahadat, Muhammad Rubayat Bin; Masnoon, Ahmed Shafkat; Ahmed, Shafkat; Morshed, A. K. M. M.

    2017-06-01

    Interstitial phenomena like different types of atoms, doping and their orientation in nano scale influence the heat transfer and these effects become very significant with the reduction of material size. Non equilibrium Molecular Dynamics (NEMD) simulation was employed in this study to understand the effects of interfacial thermal resistance named kapitza resistance on solid. Argon like solid was considered in this study and LJ potential model was employed for the calculation of atomic interaction. Doping of nanoparticles at different orientation was inserted into the solid. From the simulation, it was observed that a large interfacial mismatch due to change in orientation in homogenous solid causes distortion of phonon frequency causing an increase in thermal resistance. The position of doped particles has a profound effect on thermal conductivity of solid. Interfacial atoms positioned perpendicular to heat flow direction causes sharp reduction in thermal conductivity. Phonon scattering at the material interface has been observed.

  16. Photons transport through ultra-high molecular weight polyethylene based composite containing tungsten and boron carbide fillers

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, S.M. [National Research Center “Kurchatov Institute”, Moscow 123182 (Russian Federation); Kuznetsov, S.A. [Russian State Technological University “MATI”, Moscow 121552 (Russian Federation); Volkov, A.E.; Terekhin, P.N.; Dmitriev, S.V. [National Research Center “Kurchatov Institute”, Moscow 123182 (Russian Federation); Tcherdyntsev, V.V.; Gorshenkov, M.V. [National University of Science and Technology “MISIS”, Moscow 119049 (Russian Federation); Boykov, A.A., E-mail: kink03@gmail.com [National University of Science and Technology “MISIS”, Moscow 119049 (Russian Federation)

    2014-02-15

    Highlights: • The developed method for predicting X-ray properties of the polymer. • Higher content of the fillers results in an increase of mechanical properties. • X-ray defensive properties of the samples were investigated experimentally. -- Abstract: Polymers are a base for creating of composite materials with high mechanical and chemical properties. Using the heavy metals as filler in these composites can give them X-ray protective properties. These materials have high deactivation rates and can be used to create Personal Protective Equipment (PPE) used in aggressive environments. It was proposed a model for calculation of X-ray protection properties of the polymer-based nanocomposite materials with ultra-high molecular weight polyethylene (UHMWPE) matrix, filled with tungsten and boron carbide particles. X-ray protective properties were calculated in a wide range of filler content using the developed model. Results of calculations allow selecting most effective compounds of X-ray protective UHMWPE based composites.

  17. Blood-brain barrier transport studies, aggregation, and molecular dynamics simulation of multiwalled carbon nanotube functionalized with fluorescein isothiocyanate.

    Science.gov (United States)

    Shityakov, Sergey; Salvador, Ellaine; Pastorin, Giorgia; Förster, Carola

    2015-01-01

    In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT-FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood-brain barrier. The results indicated that the MWCNT-FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell(®) system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT-FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT-FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCNT-FITC rapid dissociation as an intermediate phase.

  18. 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

  19. Electrostatic and magnetic measurements of turbulence and transport in Extrap T2

    Science.gov (United States)

    Möller, Anders; Sallander, Eva

    1999-10-01

    Langmuir probe and magnetic pick-up coil measurements are used to study edge turbulence in the Extrap T2 reversed field pinch. Magnetic fluctuations resonant outside the toroidal field reversal surface are observed where previously only fluctuations in the spectra of potential and electron density and temperature have been measured. Results are presented which imply that these fluctuations are coupled to and also correlated to the internally resonant tearing mode fluctuations. Evidence of coupling between low-frequency (<100 kHz) and high-frequency fluctuations is also presented. The normalized floating potential fluctuations are seen to increase with the edge electron temperature. This causes an increase of the potential and density fluctuation driven transport with the temperature which is faster than linear. These results, in combination, are consistent with a picture where internally resonant fluctuations couple to edge fluctuations through radial heat conduction from the stochastic core to the edge.

  20. Scalar arguments of the mathematical functions defining molecular and turbulent transport of heat and mass in compressible fluids

    Science.gov (United States)

    Kowalski, Andrew S.; Argüeso, Daniel

    2011-11-01

    The advection-diffusion equations defining control volume conservation laws in micrometeorological research are analysed to resolve discrepancies in their appropriate scalar variables for heat and mass transport. A scalar variable that is conserved during vertical motions enables the interpretation of turbulent mixing as ‘diffusion’. Gas-phase heat advection is shown to depend on gradients in the potential temperature (θ), not the temperature (T). Since conduction and radiation depend on T, advection-diffusion of heat depends on gradients of both θ and T. Conservation of θ (the first Law of Thermodynamics) requires including a pressure covariance term in the definition of the turbulent heat flux. Mass advection and diffusion are universally agreed to depend directly on gradients in the gas ‘concentration’ (c), a nonetheless ambiguous term. Depending upon author, c may be defined either as a dimensionless proportion or as a dimensional density, with non-trivial differences for the gas phase. Analyses of atmospheric law, scalar conservation and similarity theory demonstrate that mass advection-diffusion in gases depends on gradients, not in density but rather in a conserved proportion. Flux-tower researchers are encouraged to respect the meteorological tradition of writing conservation equations in terms of scalar variables that are conserved through simple air motions.

  1. Role of Histidine 547 of Human Dopamine Transporter in Molecular Interaction with HIV-1 Tat and Dopamine Uptake.

    Science.gov (United States)

    Yuan, Yaxia; Quizon, Pamela M; Sun, Wei-Lun; Yao, Jianzhuang; Zhu, Jun; Zhan, Chang-Guo

    2016-06-02

    HIV-1 Tat plays an important role in HIV-associated neurocognitive disorders (HAND) by disrupting neurotransmission including dopamine uptake by human dopamine transporter (hDAT). Previous studies have demonstrated that HIV-1 Tat directly binds to hDAT and some amino-acid mutations that attenuate the hDAT-Tat binding also significantly decreased dopamine uptake activity of hDAT. This combined computational-experimental study demonstrates that histidine-547 (H547) of hDAT plays a crucial role in the hDAT-Tat binding and dopamine uptake by hDAT, and that the H547A mutation can not only considerably attenuate Tat-induced inhibition of dopamine uptake, but also significantly increase the Vmax of hDAT for dopamine uptake. The finding of such an unusual hDAT mutant capable of both increasing the Vmax of hDAT for dopamine uptake and disrupting the hDAT-Tat binding may provide an exciting knowledge basis for development of novel concepts for therapeutic treatment of the HAND.

  2. 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.

  3. Sheetflow Effects and Canal Backfilling on Sediment Source and Transport in Everglades Freshwater Marshes: Analysis of Molecular Organic Biomarkers

    Science.gov (United States)

    Regier, P.; He, D.; Saunders, C.; Coronado-Molina, C.; Jara, B.; Jaffe, R.

    2014-12-01

    Historic freshwater sheetflow in the Florida Everglades distributed sediment to form a ridge-and-slough landscape. However, drainage along with reduction and obstruction of flow has resulted in degradation of this ridged topography. The DECOMP Physical Model is a landscape-scale project aiming to reestablish natural sheetflow to the central and southern Everglades by redesigning barriers to flow. To validate proof of concept that increased flow will rebuild ridge-slough microtopography, biomarker proxies were established for ridge and slough organic matter sources. In addition, partial and complete canal backfill options were assessed via sediment trap accumulation in each backfill treatment area. Flocculent matter (floc) and sediment samples were collected, solvent extracted, chromatographically separated, and analyzed on a GC/MS using internal standard for quantification. Four molecular organic biomarkers were evaluated: the aquatic proxy (Paq), highly-branched isoprenoids (C20 HBI), kaurenes and botyrococcenes. Paq, an aquatic proxy of mid to long-chain n-alkanes, was shown to clearly differentiate between ridge-derived and slough-derived organic matter with Paq values increasing along ridge-to-slough transects. Kaurenes indicated presence of ridge-derived organic matter while C20 HBI and botyrococcenes were indicative of periphyton-derived organic matter which is commonly more abundant in sloughs. Biomarker distributions during both low (present day) and high (managed) water flow through the DECOMP experimental parcel were determined and discussed comparatively.

  4. A molecular dynamics study on the transport of a charged biomolecule in a polymeric adsorbent medium and its adsorption onto a charged ligand.

    Science.gov (United States)

    Riccardi, E; Wang, J-C; Liapis, A I

    2010-08-28

    The transport of a charged adsorbate biomolecule in a porous polymeric adsorbent medium and its adsorption onto the covalently immobilized ligands have been modeled and investigated using molecular dynamics modeling and simulations as the third part of a novel fundamental methodology developed for studying ion-exchange chromatography based bioseparations. To overcome computational challenges, a novel simulation approach is devised where appropriate atomistic and coarse grain models are employed simultaneously and the transport of the adsorbate is characterized through a number of locations representative of the progress of the transport process. The adsorbate biomolecule for the system studied in this work changes shape, orientation, and lateral position in order to proceed toward the site where adsorption occurs and exhibits decreased mass transport coefficients as it approaches closer to the immobilized ligand. Furthermore, because the ligands are surrounded by counterions carrying the same type of charge as the adsorbate biomolecule, it takes the biomolecule repeated attempts to approach toward a ligand in order to displace the counterions in the proximity of the ligand and to finally become adsorbed. The formed adsorbate-ligand complex interacts with the counterions and polymeric molecules and is found to evolve slowly and continuously from one-site (monovalent) interaction to multisite (multivalent) interactions. Such a transition of the nature of adsorption reduces the overall adsorption capacity of the ligands in the adsorbent medium and results in a type of surface exclusion effect. Also, the adsorption of the biomolecule also presents certain volume exclusion effects by not only directly reducing the pore volume and the availability of the ligands in the adjacent regions, but also causing the polymeric molecules to change to more compact structures that could further shield certain ligands from being accessible to subsequent adsorbate molecules. These

  5. Dominance induction of fruitlet shedding in Malus × domestica (L. Borkh: molecular changes associated with polar auxin transport

    Directory of Open Access Journals (Sweden)

    Velasco Riccardo

    2009-11-01

    Full Text Available Abstract Background Apple fruitlet abscission is induced by dominance, a process in which hormones such as auxin, cytokinins and strigolactone play a pivotal role. The response to these hormones is controlled by transcription regulators such as Aux/IAA and ARR, whereas auxin transport is controlled by influx and efflux carriers. Results Seven partial clones encoding auxin efflux carriers (MdPIN1_A, MdPIN1_B, MdPIN10_A, MdPIN10_B, MdPIN4, MdPIN7_A and MdPIN7_B, three encoding auxin influx carriers (MdLAX1, MdLAX2 and MdLAX3 and three encoding type A ARR cytokinin response regulators (MdARR3, MdARR4 and MdARR6 were isolated by the use of degenerate primers. The organization of the PIN multigene family in apple is closer to Medicago truncatula than to Arabidopsis thaliana. The genes are differentially expressed in diverse plant organs and at different developmental stages. MdPIN1 and MdPIN7 are largely more expressed than MdPIN10 and MdPIN4. During abscission, the transcription of these genes increased in the cortex whereas in the seed a sharp fall was observed. The expression of these genes was found to be at least partially controlled by ethylene and auxin. Conclusion The ethylene burst preceding abscission of fruitlets may be responsible for the decrease in transcript level of MDPIN1, MDARR5 and MDIAA3 in seed. This situation modulates the status of the fruitlet and its fate by hampering the PAT from the seeds down through the abscission zone (AZ and this brings about the shedding of the fruitlet.

  6. Molecular Dynamics Simulation of Thermal Transport in UO2 Containing Uranium, Oxygen, and Fission-product Defects

    Science.gov (United States)

    Liu, X.-Y.; Cooper, M. W. D.; McClellan, K. J.; Lashley, J. C.; Byler, D. D.; Bell, B. D. C.; Grimes, R. W.; Stanek, C. R.; Andersson, D. A.

    2016-10-01

    Uranium dioxide (UO2 ) is the most commonly used fuel in light-water nuclear reactors and thermal conductivity controls the removal of heat produced by fission, thereby governing fuel temperature during normal and accident conditions. The use of fuel performance codes by the industry to predict operational behavior is widespread. A primary source of uncertainty in these codes is thermal conductivity, and optimized fuel utilization may be possible if existing empirical models are replaced with models that incorporate explicit thermal-conductivity-degradation mechanisms during fuel burn up. This approach is able to represent the degradation of thermal conductivity due to each individual defect type, rather than the overall burn-up measure typically used, which is not an accurate representation of the chemical or microstructure state of the fuel that actually governs thermal conductivity and other properties. To generate a mechanistic thermal conductivity model, molecular dynamics (MD) simulations of UO2 thermal conductivity including representative uranium and oxygen defects and fission products are carried out. These calculations employ a standard Buckingham-type interatomic potential and a potential that combines the many-body embedded-atom-method potential with Morse-Buckingham pair potentials. Potential parameters for UO2 +x and ZrO2 are developed for the latter potential. Physical insights from the resonant phonon-spin-scattering mechanism due to spins on the magnetic uranium ions are introduced into the treatment of the MD results, with the corresponding relaxation time derived from existing experimental data. High defect scattering is predicted for Xe atoms compared to that of La and Zr ions. Uranium defects reduce the thermal conductivity more than oxygen defects. For each defect and fission product, scattering parameters are derived for application in both a Callaway model and the corresponding high-temperature model typically used in fuel-performance codes

  7. Gene amplification, ABC transporters and cytochrome P450s: unraveling the molecular basis of pyrethroid resistance in the dengue vector, Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Vassiliki Bariami

    Full Text Available BACKGROUND: Pyrethroid insecticides are widely utilized in dengue control. However, the major vector, Aedes aegypti, is becoming increasingly resistant to these insecticides and this is impacting on the efficacy of control measures. The near complete transcriptome of two pyrethroid resistant populations from the Caribbean was examined to explore the molecular basis of this resistance. PRINCIPAL FINDINGS: Two previously described target site mutations, 1016I and 1534C were detected in pyrethroid resistant populations from Grand Cayman and Cuba. In addition between two and five per cent of the Ae. aegypti transcriptome was differentially expressed in the resistant populations compared to a laboratory susceptible population. Approximately 20 per cent of the genes over-expressed in resistant mosquitoes were up-regulated in both Caribbean populations (107 genes. Genes with putative monooxygenase activity were significantly over represented in the up-regulated subset, including five CYP9 P450 genes. Quantitative PCR was used to confirm the higher transcript levels of multiple cytochrome P450 genes from the CYP9J family and an ATP binding cassette transporter. Over expression of two genes, CYP9J26 and ABCB4, is due, at least in part, to gene amplification. SIGNIFICANCE: These results, and those from other studies, strongly suggest that increases in the amount of the CYP9J cytochrome P450s are an important mechanism of pyrethroid resistance in Ae. aegypti. The genetic redundancy resulting from the expansion of this gene family makes it unlikely that a single gene or mutation responsible for pyrethroid resistance will be identified in this mosquito species. However, the results from this study do pave the way for the development of new pyrethroid synergists and improved resistance diagnostics. The role of copy number polymorphisms in detoxification and transporter genes in providing protection against insecticide exposure requires further investigation.

  8. Molecular cloning and characterization of the porcine prostaglandin transporter (SLCO2A1: evaluation of its role in F4 mediated neonatal diarrhoea

    Directory of Open Access Journals (Sweden)

    Cox Eric

    2009-10-01

    Full Text Available Abstract Background Because prostaglandins are involved in many (pathophysiological processes, SLCO2A1 was already characterized in several species in an attempt to unravel specific processes/deficiencies. Here, we describe the molecular cloning and characterization of the porcine ortholog in order to evaluate its possible involvement in F4 enterotoxigenic E. coli mediated neonatal diarrhoea, based on a positional candidate gene approach study. Results Porcine SLCO2A1 is organized in 14 exons, containing an open reading frame of 1935 bp, encoding a 12-transmembrane organic anion cell surface transporter of 644 aa. The -388 to -5 upstream region comprises a (CpG48 island containing a number of conserved promoter elements, including a TATA box. A potential alternative promoter region was found in the conserved -973 to -700 upstream region. No consensus polyadenylation signal was discovered in the 3' UTR. Repeat sequences were found in 15% of all the non coding sequences. As expected for a multifunctional protein, a wide tissue distribution was observed. mRNA expression was found in the adrenal gland, bladder, caecum, colon (centripetal coil/centrifugal coil, diaphragm, duodenum, gallbladder, heart, ileum, jejunum, kidney, liver, longissimus dorsi muscle, lung, lymph node, mesenterium, rectum, spleen, stomach, tongue and ureter, but not in the aorta, oesophagus and pancreas. The promoter region and the exons (including the splice sites of SLCO2A1 were resequenced in 5 F4ab/ac receptor positive and 5 F4ab/ac receptor negative pigs. Two silent and 2 missense (both S → L at position 360 and 633 mutations were found, but none was associated with the F4ab/ac receptor phenotype. In addition, no phenotype associated differential mRNA expression or alternative/abberant splicing/polyadenylation was found in the jejunum. Conclusion The molecular cloning and characterization of porcine SLCO2A1 not only contributes to the already existing knowledge about the

  9. Universal transport signatures in two-electron molecular quantum dots: gate-tunable Hund's rule, underscreened Kondo effect and quantum phase transitions.

    Science.gov (United States)

    Florens, Serge; Freyn, Axel; Roch, Nicolas; Wernsdorfer, Wolfgang; Balestro, Franck; Roura-Bas, Pablo; Aligia, A A

    2011-06-22

    We review here some universal aspects of the physics of two-electron molecular transistors in the absence of strong spin-orbit effects. Several recent quantum dot experiments have shown that an electrostatic backgate could be used to control the energy dispersion of magnetic levels. We discuss how the generally asymmetric coupling of the metallic contacts to two different molecular orbitals can indeed lead to a gate-tunable Hund's rule in the presence of singlet and triplet states in the quantum dot. For gate voltages such that the singlet constitutes the (non-magnetic) ground state, one generally observes a suppression of low voltage transport, which can yet be restored in the form of enhanced cotunneling features at finite bias. More interestingly, when the gate voltage is controlled to obtain the triplet configuration, spin S = 1 Kondo anomalies appear at zero bias, with non-Fermi liquid features related to the underscreening of a spin larger than 1/2. Finally, the small bare singlet-triplet splitting in our device allows fine-tuning with the gate between these two magnetic configurations, leading to an unscreening quantum phase transition. This transition occurs between the non-magnetic singlet phase, where a two-stage Kondo effect occurs, and the triplet phase, where the partially compensated (underscreened) moment is akin to a magnetically 'ordered' state. These observations are put theoretically into a consistent global picture by using new numerical renormalization group simulations, tailored to capture sharp finite-voltage cotunneling features within the Coulomb diamonds, together with complementary out-of-equilibrium diagrammatic calculations on the two-orbital Anderson model. This work should shed further light on the complicated puzzle still raised by multi-orbital extensions of the classic Kondo problem.

  10. Artificial oxygen transport protein

    Science.gov (United States)

    Dutton, P. Leslie

    2014-09-30

    This invention provides heme-containing peptides capable of binding molecular oxygen at room temperature. These compounds may be useful in the absorption of molecular oxygen from molecular oxygen-containing atmospheres. Also included in the invention are methods for treating an oxygen transport deficiency in a mammal.

  11. Time-resolved investigation of molecular components involved in the induction of NO3- high affinity transport system in maize roots

    Directory of Open Access Journals (Sweden)

    Youry Pii

    2016-11-01

    Full Text Available The induction, i.e. the rapid increase of nitrate (NO3- uptake following the exposure of roots to the anion, was studied integrating physiological and molecular levels in maize roots. Responses to NO3- treatment were characterized in terms of changes in NO3- uptake rate and plasma membrane (PM H+-ATPase activity and related to transcriptional and protein profiles of NRT2, NRT3 and PM H+-ATPase gene families. The behaviour of transcripts and proteins of ZmNRT2s and ZmNRT3s suggested that the regulation of the activity of inducible high-affinity transport system (iHATS is mainly based on the transcriptional/translational modulation of the accessory protein ZmNRT3.1A. Furthermore, ZmNRT2.1 and ZmNRT3.1A appear to be associated in a ∼ 150 kDa oligomer. The expression trend during the induction of the 11 identified PM H+-ATPase transcripts indicates that those mainly involved in the response to NO3- treatment are ZmHA2 and ZmHA4. Yet, partial correlation between the gene expression, protein levels and enzyme activity suggests an involvement of post-transcriptional and post-translational mechanisms of regulation. A nondenaturing Deriphat-PAGE approach allowed demonstrating for the first time that PM H+-ATPase can occur in vivo as hexameric complex together with the already described monomeric and dimeric forms.

  12. Targeted cutaneous delivery of ciclosporin A using micellar nanocarriers and the possible role of inter-cluster regions as molecular transport pathways.

    Science.gov (United States)

    Lapteva, Maria; Santer, Verena; Mondon, Karine; Patmanidis, Ilias; Chiriano, Gianpaolo; Scapozza, Leonardo; Gurny, Robert; Möller, Michael; Kalia, Yogeshvar N

    2014-12-28

    Oral administration of ciclosporin A (CsA) is indicated in the treatment of severe recalcitrant plaque psoriasis. However, CsA is both nephro- and hepatotoxic and its systemic administration also exposes the patient to other severe side effects. Although topical delivery of CsA, targeted directly to psoriatic skin, would offer significant advantages, there are no topical formulations approved for dermatological use. The aim of this work was to formulate CsA loaded polymeric micelles using the biodegradable and biocompatible MPEG-dihexPLA diblock copolymer and to evaluate their potential for delivering the drug selectively into the skin without concomitant transdermal permeation. Micelle formulations were characterised with respect to drug content, size and morphology. Micelle and drug penetration pathways were subsequently visualised with confocal laser scanning microscopy (CLSM) using fluorescein labelled CsA (Fluo-CsA) and Nile-Red (NR) labelled copolymer. Visualisation studies typically use fluorescent dyes as "model drugs"; however, these may have different physicochemical properties to the drug molecule under investigation. Therefore, in this study it was decided to chemically modify CsA and to use this structurally similar fluorescent analogue to visualise molecular distribution and transport pathways. Molecular modelling techniques and experimental determination of log D served as molecular scale and macroscopic methods to compare the lipophilicity of CsA and Fluo-CsA. The spherical, homogeneous and nanometre-scale micelles (with Zav from 25 to 52 nm) increased the aqueous solubility of CsA by 518-fold. Supra-therapeutic amounts of CsA were delivered to human skin (1.4±0.6 μg/cm2, cf. a statistically equivalent 1.1±0.5 μg/cm2 for porcine skin) after application of the formulation with the lowest CsA and copolymer content (1.67±0.03 mg/ml of CsA and 5mg/ml of copolymer) for only 1h without concomitant transdermal permeation. Fluo-CsA was successfully

  13. Molecular characterization of free tropospheric aerosol collected at the Pico Mountain Observatory: a case study with long range transported biomass burning plumes

    Directory of Open Access Journals (Sweden)

    K. Dzepina

    2014-09-01

    Full Text Available Free tropospheric aerosol was sampled at the Pico Mountain Observatory located at 2225 m a.m.s.l. on Pico Island of the Azores archipelago in the North Atlantic. The observatory (38°28'15'' N; 28°24'14'' W is located ∼3900 km east and downwind of North America, which enables studies of free tropospheric air transported over long distances, mainly from North America. Aerosol samples collected on filters from June to October 2012 were analyzed to characterize organic carbon, elemental carbon and inorganic ion species. The average ambient concentration of aerosol was 0.9 μg m−3; on average organic aerosol contributes the majority of mass (57%, followed by sulfate (21% and nitrate (17%. Filter-collected aerosol measurements were positively correlated (with an r2 ≥ 0.80 with continuous aerosol measurements of black carbon, aerosol light scattering and number concentration. Water-soluble organic carbon (WSOC species extracted from two aerosol samples (9/24 and 9/25 collected consecutively during a pollution event were analyzed using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry. FLEXPART retroplume analysis shows the sampled air masses were very aged (average plume age > 12 days. 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 have unsaturated structures with CHO and CHNO elemental compositions. These aged WSOC compounds have an average O / C ratio of ∼0.45, which is relatively low compared to O / C ratios of other aged aerosol and might be the result of evaporation and increased fragmentation during long-range transport. 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

  14. Molecular characterization of free tropospheric aerosol collected at the Pico Mountain Observatory: a case study with long range transported biomass burning plumes

    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.; Dziobak, M. P.; Ampadu, M. T.; Olsen, S.; Wuebbles, D. J.; Mazzoleni, L. R.

    2014-09-01

    Free tropospheric aerosol was sampled at the Pico Mountain Observatory located at 2225 m a.m.s.l. on Pico Island of the Azores archipelago in the North Atlantic. The observatory (38°28'15'' N; 28°24'14'' W) is located ∼3900 km east and downwind of North America, which enables studies of free tropospheric air transported over long distances, mainly from North America. Aerosol samples collected on filters from June to October 2012 were analyzed to characterize organic carbon, elemental carbon and inorganic ion species. The average ambient concentration of aerosol was 0.9 μg m-3; on average organic aerosol contributes the majority of mass (57%), followed by sulfate (21%) and nitrate (17%). Filter-collected aerosol measurements were positively correlated (with an r2 ≥ 0.80) with continuous aerosol measurements of black carbon, aerosol light scattering and number concentration. Water-soluble organic carbon (WSOC) species extracted from two aerosol samples (9/24 and 9/25) collected consecutively during a pollution event were analyzed using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry. FLEXPART retroplume analysis shows the sampled air masses were very aged (average plume age > 12 days). 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 have unsaturated structures with CHO and CHNO elemental compositions. These aged WSOC compounds have an average O / C ratio of ∼0.45, which is relatively low compared to O / C ratios of other aged aerosol and might be the result of evaporation and increased fragmentation during long-range transport. 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

  15. Quantum transport equation for systems with rough surfaces and its application to ultracold neutrons in a quantizing gravity field

    Energy Technology Data Exchange (ETDEWEB)

    Escobar, M.; Meyerovich, A. E., E-mail: Alexander-Meyerovich@uri.edu [University of Rhode Island, Department of Physics (United States)

    2014-12-15

    We discuss transport of particles along random rough surfaces in quantum size effect conditions. As an intriguing application, we analyze gravitationally quantized ultracold neutrons in rough waveguides in conjunction with GRANIT experiments (ILL, Grenoble). We present a theoretical description of these experiments in the biased diffusion approximation for neutron mirrors with both one- and two-dimensional (1D and 2D) roughness. All system parameters collapse into a single constant which determines the depletion times for the gravitational quantum states and the exit neutron count. This constant is determined by a complicated integral of the correlation function (CF) of surface roughness. The reliable identification of this CF is always hindered by the presence of long fluctuation-driven correlation tails in finite-size samples. We report numerical experiments relevant for the identification of roughness of a new GRANIT waveguide and make predictions for ongoing experiments. We also propose a radically new design for the rough waveguide.

  16. Charge transport along molecular wires

    NARCIS (Netherlands)

    Prins, P.

    2007-01-01

    Imagine plastic electronics ... Consumer products such as mobile phones, mp3 players and palmtop computers that do not break when you accidentally drop them, with flexible displays. Moreover, these all plastic products would be cheaper than the current products based on conventional semi conductors.

  17. Molecular Transporters for Desalination Applications

    Science.gov (United States)

    2014-08-02

    10 2011): 0. doi: 10.1021/jp201467y Xin Su, Xin Zhan, Bruce J. Hinds. Pt monolayer deposition onto carbon nanotube mattes with high...Pt monolayer deposition onto carbon nanotube mattes with high electrochemical activity” Xin Su#, Xin Zhan#, Bruce J. Hinds* J. Mater. Chem. 2012 22(16...7979-84. This work uses a newly developed Cu- underpotential method that self-limits to a monolayer of Cu(0) film that can be monotomically

  18. Electron transport in unipolar InGaN/GaN multiple quantum well structures grown by NH3 molecular beam epitaxy

    KAUST Repository

    Browne, David A.

    2015-05-14

    © 2015 AIP Publishing LLC. Unipolar-light emitting diode like structures were grown by NH3 molecular beam epitaxy on c plane (0001) GaN on sapphire templates. Studies were performed to experimentally examine the effect of random alloy fluctuations on electron transport through quantum well active regions. These unipolar structures served as a test vehicle to test our 2D model of the effect of compositional fluctuations on polarization-induced barriers. Variables that were systematically studied included varying quantum well number from 0 to 5, well thickness of 1.5 nm, 3 nm, and 4.5 nm, and well compositions of In0.14Ga0.86N and In0.19Ga0.81N. Diode-like current voltage behavior was clearly observed due to the polarization-induced conduction band barrier in the quantum well region. Increasing quantum well width and number were shown to have a significant impact on increasing the turn-on voltage of each device. Temperature dependent IV measurements clearly revealed the dominant effect of thermionic behavior for temperatures from room temperature and above. Atom probe tomography was used to directly analyze parameters of the alloy fluctuations in the quantum wells including amplitude and length scale of compositional variation. A drift diffusion Schrödinger Poisson method accounting for two dimensional indium fluctuations (both in the growth direction and within the wells) was used to correctly model the turn-on voltages of the devices as compared to traditional 1D simulation models.

  19. Introducing Thermal Wave Transport Analysis (TWTA): A Thermal Technique for Dopamine Detection by Screen-Printed Electrodes Functionalized with Molecularly Imprinted Polymer (MIP) Particles.

    Science.gov (United States)

    Peeters, Marloes M; van Grinsven, Bart; Foster, Christopher W; Cleij, Thomas J; Banks, Craig E

    2016-04-26

    A novel procedure is developed for producing bulk modified Molecularly Imprinted Polymer (MIP) screen-printed electrodes (SPEs), which involves the direct mixing of the polymer particles within the screen-printed ink. This allowed reduction of the sample preparation time from 45 min to 1 min, and resulted in higher reproducibility of the electrodes. The samples are measured with a novel detection method, namely, thermal wave transport analysis (TWTA), relying on the analysis of thermal waves through a functional interface. As a first proof-of-principle, MIPs for dopamine are developed and successfully incorporated within a bulk modified MIP SPE. The detection limits of dopamine within buffer solutions for the MIP SPEs are determined via three independent techniques. With cyclic voltammetry this was determined to be 4.7 × 10(-6) M, whereas by using the heat-transfer method (HTM) 0.35 × 10(-6) M was obtained, and with the novel TWTA concept 0.26 × 10(-6) M is possible. This TWTA technique is measured simultaneously with HTM and has the benefits of reducing measurement time to less than 5 min and increasing effect size by nearly a factor of two. The two thermal methods are able to enhance dopamine detection by one order of magnitude compared to the electrochemical method. In previous research, it was not possible to measure neurotransmitters in complex samples with HTM, but with the improved signal-to-noise of TWTA for the first time, spiked dopamine concentrations were determined in a relevant food sample. In summary, novel concepts are presented for both the sensor functionalization side by employing screen-printing technology, and on the sensing side, the novel TWTA thermal technique is reported. The developed bio-sensing platform is cost-effective and suitable for mass-production due to the nature of screen-printing technology, which makes it very interesting for neurotransmitter detection in clinical diagnostic applications.

  20. Time-Resolved Investigation of Molecular Components Involved in the Induction of NO3– High Affinity Transport System in Maize Roots

    Science.gov (United States)

    Pii, Youry; Alessandrini, Massimiliano; Dall’Osto, Luca; Guardini, Katia; Prinsi, Bhakti; Espen, Luca; Zamboni, Anita; Varanini, Zeno

    2016-01-01

    The induction, i.e., the rapid increase of nitrate (NO3–) uptake following the exposure of roots to the anion, was studied integrating physiological and molecular levels in maize roots. Responses to NO3– treatment were characterized in terms of changes in NO3– uptake rate and plasma membrane (PM) H+-ATPase activity and related to transcriptional and protein profiles of NRT2, NRT3, and PM H+-ATPase gene families. The behavior of transcripts and proteins of ZmNRT2s and ZmNRT3s suggested that the regulation of the activity of inducible high-affinity transport system (iHATS) is mainly based on the transcriptional/translational modulation of the accessory protein ZmNRT3.1A. Furthermore, ZmNRT2.1 and ZmNRT3.1A appear to be associated in a ∼150 kDa oligomer. The expression trend during the induction of the 11 identified PM H+-ATPase transcripts indicates that those mainly involved in the response to NO3– treatment are ZmHA2 and ZmHA4. Yet, partial correlation between the gene expression, protein levels and enzyme activity suggests an involvement of post-transcriptional and post-translational mechanisms of regulation. A non-denaturing Deriphat-PAGE approach allowed demonstrating for the first time that PM H+-ATPase can occur in vivo as hexameric complex together with the already described monomeric and dimeric forms. PMID:27877183