Sample records for bilayer structure determination

  1. Determination of the electronic structure of bilayer graphene from infrared spectroscopy results

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, L. M.; Li, Z. Q.; Basov, D. N.; Fogler, M. M.; Hao, Z.; Martin, Michael C.


    We present an experimental study of the infrared conductivity, transmission, and reflection of a gated bilayer graphene and their theoretical analysis within the Slonczewski-Weiss-McClure (SWMc) model. The infrared response is shown to be governed by the interplay of the interband and the intraband transitions among the four bands of the bilayer. The position of the main conductivity peak at thecharge-neutrality point is determined by the interlayer tunneling frequency. The shift of this peak as a function of the gate voltage gives information about less known parameters of the SWMc model such as those responsible for the electron-hole and sublattice asymmetries. These parameter values are shown to be consistent with recent electronic structure calculations for the bilayer graphene and the SWMc parameters commonly used for the bulk graphite.

  2. D IR Line Shapes for Determining the Structure of a Peptide in a Bilayer (United States)

    Woys, Ann Marie; Lin, Y. S.; Skinner, J. S.; Zanni, M. T.; Reddy, A. S.; de Pablo, J. J.


    Structure of the antimicrobial peptide, ovispirin, on a lipid bilayer was determined using 2D IR spectroscopy and spectra calculated from molecular dynamics simulations. Ovispirin is an 18 residue amphipathic peptide that binds parallel to the membrane in a mostly alpha helical conformation. 15 of the 18 residues were ^1^3C^1^8O isotopically labeled on the backbone to isolate the amide I vibration at each position. 2D IR spectra were collected for each labeled peptide in 3:1 POPC/POPG vesicles, and peak width along the diagonal was measured. The diagonal line width is sensitive to the vibrator's electrostatic environment, which varies through the bilayer. We observe an oscillatory line width spanning 10 to 24 cm-1 and with a period of nearly 3.6 residues. To further investigate the position of ovispirin in a bilayer, molecular dynamics simulations determined the peptide depth to be just below the lipid headgroups. The trajectory of ovispirin at this depth was used to calculate 2D IR spectra, from which the diagonal line width is measured. Both experimental and simulated line widths are similar in periodicity and suggest a kink in the peptide backbone and the tilt in the bilayer. A. Woys, Y. S. Lin, A. S. Reddy, W. Xiong, J. J. de Pablo, J. S. Skinner, and M. T. Zanni, JACS 132, 2832-2838 (2010).

  3. Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

    Energy Technology Data Exchange (ETDEWEB)

    White, S.H. [Univ. of California, Irvine, CA (United States); Wiener, M.C. [Univ. of California, San Francisco, CA (United States)


    Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining {open_quote}the structure{close_quote} of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors.

  4. Water replacement hypothesis in atomic detail--factors determining the structure of dehydrated bilayer stacks. (United States)

    Golovina, Elena A; Golovin, Andrey V; Hoekstra, Folkert A; Faller, Roland


    According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar "stacks" through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis.

  5. Water Replacement Hypothesis in Atomic Detail—Factors Determining the Structure of Dehydrated Bilayer Stacks (United States)

    Golovina, Elena A.; Golovin, Andrey V.; Hoekstra, Folkert A.; Faller, Roland


    Abstract According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar “stacks” through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis. PMID:19619463

  6. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. (United States)

    Mote, Kaustubh R; Gopinath, T; Veglia, Gianluigi


    The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments, for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ~0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional oriented solid-state NMR and magic angle spinning solid-state NMR.

  7. Structure of twisted and buckled bilayer graphene (United States)

    Jain, Sandeep K.; Juričić, Vladimir; Barkema, Gerard T.


    We study the atomic structure of twisted bilayer graphene, with very small mismatch angles (θ ∼ {0.28}0), a topic of intense recent interest. We use simulations, in which we combine a recently presented semi-empirical potential for single-layer graphene, with a new term for out-of-plane deformations, (Jain et al 2015 J. Phys. Chem. C 119 9646) and an often-used interlayer potential (Kolmogorov et al 2005 Phys. Rev. B 71 235415). This combination of potentials is computationally cheap but accurate and precise at the same time, allowing us to study very large samples, which is necessary to reach very small mismatch angles in periodic samples. By performing large scale atomistic simulations, we show that the vortices appearing in the Moiré pattern in the twisted bilayer graphene samples converge to a constant size in the thermodynamic limit. Furthermore, the well known sinusoidal behavior of energy no longer persists once the misorientation angle becomes very small (θ \\lt {1}0). We also show that there is a significant buckling after the relaxation in the samples, with the buckling height proportional to the system size. These structural properties have direct consequences on the electronic and optical properties of bilayer graphene.

  8. Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins

    DEFF Research Database (Denmark)

    Skar-Gislinge, Nicholas; Simonsen, Jens Bæk; Mortensen, Kell


    -angle neutron scattering in combination with variable-temperature studies of synchrotron small-angle X-ray scattering on nanodiscs in solution, we show that the fundamental nanodisc unit, consisting of a lipid bilayer surrounded by amphiphilic scaffold proteins, possesses intrinsically an elliptical shape....... The temperature dependence of the curvature of the nanodiscs prepared with two different phospholipid types (DLPC and POPC) shows that it is the scaffold protein that determines the overall elliptical shape and that the nanodiscs become more circular with increasing temperature. Our data also show...... that the hydrophobic bilayer thickness is, to a large extent, dictated by the scaffolding protein and adjusted to minimize the hydrophobic mismatch between protein and phospholipid. Our conclusions result from a new comprehensive and molecular-based model of the nanodisc structure and the use of this to analyze...

  9. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. II. Distribution and packing of terminal methyl groups.


    Wiener, M C; White, S H


    We continue in this paper the presentation of theoretical and experimental methods for the joint refinement of neutron and x-ray lamellar diffraction data for the analysis of fluid (L alpha phase) bilayer structure (Wiener, M. C., and S. H. White. 1991 a, b, c. Biophys. J. 59:162-173 and 174-185; Biochemistry. 30:6997-7008; Wiener, M. C., G. I. King, and S. H. White. Biophys. J. 60: 568-576). We show how to obtain the distribution and packing of the terminal methyls in the interior of a fluid...

  10. Modeling liquid crystal bilayer structures with minimal surfaces. (United States)

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W


    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  11. Band Structure Asymmetry of Bilayer Graphene Revealed by Infrared Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Li, Z.Q.; Henriksen, E.A.; Jiang, Z.; Hao, Zhao; Martin, Michael C.; Kim, P.; Stormer, H.L.; Basov, Dimitri N.


    We report on infrared spectroscopy of bilayer graphene integrated in gated structures. We observe a significant asymmetry in the optical conductivity upon electrostatic doping of electrons and holes. We show that this finding arises from a marked asymmetry between the valence and conduction bands, which is mainly due to the inequivalence of the two sublattices within the graphene layer and the next-nearest-neighbor interlayer coupling. From the conductivity data, the energy difference of the two sublattices and the interlayer coupling energy are directly determined.

  12. The effect of temperature on supported dipalmitoylphosphatidylcholine (DPPC) bilayers: structure and lubrication performance. (United States)

    Wang, Min; Zander, Thomas; Liu, Xiaoyan; Liu, Chao; Raj, Akanksha; Wieland, D C Florian; Garamus, Vasil M; Willumeit-Römer, Regine; Claesson, Per Martin; Dėdinaitė, Andra


    Phospholipids fulfill an important role in joint lubrication. They, together with hyaluronan and glycoproteins, are the biolubricants that sustain low friction between cartilage surfaces bathed in synovial fluid. In this work we have investigated how the friction force and load bearing capacity of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers on silica surfaces are affected by temperature, covering the temperature range 25-52°C. Friction forces have been determined utilizing the AFM colloidal probe technique, which showed that DPPC bilayers are able to provide low friction forces over the whole temperature interval. However, the load bearing capacity is improved at higher temperatures. We interpret this finding as being a consequence of lower rigidity and higher self-healing capacity of the DPPC bilayer in the liquid disordered state compared to the gel state. The corresponding structure of solid supported DPPC bilayers at the silica-liquid interface has been followed using X-ray reflectivity measurements, which suggests that the DPPC bilayer is in the gel phase at 25°C and 39°C and in the liquid disordered state at 55°C. Well-defined bilayer structures were observed for both phases. The deposited DPPC bilayers were also imaged using AFM PeakForce Tapping mode, and these measurements indicated a less homogeneous layer at temperatures below 37°C.

  13. Tethered and Polymer Supported Bilayer Lipid Membranes: Structure and Function

    Directory of Open Access Journals (Sweden)

    Jakob Andersson


    Full Text Available Solid supported bilayer lipid membranes are model systems to mimic natural cell membranes in order to understand structural and functional properties of such systems. The use of a model system allows for the use of a wide variety of analytical tools including atomic force microscopy, impedance spectroscopy, neutron reflectometry, and surface plasmon resonance spectroscopy. Among the large number of different types of model membranes polymer-supported and tethered lipid bilayers have been shown to be versatile and useful systems. Both systems consist of a lipid bilayer, which is de-coupled from an underlying support by a spacer cushion. Both systems will be reviewed, with an emphasis on the effect that the spacer moiety has on the bilayer properties.

  14. Structural Effects of Small Molecules on Phospholipid Bilayers Investigated by Molecular Simulations

    CERN Document Server

    Lee, B W; Sum, A K; Vattulainen, I; Patra, M; Karttunen, M; Lee, Bryan W; Faller, Roland; Sum, Amadeu K; Vattulainen, Ilpo; Patra, Michael; Karttunen, Mikko


    We summarize and compare recent Molecular Dynamics simulations on the interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid crystalline phase with a number of small molecules including trehalose, a disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar molecules tend to stabilize the structure of the bilayer as they bridge adjacent lipid headgroups. They do not strongly change the structure of the bilayer. Alcohols and DMSO destabilize the bilayer as they increase its area per molecule in the bilayer plane and decrease the order parameter. Alcohols have a stronger detrimental effect than DMSO. The observables which we compare are the area per molecule in the plane of the bilayer, the membrane thickness, and the NMR order parameter of DPPC hydrocarbon tails. The area per molecule and the order parameter are very well correlated whereas the bilayer thickness is not necessarily correlated with them.

  15. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

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    Ratna Juwita


    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  16. Bilayer fractal structure with multiband left-handed characteristics. (United States)

    Du, Qiujiao; Liu, Jinsong; Yang, Hongwu; Yi, Xunong


    We present a bilayer fractal structure for the realization of multiband left-handed metamaterial at terahertz frequencies. The structure is composed of metallic H-fractal pairs separated by a dielectric layer. The electromagnetic properties of periodic H-fractal pairs have been investigated by numerical simulation. The period in the propagation direction is extremely small as compared to the wavelength at the operational frequency. Under the electromagnetic wave normal incidence, the material exhibits negative refraction simultaneously around the frequencies of 0.10 and 0.15 THz for parallel polarization, and around the frequencies of 0.19 and 0.38 THz for perpendicular polarization. The design provides a left-handed metamaterial suitable for multiband and compact devices at terahertz frequencies.

  17. The Mechanical Aspects of Formation and Application of PDMS Bilayers Rolled into a Cylindrical Structure

    Directory of Open Access Journals (Sweden)

    Dongwon Kang


    Full Text Available A polydimethylsiloxane (PDMS film with its surface being oxidized by a plasma treatment or a UV-ozone (UVO treatment, that is, a bilayer made of PDMS and its oxidized surface layer, is known to roll into a cylindrical structure upon exposure to the chloroform vapor due to the mismatch in the swelling ratio between PDMS and the oxidized layer by the chloroform vapor. Here we analyzed the formation of the rolled bilayer with the mechanical aspects: how the mismatch in the swelling ratio of the bilayer induces rolling of the bilayer, why any form of trigger that breaks the symmetry in the in-plane stress level is needed to roll the bilayer uniaxially, why the rolled bilayer does not unroll in the dry state when there is no more mismatch in the swelling ratio, and how the measured curvature of rolled bilayer matches well with the prediction by the theory. Moreover, for the use of the rolled bilayer as the channel of the microfluidic device, we examined whether the rolled bilayer deforms or unrolls by the flow of the aqueous solution that exerts the circumferential stress on the rolled bilayer.

  18. Modeling Kinetics of Distortion in Porous Bi-layered Structures

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Frandsen, Henrik Lund; Bjørk, Rasmus;


    Shape distortions during constrained sintering experiment of bi-layer porous and dense cerium gadolinium oxide (CGO) structures have been modeled. Technologies like solid oxide fuel cells require co-firing thin layers with different green densities, which often exhibit differential shrinkage...... because of different sintering rates of the materials resulting in undesired distortions of the component. An analytical model based on the continuum theory of sintering has been developed to describe the kinetics of densification and distortion in the sintering processes. A new approach is used...... to extract the material parameters controlling shape distortion through optimizing the model to experimental data of free shrinkage strains. The significant influence of weight of the sample (gravity) on the kinetics of distortion is taken in to consideration. The modeling predictions indicate good agreement...

  19. Effect of monoglyceride structure and cholesterol content on water permeability of the droplet bilayer. (United States)

    Michalak, Zuzanna; Muzzio, Michelle; Milianta, Peter J; Giacomini, Rosario; Lee, Sunghee


    The process of water permeation across lipid membranes has significant implications for cellular physiology and homeostasis, and its study may lead to a greater understanding of the relationship between the structure of lipid bilayer and the role that lipid structure plays in water permeation. In this study, we formed a droplet interface bilayer (DIB) by contacting two aqueous droplets together in an immiscible solvent (squalane) containing bilayer-forming surfactant (monoglycerides). Using the DIB model, we present our results on osmotic water permeabilities and activation energy for water permeation of an associated series of unsaturated monoglycerides as the principal component of droplet bilayers, each having the same chain length but differing in the position and number of double bonds, in the absence and presence of a varying concentration of cholesterol. Our findings suggest that the tailgroup structure in a series of monoglyceride bilayers is seen to affect the permeability and activation energy for the water permeation process. Moreover, we have also established the insertion of cholesterol into the droplet bilayer, and have detected its presence via its effect on water permeability. The effect of cholesterol differs depending on the type of monoglyceride. We demonstrate that the DIB can be employed as a convenient model membrane to rapidly explore subtle structural effects on bilayer water permeability.

  20. Phase Transition of MoS2 Bilayer Structures

    DEFF Research Database (Denmark)

    Pandey, Mohnish; Bothra, Pallavi; Pati, Swapan K.


    In the present study, using density functional calculations we have investigated a possible mechanism for the structural phase transition of the semiconducting bilayer 2H-MoS2 via lithiation. The results indicate that the addition of lithium to the bilayer 2H-MoS2 transforms the bilayer to a hete...... microscopic mechanism of the phase transition in MoS2 and enriches the atomic scale understanding of the interaction of MoS2 with the alkali ions and other transition metal dichalcogenides manifesting a similar phase transition....

  1. Structure and Dynamics in Amphiphilic Bilayers: NMR and MD simulation Studies



    Solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations were employed to study molecular structure and dynamics in amphiphilic bilayers. This thesis reports on method development and practical applications to two types of bilayer systems: simple cell membrane models composed of phosphatidylcholine lipids and cholesterol; and liquid crystals composed of ethyleneoxide-based surfactants often used in technological applications and in fundamental studies ...

  2. Modeling constrained sintering of bi-layered tubular structures

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Kothanda Ramachandran, Dhavanesan; Ni, De Wei;


    . Furthermore, the model is validated using densification results from sintering of bi-layered tubular ceramic oxygen membrane based on porous MgO and Ce0.9Gd0.1O1.95-d layers. Model input parameters, such as the shrinkage kinetics and viscous parameters are obtained experimentally using optical dilatometry...

  3. Linking lipid architecture to bilayer structure and mechanics using self-consistent field modelling

    Energy Technology Data Exchange (ETDEWEB)

    Pera, H.; Kleijn, J. M.; Leermakers, F. A. M., E-mail: [Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6307 HB Wageningen (Netherlands)


    To understand how lipid architecture determines the lipid bilayer structure and its mechanics, we implement a molecularly detailed model that uses the self-consistent field theory. This numerical model accurately predicts parameters such as Helfrichs mean and Gaussian bending modulus k{sub c} and k{sup ¯} and the preferred monolayer curvature J{sub 0}{sup m}, and also delivers structural membrane properties like the core thickness, and head group position and orientation. We studied how these mechanical parameters vary with system variations, such as lipid tail length, membrane composition, and those parameters that control the lipid tail and head group solvent quality. For the membrane composition, negatively charged phosphatidylglycerol (PG) or zwitterionic, phosphatidylcholine (PC), and -ethanolamine (PE) lipids were used. In line with experimental findings, we find that the values of k{sub c} and the area compression modulus k{sub A} are always positive. They respond similarly to parameters that affect the core thickness, but differently to parameters that affect the head group properties. We found that the trends for k{sup ¯} and J{sub 0}{sup m} can be rationalised by the concept of Israelachivili's surfactant packing parameter, and that both k{sup ¯} and J{sub 0}{sup m} change sign with relevant parameter changes. Although typically k{sup ¯}<0, membranes can form stable cubic phases when the Gaussian bending modulus becomes positive, which occurs with membranes composed of PC lipids with long tails. Similarly, negative monolayer curvatures appear when a small head group such as PE is combined with long lipid tails, which hints towards the stability of inverse hexagonal phases at the cost of the bilayer topology. To prevent the destabilisation of bilayers, PG lipids can be mixed into these PC or PE lipid membranes. Progressive loading of bilayers with PG lipids lead to highly charged membranes, resulting in J{sub 0}{sup m}≫0, especially at low ionic

  4. Monolayer to Bilayer Structural Transition in Confined Pyrrolidinium-Based Ionic Liquids. (United States)

    Smith, Alexander M; Lovelock, Kevin R J; Gosvami, Nitya Nand; Licence, Peter; Dolan, Andrew; Welton, Tom; Perkin, Susan


    Ionic liquids can be intricately nanostructured in the bulk and at interfaces resulting from a delicate interplay between interionic and surface forces. Here we report the structuring of a series of dialkylpyrrolidinium-based ionic liquids induced by confinement. The ionic liquids containing cations with shorter alkyl chain substituents form alternating cation-anion monolayer structures on confinement to a thin film, whereas a cation with a longer alkyl chain substituent leads to bilayer formation. The crossover from monolayer to bilayer structure occurs between chain lengths of n = 8 and 10 for these pyrrolidinium-based ionic liquids. The bilayer structure for n = 10 involves full interdigitation of the alkyl chains; this is in contrast with previous observations for imidazolium-based ionic liquids. The results are pertinent to these liquids' application as electrolytes, where the electrolyte is confined inside the pores of a nanoporous electrode, for example, in devices such as supercapacitors or batteries.

  5. Monolayer and bilayer structures in ionic liquids and their mixtures confined to nano-films. (United States)

    Smith, Alexander M; Lovelock, Kevin R J; Perkin, Susan


    The confinement of liquids to thin films can lead to dramatic changes in their structural arrangement and dynamic properties. Ionic liquids display nano-structures in the bulk of the liquid, consisting of polar and non-polar domains, whereas a solid surface can induce layered structures in the near-surface liquid. Here we compare and contrast the layer structures in a series of imidazolium and pyrrolidinium-based ionic liquids upon confinement of the liquids to films of approximately 0-20 nm between two negatively charged mica surfaces. Using a surface force balance (SFB) we measured the force between the two atomically smooth mica surfaces with ionic liquid between, directly revealing the ion packing and dimensions of layered structures for each liquid. The ionic liquids with shorter alkyl chain substituents form alternating cation-anion monolayer structures on confinement, whilst a longer alkyl chain leads to alignment of the cations in bilayer formation. The crossover from monolayers to bilayers, however, occurs at different alkyl chain lengths for imidazolium- and pyrrolidinium-based ionic liquids with a common anion. In addition, we find that imidazolium cation bilayers are arranged in toe-to-toe orientation, whereas pyrrolidinium cations form bilayers consisting of fully interdigitated alkyl chains. Results for a mixture of monolayer-preferring (i.e. short alkyl chain) and bilayer-preferring (i.e. long alkyl chain) liquids indicate alkyl chain segregation and bilayer-like structures. We discuss the driving forces for these self-assembly effects, and the contrasting behaviour of the imidazolium and pyrrolidinium-type ionic liquids.

  6. Inverse Proximity Effect in Superconductor-ferromagnet Bilayer Structures

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Jing


    Measurements of the polar Kerr effect using a zero-area-loop Sagnac magnetometer on Pb/Ni and Al/(Co-Pd) proximity-effect bilayers show unambiguous evidence for the 'inverse proximity effect,' in which the ferromagnet (F) induces a finite magnetization in the superconducting (S) layer. To avoid probing the magnetic effects in the ferromagnet, the superconducting layer was prepared much thicker than the light's optical penetration depth. The sign and size of the effect, as well as its temperature dependence agree with recent predictions by Bergeret et al.[1].

  7. Improved Modeling Approaches for Constrained Sintering of Bi-Layered Porous Structures

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Frandsen, Henrik Lund; Esposito, Vincenzo;


    Shape instabilities during constrained sintering experiment of bi-layer porous and dense cerium gadolinium oxide (CGO) structures have been analyzed. An analytical and a numerical model based on the continuum theory of sintering has been implemented to describe the evolution of bow and densificat......Shape instabilities during constrained sintering experiment of bi-layer porous and dense cerium gadolinium oxide (CGO) structures have been analyzed. An analytical and a numerical model based on the continuum theory of sintering has been implemented to describe the evolution of bow...

  8. Electronic band structure effects in monolayer, bilayer, and hybrid graphene structures (United States)

    Puls, Conor

    Since its discovery in 2005, graphene has been the focus of intense theoretical and experimental study owing to its unique two-dimensional band structure and related electronic properties. In this thesis, we explore the electronic properties of graphene structures from several perspectives including the magnetoelectrical transport properties of monolayer graphene, gap engineering and measurements in bilayer graphene, and anomalous quantum oscillation in the monolayer-bilayer graphene hybrids. We also explored the device implications of our findings, and the application of some experimental techniques developed for the graphene work to the study of a complex oxide, Ca3Ru2O7, exhibiting properties of strongly correlated electrons. Graphene's high mobility and ballistic transport over device length scales, make it suitable for numerous applications. However, two big challenges remain in the way: maintaining high mobility in fabricated devices, and engineering a band gap to make graphene compatible with logical electronics and various optical devices. We address the first challenge by experimentally evaluating mobilities in scalable monolayer graphene-based field effect transistors (FETs) and dielectric-covered Hall bars. We find that the mobility is limited in these devices, and is roughly inversely proportional to doping. By considering interaction of graphene's Dirac fermions with local charged impurities at the interface between graphene and the top-gate dielectric, we find that Coulomb scattering is responsible for degraded mobility. Even in the cleanest devices, a band gap is still desirable for electronic applications of graphene. We address this challenge by probing the band structure of bilayer graphene, in which a field-tunable energy band gap has been theoretically proposed. We use planar tunneling spectroscopy of exfoliated bilayer graphene flakes demonstrate both measurement and control of the energy band gap. We find that both the Fermi level and

  9. Structure and dynamics of POPC bilayers in water solutions of room temperature ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Benedetto, Antonio [School of Physics, University College Dublin, Dublin 4 (Ireland); Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen (Switzerland); Bingham, Richard J. [York Centre for Complex Systems Analysis, University of York, York YO10 5GE (United Kingdom); Ballone, Pietro [Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia (IIT), 00185 Roma (Italy); Department of Physics, Università di Roma “La Sapienza,” 00185 Roma (Italy)


    Molecular dynamics simulations in the NPT ensemble have been carried out to investigate the effect of two room temperature ionic liquids (RTILs), on stacks of phospholipid bilayers in water. We consider RTIL compounds consisting of chloride ([bmim][Cl]) and hexafluorophosphate ([bmim][PF{sub 6}]) salts of the 1-buthyl-3-methylimidazolium ([bmim]{sup +}) cation, while the phospholipid bilayer is made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our investigations focus on structural and dynamical properties of phospholipid and water molecules that could be probed by inelastic and quasi-elastic neutron scattering measurements. The results confirm the fast incorporation of [bmim]{sup +} into the lipid phase already observed in previous simulations, driven by the Coulomb attraction of the cation for the most electronegative oxygens in the POPC head group and by sizeable dispersion forces binding the neutral hydrocarbon tails of [bmim]{sup +} and of POPC. The [bmim]{sup +} absorption into the bilayer favours the penetration of water into POPC, causes a slight but systematic thinning of the bilayer, and further stabilises hydrogen bonds at the lipid/water interface that already in pure samples (no RTIL) display a lifetime much longer than in bulk water. On the other hand, the effect of RTILs on the diffusion constant of POPC (D{sub POPC}) does not reveal a clearly identifiable trend, since D{sub POPC} increases upon addition of [bmim][Cl] and decreases in the [bmim][PF{sub 6}] case. Moreover, because of screening, the electrostatic signature of each bilayer is only moderately affected by the addition of RTIL ions in solution. The analysis of long wavelength fluctuations of the bilayers shows that RTIL sorption causes a general decrease of the lipid/water interfacial tension and bending rigidity, pointing to the destabilizing effect of RTILs on lipid bilayers.

  10. On the determination of Poisson's ratio of stressed monolayer and bilayer submicron thick films

    CERN Document Server

    Martins, P; Brida, S; Barbier, D


    In this paper, the bulge test is used to determine the mechanical properties of very thin dielectric membranes. Commonly, this experimental method permits to determine the residual stress (s0) and biaxial Young's modulus (E/(1-u)). Associating square and rectangular membranes with different length to width ratios, the Poisson's ratio (u) can also be determined. LPCVD Si3N4 monolayer and Si3N4/SiO2 bilayer membranes, with thicknesses down to 100 nm, have been characterized giving results in agreement with literature for Si3N4, E = 212 $\\pm$ 14 GPa, s0 = 420 $\\pm$ 8 and u = 0.29.

  11. Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes (United States)

    Kel, Oksana; Tamimi, Amr; Fayer, Michael D.


    The ultrafast structural dynamics inside the bilayers of dilauroylphosphatidylcholine (DLPC) and dipalmitoylphosphatidylcholine vesicles with 70, 90, and 125 nm diameters were directly measured with 2D IR vibrational echo spectroscopy. The antisymmetric CO stretch of tungsten hexacarbonyl was used as a vibrational probe and provided information on spectral diffusion (structural dynamics) in the alkyl region of the bilayers. Although the CO stretch absorption spectra remain the same, the interior structural dynamics become faster as the size of the vesicles decrease, with the size dependence greater for dipalmitoylphosphatidylcholine than for DLPC. As DLPC vesicles become larger, the interior dynamics approach those of the planar bilayer. PMID:24395796

  12. Ferromagnetic/superconducting bilayer structure: A model system for spin diffusion length estimation

    CERN Document Server

    Soltan, S; Habermeier, H U


    We report detailed studies on ferromagnet--superconductor bilayer structures. Epitaxial bilayer structures of half metal--colossal magnetoresistive La$_{\\mathrm{2/3}}$Ca$_{\\mathrm{1/3}}$MnO$_{\\mathrm{3}}$ (HM--CMR) and high--$T_{\\mathrm{c}}$ superconducting YBa$_{\\mathrm{2}}$Cu$_{\\mathrm{3}}$O$_{\\mathrm{7-\\delta}}$(HTSC) are grown on SrTiO$_3$ (100) single--crystalline substrates using pulsed laser deposition. Magnetization $M$(T) measurements show the coexistence of ferromagnetism and superconductivity in these structures at low temperatures. Using the HM--CMR layer as an electrode for spin polarized electrons, we discuss the role of spin polarized self injection into the HTSC layer. The experimental results are in good agreement with a presented theoretical estimation, where the spin diffusion length $\\xi_{\\mathrm {FM}}$ is found to be in the range of $\\xi_{\\mathrm{FM}} \\approx$ 10 nm.

  13. Relation between interfacial structure and mechanical properties in AlN/TiN bilayers investigated by EXAFS

    Energy Technology Data Exchange (ETDEWEB)

    Ersen, O. [Equipe de Recherche Mecanique, Materiaux et Procedes de Fabrication, 61, rue Albert Camus, F-68093 Mulhouse (France)]. E-mail:; Tuilier, M.-H. [Equipe de Recherche Mecanique, Materiaux et Procedes de Fabrication, 61, rue Albert Camus, F-68093 Mulhouse (France); Thobor-Keck, A. [Centre de Recherche sur les Ecoulements les Surfaces et les Transferts (UMR CNRS 6000), ITSFC, 4, place Tharradin, BP 71427, F-25211 Montbeliard (France); Rousselot, C. [Centre de Recherche sur les Ecoulements les Surfaces et les Transferts (UMR CNRS 6000), ITSFC, 4, place Tharradin, BP 71427, F-25211 Montbeliard (France); Cortes, R. [Laboratoire de Physique de la Matiere Condensee (UMR CNRS 7643), Ecole Polytechnique, F-91128 Palaiseau cedex (France)


    The relation between the mechanical properties and the structure of AlN/TiN bilayers prepared by reactive magnetron sputtering in the 600 nm range is investigated. Al and Ti K-edge extended X-ray absorption fine structure is used in order to determine the local order around Al and Ti by comparison with 300 nm thick AlN and TiN single layers. The use of this powerful local probe allows the evidence of intermixing between AlN and TiN deposited layers, which is suggested by glow discharge optical emission spectroscopy experiments. The effect of ionic bombardment applied at various steps of the deposition process is studied. The ionic bombardment applied during the deposit induces substantial changes in the absorption spectra that are assigned to a decrease of intermixing and an improvement of local order. Simulations of (Al, Ti)N ternary alloys Al and Ti K-edge absorption spectra for increasing mean occupation factors C {sub Ti} (C {sub Al}) of Ti(Al) substituting Al(Ti) in hexagonal AlN (cubic TiN) lattice are performed in order to determine the initial parameters for the fit of the experimental data. The refinements performed by using FEFFIT software demonstrate that an ionic bombardment applied during the deposition phase results in a significant reduction of the number of Al-Ti pairs within the bilayer and an improvement of the local order around Ti and Al, which is quantified by a decrease of the Debye-Waller parameters. This structural evolution is tentatively correlated with the improvement of mechanical properties of the bilayers.

  14. Structure and dynamics of Penetratin's association and translocation to a lipid bilayer (United States)

    Ignacio J., General; Asciutto, Eliana K.


    Penetratin belongs to the important class of small and positively charged peptides, capable of entering cells. The determination of the optimal peptidic structure for translocation is challenging; results obtained so far are varied and dependent on several factors. In this work, we review the dynamics of association of Penetratin with a modeled dioleoyl-phosphatidylcholine (DOPC) lipid membrane using molecular dynamics simulations with last generation force fields. Penetratin's structural preferences are determined using a Markov state model. It is observed that the peptide retains a helical form in the membrane associated state, just as in water, with the exception of both termini which lose helicity, facilitating the interaction of terminal residues with the phosphate groups on the membrane's outer layer. The optimal orientation for insertion is found to be with the peptide's axis forming a small angle with the interface, and with R1 stretching toward the bilayer. The interaction between arginine side-chains and phosphate groups is found to be greater than the corresponding to lysine, mainly due to a higher number of hydrogen bonds between them. The free energy profile of translocation is qualitatively studied using Umbrella Sampling. It is found that there are different paths of penetration, that greatly differ in size of free energy barrier. The lowest path is compatible with residues R10 to K13 leading the way through the membrane and pulling the rest of the peptide. When the other side is reached, the C-terminus overtakes those residues, and finally breaks out of the membrane. The peptide's secondary structure during this traversal suffers some changes with respect to the association structure but, overall, conserves its helicity, with both termini in a more disordered state.

  15. Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers. (United States)

    Leekumjorn, Sukit; Sum, Amadeu K


    Molecular dynamics simulations were used for a comprehensive study of the structural properties of monounsaturated POPC and POPE bilayers in the gel and liquid-crystalline state at a number of temperatures, ranging from 250 to 330 K. Though the chemical structures of POPC and POPE are largely similar (choline versus ethanolamine headgroup), their transformation processes from a gel to a liquid-crystalline state are contrasting. In the similarities, the lipid tails for both systems are tilted below the phase transition and become more random above the phase transition temperature. The average area per lipid and bilayer thickness were found less sensitive to phase transition changes as the unsaturated tails are able to buffer reordering of the bilayer structure, as observed from hysteresis loops in annealing simulations. For POPC, changes in the structural properties such as the lipid tail order parameter, hydrocarbon trans-gauche isomerization, lipid tail tilt-angle, and level of interdigitation identified a phase transition at about 270 K. For POPE, three temperature ranges were identified, in which the lower one (270-280 K) was associated with a pre-transition state and the higher (290-300 K) with the post-transition state. In the pre-transition state, there was a significant increase in the number of gauche arrangements formed along the lipid tails. Near the main transition (280-290 K), there was a lowering of the lipid order parameters and a disappearance of the tilted lipid arrangement. In the post-transition state, the carbon atoms along the lipid tails became less hindered as their density profiles showed uniform distributions. This study also demonstrates that atomistic simulations of current lipid force fields are capable of capturing the phase transition behavior of lipid bilayers, providing a rich set of molecular and structural information at and near the main transition state.

  16. Improve the operational stability of the inverted organic solar cells using bilayer metal oxide structure. (United States)

    Chang, Jingjing; Lin, Zhenhua; Jiang, Changyun; Zhang, Jie; Zhu, Chunxiang; Wu, Jishan


    Operational stability is a big obstacle for the application of inverted organic solar cells (OSCs), however, less talked about in the research reports. Due to photoinduced degradation of the metal oxide interlayer, which can cause shunts generation and degeneration in ZnO interlayer, a significant degradation of open circuit voltage (Voc) and fill factor (FF) has been observed by in situ periodic measurements of the device current density-voltage (J-V) curves with light illumination. By combining TiOx and ZnO to form bilayer structures on ITO, the photovoltaic performance is improved and the photoinduced degradation is reduced. It was found that the device based on ZnO/TiOx bilayer structure achieved better operational stability as compared to that with ZnO or TiOx interlayer.

  17. Microfluidic anodization of aluminum films for the fabrication of nanoporous lipid bilayer support structures

    Directory of Open Access Journals (Sweden)

    Jaydeep Bhattacharya


    Full Text Available Solid state nanoporous membranes show great potential as support structures for biointerfaces. In this paper, we present a technique for fabricating nanoporous alumina membranes under constant-flow conditions in a microfluidic environment. This approach allows the direct integration of the fabrication process into a microfluidic setup for performing biological experiments without the need to transfer the brittle nanoporous material. We demonstrate this technique by using the same microfluidic system for membrane fabrication and subsequent liposome fusion onto the nanoporous support structure. The resulting bilayer formation is monitored by impedance spectroscopy across the nanoporous alumina membrane in real-time. Our approach offers a simple and efficient methodology to investigate the activity of transmembrane proteins or ion diffusion across membrane bilayers.

  18. Microfluidic anodization of aluminum films for the fabrication of nanoporous lipid bilayer support structures. (United States)

    Bhattacharya, Jaydeep; Kisner, Alexandre; Offenhäusser, Andreas; Wolfrum, Bernhard


    Solid state nanoporous membranes show great potential as support structures for biointerfaces. In this paper, we present a technique for fabricating nanoporous alumina membranes under constant-flow conditions in a microfluidic environment. This approach allows the direct integration of the fabrication process into a microfluidic setup for performing biological experiments without the need to transfer the brittle nanoporous material. We demonstrate this technique by using the same microfluidic system for membrane fabrication and subsequent liposome fusion onto the nanoporous support structure. The resulting bilayer formation is monitored by impedance spectroscopy across the nanoporous alumina membrane in real-time. Our approach offers a simple and efficient methodology to investigate the activity of transmembrane proteins or ion diffusion across membrane bilayers.

  19. In vitro determination of the solubility limit of cholesterol in phospholipid bilayers. (United States)

    Epand, Richard M; Bach, Diana; Wachtel, Ellen


    Cholesterol has limited solubility in phospholipid bilayers. The solubility limit is strongly dependent on the nature of the lipid with which the cholesterol is mixed while properties of the crystals formed can be modified by phospholipid-cholesterol interactions. In this review we summarize the various methods that have been developed to prepare hydrated mixtures of cholesterol and phospholipid. We point out some of the factors that determine the form adopted when cholesterol crystallizes in such mixtures, i.e. two- or three-dimensional, monohydrate or anhydrous. These differences can greatly affect the ability to experimentally detect the presence of these crystals in a membrane. Several methods for detecting cholesterol crystals are discussed and compared including DSC, X-ray and GIXRD diffraction methods, NMR and EPR spectroscopy. The importance of the history of the sample in determining the amount and nature of the cholesterol crystals formed is emphasized.

  20. Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu; Sugiura, Ryuta; Sasaki, Nobuaki; Misawa, Nobuo; Tero, Ryugo; Urisu, Tsuneo; Gardiner, Alastair T; Cogdell, Richard J; Hashimoto, Hideki; Nango, Mamoru


    The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.

  1. Structure and Dynamics Studies of Cytolytic Peptides in Lipid Bilayers using NMR Spectroscopy

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh


    Millions of people around the world take antimicrobial drugs every day to fight off bacterial infections. However, the microbes are starting to fight back and to develop resistance towards conventional antibiotics, posing a major challenge in the future. Therefore, there is a need for exploring...... the opportunities for alternative drugs that cannot be overcome by the bacteria. In this context, cytolytic peptides are being investigated and designed to target cell membranes of microbes specifically. In the search for information about the structure and dynamics of membrane-active peptides, three highly...... to characterize different properties of these peptides. Owing to the membrane-active nature of all three, the peptides were studied in model membranes including isotropic bicelles, magnetically aligned bilayers and mechanically aligned bilayers, employing a diverse set of NMR experiments on unlabeled and 15N...

  2. Structural modifications to enhance the exciton diffusion in bilayer porphyrin fullerene thin films (United States)

    Kaushal, Meesha; Srinivasamurthy, Praveen; Walter, Michael G.


    The effects of peripheral alkyl groups and thermal annealing on the exciton quenching efficiency in bilayer porphyrinfullerene thin films has been investigated. The thin film UV-vis absorbance spectra, steady-state fluorescence emission, and thermal properties of three carboalkoxyphenyl porphyrin derivatives have been studied: tetra(4-carbohexoxyphenyl)porphyrin (TCH4PP), tetra(4-carbo-2-ethylhexoxyphenyl)porphyrin (TCEH4PP), and tetra(4-carbooctoxyphenyl)-porphyrin (TCO4PP). The quenching efficiencies of these three derivatives have been calculated from their steady-state emission using pristine spin cast films and films with an evaporated C60 bilayer. Structural analyses have been performed using X-ray diffraction (XRD), UV-vis spectroscopy, and thermal properties were studied using differential scanning calorimetry measurements (DSC). Annealing the films caused significant structural changes as was observed in the UV-vis absorbance spectra and XRD diffraction patterns. Prior to thermal annealing, quenching efficiencies are greatest for the TCH4PP and TCO4PP (hexyl and octyl derivatives), which is in agreement with previous bulk quenching experiments to calculate exciton diffusion lengths.1 After annealing, the hexyl derivative (TCH4PP) showed the lowest bilayer quenching efficiency and indicated evidence of significant molecular rearrangements.

  3. The impact of cell-penetrating peptides on membrane bilayer structure during binding and insertion. (United States)

    Hirst, Daniel J; Lee, Tzong-Hsien; Kulkarni, Ketav; Wilce, Jacqueline A; Aguilar, Marie-Isabel


    We have studied the effect of penetratin and a truncated analogue on the bilayer structure using dual polarisation interferometry, to simultaneously measure changes in mass per unit area and birefringence (an optical parameter representing bilayer order) with high sensitivity during the binding and dissociation from the membrane. Specifically, we studied penetratin (RQIKIWFQNRRMKWKK), along with a shortened and biotinylated version known as R8K-biotin (RRMKWKKK(Biotin)-NH2). Overall both peptides bound only weakly to the neutral DMPC and POPC bilayers, while much higher binding was observed for the anionic DMPC/DMPG and POPC/POPG. The binding of penetratin to gel-phase DMPC/DMPG was adequately represented by a two-state model, whereas on the fluid-phase POPC/POPG it exhibited a distinctly different binding pattern, best represented by a three-state kinetic model. However, R8K-biotin did not bind well to DMPC/DMPG and showed a more transitory and superficial binding to POPC/POPG. Comparing the modelling results for both peptides binding to POPC/POPG suggests an important role for a securely bound intermediate prior to penetratin insertion and translocation. Overall these results further elucidate the mechanism of penetratin, and provide another example of the significance of the ability of DPI to measure structural changes and the use of kinetic analysis to investigate the stages of peptide-membrane interactions.

  4. Intercalation of small hydrophobic molecules in lipid bilayers containing cholesterol

    Energy Technology Data Exchange (ETDEWEB)

    Worcester, D.L.; Hamacher, K.; Kaiser, H.; Kulasekere, R.; Torbet, J. [Univ. of Missouri, Columbia, MO (United States)


    Partitioning of small hydrophobic molecules into lipid bilayers containing cholesterol has been studied using the 2XC diffractometer at the University of Missouri Research Reactor. Locations of the compounds were determined by Fourier difference methods with data from both deuterated and undeuterated compounds introduced into the bilayers from the vapor phase. Data fitting procedures were developed for determining how well the compounds were localized. The compounds were found to be localized in a narrow region at the center of the hydrophobic layer, between the two halves of the bilayer. The structures are therefore intercalated structures with the long axis of the molecules in the plane of the bilayer.

  5. Reconstitution of rhodopsin into polymerizable planar supported lipid bilayers: influence of dienoyl monomer structure on photoactivation. (United States)

    Subramaniam, Varuni; D'Ambruoso, Gemma D; Hall, H K; Wysocki, Ronald J; Brown, Michael F; Saavedra, S Scott


    G-protein-coupled receptors (GPCRs) play key roles in cellular signal transduction and many are pharmacologically important targets for drug discovery. GPCRs can be reconstituted in planar supported lipid bilayers (PSLBs) with retention of activity, which has led to development of GPCR-based biosensors and biochips. However, PSLBs composed of natural lipids lack the high stability desired for many technological applications. One strategy is to use synthetic lipid monomers that can be polymerized to form robust bilayers. A key question is how lipid polymerization affects GPCR structure and activity. Here we have investigated the photochemical activity of bovine rhodopsin (Rho), a model GPCR, reconstituted into PSLBs composed of lipids having one or two polymerizable dienoyl moieties located in different regions of the acyl chains. Plasmon waveguide resonance spectroscopy was used to compare the degree of Rho photoactivation in fluid and poly(lipid) PSLBs. The position of the dienoyl moiety was found to have a significant effect: polymerization near the glycerol backbone significantly attenuates Rho activity whereas polymerization near the acyl chain termini does not. Differences in cross-link density near the acyl chain termini also do not affect Rho activity. In unpolymerized PSLBs, an equimolar mixture of phosphatidylethanolamine and phosphatidylcholine (PC) lipids enhances activity relative to pure PC; however after polymerization, the enhancement is eliminated which is attributed to stabilization of the membrane lamellar phase. These results should provide guidance for the design of robust lipid bilayers functionalized with transmembrane proteins for use in membrane-based biochips and biosensors.

  6. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. (United States)

    Ollila, O H Samuli; Pabst, Georg


    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at and This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  7. Structural and superconducting properties of ion beam sputtered Nb thin films and Nb/Cu bilayers (United States)

    Nath, S. K.; Dhawan, R.; Rai, S.; Lodha, G. S.; Sokhey, K. J. S.


    We present the results of a study of structural and superconducting properties of polycrystalline Nb thin films (200 Å, 300 Å, 400 Å, 700 Å and 1000 Å) and Nb/Cu bilayers (300 Å/300 Å and 400 Å/300 Å) prepared on Si substrates by ion beam sputtering at room temperature. The thicknesses, roughnesses at the surfaces and interfaces were determined by X-ray reflectivity whereas the grain sizes were determined from grazing incidence X-ray diffraction and transmission electron microscopic studies. The superconducting transition temperature ( T C) of Nb thin films are smaller than T C of bulk Nb. The Nb-200 Å sample does not show T C down to 2.3 K. The average size of the grains varies from 42 Å for Nb-200 Å sample to 69 Å for Nb-1000 Å sample. Our results show that the T C in these polycrystalline films is not only limited by its thickness but also by the size of the grains. The Nb films deposited in situ on the Cu layer (Nb/Cu) show a marginal increase in average sizes of the grains as compare to their respective values in Nb films of same thicknesses. As a result a marginal increase in T C of these films is also observed. The maximum decrease in T C due to oxygen intake during deposition should be about 0.5 K from its bulk value (9.28 K). We have attributed the large decrease in T C in our case on the basis of decrease in the Debye temperature and density of states at the Fermi level for Nb thin films as compared to their respective values for bulk Nb.

  8. Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Ronak Y. Patel


    Full Text Available Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

  9. Compositional and structural characterization of monolayers and bilayers composed of native pulmonary surfactant from wild type mice

    DEFF Research Database (Denmark)

    Bernardino de la Serna, Jorge; Hansen, Soren; Berzina, Zane


    This work comprises a structural and dynamical study of monolayers and bilayers composed of native pulmonary surfactant from mice. Spatially resolved information was obtained using fluorescence (confocal, wide field and two photon excitation) and atomic force microscopy methods. Lipid mass...... spectrometry experiments were also performed in order to obtain relevant information on the lipid composition of this material. Bilayers composed of mice pulmonary surfactant showed coexistence of distinct domains at room temperature, with morphologies and lateral packing resembling the coexistence of liquid...... between mono- and bi-layers composed of mice pulmonary surfactant were observed when the monolayers reach a surface pressure of 30 mN/m. This value is in line with theoretically predicted and recently measured surface pressures, where the monolayer-bilayer equivalence occurs in samples composed of single...

  10. Exchange-bias field induced by surface inhomogeneities in ferromagnetic/charge-ordered bilayer structure

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Haiou, E-mail: [Institute of Materials Physics, Hangzhou Dianzi University, Hangzhou, 310018 (China); Key Laboratory of Soft Chemistry and Functional Materials, Ministry of Education, Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, 210094 (China); Yang, Weifeng; Su, Kunpeng [Institute of Materials Physics, Hangzhou Dianzi University, Hangzhou, 310018 (China); Huo, Dexuan, E-mail: [Institute of Materials Physics, Hangzhou Dianzi University, Hangzhou, 310018 (China); Tan, Weishi [Key Laboratory of Soft Chemistry and Functional Materials, Ministry of Education, Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, 210094 (China)


    Epitaxial bilayer structure consisting of ferromagnetic metallic Pr{sub 0.7}Sr{sub 0.3}MnO{sub 3} (PSMO) and charge-ordered insulator La{sub 0.5}Ca{sub 0.5}MnO{sub 3} (LCMO) was fabricated on (001) SrTiO{sub 3} substrate by pulsed laser deposition. High-resolution synchrotron X-ray diffraction showed high quality of epitaxial layer. However, besides diffraction peaks from PSMO layer, LCMO layer and SrTiO{sub 3} substrate, we observed an additional shoulder peak, which might stem from the inhomogeneities of composition in PSMO/LCMO. Further the atomic force microscopy measurement showed the presence of non-stoichiometric large particulates at surface, imparting an overall inhomogeneous composition to the film. This implied that the variation of crystalline structure of PSMO/LCMO occurred due to inhomogeneous composition. Moreover, studies on magnetic properties showed that surface inhomogeneities and ferromagnetic clusters at the PSMO/LCMO interface probably influenced the ferromagnetism of the bilayer film together, tuning exchange bias effect. - Highlights: • We report the epitaxial growth of Pr{sub 0.7}Sr{sub 0.3}MnO{sub 3}/La{sub 0.5}Ca{sub 0.5}MnO{sub 3} bilayer on SrTiO{sub 3}. • The non-stoichiometric particulates at surface impart inhomogeneous composition. • Inhomogeneities in the film lead to the variation of crystalline structure. • Surface inhomogeneities reduce ferromagnetism and enhance exchange bias effect.

  11. Composition, structure and properties of POPC–triolein mixtures. Evidence of triglyceride domains in phospholipid bilayers

    DEFF Research Database (Denmark)

    Duelund, Lars; Jensen, Grethe Vestergaard; Hannibal-Bach, Hans Kristian;


    We have in this study investigated the composition, structure and spectroscopical properties of multilamellar vesicles composed of a phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and up to 10mol% of triolein (TO), a triglyceride. We found in agreement with previous result......% TO contained pure TO domains. These observations are consistent with an earlier MD simulation study by us and our co-workers suggesting triglycerides to be located in lens shaped, blister-like domains between the two lipid bilayer leaflets (Khandelia et al. (2010) [26])....

  12. Sintering of bi-layered porous structures: Stress development and shape evolution

    DEFF Research Database (Denmark)

    Ni, De Wei; Esposito, Vincenzo; Ramousse, Severine;

    Ce0.9Gd0.1O1.95 (CGO) and (La, Sr)MnO3 (LSM) are electro-ceramics materials with high potential for several electrochemical applications such as solid Oxide Fuel Cell (SOFC), gas separation membranes, and flue gas purification application. In the latter case, these materials are shaped as thick...... porous layers and sintered by co-firing process. In this work, porous CGO and LSM/CGO single layers were prepared by tape casting, and CGO-LSM/CGO bi-layer structures were obtained by lamination. The shrinkage characteristics of individual layers were measured by optical dilatometry and the uniaxial...

  13. Nanoporous Au structures by dealloying Au/Ag thermal- or laser-dewetted bilayers on surfaces (United States)

    Ruffino, F.; Torrisi, V.; Grillo, R.; Cacciato, G.; Zimbone, M.; Piccitto, G.; Grimaldi, M. G.


    Nanoporous Au attracts great technological interest and it is a promising candidate for optical and electrochemical sensors. In addition to nanoporous Au leafs and films, recently, interest was focused on nanoporous Au micro- and nano-structures on surfaces. In this work we report on the study of the characteristics of nanoporous Au structures produced on surfaces. We developed the following procedures to fabricate the nanoporous Au structures: we deposited thin Au/Ag bilayers on SiO2 or FTO (fluorine-doped tin oxide) substrates with thickness xAu and xAg of the Au and Ag layers; we induced the alloying and dewetting processes of the bilayers by furnace annealing processes of the bilayers deposited on SiO2 and by laser irradiations of the bilayers deposited on FTO; the alloying and dewetting processes result in the formation of AuxAgy alloy sub-micron particles being x and y tunable by xAu and xAg. These particles are dealloyed in HNO3 solution to remove the Ag atoms. We obtain, so, nanoporous sub-micron Au particles on the substrates. Analyzing the characteristics of these particles we find that: a) the size and shape of the particles depend on the nature of the dewetting process (solid-state dewetting on SiO2, molten-state dewetting on FTO); b) the porosity fraction of the particles depends on how the alloying process is reached: about 32% of porosity for the particles fabricated by the furnace annealing at 900 °C, about 45% of porosity for the particles fabricated by the laser irradiation at 0.5 J/cm2, in both cases independently on the Ag concentration in the alloy; c) After the dealloying process the mean volume of the Au particles shrinks of about 39%; d) After an annealing at 400 °C the nanoporous Au particles reprise their initial volume while the porosity fraction is reduced. Arguments to justify these behaviors are presented.

  14. Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

    DEFF Research Database (Denmark)

    Zhao, W.; Gurtovenko, A. A.; Vattulainen, I.


    of 0.4, that is, at lower TAP fractions compared with saturated PC/TAP bilayers. Adding unsaturated DOTAP lipids into DMPC bilayers was found to promote lipid chain interdigitation and to fluidize lipid bilayers, as seen through enhanced lateral lipid diffusion. The speed-up in lateral diffusion...

  15. Growth, structure and magnetic properties of single crystalline Fe/CoO/Ag(001) bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Abrudan, R.M.


    The structural and magnetic properties of epitaxially deposited single-crystalline CoO layers and Fe/CoO bilayers on Ag(001) were investigated. CoO films on Ag(001) exhibit (1 x 1) Low Energy Electron Diffraction (LEED) patterns similar to the clean Ag(001) substrate. The vertical interlayer spacing of the CoO films, deduced from a kinematic analysis of LEED I(E) curves, is a {sub perpendicular} {sub to} /2=2.17 Aa, slightly expanded along the film normal. Scanning Tunneling Microscopy (STM) show a big improvement in the surface roughness after annealing the CoO films at 750 K in oxygen atmosphere. Magnetic measurements using the magneto-optical Kerr effect (MOKE) show a characteristic increase of the coercive field when the Fe/CoO bilayer system is cooled down from room temperature to 150 K. The ordering temperature for the antiferromagnetic layer is in the same range as the Neel temperature for bulk CoO (T{sub N}=290 K). X-ray absorption spectroscopy was employed to probe magnetic and electronic properties with elemental selectivity. Absorption spectra taken from bilayers with different amounts of deposited Fe show only a weak indication for the formation of Fe oxide at the Fe/CoO interface (0.3 ML Fe). From the spectral shape it is concluded that an FeO type of oxide is formed. X-ray Magnetic Circular Dichroism (XMCD) measurements exhibit a sizeable induced ferromagnetic signal at the Co L{sub 2,3} absorption edge, corresponding to an interface layer of 1.1 ML in which the magnetic spins couple with the Fe layer. The angular dependence of the X-ray Magnetic Linear Dichroism (XMLD) and X-ray Magnetic Circular Dichroism XMCD at both the Co and Fe L{sub 2,3} edges shows the orientation of the Co and Fe moments in the bilayers with respect to the crystallographic direction. PhotoElectron Emission Microscope (PEEM) is used to image each ferromagnetic and antiferromagnetic layer separately. Magnetic contrast due to the induced magnetic spins at the interface is also

  16. Computational criterion for application of the characteristic effective medium approximation to ultrathin Co-Au multi-bilayer structures

    Energy Technology Data Exchange (ETDEWEB)

    Haija, A.J. [Physics Department, Indiana University of Pennsylvania, 975 Oakland Avenue, Weyandt Hall-Rm 40, Indiana, PA 15705-1087 (United States)], E-mail:; Larry Freeman, W.; DeNinno, Matthew [Physics Department, Indiana University of Pennsylvania, 975 Oakland Avenue, Weyandt Hall-Rm 40, Indiana, PA 15705-1087 (United States)


    The basic optical properties, reflectivity and transmissivity, of three sets of Co-Au bilayer structures are calculated for normal incidence in the wavelength range 300-700 nm. Each set consists of a total number of bilayer identity periods m=1, 2, 3, 4, 5, 6. The thickness of the bilayer in each set is 5, 7, and 9 nm. The composition of the bilayer is kept fixed: 40% Co and 60% Au. The calculations are done for ideal layered Co-Au stacks using the characteristic matrix technique. Calculations for each stack based on the thicknesses of the two composite layers and their optical constants are contrasted against calculations using the characteristic effective medium approximation, CEMA. A third calculation of the optical properties for each stack is performed, again using the CEMA, but when the whole stack, called the effective stack, ES, is treated as one uniform medium of effective optical constants. The comparison of the three sets of calculations for all sets is intended to shed more light onto the validity of the CEMA approximation that has been established for thin bilayer structures whose constituents have thicknesses much less than the wavelength of the incident radiation. The study establishes a limit based on the product of the number of layers m and the identity period of the stack h, beyond which the CEMA approximation cannot be applied. This limit is consistent with a previous study carried out on Ag-SiO ultrathin stacks.

  17. Computational criterion for application of the characteristic effective medium approximation to ultrathin Co Au multi-bilayer structures (United States)

    Haija, A. J.; Larry Freeman, W.; DeNinno, Matthew


    The basic optical properties, reflectivity and transmissivity, of three sets of Co-Au bilayer structures are calculated for normal incidence in the wavelength range 300-700 nm. Each set consists of a total number of bilayer identity periods m=1, 2, 3, 4, 5, 6. The thickness of the bilayer in each set is 5, 7, and 9 nm. The composition of the bilayer is kept fixed: 40% Co and 60% Au. The calculations are done for ideal layered Co-Au stacks using the characteristic matrix technique. Calculations for each stack based on the thicknesses of the two composite layers and their optical constants are contrasted against calculations using the characteristic effective medium approximation, CEMA. A third calculation of the optical properties for each stack is performed, again using the CEMA, but when the whole stack, called the effective stack, ES, is treated as one uniform medium of effective optical constants. The comparison of the three sets of calculations for all sets is intended to shed more light onto the validity of the CEMA approximation that has been established for thin bilayer structures whose constituents have thicknesses much less than the wavelength of the incident radiation. The study establishes a limit based on the product of the number of layers m and the identity period of the stack h, beyond which the CEMA approximation cannot be applied. This limit is consistent with a previous study carried out on Ag-SiO ultrathin stacks.

  18. Bilayer Structure and Lipid Dynamics in a Model Stratum Corneum with Oleic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Hoopes, Matthew I.; Noro, Massimo G.; Longo, Marjorie L.; Faller, Roland


    The stratum corneum is the uppermost layer of the skin and acts as a barrier to keep out contaminants and retain moisture. Understanding the molecular structure and behavior of this layer will provide guidance for optimizing its biological function. In this study we use a model mixture comprised of equimolar portions of ceramide NS (24:0), lignoceric acid, and cholesterol to model the effect of the addition of small amounts of oleic acid to the bilayer at 300 and 340 K. Five systems at each temperature have been simulated with concentrations between 0 and 0.1 mol % oleic acid. Our major finding is that subdiffusive behavior over the 200 ns time scale is evident in systems at 340 K, with cholesterol diffusion being enhanced with increased oleic acid. Importantly, cholesterol and other species diffuse faster when radial densities indicate nearest neighbors include more cholesterol. We also find that, with the addition of oleic acid, the bilayer midplane and interfacial densities are reduced and there is a 3% decrease in total thickness occurring mostly near the hydrophilic interface at 300 K with reduced overall density at 340 K. Increased interdigitation occurs independent of oleic acid with a temperature increase. Slight ordering of the long non-hydroxy fatty acid of the ceramide occurs near the hydrophilic interface as a function of the oleic acid concentration, but no significant impact on hydrogen bonding is seen in the chosen oleic acid concentrations.

  19. Optical and structural investigations of self-assembled Ge/Si bi-layer containing Ge QDs

    Energy Technology Data Exchange (ETDEWEB)

    Samavati, Alireza, E-mail: [Ibn Sina Institute for Fundamental Science Studies, Universiti Teknologi Malaysia, Skudai 81310, Johor (Malaysia); Othaman, Z., E-mail: [Ibn Sina Institute for Fundamental Science Studies, Universiti Teknologi Malaysia, Skudai 81310, Johor (Malaysia); Ghoshal, S.K.; Dousti, M.R. [Advanced Optical Material Research Group, Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor (Malaysia)


    We report the influence of Si spacer thickness variation (10–40 nm) on structural and optical properties of Ge quantum dots (QDs) in Ge/Si(1 0 0) bi-layer grown by radio frequency magnetron sputtering. AFM images reveal the spacer dependent width, height, root mean square roughness and number density of QDs vary in the range of ∼12–25 nm, ∼2–6 nm, ∼1.95–1.05 nm and ∼0.55×10{sup 11}–2.1×10{sup 11} cm{sup −2}, respectively. XRD patterns exhibit the presence of poly-oriented structures of Ge with preferred growth along (1 1 1) direction accompanied by a reduction in strain from 4.9% to 1.2% (estimated from Williamson–Hall plot) due to bi-layering. The room temperature luminescence displays strong blue–violet peak associated with a blue shift as much as 0.05 eV upon increasing the thickness of Si spacer. This shift is attributed to the quantum size effect, the material intermixing and the strain mediation. Raman spectra for both mono and bi-layer samples show intense Ge–Ge optical phonon mode that is shifted towards higher frequency. Furthermore, the first order features of Raman spectra affirm the occurrence of interfacial intermixing and phase formation during deposition. The excellent features of the results suggest that our systematic method may constitute a basis for the tunable growth of Ge QDs suitable in nanophotonics. - Highlights: • High quality bilayered hetero-structure Ge/Si using economic and easy rf magnetron sputtering fabrication method. • The role of phonon-confinement and strain relaxation mechanisms. • Influence of bilayering on evolutionary growth dynamics. • Band gap shift of visible PL upon bilayering.

  20. Rational Design of ZnO:H/ZnO Bilayer Structure for High-Performance Thin-Film Transistors. (United States)

    Abliz, Ablat; Huang, Chun-Wei; Wang, Jingli; Xu, Lei; Liao, Lei; Xiao, Xiangheng; Wu, Wen-Wei; Fan, Zhiyong; Jiang, Changzhong; Li, Jinchai; Guo, Shishang; Liu, Chuansheng; Guo, Tailiang


    The intriguing properties of zinc oxide-based semiconductors are being extensively studied as they are attractive alternatives to current silicon-based semiconductors for applications in transparent and flexible electronics. Although they have promising properties, significant improvements on performance and electrical reliability of ZnO-based thin film transistors (TFTs) should be achieved before they can be applied widely in practical applications. This work demonstrates a rational and elegant design of TFT, composed of poly crystalline ZnO:H/ZnO bilayer structure without using other metal elements for doping. The field-effect mobility and gate bias stability of the bilayer structured devices have been improved. In this device structure, the hydrogenated ultrathin ZnO:H active layer (∼3 nm) could provide suitable carrier concentration and decrease the interface trap density, while thick pure-ZnO layer could control channel conductance. Based on this novel structure, a high field-effect mobility of 42.6 cm(2) V(-1) s(-1), a high on/off current ratio of 10(8) and a small subthreshold swing of 0.13 V dec(-1) have been achieved. Additionally, the bias stress stability of the bilayer structured devices is enhanced compared to the simple single channel layer ZnO device. These results suggest that the bilayer ZnO:H/ZnO TFTs have a great potential for low-cost thin-film electronics.

  1. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N


    All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure of t...

  2. Preservation of bilayer structure in human erythrocytes and erythrocyte ghosts after phospholipase treatment. A 31P-NMR study. (United States)

    van Meer, G; de Kruijff, B; op den Kamp, J A; van Deenen, L L


    1. Fresh human erythrocytes were treated with lytic and non-lytic combinations of phospholipases A2, C and sphingomyelinase. The 31P-NMR spectra of ghosts derived from such erythrocytes show that, in all cases, the residual phospholipids and lysophospholipids remain organized in a bilayer configuration. 2. A bilayer configuration of the (lyso)phospholipids was also observed after treatment of erythrocyte ghosts with various phospholipases even in the case that 98% of the phospholipid was converted into lysophospholipid (72%) and ceramides (26%). 3. A slightly decreased order of the phosphate group of phospholipid molecules, seen as reduced effective chemical shift anisotropy in the 31P-NMR spectra, was found following the formation of diacyglycerols and ceramides in the membrane of intact erythrocytes. Treatment of ghosts always resulted in an extensive decrease in the order of the phosphate groups. 4. The results allow the following conclusions to made: a. Hydrolysis of phospholipids in intact red cells and ghosts does not result in the formation of non-bilayer configuration of residual phospholipids and lysophospholipids. b. Haemolysis, which is obtained by subsequent treatment of intact cells with sphingomyelinase and phospholipase A2, or with phospholipase C, cannot be ascribed to the formation of non-bilayer configuration of phosphate-containing lipids. c. Preservation of bilayer structure, even after hydrolysis of all phospholipid, shows that other membrane constitutents, e.g. cholesterol and/or membrane proteins play an important role in stabilizing the structure of the erythrocyte membrane. d. A major prerequisite for the application of phospholipases in lipid localization studies, the preservation of a bilayer configuration during phospholipid hydrolysis, is met for the erythrocyte membrane.

  3. Correlation Between Interfacial Structure and Toughness in SiC-Al Bilayers (United States)

    Kong, Yaru; Guo, Qiang; Guo, Xiaolei; Fan, Genlian; Li, Zhiqiang; Xiong, Ding-Bang; Su, Yishi; Zhang, Jie; Zhang, Di


    Reinforcement surface modification is often used to improve the mechanical properties of particle-reinforced metal matrix composites, however, the extent to which such modifications affect the interfacial properties is yet to be revealed. In this study, we fabricated SiC-Al composite bilayers where the SiC underwent different surface treatments before Al deposition. Four-point bending tests showed that the samples made from acid-pickled and thermally oxidized SiC possessed substantially higher interfacial toughness than their untreated counterpart, a presumption inferred from mechanical tests on bulk SiCp-Al composites but never justified quantitatively. These findings were rationalized by the different interfacial constituents and structure in these samples.

  4. Enhanced Performance of Dye-Sensitized Solar Cells with Graphene/ZnO Nanoparticles Bilayer Structure

    Directory of Open Access Journals (Sweden)

    Chih-Hung Hsu


    Full Text Available This study reports characteristics of dye-sensitized solar cells (DSSCs with graphene/ZnO nanoparticle bilayer structure. The enhancement of the performance of DSSCs achieved using graphene/ZnO nanoparticle films is attributable to the introduction of an electron-extraction layer and absorption of light in the visible range and especially in the range 300–420 nm. DSSC that was fabricated with graphene/ZnO nanoparticle film composite photoanodes exhibited a Voc of 0.5 V, a Jsc of 17.5 mA/cm2, an FF of 0.456, and a calculated η of 3.98%.

  5. Sputtered Pt electrode structures with smoothly tapered edges by bi-layer resist lift-off

    Energy Technology Data Exchange (ETDEWEB)

    Preiss, Elisabeth M., E-mail: [Robert Bosch GmbH, Corporate Sector Research and Advance Engineering, Robert-Bosch-Campus 1, 71272 Renningen (Germany); Saarland University, Lab for Micromechanics, Microfluidics, and Microactuators, 66123 Saarbruecken (Germany); Krauss, Andreas [Robert Bosch GmbH, Corporate Sector Research and Advance Engineering, Robert-Bosch-Campus 1, 71272 Renningen (Germany); Seidel, Helmut [Saarland University, Lab for Micromechanics, Microfluidics, and Microactuators, 66123 Saarbruecken (Germany)


    A lift-off process using a bi-layer resist consisting of an image reversal resist on top and a lift-off resist at the bottom was used to structure Ti–Pt thin films. DC magnetron sputtered metal films patterned by this process show ultra smooth edges, ideal for applications such as interdigitated electrodes in resistive gas sensors including thin-film based sensitive coatings with thicknesses below 100 nm. Profiles of processed structures were analyzed by scanning electron microscopy and surface profilometer. The thickness profile and structure width were controlled by using different resist thicknesses and undercut lengths. Results were compared with iterative simulations by a geometric shadowing model, predicting undersputtering length and profile structure of the experimentally manufactured samples in good agreement. Target-to-substrate distance variation was found to have only a minor influence on the sputtering result. - Highlights: • Ti–Pt electrode structures were prepared using sputtering bi-layer-resist lift-off. • Prepared lift-off electrodes can be used for good overgrowth of thin films. • Ultra-smoothly tapered edges were controlled by the process parameters. • Simulations using a geometric shadowing model confirm our experimental results.

  6. Synthesis, structural and optical properties of a novel bilayered organic-inorganic perovskite C{sub 5}Pb{sub 2}I{sub 5}

    Energy Technology Data Exchange (ETDEWEB)

    Elleuch, S., E-mail: slimlpa@yahoo.f [Laboratoire de Physique Appliquee, Faculte des Sciences de Sfax, 3000, BP 1171, Sfax (Tunisia); Dammak, T.; Abid, Y. [Laboratoire de Physique Appliquee, Faculte des Sciences de Sfax, 3000, BP 1171, Sfax (Tunisia); Mlayah, A. [Centre d' Elaboration de Materiaux et d' Etudes Structurales, CNRS-Universite Paul Sabatier, 29 Rue Jeanne Marvig, Toulouse 31055 (France); Boughzala, H. [Laboratoire de Materiaux et Cristallochimie, Institut Preparatoire aux etudes Ingenieur de Nabeul, 8000 Mrezga, Nabeul (Tunisia)


    Single crystals of [C{sub 5}H{sub 11}NH{sub 3}]Pb{sub 2}I{sub 5}, abbreviated C{sub 5}Pb{sub 2}I{sub 5}, have been prepared. This compound is a new member of the family of the bilayered organic-inorganic lead-iodide based perovskites. Its crystal structure has been determined by X-ray diffraction. The inorganic sub-lattice consists of periodic bilayers of iodoplumbate octahedra. Each PbI{sub 6} octahedra exhibits both edge- and corner-sharing with adjacent octahedra. The vibrational properties of this compound have been studied by Raman scattering spectroscopy. Optical absorption, photoluminescence and diffuse reflectance measurements have been performed. The room-temperature bandgap and free exciton absorption bands are observed at 2.46 and 2.23 eV, respectively. The exciton binding energy is 230 meV which is the largest value ever reported till date for the bilayered PbI based perovskites. Calculations assuming Wannier-type quasi-two-dimensional excitons and taking into account the image potential of the exciton charges showed that nearly 64% of the exciton binding energy is due to the dielectric confinement effect.

  7. Dynamical structure factors and excitation modes of the bilayer Heisenberg model (United States)

    Lohöfer, M.; Coletta, T.; Joshi, D. G.; Assaad, F. F.; Vojta, M.; Wessel, S.; Mila, F.


    Using quantum Monte Carlo simulations along with higher-order spin-wave theory, bond-operator and strong-coupling expansions, we analyze the dynamical spin structure factor of the spin-half Heisenberg model on the square-lattice bilayer. We identify distinct contributions from the low-energy Goldstone modes in the magnetically ordered phase and the gapped triplon modes in the quantum disordered phase. In the antisymmetric (with respect to layer inversion) channel, the dynamical spin structure factor exhibits a continuous evolution of spectral features across the quantum phase transition, connecting the two types of modes. Instead, in the symmetric channel, we find a depletion of the spectral weight when moving from the ordered to the disordered phase. While the dynamical spin structure factor does not exhibit a well-defined distinct contribution from the amplitude (or Higgs) mode in the ordered phase, we identify an only marginally damped amplitude mode in the dynamical singlet structure factor, obtained from interlayer bond correlations, in the vicinity of the quantum critical point. These findings provide quantitative information in direct relation to possible neutron or light scattering experiments in a fundamental two-dimensional quantum-critical spin system.

  8. The roles of bulk and interfacial molecular orientations in determining the performance of organic bilayer solar cells

    KAUST Repository

    Ngongang Ndjawa, Guy O.


    Molecular orientation plays a significant role in determining the performance of small molecule solar cells. Key photovoltaic processes in these cells are strongly dependent on how the molecules are oriented in the active layer. We isolate contributions arising from the bulk molecular orientations vs. those from interfacial orientations in ZnPc/C60 bilayer systems and we probe these contributions by comparing device pairs in which only the bulk or the interface differ. By controlling the orientation in the bulk the current can be strongly modulated, whereas controlling the interfacial molecular orientation and degree of intermixing mediate the voltage.

  9. Correlating anomalous diffusion with lipid bilayer membrane structure using single molecule tracking and atomic force microscopy (United States)

    Skaug, Michael J.; Faller, Roland; Longo, Marjorie L.


    Anomalous diffusion has been observed abundantly in the plasma membrane of biological cells, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, which are thought to be skeleton bound proteins, protein aggregates, and lipid domains, so the dynamics of diffusing particles is used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension, and correlation length. To accurately measure an anomalous diffusion exponent, we derived an expression to account for the time-averaging inherent to all single molecule tracking experiments. We show that the length of the single molecule trajectories is critical to the determination of the anomalous diffusion exponent. We further discuss our results in the context of confinement models and the generating stochastic process.

  10. What determines family structure?


    Blau, David M.; van der Klaauw, Wilbert


    We estimate the effects of policy and labor market variables on the fertility, union formation and dissolution, type of union (cohabiting versus married), and partner choices of the NLSY79 cohort of women. These demographic behaviors interact to determine the family structure experienced by the children of these women: living with the biological mother and the married or cohabiting biological father, a married or cohabiting step father, or no man. We find that the average wage rates available...

  11. Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR. (United States)

    Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio


    Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1'-(13)C-2-(15)N-labeled and 2'-(13)C-2-(15)N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on (13)C and (15)N chemical-shift anisotropies and intramolecular (13)C-(15)N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation.

  12. Bilayered graphene/h-BN with folded holes as new nanoelectronic materials: modeling of structures and electronic properties (United States)

    Chernozatonskii, Leonid A.; Demin сtor A., Vi; Bellucci, Stefano


    The latest achievements in 2-dimensional (2D) material research have shown the perspective use of sandwich structures in nanodevices. We demonstrate the following generation of bilayer materials for electronics and optoelectronics. The atomic structures, the stability and electronic properties of Moiré graphene (G)/h-BN bilayers with folded nanoholes have been investigated theoretically by ab-initio DFT method. These perforated bilayers with folded hole edges may present electronic properties different from the properties of both graphene and monolayer nanomesh structures. The closing of the edges is realized by C-B(N) bonds that form after folding the borders of the holes. Stable ≪round≫ and ≪triangle≫ holes organization are studied and compared with similar hole forms in single layer graphene. The electronic band structures of the considered G/BN nanomeshes reveal semiconducting or metallic characteristics depending on the sizes and edge terminations of the created holes. This investigation of the new types of G/BN nanostructures with folded edges might provide a directional guide for the future of this emerging area.

  13. A High-Transmission, Multiple Antireflective Surface Inspired from Bilayer 3D Ultrafine Hierarchical Structures in Butterfly Wing Scales. (United States)

    Han, Zhiwu; Mu, Zhengzhi; Li, Bo; Niu, Shichao; Zhang, Junqiu; Ren, Luquan


    A high-transmission, multiple antireflective surface inspired by bilayer 3D ultrafine hierarchical structures in butterfly wing scales is fabricated on a glass substrate using wet chemical biomimetic fabrication. Interestingly, the biomimetic antireflective surface exhibits excellent antireflective properties and high transmission, which provides better characteristics than the butterfly wings and can significantly reduce reflection without losing transparency. These findings offer a new path for generating nanostructured antireflectors with high transmission properties.

  14. General aspects of peptide selectivity towards lipid bilayers and cell membranes studied by variation of the structural parameters of amphipathic helical model peptides. (United States)

    Dathe, Margitta; Meyer, Jana; Beyermann, Michael; Maul, Björn; Hoischen, Christian; Bienert, Michael


    Model compounds of modified hydrophobicity (Eta), hydrophobic moment (mu) and angle subtended by charged residues (Phi) were synthesized to define the general roles of structural motifs of cationic helical peptides for membrane activity and selectivity. The peptide sets were based on a highly hydrophobic, non-selective KLA model peptide with high antimicrobial and hemolytic activity. Variation of the investigated parameters was found to be a suitable method for modifying peptide selectivity towards either neutral or highly negatively charged lipid bilayers. Eta and mu influenced selectivity preferentially via modification of activity on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) bilayers, while the size of the polar/hydrophobic angle affected the activity against 1-palmitoyl-2-oleoylphosphatidyl-DL-glycerol (POPG). The influence of the parameters on the activity determining step was modest in both lipid systems and the activity profiles were the result of the parameters' influence on the second less pronounced permeabilization step. Thus, the activity towards POPC vesicles was determined by the high permeabilizing efficiency, however, changes in the structural parameters preferentially influenced the relatively moderate affinity. In contrast, intensive peptide accumulation via electrostatic interactions was sufficient for the destabilization of highly negatively charged POPG lipid membranes, but changes in the activity profile, as revealed by the modification of Phi, seem to be preferentially caused by variation of the low permeabilizing efficiency. The parameters proved very effective also in modifying antimicrobial and hemolytic activity. However, their influence on cell selectivity was limited. A threshold value of hydrophobicity seems to exist which restricted the activity modifying potential of mu and Phi on both lipid bilayers and cell membranes.

  15. Temperature-controlled structure and kinetics of ripple phases in one- and two-component supported lipid bilayers

    DEFF Research Database (Denmark)

    Kaasgaard, Thomas; Leidy, Chad; Crowe, J.H.


    ripples was seen. From height profiles of the AFM images, estimates of the amplitudes of the different ripple phases are reported. To elucidate the processes of ripple formation and disappearance, a ripple-phase DPPC lipid bilayer was taken through the pretransition in the cooling and the heating...... was heated from the ripple phase and into the ripple-phase/fluid-phase coexistence temperature region, the AFM images revealed that several dynamic properties of the ripple phase are important for the melting behavior of the lipid mixture. Onset of melting is observed at grain boundaries between different......Temperature-controlled atomic force microscopy (AFM) has been used to visualize and study the structure and kinetics of ripple phases in one-component dipalmitoylphosphaticlylcholine (DPPC) and two-component dimyristoylphosphatidylcholine-distearoylphosphatidylcholine (DMPC-DSPC) lipid bilayers...

  16. Compositional and structural characterization of monolayers and bilayers composed of native pulmonary surfactant from wild type mice. (United States)

    Bernardino de la Serna, Jorge; Hansen, Soren; Berzina, Zane; Simonsen, Adam C; Hannibal-Bach, Hans K; Knudsen, Jens; Ejsing, Christer S; Bagatolli, Luis A


    This work comprises a structural and dynamical study of monolayers and bilayers composed of native pulmonary surfactant from mice. Spatially resolved information was obtained using fluorescence (confocal, wide field and two photon excitation) and atomic force microscopy methods. Lipid mass spectrometry experiments were also performed in order to obtain relevant information on the lipid composition of this material. Bilayers composed of mice pulmonary surfactant showed coexistence of distinct domains at room temperature, with morphologies and lateral packing resembling the coexistence of liquid ordered (lo)/liquid disordered (ld)-like phases reported previously in porcine lung surfactant. Interestingly, the molar ratio of saturated (mostly DPPC)/non-saturated phospholipid species and cholesterol measured in the innate material corresponds with that of a DOPC/DPPC/cholesterol mixture showing lo/ld phase coexistence at a similar temperature. This suggests that at quasi-equilibrium conditions, key lipid classes in this complex biological material are still able to produce the same scaffold observed in relevant but simpler model lipid mixtures. Also, robust structural and dynamical similarities between mono- and bi-layers composed of mice pulmonary surfactant were observed when the monolayers reach a surface pressure of 30mN/m. This value is in line with theoretically predicted and recently measured surface pressures, where the monolayer-bilayer equivalence occurs in samples composed of single phospholipids. Finally, squeezed out material attached to pulmonary surfactant monolayers was observed at surface pressures near the beginning of the monolayer reversible exclusion plateau (~40mN/m). Under these conditions this material adopts elongated tubular shapes and displays ordered lateral packing as indicated by spatially resolved LAURDAN GP measurements.

  17. Probing Structural Dynamics and Topology of the KCNE1 Membrane Protein in Lipid Bilayers via Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy. (United States)

    Sahu, Indra D; Craig, Andrew F; Dunagan, Megan M; Troxel, Kaylee R; Zhang, Rongfu; Meiberg, Andrew G; Harmon, Corrinne N; McCarrick, Robert M; Kroncke, Brett M; Sanders, Charles R; Lorigan, Gary A


    KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despite the biological significance of KCNE1, the structure and dynamic properties of its physiologically relevant native membrane-bound state are not fully understood. In this study, the structural dynamics and topology of KCNE1 in bilayered lipid vesicles was investigated using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A 53-residue nitroxide EPR scan of the KCNE1 protein sequence including all 27 residues of the transmembrane domain (45-71) and 26 residues of the N- and C-termini of KCNE1 in lipid bilayered vesicles was analyzed in terms of nitroxide side-chain motion. Continuous wave-EPR spectral line shape analysis indicated the nitroxide spin label side-chains located in the KCNE1 TMD are less mobile when compared to the extracellular region of KCNE1. The EPR data also revealed that the C-terminus of KCNE1 is more mobile when compared to the N-terminus. EPR power saturation experiments were performed on 41 sites including 18 residues previously proposed to reside in the transmembrane domain (TMD) and 23 residues of the N- and C-termini to determine the topology of KCNE1 with respect to the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayers. The results indicated that the transmembrane domain is indeed buried within the membrane, spanning the width of the lipid bilayer. Power saturation data also revealed that the extracellular region of KCNE1 is solvent-exposed with some of the portions partially or weakly interacting with the membrane surface. These results are consistent with the previously published solution NMR

  18. Structural impact of cations on lipid bilayer models: nanomechanical properties by AFM-force spectroscopy. (United States)

    Redondo-Morata, Lorena; Giannotti, Marina I; Sanz, Fausto


    Atomic Force Microscopy (AFM) has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. The main strength of AFM relies on the possibility to operate in an aqueous environment on a wide variety of biological samples, from single molecules - DNA or proteins - to macromolecular assemblies like biological membranes. Understanding the effect of mechanical stress on membranes is of primary importance in biophysics, since cells are known to perform their function under a complex combination of forces. In the later years, AFM-based Force-Spectroscopy (AFM-FS) has provided a new vista on membrane mechanics in a confined area within the nanometer realm, where most of the specific molecular interactions take place. Lipid membranes are electrostatically charged entities that physiologically coexist with electrolyte solutions. Thus, specific interactions with ions are a matter of considerable interest. The distribution of ions in the solution and their interaction with the membranes are factors that substantially modify the structure and dynamics of the cell membranes. Furthermore, signaling processes are modified by the membrane capability of retaining ions. Supported Lipid Bilayers (SLBs) are a versatile tool to investigate phospholipid membranes mimicking biological surfaces. In the present contribution, we review selected experiments on the mechanical stability of SLBs as models of lipid membranes by means of AFM-FS, with special focus on the effect of cations and ionic strength in the overall nanomechanical stability.

  19. Probing the Structure of the Mechanosensitive Channel of Small Conductance in Lipid Bilayers with Pulsed Electron-Electron Double Resonance (United States)

    Ward, Richard; Pliotas, Christos; Branigan, Emma; Hacker, Christian; Rasmussen, Akiko; Hagelueken, Gregor; Booth, Ian R.; Miller, Samantha; Lucocq, John; Naismith, James H.; Schiemann, Olav


    Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating. PMID:24559986

  20. Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion

    DEFF Research Database (Denmark)

    Parisio, Giulia; Sperotto, Maria Maddalena; Ferrarini, Alberta


    The transverse motion of molecules from one leaflet to the other of a lipid bilayer, or flip-flop, represents a putative mechanism for their transmembrane transport and may contribute to the asymmetric distribution of components in biomembranes. However, a clear understanding of this process is s...

  1. Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage (United States)

    Steinhauser, Martin O.; Schindler, Tanja


    We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction h_c of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli K_A and bending stiffnesses κ _B for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol-gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity h_c of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self

  2. Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage (United States)

    Steinhauser, Martin O.; Schindler, Tanja


    We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction h_c of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli K_A and bending stiffnesses κ_B for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol-gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity h_c of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self

  3. Label-Free Electrochemiluminescence Aptasensor for 2,4,6-Trinitrotoluene Based on Bilayer Structure of Luminescence Functionalized Graphene Hybrids. (United States)

    Li, Guixin; Yu, Xiuxia; Liu, Danqing; Liu, Xiaoying; Li, Fang; Cui, Hua


    The electrochemiluminescence (ECL) behavior of N-(aminobutyl)-N-(ethylisoluminol)/hemin dual-functionalized graphene hybrids (A-H-GNs) and luminol-functionalized silver/graphene oxide composite (luminol-AgNPs-GO) was investigated under cyclic voltammetry and pulse potential. It was found that A-H-GNs and luminol-AgNPs-GO exhibited excellent ECL activity. On this basis, a label-free ECL aptasensor for 2,4,6-trinitrotoluene (TNT) detection was developed based on bilayer structure of luminescence functionalized graphene hybrids consisting of A-H-GNs and luminol-AgNPs-GO. First, positively charged chitosan-coated A-H-GNs were modified on the surface of indium-doped tin oxide electrode by simple dripping and drying in the air; after that, the modified electrode was immersed in negatively charged luminol-AgNPs-GO modified with aptamer (apta-biotin-SA-luminol-AgNPs-GO) to form apta-biotin-SA-luminol-AgNPs-GO/CS-A-H-GNs/ITO electrode (i.e., aptasensor) by electrostatic interaction. In the presence of TNT, a remarkable decrease in ECL signals was observed due to the formation of aptamer-TNT complex. TNT could be detected based on the inhibition effect. The aptasensor exhibits a wide dynamic range from 1.0 × 10(-12) to 1.0 × 10(-9) g/mL, with a low detection limit of 6.3 × 10(-13) g/mL for the determination of TNT, which is superior to most previously reported bioassays for TNT. Moreover, the proposed aptasensor has been successfully applied to the detection of TNT in environmental water. It is sensitive, selective, and simple, avoiding complicated labeling and purification procedures. Due to the wide target recognition range of aptamer, this strategy provides a promising way to develop new aptasensor for other analytes.

  4. Interplay of curvature-induced micro- and nanodomain structures in multicomponent lipid bilayers

    CERN Document Server

    Brodbek, Leonie


    We discuss different mechanisms for curvature-induced domain formation in multicomponent lipid membranes and present a theoretical model that allows us to study the interplay between the domains. The model represents the membrane by two coupled monolayers, which each carry an additional order parameter field describing the local lipid composition. The spontaneous curvature of each monolayer is coupled to the local composition, moreover, the lipid compositions on opposing monolayers are coupled to each other. Using this model, we calculate the phase behavior of the bilayer in mean-field approximation. The resulting phase diagrams are surprisingly complex and reveal a variety of phases and phase transitions, including a decorated microdomain phase where nanodomains are aligned along the microdomain boundaries. Our results suggest that external membrane tension can be used to control the lateral organization of nanodomains (which might be associated with lipid "rafts") in a multicomponent lipid bilayer.

  5. Bi-layer structure of counterstreaming energetic electron fluxes: a diagnostic tool of the acceleration mechanism in the Earth's magnetotail

    Directory of Open Access Journals (Sweden)

    D. V. Sarafopoulos


    Full Text Available For the first time we identify a bi-layer structure of energetic electron fluxes in the Earth's magnetotail and establish (using datasets mainly obtained by the Geotail Energetic Particles and Ion Composition (EPIC/ICS instrument that it actually provides strong evidence for a purely spatial structure. Each bi-layer event is composed of two distinct layers with counterstreaming energetic electron fluxes, parallel and antiparallel to the local ambient magnetic field lines; in particular, the tailward directed fluxes always occur in a region adjacent to the lobes. Adopting the X-line as a standard reconnection model, we determine the occurrence of bi-layer events relatively to the neutral point, in the substorm frame; four (out of the shown seven events are observed earthward and three tailward, a result implying that four events probably occurred with the substorm's local recovery phase. We discuss the bi-layer events in terms of the X-line model; they add more constraints for any candidate electron acceleration mechanism. It should be stressed that until this time, none proposed electron acceleration mechanism has discussed or predicted these layered structures with all their properties. Then we discuss the bi-layer events in terms of the much promising "akis model", as introduced by Sarafopoulos (2008. The akis magnetic field topology is embedded in a thinned plasma sheet and is potentially causing charge separation. We assume that as the Rc curvature radius of the magnetic field line tends to become equal to the ion gyroradius rg, then the ions become non-adiabatic. At the limit Rc=rg the demagnetization process is also under way and the frozen-in magnetic field condition is violated by strong wave turbulence; hence, the ion particles in this geometry are stochastically scattered. In addition, ion diffusion probably takes place across the magnetic field, since an

  6. Off-easy-plane antiferromagnetic spin canting in coupled FePt/NiO bilayer structure with perpendicular exchange bias (United States)

    Gao, Tenghua; Itokawa, Nobuhide; Wang, Jian; Yu, Youxing; Harumoto, Takashi; Nakamura, Yoshio; Shi, Ji


    We report on the investigation of perpendicular exchange bias in FePt (001 ) /NiO (1 ¯1 ¯1 ) orthogonal exchange couple with FePt partially L 10 ordered. From initial magnetization curve measurement and magnetic domain imaging, we find that, for the as-grown bilayer structure, the FePt layer experiences a small-angle magnetization rotation when it is magnetized near to saturation in film normal direction. After field cooling, the bilayer structure shows a significant enhancement of perpendicular magnetic anisotropy, indicating the field mediated coupling between the spins across the FePt/NiO interface. According to Koon's theoretical calculation on the basis of lowest energy ferromagnetic/antiferromagnetic coupling configuration for compensated spins at antiferromagnetic side, we consider slightly slanted Ni spins at the interface off the (1 ¯1 ¯1 ) easy plane can stabilize the spin coupling between FePt and NiO and result in the observed exchange bias in this paper. This consideration was further confirmed by stripe domain width calculation.

  7. TiB{sub 2}/TiSi{sub 2} bilayer fabrication by various techniques: Structure and contact properties

    Energy Technology Data Exchange (ETDEWEB)

    Pelleg, Joshua [Department of Materials Engineering, Ben Gurion University of the Negev, Ben Gurion Str. 84105, Beer Sheva (Israel)]. E-mail:; Sade, G. [Department of Materials Engineering, Ben Gurion University of the Negev, Ben Gurion Str. 84105, Beer Sheva (Israel)


    TiB{sub 2}/TiSi{sub 2} films were produced by several techniques in an attempt to evaluate the most appropriate method to fabricate this system. Analysis by X-ray diffraction, Auger electron spectroscopy, transmission and high-resolution transmission electron microscopy indicate that the best method to obtain the above system is by sequential cosputtering of the layers without exposure to air between the two cosputtering sequences. Post-deposition annealing was performed to obtain a low resistive bilayer. Schottky diodes fabricated by this method provided an average barrier height of {approx}0.68 V with an ideality factor in the range of 1.0-1.04 (excluding the as-deposited specimen). In specimens fabricated by silicidation of TiB{sub 2}/Ti films formation of TiSi{sub 2} was Ti thickness dependent [G. Sade, Ph.D. Thesis, Ben Gurion University of the Negev, Beer Sheva, Israel, 1999]. Small amounts of Ti{sub 5}Si{sub 3} were observed at 1123 K. The attempts to obtain a TiB{sub 2}/TiSi{sub 2} bilayer from (Ti+B) enriched with Ti at 1073 K resulted in the formation of small amounts of Ti{sub 5}Si{sub 3}, and some crystallization of the amorphous TiB{sub 2} also occurred. Diodes fabricated by this technique showed Ohmic rather than rectifying character. The shift from rectifying to Ohmic behavior is the result of B out-diffusion to the Si and the consequent change of the substrate from an n- to a p-type Si. The results place the Fermi level of TiB{sub 2} about 0.9 eV below the silicon conduction band. A remedy to this problem could result in a challenging method of fabricating a TiB{sub 2}/TiSi{sub 2} bilayer structure in a one-step process.

  8. ATR-IR spectroscopic study of the structural changes in the hydrophobic region of ICPAN/DPPC bilayers (United States)

    Cieślik-Boczula, Katarzyna; Czarnik-Matusewicz, Bogusława; Perevozkina, Margarita; Filarowski, Aleksander; Boens, Noël; De Borggraeve, Wim M.; Koll, Aleksander


    Structural changes in the hydrophobic region in the self-aggregates of the long hydrocarbon chain ICPAN ((( N, N-dimethyl- N-octyl-2-ammonioethyl)-3-(3,5-di- tert-butyl-4-hydroxyphenyl)propionate bromide)) homologues and their interaction with a DPPC (dipalmitoylophosphatidylcholine) bilayer were the subject of detailed investigation using ATR infrared spectroscopy. On the base of analysis of the bands assigned to CH 2 stretching, scissoring, and rocking and CH wagging vibrations it was revealed that the hydrophobic parts ICPANs adopt a gauche-rich disordering structure. Moreover, it was shown that the micellar- or lamellar-like character of these structures depends on the hydrocarbon chain length. Results obtained from the ICPAN/DPPC mixtures indicate an increase in the conformational disorder in hydrophobic part compare to pure DPPC film. This effect depends on the length of the aliphatic chain of ICPAN homologues and on the relative concentrations of DPPC and ICPAN.

  9. Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

    Directory of Open Access Journals (Sweden)

    Sara Y. Cheng


    Full Text Available This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.

  10. Mechanism of unassisted ion transport across membrane bilayers (United States)

    Wilson, M. A.; Pohorille, A.


    To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

  11. Influence of an Fe cap layer on the structural and magnetic properties of Fe49Pt51/Fe bi-layers

    Institute of Scientific and Technical Information of China (English)

    Duan Chao-Yang; Ma Bin; Wei Fu-Lin; Zhang zong-Zhi; Jin Qing-Yuan


    The influences of an Fe cap layer on the structural and magnetic properties of FePt/Fe bi-layers are investigated.Compared with single FePt alloy films, a thin Fe layer can affect the crystalline orientation and improve the chemical ordering of L10 FePt films. Moreover, the coercivity increases when a thin Fe layer covers the FePt layer. Beyond a critical thickness, however, the Fe cover layer quickens the magnetization reversal of Fe49Pt51/Fe bi-layers by their exchange coupling.

  12. From lanosterol to cholesterol: Structural evolution and differential effects on lipid bilayers

    DEFF Research Database (Denmark)

    Miao, Ling; Nielsen, Morten; Thewalt, J.;


    Cholesterol is an important molecular component of the plasma membranes of mammalian cells. Its precursor in the sterol biosynthetic pathway, lanosterol, has been argued by Konrad Bloch (Bloch, K. 1965. Science. 150:19-28; 1983. CRC Crit Rev. Biochem. 14:47-92; 1994. Blonds in Venetian Paintings......-bilayer membranes. By using deuterium NMR spectroscopy on multilamellar lipid-sterol systems in combination with Monte Carlo simulations of microscopic models of lipid-sterol interactions, we demonstrate that the evolution in the molecular chemistry from lanosterol to cholesterol is manifested in the model lipid......-sterol membranes by an increase in the ability of the sterols to promote and stabilize a particular membrane phase, the liquid-ordered phase, and to induce collective order in the acyl-chain conformations of lipid molecules. We also discuss the biological relevance of our results, in particular in the context...

  13. Inter-Layer Energy Transfer through Wetting-Layer States in Bi-layer InGaAs/GaAs Quantum-Dot Structures with Thick Barriers

    DEFF Research Database (Denmark)

    Xu, Zhang-Cheng; Zhang, Ya-Ting; Hvam, Jørn Märcher


    The inter-layer energy transfer in a bi-layer InGaAs/GaAs quantum dot structure with a thick GaAs barrier is studied using temperature-dependent photoluminescence. The abnormal enhancement of the photoluminescence of the QDs in the layer with a larger amount of coverage at 110K is observed, which...

  14. Enhanced resistive switching and multilevel behavior in bilayered HfAlO/HfAlO{sub x} structures for non-volatile memory applications

    Energy Technology Data Exchange (ETDEWEB)

    Faita, F. L., E-mail: [Centre of Physics, University of Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Departamento de Física, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, SC (Brazil); Silva, J. P. B., E-mail: [Centre of Physics, University of Minho, Campus de Gualtar, 4710-057 Braga (Portugal); IFIMUP and IN-Institute of Nanoscience and Nanotechnology, Departamento de Física e Astronomia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto (Portugal); Pereira, M.; Gomes, M. J. M. [Centre of Physics, University of Minho, Campus de Gualtar, 4710-057 Braga (Portugal)


    In this work, hafnium aluminum oxide (HfAlO) thin films were deposited by ion beam sputtering deposition technique on Si substrate. The presence of oxygen vacancies in the HfAlO{sub x} layer deposited in oxygen deficient environment is evidenced from the photoluminescence spectra. Furthermore, HfAlO(oxygen rich)/HfAlO{sub x}(oxygen poor) bilayer structures exhibit multilevel resistive switching (RS), and the switching ratio becomes more prominent with increasing the HfAlO layer thickness. The bilayer structure with HfAlO/HfAlO{sub x} thickness of 30/40 nm displays the enhanced multilevel resistive switching characteristics, where the high resistance state/intermediate resistance state (IRS) and IRS/low resistance state resistance ratios are ≈10{sup 2} and ≈5 × 10{sup 5}, respectively. The switching mechanisms in the bilayer structures were investigated by the temperature dependence of the three resistance states. This study revealed that the multilevel RS is attributed to the coupling of ionic conduction and the metallic conduction, being the first associated to the formation and rupture of conductive filaments related to oxygen vacancies and the second with the formation of a metallic filament. Moreover, the bilayer structures exhibit good endurance and stability in time.

  15. Structural determination of argon trimer

    Directory of Open Access Journals (Sweden)

    Xiguo Xie


    Full Text Available Rare gas clusters are model systems to investigate structural properties at finite size. However, their structures are difficult to be determined with available experimental techniques because of the strong coupling between the vibration and the rotation. Here we experimentally investigated multiple ionization and fragmentation dynamics of argon trimer by ultrashort intense laser fields and reconstructed their structures with Coulomb explosion technique. The measured structure distribution was compared with our finite-temperature ab initio calculations and the discrepancy was discussed. The present study provides a guidance for the development of theoretical methods for exploring the geometric structure of rare gas clusters.

  16. Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

    DEFF Research Database (Denmark)

    Murtola, Teemu; Karttunen, Mikko; Vattulainen, Ilpo


    We present a two-dimensional coarse-grained (CG) model for a lipid membrane composed of phospholipids and cholesterol. The effective CG interactions are determined using radial distribution functions (RDFs) from atom-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique...... in the presence of internal states, in general, and present a modified IMC method for their inclusion. The new model agrees with the original models on large-scale structural features such as density fluctuations in pure dipalmitoylphosphocholine and cholesterol domain formation at intermediate concentrations...... and also indicates that ordered and disordered domains form at all cholesterol concentrations, even if the global density remains uniform. The inclusion of ordering also improves transferability of the interactions between different concentrations, but does not eliminate transferability problems completely...

  17. Determinants and Polynomial Root Structure (United States)

    De Pillis, L. G.


    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  18. Effects of Polyhexamethylene Biguanide and Polyquaternium-1 on Phospholipid Bilayer Structure and Dynamics. (United States)

    Horner, Ian J; Kraut, Nadine D; Hurst, Jerod J; Rook, Alyssa M; Collado, Crystal M; Atilla-Gokcumen, G Ekin; Maziarz, E Peter; Liu, X Michael; Merchea, Mohinder M; Bright, Frank V


    Multipurpose solutions (MPS) are a single solution that functions to simultaneously rinse, disinfect, clean, and store soft contact lenses. Several commercial MPS products contain polyhexamethylene biguanide (PHMB) and/or polyquaternium-1 (PQ-1) as antimicrobial agents. In this paper we have created an in vitro small unilamellar vesicle (SUV) model of the corneal epithelial surface, and we have assessed the interactions of PHMB and PQ-1 with several model biomembranes by using fluorescence spectroscopy, dynamic light scattering (DLS), and liquid chromatography-mass spectrometry (LC-MS). Steady-state and time-resolved fluorescence were used to assess the membrane acyl chain and polar headgroup region local microenvironment as a function of added PHMB or PQ-1. DLS was used to detect and quantify SUV aggregation induced by PHMB and PQ-1. LC-MS was used to determine the liposomal composition from any precipitated materials in comparison to the as-prepared SUVs. The results are consistent with PHMB adsorbing onto and PQ-1 intercalating into the biomembrane structure. The differences between the two interaction mechanisms have substantial impacts on the biomembrane dynamics and stability.

  19. Study of the influence of semiconductor material parameters on acoustic wave propagation modes in GaSb/AlSb bi-layered structures by Legendre polynomial method

    Energy Technology Data Exchange (ETDEWEB)

    Othmani, Cherif, E-mail:; Takali, Farid; Njeh, Anouar; Ben Ghozlen, Mohamed Hédi


    The propagation of Rayleigh–Lamb waves in bi-layered structures is studied. For this purpose, an extension of the Legendre polynomial (LP) method is proposed to formulate the acoustic wave equation in the bi-layered structures induced by thin film Gallium Antimonide (GaSb) and with Aluminum Antimonide (AlSb) substrate in moderate thickness. Acoustic modes propagating along a bi-layer plate are shown to be quite different than classical Lamb modes, contrary to most of the multilayered structures. The validation of the LP method is illustrated by a comparison between the associated numerical results and those obtained using the ordinary differential equation (ODE) method. The convergency of the LP method is discussed through a numerical example. Moreover, the influences of thin film GaSb parameters on the characteristics Rayleigh–Lamb waves propagation has been studied in detail. Finally, the advantages of the Legendre polynomial (LP) method to analyze the multilayered structures are described. All the developments performed in this work were implemented in Matlab software.

  20. Study of the influence of semiconductor material parameters on acoustic wave propagation modes in GaSb/AlSb bi-layered structures by Legendre polynomial method (United States)

    Othmani, Cherif; Takali, Farid; Njeh, Anouar; Ben Ghozlen, Mohamed Hédi


    The propagation of Rayleigh-Lamb waves in bi-layered structures is studied. For this purpose, an extension of the Legendre polynomial (LP) method is proposed to formulate the acoustic wave equation in the bi-layered structures induced by thin film Gallium Antimonide (GaSb) and with Aluminum Antimonide (AlSb) substrate in moderate thickness. Acoustic modes propagating along a bi-layer plate are shown to be quite different than classical Lamb modes, contrary to most of the multilayered structures. The validation of the LP method is illustrated by a comparison between the associated numerical results and those obtained using the ordinary differential equation (ODE) method. The convergency of the LP method is discussed through a numerical example. Moreover, the influences of thin film GaSb parameters on the characteristics Rayleigh-Lamb waves propagation has been studied in detail. Finally, the advantages of the Legendre polynomial (LP) method to analyze the multilayered structures are described. All the developments performed in this work were implemented in Matlab software.

  1. Effect of cholesterol on behavior of 5-fluorouracil (5-FU) in a DMPC lipid bilayer, a molecular dynamics study. (United States)

    Khajeh, Aboozar; Modarress, Hamid


    In this work, molecular dynamics (MD) simulations were performed to investigate the effects of cholesterol on the interaction between the hydrophilic anticancer drug, 5-FU, and fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer. Several structural and dynamical parameters of DMPC bilayers with varying amounts of cholesterol (0, 25, and 50mol%) in the presence and absence of drug molecules were calculated. Moreover, the free energy barriers for translocation of one 5-FU molecule from water to the lipid bilayer were determined by using the potential of mean force (PMF). PMF studies indicated that the location of the maximum free energy barrier was in the hydrophobic middle region of bilayer, while the minimums of the barrier were located at the hydrophilic part of bilayer at the interface with water. The minimum and maximum of the free energy profiles were independent of cholesterol concentration and suggested that the drug molecules 5-FU were accumulated in the vicinity of the polar head group of lipid bilayers. Moreover, the results showed that with increasing cholesterol concentration in the bilayer, the free energy barrier for translocation of 5-FU across the bilayer also increases which can be attributed to the condensing effect of the cholesterol on the bilayer.

  2. Magnetism and electronic structure of (001)- and (111)-oriented LaTiO{sub 3} bilayers sandwiched in LaScO{sub 3} barriers

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Yakui; Dong, Shuai, E-mail: [Department of Physics and Jiangsu Key Laboratory of Advanced Metallic Materials, Southeast University, Nanjing 211189 (China)


    In this study, the magnetism and electronic structure of LaTiO{sub 3} bilayers along both the (001) and (111) orientations are calculated using the density functional theory. The band insulator LaScO{sub 3} is chosen as the barrier layer and substrate to obtain the isolating LaTiO{sub 3} bilayer. For both the (001)- and (111)-oriented cases, LaTiO{sub 3} demonstrates the G-type antiferromagnetism as the ground state, similar to the bulk material. However, the electronic structure is significantly changed. The occupied bands of Ti are much narrower in the (111) case, giving a nearly flat band. As a result, the exchange coupling between nearest-neighbor Ti ions is reformed in these superlattices, which will affect the Néel temperature significantly.

  3. Inter-Layer Energy Transfer through Wetting-Layer States in Bi-layer InGaAs/GaAs Quantum-Dot Structures with Thick Barriers

    Institute of Scientific and Technical Information of China (English)

    XU Zhang-Cheng; ZHANG Ya-Ting; J(φ)rn M. Hvam; Yoshiji Horikoshi


    The inter-layer energy transfer in a bi-layer InGaAs/GaAs quantum dot structure with a thick GaAs barrier is studied using temperature-dependent photoluminescence. The abnormal enhancement of the photoluminescence of the QDs in the layer with a larger amount of coverage at 110K is observed, which can be explained by considering the resonant F(o)rster energy transfer between the wetting layer states at elevated temperatures.

  4. The influence of oscillating electromagnetic fields on membrane structure and function: Synthetic liposome and natural membrane bilayer systems with direct application to the controlled delivery of chemical agents

    Energy Technology Data Exchange (ETDEWEB)

    Liburdy, R.P.; de Manincor, D.; Fingado, B.


    Investigations have been conducted to determine if an imposed electromagnetic field can influence membrane transport, and ion and drug permeability in both synthetic and natural cell membrane systems. Microwave fields enhance accumulation of sodium in the lymphocyte and induce protein shedding at Tc. Microwaves also trigger membrane permeability of liposome systems under specific field exposure conditions. Sensitivity varies in a defined way in bilayers displaying a membrane structural phase transition temperature, Tc; maximal release was observed at or near Tc. Significantly, liposome systems without a membrane phase transition were also found to experience permeability increases but, in contrast, this response was temperature independent. The above results indicate that field-enhanced drug release occurs in liposome vesicles that possess a Tc as well as non-Tc liposomes. Additional studies extend non-Tc liposome responses to the in vivo case in which microwaves trigger Gentamicin release from a liposome depot'' placed subcutaneously in the rat hind leg. In addition, evidence is provided that cell surface sequestered liposomes can be triggered by microwave fields to release drugs directly into target cells. 24 refs., 6 figs.

  5. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers. (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep


    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  6. Structure and homogeneity of pseudo-physiological phospholipid bilayers and their deposition characteristics on carboxylic acid terminated self-assembled monolayers. (United States)

    Mechler, Adam; Praporski, Slavica; Piantavigna, Stefania; Heaton, Steven M; Hall, Kristopher N; Aguilar, Marie-Isabel; Martin, Lisandra L


    Supported phospholipid bilayers are frequently used to establish a pseudo-physiological environment required for the study of protein function or the design of enzyme-based biosensors and biocatalytic reactors. These membranes are deposited from bilayer vesicles (liposomes) that rupture and fuse into a planar membrane upon adhesion to a surface. However, the morphology and homogeneity of the resulting layer is affected by the characteristics of the precursor liposome suspension and the substrate. Here we show that two distinct liposome populations contribute to membrane formation--equilibrium liposomes and small unilamellar vesicles. Liposome deposition onto carboxylic acid terminated self-assembled monolayers resulted in planar mono- and multilayer, vesicular and composite membranes, as a function of liposome size and composition. Quartz crystal microbalance data provided estimates for layer thicknesses and sheer moduli and were used for classification of the final structure. Finally, atomic force microscopy data illustrated the inherently inhomogeneous and dynamic nature of these membranes.

  7. Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order. (United States)

    Chiantia, Salvatore; London, Erwin


    A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.

  8. Particle trapping and impedance measurement using bilayer electrodes integrated with microcavity structure (United States)

    Chen, Guan-Ting; Liu, Chia-Feng; Jang, Ling-Sheng; Li, Shun-Lai; Wang, Min-Haw


    Traditional planar electrodes for single-particle impedance measurement have difficulty in trapping and positioning particles. This paper proposes a microfluidic device for single-particle trapping and impedance measurement with a microcavity configuration. A carbon dioxide (CO2) laser technique was used to fabricate the microcavity structure, which can capture 15 µm diameter particles without requiring additional trapping structures. The measurement electrodes on both sides of the microcavity were fabricated using electroplating and deposition techniques. The advantages of the microcavity structure and electrodes are discussed. The bottom electrode spreads into the microcavity to increase measurement sensitivity and shrink the exit aperture to around 10 µm for particle trapping. The experimental results show that the device successfully captured particles and distinguished the impedance of a particle from that of phosphate-buffered saline solution.

  9. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)


    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  10. Structure and electronic properties of bilayer graphene functionalized with half-sandwiched transition metal-cyclopentadienyl complexes. (United States)

    Yao, Xiaojing; Zhang, Xiuyun; Ye, Xiaoshan; Wang, Jinlan


    Tuning the electronic and magnetic properties of graphene is a crucial problem in the design of practical on-off electronic devices. Using density functional theory calculations, we explore the electronic and magnetic properties of bilayer graphene functionalized by cyclopentadienyl (Cp = cyclopentadienyl, C5H5) based half-sandwich ligands, CpTM (TM = Sc-Ni). It is found that the adsorption of CpTM ligands can introduce high magnetic moments and open the band gap of bilayer graphene, due to the electron doping as well as the asymmetric charge distribution between two graphene layers. Furthermore, the p-n doping of bilayer graphene by co-binding F/NO2 and CpTM on two external sides of BLG can further widen the band gap up to 366.1 meV. This study proposes an effective way to the modulation of the electronic and magnetic properties of graphene.

  11. Simulations of a Membrane-Anchored Peptide: Structure, Dynamics, and Influence on Bilayer Properties

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Mouritsen, O.G.; Peters, Günther H.J.


    A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at ...

  12. Microfluidic anodization of aluminum films for the fabrication of nanoporous lipid bilayer support structures



    Solid state nanoporous membranes show great potential as support structures for biointerfaces. In this paper, we present a technique for fabricating nanoporous alumina membranes under constant-flow conditions in a microfluidic environment. This approach allows the direct integration of the fabrication process into a microfluidic setup for performing biological experiments without the need to transfer the brittle nanoporous material. We demonstrate this technique by using the same microfluidic...

  13. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    DEFF Research Database (Denmark)

    Rønnest, A. K.; Peters, Günther H.J.; Hansen, Flemming Yssing;


    the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic...... compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have...... potential within phospholipid membranes imply an enormous electric field of 108-109 V m-1, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential...

  14. Oxidation of Membrane Curvature-Regulating Phosphatidylethanolamine Lipid Results in Formation of Bilayer and Cubic Structures. (United States)

    Sankhagowit, Shalene; Lee, Ernest Y; Wong, Gerard C L; Malmstadt, Noah


    Oxidation is associated with conditions related to chronic inflammations and aging. Cubic structures have been observed in the smooth endoplasmic reticulum and mitochondrial membranes of cells under oxidative stress (e.g., tumor cells and virus-infected cells). It has been previously suspected that oxidation can result in the rearrangement of lipids from a fluid lamellar phase to a cubic structure in organelles containing membranes enriched with amphiphiles that have nonzero intrinsic curvature, such as phosphatidylethanolamine (PE) and cardiolipin. This study focuses on the oxidation of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), a lipid that natively forms an inverted hexagonal phase at physiological conditions. The oxidized samples contain an approximately 3:2 molar ratio of nonoxidized to oxidized DOPE. Optical microscopy images collected during the hydration of this mixture from a dried film suggest that the system evolves into a coexistence of a stable fluid lamellar phase and transient square lattice structures with unit cell sizes of 500-600 nm. Small-angle X-ray scattering of the same lipid mixture yielded a body-centered Im3m cubic phase with the lattice parameter of 14.04 nm. On average, the effective packing parameter of the oxidized DOPE species was estimated to be 0.657 ± 0.069 (standard deviation). This suggests that the oxidation of PE leads to a group of species with inverted molecular intrinsic curvature. Oxidation can create amphiphilic subpopulations that potently impact the integrity of the membrane, since negative Gaussian curvature intrinsic to cubic phases can enable membrane destabilization processes.

  15. Effect of biocompatible polymers on the structural integrity of lipid bilayers under external stimuli (United States)

    Wang, Jia-Yu; Kausik, Ravinath; Chen, Chi-Yuan; Han, Song-I.; Marks, Jeremy; Lee, Ka Yee


    Cell membrane dysfunction due to loss of structural integrity is the pathology of tissue death in trauma and common diseases. It is now established that certain biocompatible polymers, such as Poloxamer 188, Poloxamine 1107 and polyethylene glycol (PEG), are effective in sealing of injured cell membranes, and able to prevent acute necrosis. Despite these broad applications of these polymers for human health, the fundamental mechanisms by which these polymers interact with cell membranes are still under debate. Here, the effects of a group of biocompatible polymers on phospholipid membrane integrity under osmotic and oxidative stress were explored using giant unilamellar vesicles as model cell membranes. Our results suggest that the adsorption of the polymers on the membrane surface is responsible for the cell membrane resealing process due to its capability of slowing down the surface hydration dynamics.

  16. Effects of annealing time on the structure, morphology, and stress of gold-chromium bilayer film (United States)

    Zhang, Hong; Jin, Yun-Xia; Wang, Hu; Kong, Fang-Yu; Huang, Hao-Peng; Cui, Yun


    In this work, a 200-nm-thick gold film with a 10-nm-thick chromium layer used as an adhesive layer is fabricated on fused silica by the electron beam evaporation method. The effects of annealing time at 300 °C on the structure, morphology and stress of the film are studied. We find that chromium could diffuse to the surface of the film by formatting a solid solution with gold during annealing. Meanwhile, chromium is oxidized on the surface and diffused downward along the grain grooves in the gold film. The various operant mechanisms that change the residual stresses of gold films for different annealing times are discussed. Project supported by the National Natural Science Foundation of China (Grant No. 61405225).

  17. Molecular simulations of lipid systems: Edge stability and structure in pure and mixed bilayers (United States)

    Jiang, Yong


    Understanding the structural, mechanical and dynamical properties of lipid self-assembled systems is fundamental to understand the behavior of the cell membrane. This thesis has investigated the equilibrium properties of lipid systems with edge defects through various molecular simulation techniques. The overall goal of this study is to understand the free energy terms of the edges and to develop efficient methods to sample equilibrium distributions of mixed-lipid systems. In the first main part of my thesis, an atomistic molecular model is used to study lipid ribbon which has two edges on both sides. Details of the edge structures, such as area per lipid and tail torsional statistics are presented. Line tension, calculated from pressure tensor in MD simulation has good agreement with result from other sources. To further investigate edge properties on a longer timescale and larger length scale, we have applied a coarse-grained forcefield on mixed lipid systems and try to interpret the edge fluctuations in terms of free energy parameters such as line tension and bending modulus. We have identified two regimes with quite different edge behavior: a high line tension regime and a low line tension regime. The last part of this thesis focuses on a hybrid Molecular dynamics and Configurational-bias Monte Carlo (MCMD) simulation method in which molecules can change their type by growing and shrinking the terminal acyl united carbon atoms. A two-step extension of the MCMD method has been developed to allow for a larger difference in the components' tail lengths. Results agreed well with previous one-step mutation results for a mixture with a length difference of four carbons. The current method can efficiently sample mixtures with a length difference of eight carbons, with a small portion of lipids of intermediate tail length. Preliminary results are obtained for "bicelle"-type (DMPC/DHPC) ribbons.

  18. Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails. (United States)

    Paloncýová, Markéta; Vávrová, Kateřina; Sovová, Žofie; DeVane, Russell; Otyepka, Michal; Berka, Karel


    Ceramides are indispensable constituents of the stratum corneum (SC), the uppermost impermeable layer of human skin. Ceramides with shorter (four- to eight-carbon acyl chains) fatty acid chains increase skin and model membrane permeability, while further shortening of the chain leads to increased resistance to penetration almost as good as that of ceramides from healthy skin (24 carbons long on average). Here we address the extent to which the atomistic CHARMM36 and coarse-grain MARTINI molecular dynamics (MD) simulations reflect the skin permeability data. As a result, we observed the same bell-shaped permeability trend for water that was observed in the skin and multilayer membrane experiments for model compounds. We showed that the enhanced permeability of the short ceramides is mainly caused by the disturbance of their headgroup conformation because of their inability to accommodate the shorter lipid acyl chain into a typical hairpin conformation, which further led to their destabilization and phase separation. As MD simulations described well delicate structural features of SC membranes, they seem to be suitable for further studies of the SC superstructure, including the development of skin penetration enhancers for transdermal drug delivery and skin toxicity risk assessment studies.

  19. Origin of spontaneous exchange bias in Co/NiMn bilayer structure (United States)

    Akbulut, A.; Akbulut, S.; Yildiz, F.


    Spontaneous exchange bias (EB) is reported for as deposited Si/Pt(tPt)/Ni45Mn55(tAFM/Co(tFM)/Pt(30 Å) thin film system without requiring any post annealing, deposition with field or field cooling procedures. Magnetic properties of this system were investigated with respect to thicknesses of buffer Pt layer (tPt), antiferromagnetic NiMn layer (tAFM) and ferromagnetic Co layer (tFM). Exchange coupling between NiMn and Co layers enhanced considerably by increasing tPt. In order to observe a spontaneous EB in the system, Pt buffer layer must be thicker than a certain thickness, and NiMn layer must be grown directly on the buffer layer. On the other hand, significant increments in the coercive fields (HC) were reported for thinner Pt buffer layers. The thickness ranges for Co and NiMn layers were also determined to obtain spontaneous EB. This spontaneous EB is discussed to be a result of NiMn (111) texture which is induced by Pt buffer layer. Greater EB fields (HEB) are measured for the samples in the negative field direction by the effect of annealing and field cooling (from 400 K to 300 K at 2 kOe).

  20. The structural role of cholesterol in cell membranes: from condensed bilayers to lipid rafts. (United States)

    Krause, Martin R; Regen, Steven L


    CONSPECTUS: Defining the two-dimensional structure of cell membranes represents one of the most daunting challenges currently facing chemists, biochemists, and biophysicists. In particular, the time-averaged lateral organization of the lipids and proteins that make up these natural enclosures has yet to be established. As the classic Singer-Nicolson model of cell membranes has evolved over the past 40 years, special attention has focused on the structural role played by cholesterol, a key component that represents ca. 30% of the total lipids that are present. Despite extensive studies with model membranes, two fundamental issues have remained a mystery: (i) the mechanism by which cholesterol condenses low-melting lipids by uncoiling their acyl chains and (ii) the thermodynamics of the interaction between cholesterol and high- and low-melting lipids. The latter bears directly on one of the most popular notions in modern cell biology, that is, the lipid raft hypothesis, whereby cholesterol is thought to combine with high-melting lipids to form "lipid rafts" that float in a "sea" of low-melting lipids. In this Account, we first describe a chemical approach that we have developed in our laboratories that has allowed us to quantify the interactions between exchangeable mimics of cholesterol and low- and high-melting lipids in model membranes. In essence, this "nearest-neighbor recognition" (NNR) method involves the synthesis of dimeric forms of these lipids that contain a disulfide moiety as a linker. By means of thiolate-disulfide interchange reactions, equilibrium mixtures of dimers are then formed. These exchange reactions are initiated either by adding dithiothreitol to a liposomal dispersion to generate a small amount of thiol monomer or by including a small amount of thiol monomer in the liposomes at pH 5.0 and then raising the pH to 7.4. We then show how such NNR measurements have allowed us to distinguish between two very different mechanisms that have been

  1. Structural determinants of glomerular permeability. (United States)

    Deen, W M; Lazzara, M J; Myers, B D


    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  2. Electrostatics of cell membrane recognition: structure and activity of neutral and cationic rigid push-pull rods in isoelectric, anionic, and polarized lipid bilayer membranes. (United States)

    Sakai, N; Gerard, D; Matile, S


    Design, synthesis, and structural and functional studies of rigid-rod ionophores of different axial electrostatic asymmetry are reported. The employed design strategy emphasized presence of (a) a rigid scaffold to minimize the conformational complexity, (b) a unimolecular ion-conducting pathway to minimize the suprastructural complexity and monitor the function, (c) an extended fluorophore to monitor structure, (d) variable axial rod dipole, and (e) variable terminal charges to create axial asymmetry. Studies in isoelectric, anionic, and polarized bilayer membranes confirmed a general increase in activity of uncharged rigid push-pull rods in polarized bilayers. The similarly increased activity of cationic rigid push-pull rods with an electrostatic asymmetry comparable to that of alpha-helical bee toxin melittin (positive charge near negative axial dipole terminus) is shown by fluorescence-depth quenching experiments to originate from the stabilization of transmembrane rod orientation by the membrane potential. The reduced activity of rigid push-pull rods having an electrostatic asymmetry comparable to that in alpha-helical natural antibiotics (a positive charge near the positive axial dipole terminus) is shown by structural studies to originate from rod "ejection" by membrane potentials comparable to that found in mammalian plasma membranes. This structural evidence for cell membrane recognition by asymmetric rods is unprecedented and of possible practical importance with regard to antibiotic resistance.

  3. Analysis of the sintering stresses and shape distortion produced in co-firing of CGO-LSM/CGO bi-layer porous structures

    DEFF Research Database (Denmark)

    Ni, De Wei; Esposito, Vincenzo; Schmidt, Cristine Grings;

    electrochemical flue gas purification devices, multilayer structures with alternating porous layers of CGO and a LSM/CGO mixture are used to achieve specific functional requirements. In a manufacturing process of such ceramic multilayer devices, co-firing is one of the critical steps as many defects...... such as cracks, de-lamination and shape distortion can result as a consequence of sintering mismatch stresses caused by the strain rate difference between layers. This work seeks to understand the underlying mechanisms that occur during the co-firing of porous CGO-LSM/CGO bi-layer laminates, by evaluating...

  4. Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry


    Guo, Shan; Moore, Timothy C.; Iacovella, Christopher R.; Strickland, L. Anderson; McCabe, Clare


    Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field o...

  5. The structure of the CD3 ζζ transmembrane dimer in POPC and raft-like lipid bilayer: a molecular dynamics study. (United States)

    Petruk, Ariel Alcides; Varriale, Sonia; Coscia, Maria Rosaria; Mazzarella, Lelio; Merlino, Antonello; Oreste, Umberto


    Plasma membrane lipids significantly affect assembly and activity of many signaling networks. The present work is aimed at analyzing, by molecular dynamics simulations, the structure and dynamics of the CD3 ζζ dimer in palmitoyl-oleoyl-phosphatidylcholine bilayer (POPC) and in POPC/cholesterol/sphingomyelin bilayer, which resembles the raft membrane microdomain supposed to be the site of the signal transducing machinery. Both POPC and raft-like environment produce significant alterations in structure and flexibility of the CD3 ζζ with respect to nuclear magnetic resonance (NMR) model: the dimer is more compact, its secondary structure is slightly less ordered, the arrangement of the Asp6 pair, which is important for binding to the Arg residue in the alpha chain of the T cell receptor (TCR), is stabilized by water molecules. Different interactions of charged residues with lipids at the lipid-cytoplasm boundary occur when the two environments are compared. Furthermore, in contrast to what is observed in POPC, in the raft-like environment correlated motions between transmembrane and cytoplasmic regions are observed. Altogether the data suggest that when the TCR complex resides in the raft domains, the CD3 ζζ dimer assumes a specific conformation probably necessary to the correct signal transduction.

  6. Hydrophobic silver nanoparticles trapped in lipid bilayers: Size distribution, bilayer phase behavior, and optical properties

    Directory of Open Access Journals (Sweden)

    Bothun Geoffrey D


    Full Text Available Abstract Background Lipid-based dispersion of nanoparticles provides a biologically inspired route to designing therapeutic agents and a means of reducing nanoparticle toxicity. Little is currently known on how the presence of nanoparticles influences lipid vesicle stability and bilayer phase behavior. In this work, the formation of aqueous lipid/nanoparticle assemblies (LNAs consisting of hydrophobic silver-decanethiol particles (5.7 ± 1.8 nm embedded within 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC bilayers is demonstrated as a function of the DPPC/Ag nanoparticle (AgNP ratio. The effect of nanoparticle loading on the size distribution, bilayer phase behavior, and bilayer fluidity is determined. Concomitantly, the effect of bilayer incorporation on the optical properties of the AgNPs is also examined. Results The dispersions were stable at 50°C where the bilayers existed in a liquid crystalline state, but phase separated at 25°C where the bilayers were in a gel state, consistent with vesicle aggregation below the lipid melting temperature. Formation of bilayer-embedded nanoparticles was confirmed by differential scanning calorimetry and fluorescence anisotropy, where increasing nanoparticle concentration suppressed the lipid pretransition temperature, reduced the melting temperature, and disrupted gel phase bilayers. The characteristic surface plasmon resonance (SPR wavelength of the embedded nanoparticles was independent of the bilayer phase; however, the SPR absorbance was dependent on vesicle aggregation. Conclusion These results suggest that lipid bilayers can distort to accommodate large hydrophobic nanoparticles, relative to the thickness of the bilayer, and may provide insight into nanoparticle/biomembrane interactions and the design of multifunctional liposomal carriers.

  7. In situ atomic force microscope imaging of supported lipid bilayers

    DEFF Research Database (Denmark)

    Kaasgaard, Thomas; Leidy, Chad; Ipsen, John Hjorth


    In situ AFM images of phospholipase A/sub 2/ (PLA/sub 2/) hydrolysis of mica-supported one- and two-component lipid bilayers are presented. For one-component DPPC bilayers an enhanced enzymatic activity is observed towards preexisting defects in the bilayer. Phase separation is observed in two......-component DMPC-DSPC bilayers and a remarkable enhanced hydrolytic activity of the PLA/sub 2/-enzyme for the DMPC-rich phase is seen. Furthermore, in a supported double bilayer system a characteristic ripple structure, most likely related to the formation of the P/sub beta /-ripple phase is observed....

  8. Water Replacement Hypothesis in Atomic Detail - Factors Determining the Structure of Dehydrated Bilayer Stacks

    NARCIS (Netherlands)

    Golovina, E.A.; Golovin, A.; Hoekstra, F.A.; Faller, R.


    According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related st

  9. Berry phase transition in twisted bilayer graphene (United States)

    Rode, Johannes C.; Smirnov, Dmitri; Schmidt, Hennrik; Haug, Rolf J.


    The electronic dispersion of a graphene bilayer is highly dependent on rotational mismatch between layers and can be further manipulated by electrical gating. This allows for an unprecedented control over electronic properties and opens up the possibility of flexible band structure engineering. Here we present novel magnetotransport data in a twisted bilayer, crossing the energetic border between decoupled monolayers and coupled bilayer. In addition a transition in Berry phase between π and 2π is observed at intermediate magnetic fields. Analysis of Fermi velocities and gate induced charge carrier densities suggests an important role of strong layer asymmetry for the observed phenomena.

  10. Small-angle and wide-angle X-ray scattering study on the bilayer structure of synthetic and bovine heart cardiolipins

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Hiroshi [Biophysics Laboratory, Department of Chemistry and Chemical Biology, Gunma University, Maebashi, Gunma, 371-8510 (Japan); Hayakawa, Tomohiro [Life Science Laboratory, Advanced Materials Laboratories, Sony Corporation, Yushima, Bunkyo-ku, Tokyo, 113-8510 (Japan); Ito, Kazuki; Takata, Masaki [Structural Materials Science Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo 679-5148 (Japan); Kobayashi, Toshihide, E-mail: [Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198 (Japan)


    Cardiolipin (CL) is a membrane phospholipid containing four fatty acid chains. CL plays an important role in energy transformation in mitochondria. The disorder of CL biosynthesis is involved in a genetic disease, Barth syndrome. Alteration of fatty acid composition of CLs has been found in Barth syndrome patients, i.e., the decrease of unsaturated fatty acid chains. In this study, we investigated how the degree of saturation alters the structure of CL bilayers by using X-ray scattering. Bovine heart CL and two synthetic CLs were compared. Fatty acid compositions of these three CLs have different saturation. Small-angle X-ray scattering data showed that the decrease of the number of double bonds in the unsaturated fatty acid chains causes to thicken the CL bilayers. In addition, wide-angle X-ray scattering data suggested that the decrease reduces the degree of disorder of the hydrophobic region in a liquid crystalline phase. These results may be related to the dysfunction of mitochondria in Barth syndrome.

  11. Structure determination of enterovirus 71


    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G


    Determination of the orientation of the enterovirus 71 virions in the crystal required the calculation of a locked rotation function that included only icosahedral threefold and fivefold symmetry axes. Otherwise, misleading high rotation-function values were produced by accidental alignment of icosahedral and crystallographic twofold axes.

  12. A high performance transparent resistive switching memory made from ZrO2/AlON bilayer structure (United States)

    Tsai, Tsung-Ling; Chang, Hsiang-Yu; Lou, Jesse Jen-Chung; Tseng, Tseung-Yuen


    In this study, the switching properties of an indium tin oxide (ITO)/zirconium oxide (ZrO2)/ITO single layer device and those of a device with an aluminum oxynitride (AlON) layer were investigated. The devices with highly transparent characteristics were fabricated. Compared with the ITO/ZrO2/ITO single layer device, the ITO/ZrO2/AlON/ITO bilayer device exhibited a larger ON/OFF ratio, higher endurance performance, and superior retention properties by using a simple two-step forming process. These substantial improvements in the resistive switching properties were attributed to the minimized influence of oxygen migration through the ITO top electrode (TE), which can be realized by forming an asymmetrical conductive filament with the weakest part at the ZrO2/AlON interface. Therefore, in the ITO/ZrO2/AlON/ITO bilayer device, the regions where conductive filament formation and rupture occur can be effectively moved from the TE interface to the interior of the device.

  13. Magnetic properties and structure of Ni80Fe20/Ni48Fe12Cr40 bilayer films deposited on SiO2/Si(100) by electron beam evaporation

    Institute of Scientific and Technical Information of China (English)

    WU Ping; GAO Yanqing; QIU Hong; PAN Liqing; TIAN Yue; Wang Fengping


    Ni80Fe20/Ni48Fe12Cr40 bilayer films and Ni80Fe20 monolayer films were deposited at room temperature on SiO2/Si(100) substrates by electron beam evaporation. The influence of the thickness of the Ni48Fe12Cr40underlayer on the structure, magnetization, and magnetoresistance of the Ni80Fe20/Ni48Fe12Cr40 bilayer film was investigated. The thickness of the Ni48Fe12Cr40 layer varied from about 1 nm to 18 nm while the Ni80Fe20 layer thickness was fixed at 45 nm. For the as-deposited bilayer films the introducing of the Ni48Fe12Cr40 underlayer promotes both the (111) texture and grain growth in the Ni80Fe20 layer. The Ni48Fe12Cr40 underlayer has no significant influence on the magnetic moment of the Ni80Fe20/Ni48Fe12Cr40 bilayer film. However, the coercivity of the bilayer film changes with the thickness of the Ni48Fe12Cr40underlayer. The optimum thickness of the Ni48Fe12Cr40 underlayer for improving the anisotropic magnetoresistance effect of the Ni80Fe20/Ni48Fe12Cr40 bilayer film is about 5 nm. With a decrease in temperature from 300 K to 81 K, the anisotropic magnetoresistance ratio of the Ni80Fe20 (45 nm)/Ni48Fe12Cr40 (5 nm) bilayer film increases linearly from 2.1% to 4.8% compared with that of the Ni80Fe20 monolayer film from 1.7% to 4.0%.


    NARCIS (Netherlands)



    The structure of tin zirconium trisulfide is of the NH4CdCl3 type with double columns of edge-sharing Zr octahedra. These columns are linked together by Sn atoms. Sn is coordinated to three S atoms at 2 x 2.619 (2) and 2.765 (2) angstrom; a fourth S atom is at 3.065 (2) angstrom. The zirconium coord

  15. Equilibrium insertion of nanoscale objects into phospholipid bilayers

    CERN Document Server

    Pogodin, Sergey


    Certain membrane proteins, peptides, nanoparticles and nanotubes have rigid structure and fixed shape. They are often viewed as spheres and cylinders with certain surface properties. Single Chain Mean Field theory is used to model the equilibrium insertion of nanoscale spheres and rods into the phospholipid bilayer. The equilibrium structures and the resulting free energies of the nano-objects in the bilayer allow to distinguish different orientations in the bilayer and estimate the energy barrier of insertion.

  16. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz


    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  17. Structural determinants of hospital closure. (United States)

    Longo, D R; Chase, G A


    In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

  18. Coupling Optical and Electrical Measurements in Artificial Membranes: Lateral Diffusion of Lipids and Channel Forming Peptides in Planar Bilayers

    Directory of Open Access Journals (Sweden)

    Duclohier H


    Full Text Available Planar lipid bilayers (PLB were prepared by the Montal-Mueller technique in a FRAP system designed to simultaneously measure conductivity across, and lateral diffusion of, the bilayer. In the first stage of the project the FRAP system was used to characterise the lateral dynamics of bilayer lipids with regards to phospholipid composition (headgroup, chain unsaturation etc., presence of cholesterol and the effect of divalent cations on negatively-charged bilayers. In the second stage of the project, lateral diffusion of two fluorescently-labelled voltage-dependent pore-forming peptides (alamethicin and S4s from Shaker K+ channel was determined at rest and in the conducting state. This study demonstrates the feasibility of such experiments with PLBs, amenable to physical constraints, and thus offers new opportunities for systematic studies of structure-function relationships in membrane-associating molecules.

  19. Cholesterol enhances surface water diffusion of phospholipid bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Chi-Yuan; Kausik, Ravinath; Han, Songi, E-mail: [Department of Chemistry and Biochemistry and Materials Research Laboratory, University of California, Santa Barbara, California 93106 (United States); Olijve, Luuk L. C. [Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven (Netherlands)


    Elucidating the physical effect of cholesterol (Chol) on biological membranes is necessary towards rationalizing their structural and functional role in cell membranes. One of the debated questions is the role of hydration water in Chol-embedding lipid membranes, for which only little direct experimental data are available. Here, we study the hydration dynamics in a series of Chol-rich and depleted bilayer systems using an approach termed {sup 1}H Overhauser dynamic nuclear polarization (ODNP) NMR relaxometry that enables the sensitive and selective determination of water diffusion within 5–10 Å of a nitroxide-based spin label, positioned off the surface of the polar headgroups or within the nonpolar core of lipid membranes. The Chol-rich membrane systems were prepared from mixtures of Chol, dipalmitoyl phosphatidylcholine and/or dioctadecyl phosphatidylcholine lipid that are known to form liquid-ordered, raft-like, domains. Our data reveal that the translational diffusion of local water on the surface and within the hydrocarbon volume of the bilayer is significantly altered, but in opposite directions: accelerated on the membrane surface and dramatically slowed in the bilayer interior with increasing Chol content. Electron paramagnetic resonance (EPR) lineshape analysis shows looser packing of lipid headgroups and concurrently tighter packing in the bilayer core with increasing Chol content, with the effects peaking at lipid compositions reported to form lipid rafts. The complementary capability of ODNP and EPR to site-specifically probe the hydration dynamics and lipid ordering in lipid membrane systems extends the current understanding of how Chol may regulate biological processes. One possible role of Chol is the facilitation of interactions between biological constituents and the lipid membrane through the weakening or disruption of strong hydrogen-bond networks of the surface hydration layers that otherwise exert stronger repulsive forces, as reflected in

  20. Stability Test of White LED with Bilayer Structure of Red InP Quantum Dots and Yellow YAG:Ce3+ Phosphor. (United States)

    Park, Kwangwon; Deressa, Gemechu; Kim, Daehan; Kim, Jongsu; Kim, Jihoon; Kim, Taehoon


    The white-light-emitting diode (white LED), based on the bilayer structure of red InP quantum dots (QDs) with 610 nm peak, and yellow YAG:Ce3+ phosphor with 550 nm peak, were fabricated through a conventional 5050 type LED fabrication process. The white LED exhibited high luminous efficiency of >130 Im/W and high color rendering index of >80 under operating current of 60 mA and color temperature of 5800 K. As an increase of QDs concentrations, the white LED showed higher color rendering index along with lower luminous efficiency, and the energy loss in the reabsorption process between yellow YAG:Ce3+ emission and red QD absorption was observed. As the temperature increases, the x-color coordinates were significantly changed, indicating that the InP QDs still have lower thermal stability. Also our white LED showed about 50% lumen maintenance after 45,000 hours of normal operation.

  1. The determinants of Dutch capital structure choice

    NARCIS (Netherlands)

    Chen, Linda H.; Jiang, George J.


    This paper uses the structural equation modeling (SEM) technique to empirically test the determinants of capital structure choice for Dutch firms. We include major factors identified by capital structure theories and construct proxies for these factors with consideration of specific institutional se

  2. Bias induced modulation of electrical and thermal conductivity and heat capacity of BN and BN/graphene bilayers (United States)

    Chegel, Raad


    By using the tight binding approximation and Green function method, the electronic structure, density of state, electrical conductivity, heat capacity of BN and BN/graphene bilayers are investigated. The AA-, AB1- and AB2- BN/graphene bilayers have small gap unlike to BN bilayers which are wide band gap semiconductors. Unlike to BN bilayer, the energy gap of graphene/BN bilayers increases with external field. The magnitude of the change in the band gap of BN bilayers is much higher than the graphene/BN bilayers. Near absolute zero, the σ(T) is zero for BN bilayers and it increases with temperature until reaches maximum value then decreases. The BN/graphene bilayers have larger electrical conductivity larger than BN bilayers. For both bilayers, the specific heat capacity has a Schottky anomaly.

  3. Application of self-consistent field theory to self-assembled bilayer membranes (United States)

    Zhang, Ping-Wen; Shi, An-Chang


    Bilayer membranes self-assembled from amphiphilic molecules such as lipids, surfactants, and block copolymers are ubiquitous in biological and physiochemical systems. The shape and structure of bilayer membranes depend crucially on their mechanical properties such as surface tension, bending moduli, and line tension. Understanding how the molecular properties of the amphiphiles determine the structure and mechanics of the self-assembled bilayers requires a molecularly detailed theoretical framework. The self-consistent field theory provides such a theoretical framework, which is capable of accurately predicting the mechanical parameters of self-assembled bilayer membranes. In this mini review we summarize the formulation of the self-consistent field theory, as exemplified by a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents, and its application to the study of self-assembled bilayer membranes. Project supported by the National Natural Science Foundation of China (Grant Nos. 11421101 and 21274005) and the Natural Sciences and Engineering Research Council (NSERC) of Canada.

  4. Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Ryan W. (University of New Mexico, Albuquerque, NM); Brozik, James A. (University of New Mexico, Albuquerque, NM); Brozik, Susan Marie; Cox, Jason M. (University of New Mexico, Albuquerque, NM); Lopez, Gabriel P. (University of New Mexico, Albuquerque, NM); Barrick, Todd A. (University of New Mexico, Albuquerque, NM); Flores, Adrean (University of New Mexico, Albuquerque, NM)


    The introduction of functional transmembrane proteins into supported bilayer-based biomimetic systems presents a significant challenge for biophysics. Among the various methods for producing supported bilayers, liposomal fusion offers a versatile method for the introduction of membrane proteins into supported bilayers on a variety of substrates. In this study, the properties of protein containing unilamellar phosphocholine lipid bilayers on nanoporous silica microspheres are investigated. The effects of the silica substrate, pore structure, and the substrate curvature on the stability of the membrane and the functionality of the membrane protein are determined. Supported bilayers on porous silica microspheres show a significant increase in surface area on surfaces with structures in excess of 10 nm as well as an overall decrease in stability resulting from increasing pore size and curvature. Comparison of the liposomal and detergent-mediated introduction of purified bacteriorhodopsin (bR) and the human type 3 serotonin receptor (5HT3R) are investigated focusing on the resulting protein function, diffusion, orientation, and incorporation efficiency. In both cases, functional proteins are observed; however, the reconstitution efficiency and orientation selectivity are significantly enhanced through detergent-mediated protein reconstitution. The results of these experiments provide a basis for bulk ionic and fluorescent dye-based compartmentalization assays as well as single-molecule optical and single-channel electrochemical interrogation of transmembrane proteins in a biomimetic platform.

  5. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.


    We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at ...

  6. Optimization of poly(L-lactic acid)/segmented polyurethane electrospinning process for the production of bilayered small-diameter nanofibrous tubular structures. (United States)

    Montini Ballarin, F; Caracciolo, P C; Blotta, E; Ballarin, V L; Abraham, G A


    The present study is focused on the electrospinning process as a versatile technique to obtain nanofibrous tubular structures for potential applications in vascular tissue engineering. A bilayered scaffolding structure composed of poly(L-lactic acid) (PLLA)/bioresorbable segmented polyurethane (SPEU) blends for small-diameter (5mm) vascular bypass grafts was obtained by multilayering electrospinning. Polymer blend ratios were chosen to mimic the media and adventitia layers. The influence of the different electrospinning parameters into the fiber formation, fiber morphology and fiber mean diameter for PLLA, SPEU and two PLLA/SPEU blends were studied. Flat and two-parallel plate collectors were used to analyze the effect of the electrostatic field on the PLLA nanofiber alignment in the rotating mandrel. Membrane topography resulted in random or aligned nanofibrous structures depending on the auxiliary collector setup used. Finally, composition, surface hydrophilicity, thermal properties and morphology of nanofibrous scaffolds were characterized and discussed. Since the development of tissue engineered microvascular prostheses is still a challenge, the prepared scaffolding tubular structures are promising candidates for vascular tissue engineering.

  7. Pair interaction of bilayer-coated nanoscopic particles

    Institute of Scientific and Technical Information of China (English)

    Zhang Qi-Yi


    The pair interaction between bilayer membrane-coated nanosized particles has been explored by using the self-consistent field (SCF) theory. The bilayer membranes are composed of amphiphilic polymers. For different system parameters, the pair-interaction free energies are obtained. Particular emphasis is placcd on the analysis of a sequence of structural transformations of bilayers on spherical particles, which occur during their approaching processes. For different head fractions of amphiphilcs, the asymmetrical morphologies between bilayers on two particles and the inverted micellar intermediates have been found in the membrane fusion pathway. These results can benefit the fabrication of vesicles as encapsulation vectors for drug and gene delivery.

  8. The Power of Asymmetry: Architecture and Assembly of the Gram-Negative Outer Membrane Lipid Bilayer. (United States)

    Henderson, Jeremy C; Zimmerman, Shawn M; Crofts, Alexander A; Boll, Joseph M; Kuhns, Lisa G; Herrera, Carmen M; Trent, M Stephen


    Determining the chemical composition of biological materials is paramount to the study of natural phenomena. Here, we describe the composition of model gram-negative outer membranes, focusing on the predominant assembly, an asymmetrical bilayer of lipid molecules. We also give an overview of lipid biosynthetic pathways and molecular mechanisms that organize this material into the outer membrane bilayer. An emphasis is placed on the potential of these pathways as targets for antibiotic development. We discuss deviations in composition, through bacterial cell surface remodeling, and alternative modalities to the asymmetric lipid bilayer. Outer membrane lipid alterations of current microbiological interest, such as lipid structures found in commensal bacteria, are emphasized. Additionally, outer membrane components could potentially be engineered to develop vaccine platforms. Observations related to composition and assembly of gram-negative outer membranes will continue to generate novel discoveries, broaden biotechnologies, and reveal profound mysteries to compel future research.

  9. Direct atomic structure determination by the inspection of structural phase. (United States)

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne


    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  10. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  11. Simple approach for ranking structure determining residues

    Directory of Open Access Journals (Sweden)

    Oscar D. Luna-Martínez


    Full Text Available Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  12. Simple approach for ranking structure determining residues. (United States)

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar


    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  13. Thermotropic and Barotropic Phase Behavior of Phosphatidylcholine Bilayers

    Directory of Open Access Journals (Sweden)

    Nobutake Tamai


    Full Text Available Bilayers formed by phospholipids are frequently used as model biological membranes in various life science studies. A characteristic feature of phospholipid bilayers is to undergo a structural change called a phase transition in response to environmental changes of their surroundings. In this review, we focus our attention on phase transitions of some major phospholipids contained in biological membranes, phosphatidylcholines (PCs, depending on temperature and pressure. Bilayers of dipalmitoylphosphatidylcholine (DPPC, which is the most representative lipid in model membrane studies, will first be explained. Then, the bilayer phase behavior of various kinds of PCs with different molecular structures is revealed from the temperature–pressure phase diagrams, and the difference in phase stability among these PC bilayers is discussed in connection with the molecular structure of the PC molecules. Furthermore, the solvent effect on the phase behavior is also described briefly.

  14. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)


    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced fr

  15. Use of the parallax-quench method to determine the position of the active-site loop of cholesterol oxidase in lipid bilayers. (United States)

    Chen, X; Wolfgang, D E; Sampson, N S


    To elucidate the cholesterol oxidase-membrane bilayer interaction, a cysteine was introduced into the active site lid at position-81 using the Brevibacterium enzyme. To eliminate the possibility of labeling native cysteine, the single cysteine in the wild-type enzyme was mutated to a serine without any change in activity. The loop-cysteine mutant was then labeled with acrylodan, an environment-sensitive fluorescence probe. The fluorescence increased and blue-shifted upon binding to lipid vesicles, consistent with a change into a more hydrophobic, i.e., lipid, environment. This acrylodan-labeled cholesterol oxidase was used to explore the pH, ionic strength, and headgroup dependence of binding. Between pH 6 and 10, there was no significant change in binding affinity. Incorporation of anionic lipids (phosphatidylserine) into the vesicles did not increase the binding affinity nor did altering the ionic strength. These experiments suggested that the interactions are primarily driven by hydrophobic effects not ionic effects. Using vesicles doped with either 5-doxyl phosphatidylcholine, 10-doxyl phosphatidylcholine, or phosphatidyl-tempocholine, quenching of acrylodan fluorescence was observed upon binding. Using the parallax method of London [Chattopadhyay, A., and London, E. (1987) Biochemistry 26, 39-45], the acrylodan ring is calculated to be 8.1 +/- 2.5 A from the center of the lipid bilayer. Modeling the acrylodan-cysteine residue as an extended chain suggests that the backbone of the loop does not penetrate into the lipid bilayer but interacts with the headgroups, i.e., the choline. These results demonstrate that cholesterol oxidase interacts directly with the lipid bilayer and sits on the surface of the membrane.

  16. Confocal Raman Microscopy of Hybrid-Supported Phospholipid Bilayers within Individual C18-Functionalized Chromatographic Particles. (United States)

    Kitt, Jay P; Harris, Joel M


    Measuring lipid-membrane partitioning of small molecules is critical to predicting bioavailability and investigating molecule-membrane interactions. A stable model membrane for such studies has been developed through assembly of a phospholipid monolayer on n-alkane-modified surfaces. These hybrid bilayers have recently been generated within n-alkyl-chain (C18)-modified porous silica and used in chromatographic retention studies of small molecules. Despite their successful application, determining the structure of hybrid bilayers within chromatographic silica is challenging because they reside at buried interfaces within the porous structure. In this work, we employ confocal Raman microscopy to investigate the formation and temperature-dependent structure of hybrid-phospholipid bilayers in C18-modified, porous-silica chromatographic particles. Porous silica provides sufficient surface area within a confocal probe volume centered in an individual particle to readily measure, with Raman microscopy, the formation of an ordered hybrid bilayer of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with the surface C18 chains. The DMPC surface density was quantified from the relative Raman scattering intensities of C18 and phospholipid acyl chains and found to be ∼40% of a DMPC vesicle membrane. By monitoring Raman spectra acquired versus temperature, the bilayer main phase transition was observed to be broadened and shifted to higher temperature compared to a DMPC vesicle, in agreement with differential scanning calorimetry (DSC) results. Raman scattering of deuterated phospholipid was resolved from protonated C18 chain scattering, showing that the lipid acyl and C18 chains melt simultaneously in a single phase transition. The surface density of lipid in the hybrid bilayer, the ordering of both C18 and lipid acyl chains upon bilayer formation, and decoupling of C18 methylene C-H vibrations by deuterated lipid acyl chains all suggest an interdigitated acyl chain

  17. Advances on surface structural determination by LEED. (United States)

    Soares, Edmar A; de Castilho, Caio M C; de Carvalho, Vagner E


    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail.

  18. Advances on surface structural determination by LEED

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Edmar A; De Carvalho, Vagner E [Departamento de Fisica, ICEX, Universidade Federal de Minas Gerais, 31270-090, Belo Horizonte, MG (Brazil); De Castilho, Caio M C, E-mail: [Grupo de Fisica de SuperfIcies e Materiais, Instituto de Fisica and Instituto Nacional de Ciencia e Tecnologia em Energia e Ambiente (CIENAM)INCT-E and A, Universidade Federal da Bahia, Campus Universitario da Federacao, 40170-115, Salvador, BA (Brazil)


    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail. (topical review)

  19. Bi-layer channel structure-based oxide thin-film transistors consisting of ZnO and Al-doped ZnO with different Al compositions and stacking sequences (United States)

    Cho, Sung Woon; Yun, Myeong Gu; Ahn, Cheol Hyoun; Kim, So Hee; Cho, Hyung Koun


    Zinc oxide (ZnO)-based bi-layers, consisting of ZnO and Al-doped ZnO (AZO) layers grown by atomic layer deposition, were utilized as the channels of oxide thin-film transistors (TFTs). Thin AZO layers (5 nm) with different Al compositions (5 and 14 at. %) were deposited on top of and beneath the ZnO layers in a bi-layer channel structure. All of the bi-layer channel TFTs that included the AZO layers showed enhanced stability (Δ V Th ≤ 3.2 V) under a positive bias stress compared to the ZnO single-layer channel TFT (Δ V Th = 4.0 V). However, the AZO/ZnO bi-layer channel TFTs with an AZO interlayer between the gate dielectric and the ZnO showed a degraded field effect mobility (0.3 cm2/V·s for 5 at. % and 1.8 cm2/V·s for 14 at. %) compared to the ZnO single-layer channel TFT (5.5 cm2/V·s) due to increased scattering caused by Al-related impurities near the gate dielectric/channel interface. In contrast, the ZnO/AZO bi-layer channel TFTs with an AZO layer on top of the ZnO layer exhibited an improved field effect mobility (7.8 cm2/V·s for 14 at. %) and better stability. [Figure not available: see fulltext.

  20. Density imbalances and free energy of lipid transfer in supported lipid bilayers (United States)

    Xing, Chenyue; Faller, Roland


    Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and at the same time have a fundamental structure approximating cell membranes. However, in computer simulations these systems have been studied only rarely up to now. An important property, which cannot be easily determined by molecular dynamics or experiments, is the unsymmetrical density profiles of bilayer leaflets (density imbalance) inflicted on the membrane by the support. This imbalance in the leaflets composition has consequences for membrane structure and phase behavior, and therefore we need to understand it in detail. The free energy can be used to determine the equilibrium structure of a given system. We employ an umbrella sampling approach to obtain the free energy of a lipid crossing the membrane (i.e., lipid flip-flop) as a function of bilayer composition and hence the equilibrium composition of the supported bilayers. In this paper, we use a variant of the coarse-grained Martini model. The results of the free energy calculation lead to a 5% higher density in the proximal leaflet. Recent data obtained by large scale modeling using a water free model suggested that the proximal leaflet had 3.2% more lipids than the distal leaflet [Hoopes et al., J. Chem. Phys. 129, 175102 (2008)]. Our findings are in line with these results. We compare results of the free energy of transport obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences, but the overall picture is consistent. We additionally characterize the intermediate states, which determine the barrier height and therefore the rate of translocation. Calculations on unsupported bilayers are used to validate the approach and to determine the barrier to flip-flop in a free membrane.

  1. Electronic and optical studies of pulse laser deposited ZnO/NiO bilayer film (United States)

    Baraskar, P.; Dar, T. A.; Choudhary, R. J.; Sen, P. K.; Sen, P.


    We report the structural, optical and electronic properties of polycrystalline ZnO and NiO thin films and amorphous ZnO/NiO bilayer film, prepared by pulsed laser deposition technique. Despite of the presence of both Zn and Ni in +2 state in the bilayer film, the grown bilayer shows no reflections (in XRD) corresponding to ZnO or NiO. The difference in crystal structure of ZnO and NiO leads to the strain in the grown bilayer film. An increase in the band gap has been observed in bilayer film which can be attributed to the amorphous nature of the structure.

  2. 单双层结构的石墨烯纳米带边界态的第一原理研究%First-principles studies on edge states of zigzag graphene nanoribbons with monolayer and bilayer structures

    Institute of Scientific and Technical Information of China (English)

    陆肖励; 张燕娜; 姚志东


    This paper studies the stable structure and electronic structure of monolayer and bilayer zigzag graphene nanoribbons based on the first-principle calculation of density functional theory. The result shows that the bilayer with a-alignment edge attracts e%利用基于密度泛函理论的第一性计算,对单双层结构的石墨烯纳米带的稳态结构和电子结构进行了研究。研究表明:α型的边界层的吸引使体系发生边界弯曲并存在非零能量边界态,届型的边界体系保持结构平整。它们都在单双层边界存在零能量的边界态。

  3. Representing Personal Determinants in Causal Structures. (United States)

    Bandura, Albert


    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  4. Finite-size effects on electronic structure and local properties in passivated AA-stacked bilayer armchair-edge graphene nanoribbons (United States)

    Chen, Xiongwen; Shi, Zhengang; Xiang, Shaohua; Song, Kehui; Zhou, Guanghui


    Based on the tight-binding model and dual-probe scanning tunneling microscopy technology, we theoretically investigate the electronic structure and local property in the passivated AA-stacked bilayer armchair-edge graphene nanoribbons (AABLAGNRs). We show that they are highly sensitive to the size of the ribbons, which is evidently different from the single-layer armchair-edge graphene nanoribbons. The ‘3p’ rule only applies to the narrow AABLGNRs. Namely, in the passivated 3p- and (3p  +  1)-AABLGNRs, the narrow ribbons are semiconducting while the medium and wide ribbons are metallic. Although the passivated (3p  +  2)-AABLGNRs are metallic, the ‘3j’ rule only applies to the narrow and medium ribbons. Namely, electrons are in the semiconducting states at sites of line 3j while they are in the metallic states at other sites. This induces a series of parallel and discrete metallic channels, consisting of lines 3j  -  1 and 3j  -  2, for the low-energy electronic transports. In the passivated wide (3p  +  2)-AABLGNRs, all electrons are in the metallic states. Additionally, the ‘3p’ and ‘3j’ rules are controllable to disappear and reappear by applying an external perpendicular electric field. Resultantly, an electric filed-driven current switch can be realized in the passivated narrow and medium (3p  +  2)-AABLGNRs.

  5. Structural characterization of hemoglobins from Monilifera and Frenulata tubeworms (Siboglinids): first discovery of giant hexagonal-bilayer hemoglobin in the former "Pogonophora" group. (United States)

    Meunier, Cédric; Andersen, Ann C; Bruneaux, Matthieu; Le Guen, Dominique; Terrier, Peran; Leize-Wagner, Emmanuelle; Zal, Franck


    Siboglinids are symbiotic polychete annelids having hemoglobins as essential oxygen- and sulfide-carriers for their endosymbiotic bacteria. We analyzed the structure of the hemoglobins from two species of siboglinids: the monilifera Sclerolinum contortum and the frenulata Oligobrachia webbi (i.e. haakonmosbiensis) from Norwegian cold seeps. Measured by Multi-Angle Laser Light Scattering (MALLS), Sclerolinum shows a 3190+/-50 kDa hexagonal bilayer hemoglobin (HBL-Hb) and a 461+/-46 kDa ring-Hb, just as vestimentifera, whereas Oligobrachia has a 409+/-3.7 kDa ring-Hb only. Electrospray Ionization-Mass Spectrometry (ESI-MS) showed Sclerolinum HBL-Hb composed of seven monomeric globins (15-16 kDa), three disulfide-bonded globin heterodimers and three linkers. The heterodimers always contain globin-b (15814.4+/-1.5 Da). Sclerolinum ring-Hb is composed of globins and dimers with identical masses as its HBL-Hb, but lacks linkers. Oligobrachia ring-Hb has three globin monomers (14-15 kDa) only, with no disulfide-bonded dimers. Comparison of Sclerolinum hemoglobins between Storegga and Haakon Mosby Mud Volcano, using the normalized height of deconvoluted ESI-MS peaks, shows differences in globin monomers abundances that could reflect genetic differences or differential gene expression between distinct seep populations. The discovery of HBL-Hb in Sclerolinum is a new element supporting the hypothesis of monilifera being phylogenetically more closely related to vestimentifera, than to frenulata.

  6. Optimizing non-Pb radiation shielding materials using bilayers

    Energy Technology Data Exchange (ETDEWEB)

    McCaffrey, J. P.; Mainegra-Hing, E.; Shen, H. [Institute for National Measurement Standards, National Research Council of Canada, Building M-35, 1200 Montreal Road, Ottawa K1A 0R6 (Canada)


    Purpose: The objective of this study was to demonstrate that the weight of non-Pb radiation shielding materials can be minimized by structuring the material as a bilayer composed of different metal-powder-embedded elastomer layers. Methods: Measurements and Monte Carlo (MC) calculations were performed to study the attenuation properties of several non-Pb metal bilayers over the x-ray energy range 30-150 keV. Metals for the layers were chosen on the basis of low cost, nontoxicity, and complementary photoelectric absorption characteristics. The EGSnrc user code cavity.cpp was used to calculate the resultant x-ray fluence spectra after attenuation by these metal layers. Air kerma attenuation was measured using commercially manufactured metal/elastomer test layers. These layers were irradiated using the primary standard calibration beams at the Institute for National Measurement Standards in Ottawa, Canada utilizing the six x-ray beam qualities recommended in the German Standard DIN 6857. Both the measurements and the calculations were designed to approximate surface irradiation as well as penetrating radiation at 10 mm depth in soft tissue. The MC modeling point and the position of the measurement detector for surface irradiation were both directly against the downstream face of the attenuating material, as recommended in DIN 6857. Results: The low-Z upstream/high-Z downstream ordering of the metal bilayers provided substantially more attenuation than the reverse order. Optimal percentages of each metal in each bilayer were determined for each x-ray radiation beam quality. Conclusions: Depending on the x-ray quality, appropriate choices of two complementary metal-embedded elastomer layers can decrease the weight of radiation shielding garments by up to 25% compared to Pb-based elastomer garments while providing equivalent attenuation.

  7. Microstructure and mechanical behavior of a shape memory Ni-Ti bi-layer thin film

    Energy Technology Data Exchange (ETDEWEB)

    Mohri, Maryam [School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran (Iran, Islamic Republic of); Karlsruhe Institute of Technology, Institute of Nanotechnology, 76021 Karlsruhe (Germany); Nili-Ahmadabadi, Mahmoud, E-mail: [School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran (Iran, Islamic Republic of); Center of Excellence for High Performance Materials, University of Tehran, Tehran (Iran, Islamic Republic of); Ivanisenko, Julia [Karlsruhe Institute of Technology, Institute of Nanotechnology, 76021 Karlsruhe (Germany); Schwaiger, Ruth [Karlsruhe Institute of Technology, Institute for Applied Materials, 76021 Karlsruhe (Germany); Hahn, Horst; Chakravadhanula, Venkata Sai Kiran [Karlsruhe Institute of Technology, Institute of Nanotechnology, 76021 Karlsruhe (Germany)


    Two different single-layers and a bi-layer Ni-Ti thin films with chemical compositions of Ni{sub 45}Ti{sub 50}Cu{sub 5}, Ni{sub 50.8}Ti{sub 49.2} and Ni{sub 50.8}Ti{sub 49.2}/Ni{sub 45}Ti{sub 50}Cu{sub 5} (numbers indicate at.%) determined by energy dispersive X-ray spectroscopy were deposited on Si (111) substrates using DC magnetron sputtering. The structures, surface morphology and transformation temperatures of annealed thin films at 500 °C for 15 min and 1 h were studied using grazing incidence X-ray diffraction, transmission electron microscopy (TEM), atomic force microscopy and differential scanning calorimetry (DSC), respectively. Nanoindentation was used to characterize the mechanical properties. The DSC and X-ray diffraction results indicated the austenitic structure of the Ni{sub 50.8}Ti{sub 49.2} and martensitic structure of the Ni{sub 45}Ti{sub 50}Cu{sub 5} thin films while the bi-layer was composed of austenitic and martensitic thin films. TEM study revealed that copper encourages crystallization in the bi-layer such that crystal structure containing nano-precipitates in the Ni{sub 45}Ti{sub 50}Cu{sub 5} layer was detected after 15 min annealing while the Ni{sub 50.8}Ti{sub 49.2} layer crystallized after 60 min at 500 °C. Furthermore, after annealing at 500 °C for 15 min, a precipitate free zone and thin layer amorphous were observed closely to the interface in the top layer. The bi-layer was completely crystallized at 500 °C for 1 h and the orientation of the Ni-rich precipitates indicated a stress gradient in the bi-layer. The bi-layer thin film showed different transformation temperatures and mechanical behavior from the single-layers. The developed bi-layer has different phase transformation temperatures, the higher temperatures of shape memory effect and lower temperature of pseudo-elastic behavior compared to the single-layers. Also, the bi-layer thin film exhibited a combined pseudo-elastic behavior and shape memory effect with a reduced

  8. Crystal structure of meteoritic schreibersites: determination of absolute structure (United States)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  9. Multiscale Modeling of supported bilayers (United States)

    Faller, Roland; Xing, Chenyue; Hoopes, Matthew I.


    Supported Lipid Bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability. We studied systematically the changes that a support induces on a phospholipid bilayer using coarse-grained molecular modeling on different levels. We characterize the density and pressure profiles as well as the density imbalance inflicted on the membrane by the support. We also determine the diffusion coefficients and characterize the influence of different corrugations of the support. We then determine the free energy of transfer of phospholipids between the proximal and distal leaflet of a supported membrane using the coarse-grained Martini model. It turns out that there is at equilibrium about a 2-3% higher density in the proximal leaflet. These results are in favorable agreement with recent data obtained by very large scale modeling using a water free model where flip-flop can be observed directly. We compare results of the free energy of transfer obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences but the overall picture is consistent. We are additionally characterizing the intermediate states which determine the barrier height and therefore the rate of translocation.

  10. Bilayer graphene quantum dot defined by topgates

    Energy Technology Data Exchange (ETDEWEB)

    Müller, André; Kaestner, Bernd; Hohls, Frank; Weimann, Thomas; Pierz, Klaus; Schumacher, Hans W., E-mail: [Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig (Germany)


    We investigate the application of nanoscale topgates on exfoliated bilayer graphene to define quantum dot devices. At temperatures below 500 mK, the conductance underneath the grounded gates is suppressed, which we attribute to nearest neighbour hopping and strain-induced piezoelectric fields. The gate-layout can thus be used to define resistive regions by tuning into the corresponding temperature range. We use this method to define a quantum dot structure in bilayer graphene showing Coulomb blockade oscillations consistent with the gate layout.

  11. Design of Asymmetric Peptide Bilayer Membranes. (United States)

    Li, Sha; Mehta, Anil K; Sidorov, Anton N; Orlando, Thomas M; Jiang, Zhigang; Anthony, Neil R; Lynn, David G


    Energetic insights emerging from the structural characterization of peptide cross-β assemblies have enabled the design and construction of robust asymmetric bilayer peptide membranes. Two peptides differing only in their N-terminal residue, phosphotyrosine vs lysine, coassemble as stacks of antiparallel β-sheets with precisely patterned charged lattices stabilizing the bilayer leaflet interface. Either homogeneous or mixed leaflet composition is possible, and both create nanotubes with dense negative external and positive internal solvent exposed surfaces. Cross-seeding peptide solutions with a preassembled peptide nanotube seed leads to domains of different leaflet architecture within single nanotubes. Architectural control over these cross-β assemblies, both across the bilayer membrane and along the nanotube length, provides access to highly ordered asymmetric membranes for the further construction of functional mesoscale assemblies.

  12. Bilayer-thickness-mediated interactions between integral membrane proteins. (United States)

    Kahraman, Osman; Koch, Peter D; Klug, William S; Haselwandter, Christoph A


    Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane

  13. Nanostructured antireflective bilayers: Optical design and preparation

    Energy Technology Data Exchange (ETDEWEB)

    Detrich, Ádám [Budapest University of Technology and Economics, Department of Physical Chemistry and Materials Science, Centre for Colloid Chemistry, H-1521 Budapest (Hungary); Nagy, Norbert [Research Centre for Natural Sciences (MTA TTK), Institute for Technical Physics and Materials Science (MFA), P.O. Box 49, H-1525 Budapest (Hungary); Nyári, Mária; Albert, Emőke; Zámbó, Dániel [Budapest University of Technology and Economics, Department of Physical Chemistry and Materials Science, Centre for Colloid Chemistry, H-1521 Budapest (Hungary); Hórvölgyi, Zoltán, E-mail: [Budapest University of Technology and Economics, Department of Physical Chemistry and Materials Science, Centre for Colloid Chemistry, H-1521 Budapest (Hungary)


    We show different methods for tailoring and fabrication of various cost-effective antireflective nanocoatings on transparent and non-transparent substrates. The main purpose was to prepare coatings with decreased reflectance in the full visible wavelength range using simple wet layer deposition techniques. Structure of coatings was designed by optical simulations applying simplified calculations. The refractive index of substrates was also considered for the calculations. The advantageous optical properties were achieved by bilayered structures combining compact and porous sol–gel derived oxide layers and nanoparticulate films. The bilayered structures enhance the flexibility of design by not only the selection of the layer thicknesses but also by different ways of adjusting the effective refractive index of the layers. Furthermore, chemical stability of the coatings was also investigated. The optical and structural properties of prepared films and bilayered coatings were studied by UV–vis spectroscopy and scanning electron microscopy, respectively. The transmittance of coated glass substrates was above 97.5%, while the reflectance of coated silicon substrates was below 4% between 450 nm and 900 nm. - Highlights: • Designed antireflective bilayered coatings on glass and silicon. • Simple, colloid chemical approaches to preparation. • Favorable optical properties by combining compact and porous oxide layers. • Different ways for adjusting the effective refractive index. • Strong chemical resistance against acidic effects.

  14. Topological transformation of a surfactant bilayer

    DEFF Research Database (Denmark)

    Le, T.D.; Olsson, U.; Mortensen, K.


    Surfactant lamellar phases are often complicated by the formation of multilamellar (onions) under shear, which can originate simply by shaking the sample. A systematic study has been performed on the C10E3-D2O system in which different bilayer structures under a steady shear flow were investigated...

  15. Tunable Fermi surface topology and Lifshitz transition in bilayer graphene


    Varlet, Anastasia; Mucha-Kruczyński, Marcin; Bischoff, Dominik; Simonet, Pauline; Taniguchi, Takashi; Watanabe, Kenji; Fal'ko, Vladimir; Ihn, Thomas; Ensslin, Klaus


    Bilayer graphene is a highly tunable material: not only can one tune the Fermi energy using standard gates, as in single-layer graphene, but the band structure can also be modified by external perturbations such as transverse electric fields or strain. We review the theoretical basics of the band structure of bilayer graphene and study the evolution of the band structure under the influence of these two external parameters. We highlight their key role concerning the ease to experimentally pro...

  16. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.;


    Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation in the dete......Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation...... in the determinants of community structure. In this study, we first examined the relative importance of environmental gradients, microclimate, and food resources in driving spatial variation in the structure of detrital communities in forests of the southeastern USA. Then, in order to assess whether the determinants...... for the effect of climatic variation along the elevational gradient, food resource addition and microclimate alteration influenced the richness and abundance of some taxa. However, the effect of food resource addition and microclimate alteration on the richness and abundance of arthropods did not vary...

  17. Water Replacement Hypothesis in Atomic Details: Effect of Trehalose on the Structure of Single Dehydrated POPC Bilayers

    NARCIS (Netherlands)

    Golovina, E.A.; Golovin, A.; Hoekstra, F.A.; Faller, R.


    We present molecular dynamics (MD) simulations to study the plausibility of the water replacement hypothesis (WRH) from the viewpoint of structural chemistry. A total of 256 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) lipids were modeled for 400 ns at 11.7 or 5.4 waters/lipid. To obtain

  18. Nanocrystal bilayer for tandem catalysis. (United States)

    Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu; Huo, Ziyang; Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Somorjai, Gabor A; Yang, Peidong


    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO(2)-Pt and Pt-SiO(2), can be used to catalyse two distinct sequential reactions. The CeO(2)-Pt interface catalysed methanol decomposition to produce CO and H(2), which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO(2) interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts.

  19. "Nanocrystal bilayer for tandem catalysis"

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong


    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  20. Possible influence of the ferromagnetic/antiferromagnetic interface on the effective critical behavior of bilayers based on La{sub 1−x}Sr{sub x}MnO{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Álvarez Miño, Lucero, E-mail: [Universidad Nacional de Colombia, Sede Manizales, Cra. 27 #64-60, Manizales (Colombia); Grupo de Superconductividad y Nuevos Materiales, Universidad Nacional de Colombia, Sede Bogotá, Avenida Carrera 30 #45, Bogotá (Colombia); Mulcué-Nieto, Luis Fernando, E-mail: [Laboratorio de Magnetismo y Materiales Avanzados, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Colombia, Sede Manizales, Cra. 27 #64-60, Manizales (Colombia)


    In this work, the effective critical exponent of the spontaneous magnetization, β, and the transition temperature, T{sub C}, were calculated from magnetization measurements of three bilayers based on La{sub 1−x}Sr{sub x}MnO{sub 3} (LSMO). The bilayers structure is a ferromagnetic (FM) LSMO film grown on top of an antiferromagnetic (AF) LSMO film. The value of the antiferromagnetic film thickness was kept the same for the three samples, while the ferromagnetic film had different thickness for each bilayer. Applying a method of calculation based on a linear superposition of the magnetization close to the critical temperature, a β value corresponding to the 3D Ising model was found for the bilayer with the thinnest ferromagnetic film. This result, and the other obtained values are explained taking into account the possible influence of the FM/AF interface on the magnetic and crystal orderings. - Highlights: • The critical exponent β of three LSMO bilayers was determined. • Two bilayers with the thinner FM layer have very similar transition temperature. • Two bilayers with the thinner FM layer have very similar width values. • We have found values of β of the 3D Ising model. • Interface also seems to be responsible for some structural disorder.

  1. Adsorption of α-synuclein to supported lipid bilayers: positioning and role of electrostatics. (United States)

    Hellstrand, Erik; Grey, Marie; Ainalem, Marie-Louise; Ankner, John; Forsyth, V Trevor; Fragneto, Giovanna; Haertlein, Michael; Dauvergne, Marie-Therese; Nilsson, Hanna; Brundin, Patrik; Linse, Sara; Nylander, Tommy; Sparr, Emma


    An amyloid form of the protein α-synuclein is the major component of the intraneuronal inclusions called Lewy bodies, which are the neuropathological hallmark of Parkinson's disease (PD). α-Synuclein is known to associate with anionic lipid membranes, and interactions between aggregating α-synuclein and cellular membranes are thought to be important for PD pathology. We have studied the molecular determinants for adsorption of monomeric α-synuclein to planar model lipid membranes composed of zwitterionic phosphatidylcholine alone or in a mixture with anionic phosphatidylserine (relevant for plasma membranes) or anionic cardiolipin (relevant for mitochondrial membranes). We studied the adsorption of the protein to supported bilayers, the position of the protein within and outside the bilayer, and structural changes in the model membranes using two complementary techniques-quartz crystal microbalance with dissipation monitoring, and neutron reflectometry. We found that the interaction and adsorbed conformation depend on membrane charge, protein charge, and electrostatic screening. The results imply that α-synuclein adsorbs in the headgroup region of anionic lipid bilayers with extensions into the bulk but does not penetrate deeply into or across the hydrophobic acyl chain region. The adsorption to anionic bilayers leads to a small perturbation of the acyl chain packing that is independent of anionic headgroup identity. We also explored the effect of changing the area per headgroup in the lipid bilayer by comparing model systems with different degrees of acyl chain saturation. An increase in area per lipid headgroup leads to an increase in the level of α-synuclein adsorption with a reduced water content in the acyl chain layer. In conclusion, the association of α-synuclein to membranes and its adsorbed conformation are of electrostatic origin, combined with van der Waals interactions, but with a very weak correlation to the molecular structure of the anionic

  2. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C


    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  3. Spin dynamics of bilayer manganites

    Indian Academy of Sciences (India)

    Tapan Chatterji


    The results of inelastic and quasi-elastic neutron scattering investigations on the 40% hole-doped quasi-2D bilayer manganites La1.2Sr1.8Mn2O7 have been reviewed. The complete set of exchange interactions have been determined on the basis of a localized Heisenberg model. However, the spin wave dispersion in La1.2Sr1.8Mn2O7 shows softening close to the zone boundary and are also heavily damped especially close to the zone boundary and deviate from that expected for a simple Heisenberg model. A minimal double exchange model including quantum corrections can reproduce these effects qualitatively but falls short of quantitative agreement.

  4. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

    LEI XianRong; YANG JianHua; LIN Xiang; DAI Qin; CHENG Qiang; GUO LingHong; LI Hui


    Optimum resolution data of powder X-ray diffraction (PXRD) for Jatrorrhizine (Jat) were collected by an X' Pert Pro MPD diffractometer with an X'celerator detector under the stepwise scanning condition as 8.255 ms and 0.00836°per step,2θrange of 50°-80° and total scanning period of 8-10 min. Indexing of the crystal system and a search of the space group from the powder X-ray diffraction data were conducted by the computational crystallography method. The pilot crystal models of Jat were globally optimized with Monte Carlo method and then refined with the Rietveld method. In parallel with PXRD test,single crystals of Jat were cultured in an aqueous solution by a slow-decreasing temperature method,then its crystal structure was determined by single crystal X-ray diffraction (SCXRD). Both crystal structures from PXRD and SCXRD are identical. The results show that the crystal structure of Jat belongs to a monoclinic system and the space group P21/c. The parameters of cell dimensions from PXRD are a=7.69(A),b= 12.55(A),c=20.89(A),β=106.53°,Z=4,and V=1933.4(A)3,meanwhile the parameters from SCXRD are a=7.72(A),b=12.61(A),c=20.99(A),β=106.38°,Z=4,and V=1961.3(A)3.

  5. Nanoparticle-lipid bilayer interactions studied with lipid bilayer arrays (United States)

    Lu, Bin; Smith, Tyler; Schmidt, Jacob J.


    The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which can provide insight into the nature of the particle-membrane interaction through variation of membrane and solution properties not possible with cell-based assays. However, the scope of these studies can be limited because of the low throughput characteristic of lipid bilayer platforms. We have recently described an easy to use, parallel lipid bilayer platform which we have used to electrically investigate the activity of 60 nm diameter amine and carboxyl modified polystyrene nanoparticles (NH2-NP and COOH-NP) with over 1000 lipid bilayers while varying lipid composition, bilayer charge, ionic strength, pH, voltage, serum, particle concentration, and particle charge. Our results confirm recent studies finding activity of NH2-NP but not COOH-NP. Detailed analysis shows that NH2-NP formed pores 0.3-2.3 nm in radius, dependent on bilayer and solution composition. These interactions appear to be electrostatic, as they are regulated by NH2-NP surface charge, solution ionic strength, and bilayer charge. The ability to rapidly measure a large number of nanoparticle and membrane parameters indicates strong potential of this bilayer array platform for additional nanoparticle bilayer studies.The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which

  6. The use of virtual ground to control transmembrane voltages and measure bilayer currents in serial arrays of droplet interface bilayers (United States)

    Sarles, Stephen A.


    The droplet interface bilayer (DIB) is a simple technique for constructing a stable lipid bilayer at the interface of two lipid-encased water droplets submerged in oil. Networks of DIBs formed by connecting more than two droplets constitute a new form of modular biomolecular smart material, where the transduction properties of a single lipid bilayer can affect the actions performed at other interface bilayers in the network via diffusion through the aqueous environments of shared droplet connections. The passive electrical properties of a lipid bilayer and the arrangement of droplets that determine the paths for transport in the network require specific electrical control to stimulate and interrogate each bilayer. Here, we explore the use of virtual ground for electrodes inserted into specific droplets in the network and employ a multichannel patch clamp amplifier to characterize bilayer formation and ion-channel activity in a serial DIB array. Analysis of serial connections of DIBs is discussed to understand how assigning electrode connections to the measurement device can be used to measure activity across all lipid membranes within a network. Serial arrays of DIBs are assembled using the regulated attachment method within a multi-compartment flexible substrate, and wire-type electrodes inserted into each droplet compartment of the substrate enable the application of voltage and measurement of current in each droplet in the array.

  7. Boron doped Si rich oxide/SiO{sub 2} and silicon rich nitride/SiN{sub x} bilayers on molybdenum-fused silica substrates for vertically structured Si quantum dot solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Ziyun, E-mail:; Wu, Lingfeng; Jia, Xuguang; Zhang, Tian; Puthen-Veettil, Binesh; Yang, Terry Chien-Jen; Conibeer, Gavin; Perez-Wurfl, Ivan [School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Building H6, Tyree Energy Technologies Building, Kensington, New South Wales 2052 (Australia)


    Vertically structured Si quantum dots (QDs) solar cells with molybdenum (Mo) interlayer on quartz substrates would overcome current crowding effects found in mesa-structured cells. This study investigates the compatibility between boron (B) doped Si QDs bilayers and Mo-fused silica substrate. Both Si/SiO{sub 2} and Si/SiN{sub x} based QDs bilayers were studied. The material compatibility under high temperature treatment was assessed by examining Si crystallinity, microstress, thin film adhesion, and Mo oxidation. It was observed that the presence of Mo interlayer enhanced the Si QDs size confinement, crystalline fraction, and QDs size uniformity. The use of B doping was preferred compared to phosphine (PH{sub 3}) doping studied previously in terms of better surface and interface properties by reducing oxidized spots on the film. Though crack formation due to thermal mismatch after annealing remained, methods to overcome this problem were proposed in this paper. Schematic diagram to fabricate full vertical structured Si QDs solar cells was also suggested.

  8. Molecular Dynamics of Lipid Bilayers (United States)


    The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.

  9. Multiscale Modeling of Supported Lipid Bilayers (United States)

    Hoopes, Matthew I.; Xing, Chenyue; Faller, Roland

    Cell membranes consist of a multitude of lipid molecules that serve as a framework for the even greater variety of membrane associated proteins [1-4]. As this highly complex (nonequilibrium) system cannot easily be understood and studied in a controlled way, a wide variety of model systems have been devised to understand the dynamics, structure, and thermodynamics in biological membranes. One such model system is a supported lipid bilayer (SLB), a two-dimensional membrane suspended on a surface. SLBs have been realized to be manageable experimentally while reproducing many of the key features of real biological membranes [5,6]. One of the main advantages of supported bilayers is the physical stability due to the solid support that enables a wide range of surface characterization techniques not available to free or unsupported membranes. As SLBs maintain some of the crucial structural and dynamic properties of biological membranes, they provide an important bridge to natural systems. In order to mimic cell membranes reliably, certain structural and dynamic features have to be reliably reproduced in the artificially constructed lipid bilayers. SLBs should display lateral mobility as in living cells, because many membrane activities involve transport, recruitment, or assembly of specific components. It is also critical for membranes to exhibit the correct thermodynamic phase, namely, a fluid lipid bilayer, to respond to environmental stress such as temperature and pressure changes [7]. There are several ways to fabricate supported lipid bilayers (SLBs) on planar substrates. One can use vesicle fusion on solid substrates [5,8-10] as well as Langmuir-Blodgett deposition [11,12]. Proteoliposome adsorption and subsequent membrane formation on a mica surface was first demonstrated by Brian and McConnell [13]. Because of its simplicity and reproducibility, this is one of the most common approaches to prepare supported membranes. A diverse range of different solid substrates

  10. Electronic properties of asymmetrically doped twisted graphene bilayers (United States)

    Trambly de Laissardière, Guy; Namarvar, Omid Faizy; Mayou, Didier; Magaud, Laurence


    Rotated graphene bilayers form an exotic class of nanomaterials with fascinating electronic properties governed by the rotation angle θ . For large rotation angles, the electron eigenstates are restricted to one layer and the bilayer behaves like two decoupled graphene layers. At intermediate angles, Dirac cones are preserved but with a lower velocity and van Hove singularities are induced at energies where the two Dirac cones intersect. At very small angles, eigenstates become localized in peculiar moiré zones. We analyze here the effect of an asymmetric doping for a series of commensurate rotated bilayers on the basis of tight-binding calculations of their band dispersions, density of states, participation ratio, and diffusive properties. While a small doping level preserves the θ dependence of the rotated bilayer electronic structure, larger doping induces a further reduction of the band velocity in the same way as a further reduction of the rotation angle.

  11. The effect of calcium on the properties of charged phospholipid bilayers

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Leidy, Chad; Westh, P.


    We have performed molecular dynamics simulations to investigate the structure and dynamics of charged bilayers as well as the distribution of counterions at the bilayer interface. For this, we have considered the negatively charged di-myristoyl-phosphatidyl-glycerol (DMPG) and di-myristoyl-phosph......We have performed molecular dynamics simulations to investigate the structure and dynamics of charged bilayers as well as the distribution of counterions at the bilayer interface. For this, we have considered the negatively charged di-myristoyl-phosphatidyl-glycerol (DMPG) and di...

  12. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding. (United States)

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming


    Graphene and its bilayer structure are the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. Their realistic applications in emerging nanoelectronics usually call for thermal transport manipulation in a controllable and precise manner. In this paper we systematically studied the effect of interlayer covalent bonding, in particular different interlay bonding arrangement, on the thermal conductivity of bilayer graphene using equilibrium molecular dynamics simulations. It is revealed that, the thermal conductivity of randomly bonded bilayer graphene decreases monotonically with the increase of interlayer bonding density, however, for the regularly bonded bilayer graphene structure the thermal conductivity possesses unexpectedly non-monotonic dependence on the interlayer bonding density. The results suggest that the thermal conductivity of bilayer graphene depends not only on the interlayer bonding density, but also on the detailed topological configuration of the interlayer bonding. The underlying mechanism for this abnormal phenomenon is identified by means of phonon spectral energy density, participation ratio and mode weight factor analysis. The large tunability of thermal conductivity of bilayer graphene through rational interlayer bonding arrangement paves the way to achieve other desired properties for potential nanoelectronics applications involving graphene layers.

  13. PI3 kinase enzymology on fluid lipid bilayers. (United States)

    Dutta, Debjit; Pulsipher, Abigail; Luo, Wei; Yousaf, Muhammad N


    We report the use of fluid lipid bilayer membrane as a model platform to study the influence of the bilayer microenvironment and composition on the enzymology in membrane. As a model system we determined the enzyme kinetics on membranes for the transformation of bilayers containing phosphoinositol(4,5)-bisphosphate (PI(4,5)P2) to phosphoinositol(3,4,5)-trisphosphate (PI(3,4,5)P3) by the enzyme phosphoinositol-3-kinase (PI3K) using radiolabeled ATP. The activity of the enzyme was monitored as a function of the radioactivity incorporated within the bilayer. The transformation of PI(4,5)P2 to PI(3,4,5)P3 was determined using a mass strip assay. The fluidity of the bilayer was confirmed by Fluorescence Recovery After Photobleaching (FRAP) experiments. Kinetic simulations were performed based on Langmuir adsorption and Michaelis-Menton kinetics equations to generate the rate constants for the enzymatic reaction. The effect of cholesterol on the enzyme kinetics was studied by doping the bilayer with 1% cholesterol. This leads to significant reduction in reaction rate due to change in membrane microenvironment. This strategy provides a method to study the enzymology of various kinases and phosphatases occurring at the membrane and also how these reactions are affected by the membrane composition and surface microenvironment.

  14. Structure of pure SDS and DTAB micelles in brine determined by small-angle neutron scattering (SANS)

    DEFF Research Database (Denmark)

    Bergström, M.; Pedersen, J.S.


    The geometrical structure of pure SDS and DTAB surfactant micelles in the absence of added salt as well as its dependence on the concentration of NaBr have been investigated at 40 degrees C using small-angle neutron scattering (SANS). In contrast to previous SANS measurements on the same systems we...... have analysed the scattering data in the entire regime of scattering vectors that are relevant for determining the structure of the micelles. Our obtained results for pure surfactant micelles, as well as those of mixed catanionic micelles presented in a recent study, show somewhat unexpectedly...... that ordinary surfactant micelles are shaped as circular or elongated bilayers (tablets). Both SDS and DTAB micelles appeared to be disk-like in pure D2O and the corresponding data were best fitted with a model for (monodisperse) oblate ellipsoids of revolution with half axes a=12.0 Angstrom, b=20.3 Angstrom...

  15. Bursting Bubbles and Bilayers

    Directory of Open Access Journals (Sweden)

    Steven P. Wrenn, Stephen M. Dicker, Eleanor F. Small, Nily R. Dan, Michał Mleczko, Georg Schmitz, Peter A. Lewin


    Full Text Available This paper discusses various interactions between ultrasound, phospholipid monolayer-coated gas bubbles, phospholipid bilayer vesicles, and cells. The paper begins with a review of microbubble physics models, developed to describe microbubble dynamic behavior in the presence of ultrasound, and follows this with a discussion of how such models can be used to predict inertial cavitation profiles. Predicted sensitivities of inertial cavitation to changes in the values of membrane properties, including surface tension, surface dilatational viscosity, and area expansion modulus, indicate that area expansion modulus exerts the greatest relative influence on inertial cavitation. Accordingly, the theoretical dependence of area expansion modulus on chemical composition - in particular, poly (ethylene glyclol (PEG - is reviewed, and predictions of inertial cavitation for different PEG molecular weights and compositions are compared with experiment. Noteworthy is the predicted dependence, or lack thereof, of inertial cavitation on PEG molecular weight and mole fraction. Specifically, inertial cavitation is predicted to be independent of PEG molecular weight and mole fraction in the so-called mushroom regime. In the “brush” regime, however, inertial cavitation is predicted to increase with PEG mole fraction but to decrease (to the inverse 3/5 power with PEG molecular weight. While excellent agreement between experiment and theory can be achieved, it is shown that the calculated inertial cavitation profiles depend strongly on the criterion used to predict inertial cavitation. This is followed by a discussion of nesting microbubbles inside the aqueous core of microcapsules and how this significantly increases the inertial cavitation threshold. Nesting thus offers a means for avoiding unwanted inertial cavitation and cell death during imaging and other applications such as sonoporation. A review of putative sonoporation mechanisms is then presented

  16. Time-resolved photoresponse of nanometer-thick Nb/NiCu bilayers (United States)

    Parlato, L.; Pepe, G. P.; Latempa, R.; De Lisio, C.; Altucci, C.; D'Acunto, P.; Peluso, G.; Barone, A.; Taneda, T.; Sobolewski, R.


    We present femtosecond optical time-resolved pump-probe investigations of superconducting hybrids structures consisting of Nb/NiCu bilayers with various thickness. Measurements performed on pure Nb and NiCu films are also given. The photoresponse experiments provide the quasiparticle relaxation times in bilayers of different thickness ratios. The study of the photoresponse as a function of the temperature reveals the spatial evolution of the superconductor order parameter across the bilayers.

  17. Study of annealing effects in Al–Sb bilayer thin films

    Indian Academy of Sciences (India)

    R K Mangal; B Tripathi; M Singh; Y K Vijay


    In this paper, we present preparation and characterization of Al–Sb bilayer thin films. Thin films of thicknesses, 3000/1000 Å and 3000/1500 Å, were obtained by the thermal evaporation (resistive heating) method. Vacuum annealing and rapid thermal annealing methods were used to mix bilayer thin film structure. Results obtained from optical band gap data and Rutherford back scattering spectrometry showed mixing of Al–Sb bilayer system.

  18. Fluctuations in lipid bilayers: Are they understood?

    CERN Document Server

    Schmid, Friederike


    We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local "protrusions" and/or density fluctuations. Such models provide an excellent basis for describing the fluctuations of tensionless bilayers in the fluid phase at a quantitative level. However, this description is found to fail for membranes in the gel phase and for membranes subject to high tensions. The fluctuations of tilted gel membranes show a signature of the modulated ripple structure, which is a nearby phase observed in the pretransition regime between the fluid and tilted gel state. This complicates a quantitative analysis on mesoscopic length scales. In the case of fluid membranes under tension, the large-wavelength fluctuation modes are found to be significantly softer than predicted by theory. In the latter context, we also address the general problem of the relat...

  19. Surface and interfacial creases in a bilayer tubular soft tissue (United States)

    Razavi, Mir Jalil; Pidaparti, Ramana; Wang, Xianqiao


    Surface and interfacial creases induced by biological growth are common types of instability in soft biological tissues. This study focuses on the criteria for the onset of surface and interfacial creases as well as their morphological evolution in a growing bilayer soft tube within a confined environment. Critical growth ratios for triggering surface and interfacial creases are investigated both analytically and numerically. Analytical interpretations provide preliminary insights into critical stretches and growth ratios for the onset of instability and formation of both surface and interfacial creases. However, the analytical approach cannot predict the evolution pattern of the model after instability; therefore nonlinear finite element simulations are carried out to replicate the poststability morphological patterns of the structure. Analytical and computational simulation results demonstrate that the initial geometry, growth ratio, and shear modulus ratio of the layers are the most influential factors to control surface and interfacial crease formation in this soft tubular bilayer. The competition between the stretch ratios in the free and interfacial surfaces is one of the key driving factors to determine the location of the first crease initiation. These findings may provide some fundamental understanding in the growth modeling of tubular biological tissues such as esophagi and airways as well as offering useful clues into normal and pathological functions of these tissues.

  20. Stokesian jellyfish: Viscous locomotion of bilayer vesicles

    CERN Document Server

    Evans, Arthur A; Lauga, Eric


    Motivated by recent advances in vesicle engineering, we consider theoretically the locomotion of shape-changing bilayer vesicles at low Reynolds number. By modulating their volume and membrane composition, the vesicles can be made to change shape quasi-statically in thermal equilibrium. When the control parameters are tuned appropriately to yield periodic shape changes which are not time-reversible, the result is a net swimming motion over one cycle of shape deformation. For two classical vesicle models (spontaneous curvature and bilayer coupling), we determine numerically the sequence of vesicle shapes through an enthalpy minimization, as well as the fluid-body interactions by solving a boundary integral formulation of the Stokes equations. For both models, net locomotion can be obtained either by continuously modulating fore-aft asymmetric vesicle shapes, or by crossing a continuous shape-transition region and alternating between fore-aft asymmetric and fore-aft symmetric shapes. The obtained hydrodynamic e...

  1. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene (United States)

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng


    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  2. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

    DEFF Research Database (Denmark)

    Sonne, Jacob; Jensen, M.Ø.; Hansen, Flemming Yssing;


    represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting...... method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per...... fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field....

  3. Oxygen as a paramagnetic probe for nuclear magnetic resonance: structure and paramagnetic profile of a lipid bilayer/membrane model system

    Energy Technology Data Exchange (ETDEWEB)

    Al-Abdul Wahid, M.S


    Paramagnetic contact shifts and relaxation rate enhancements from molecular oxygen dissolved in a model membrane, were studied by nuclear magnetic resonance spectroscopy. The model membrane system was an isotropic bicelle formed using 1-myristelaidoyl-2-myristoyl-d27-sn- glycero-3-phosphocholine (MLMPC), a custom phospholipid, and 1-2-dihexanoyl-d22-sn-glycero-3-phosphocholine (DHPC). The {sup 13}C and {sup 1}H spectra of MLMPC were assigned. Molecular oxygen was delivered at external pressures of 20 and 50 atm. Paramagnetic contact shifts were found to scale with the oxygen solubility gradient in the lipid bilayer, were found to be invariant to temperature changes in the region studied (288K to 331K), and scaled linearly with changes in oxygen pressure. Relaxation rate enhancements from oxygen were low in the headgroup region and increased to a roughly constant rate in the acyl chain region. Rates were comparable to values predicted by simple thermodynamic theories which take into account the observed gradients in diffusion rates and solubility of oxygen in bilayers. (author)

  4. Molecular Dynamics of a Water-Lipid Bilayer Interface (United States)

    Wilson, Michael A.; Pohorille, Andrew


    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  5. Different oxidized phospholipid molecules unequally affect bilayer packing. (United States)

    Megli, Francesco M; Russo, Luciana


    The aim of this study was to gain more detailed knowledge about the effect of the presence of defined oxidized phospholipid molecules in phospholipid bilayers. After chromatographic and mass spectrometry analysis, the previously used product of the Fenton reaction with unsaturated lecithins proved to consist of a plethora of oxidatively modified lecithins, useless either for the detailed study of the effects brought about in the bilayer or as the source of defined oxidized phospholipid molecules. The latter, particularly 2-(omega-carboxyacyl)- and 2-(n-hydroperoxyacyl)-lecithins, can be more conveniently prepared by chemical or enzymatic synthesis rather than by chemical or physical oxidation. The effect of those molecules and of commercially available 12-hydroxy-stearic and dodecanedioic acid was studied in planar supported phospholipid bilayers (SPBs) by use of EPR spectrometry. The SPBs also contained 2-(5-doxylstearoyl)-lecithin as the spin probe, and the EPR spectral anisotropy loss, indicative of bilayer disordering, was measured as a function of the molar percentage of oxidized lipid. Most oxidized lipid molecules examined in this study were able to induce bilayer disordering, while hydroperoxyl group-bearing acyl chains appeared to be much less effective. It is concluded that the effects of different oxidized phospholipids on phospholipid bilayer structure cannot be generalized, as happens with batch-oxidized phospholipids, and that the use of defined oxidized phospholipid molecular species for membrane oxidative stress guarantees a more reliable and detailed response.

  6. Predicting proton titration in cationic micelle and bilayer environments

    Energy Technology Data Exchange (ETDEWEB)

    Morrow, Brian H.; Shen, Jana K. [Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201 (United States); Eike, David M.; Murch, Bruce P.; Koenig, Peter H. [Computational Chemistry, Modeling and Simulation GCO, Procter and Gamble, Cincinnati, Ohio 45201 (United States)


    Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pK{sub a}’s in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pK{sub a} of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pK{sub a} of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.

  7. Stealth carriers for low-resolution structure determination of membrane proteins in solution

    DEFF Research Database (Denmark)

    Maric, Selma; Skar-Gislinge, Nicholas; Midtgaard, Søren;


    Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering...... techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity......O at the length scales relevant to SANS. These 'stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins. © 2014 International Union of Crystallography....

  8. Lipid bilayers on nano-templates (United States)

    Noy, Aleksandr; Artyukhin, Alexander B.; Bakajin, Olgica; Stoeve, Pieter


    A lipid bilayer on a nano-template comprising a nanotube or nanowire and a lipid bilayer around the nanotube or nanowire. One embodiment provides a method of fabricating a lipid bilayer on a nano-template comprising the steps of providing a nanotube or nanowire and forming a lipid bilayer around the polymer cushion. One embodiment provides a protein pore in the lipid bilayer. In one embodiment the protein pore is sensitive to specific agents


    Institute of Scientific and Technical Information of China (English)

    WANG De-ming; GAI Bing-zheng


    For calculating the stiffness function of a structure, the differential equation of the vibration of the structure was divided into the differential equation on the original stiffness function that was known, and Fredholm integral equation of the first kind on the undetermined stiffness function that was unknown. And the stable solutions of the integral equation, when the smooth factor was equal to zero, was solved by the extrapolation with p smooth factors. So the stiffness function of the structure is obtained. Applied examples show that the method is feasible and effective.

  10. Determining crystal structures through crowdsourcing and coursework (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.


    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  11. Determining crystal structures through crowdsourcing and coursework



    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit pla...


    Directory of Open Access Journals (Sweden)

    Pejman Kamkarian


    Full Text Available This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.



    Pejman Kamkarian; Henry Hexmoor


    This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.

  14. Self-folding graphene-polymer bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Tao [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Yoon, ChangKyu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Jin, Qianru [Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Li, Mingen [Department of Physics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Liu, Zewen [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Gracias, David H., E-mail: [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)


    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  15. Self-folding graphene-polymer bilayers (United States)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.


    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  16. Formation of supported lipid bilayers containing phase-segregated domains and their interaction with gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Melby, Eric S.; Mensch, Arielle C.; Lohse, Samuel E.; Hu, Dehong; Orr, Galya; Murphy, Catherine J.; Hamers, Robert J.; Pedersen, Joel A.


    The cell membrane represents an important biological interface that nanoparticles may encounter after being released into the environment. Interaction of nanoparticles with cellular membranes may alter membrane structure and function, lead to their uptake into cells, and elicit adverse biological responses. Supported lipid bilayers have proven to be valuable ex vivo models for biological membranes, allowing investigation of their mechanisms of interaction with nanoparticles with a degree of control impossible in living cells. To date, the majority of research on nanoparticle interaction with supported lipid bilayers has employed membranes composed of single or binary mixtures of phospholipids. Cellular membranes contain a wide variety of lipids and exhibit lateral organization. Ordered membrane domains enriched in specific membrane components are referred to as lipid rafts and have not been explored with respect to their interaction with nanoparticles. Here we develop model lipid raft-containing membranes amenable to investigation by a variety of surface-sensitive analytical techniques and demonstrate that lipid rafts influence the extent of nanoparticle attachment to model membranes. We determined conditions that allow reliable formation of bilayers containing rafts enriched in sphingomyelin and cholesterol and confirmed their morphology by structured illumination and atomic force microscopies. We demonstrate that lipid rafts increase attachment of cationic gold nanoparticles to model membranes under near physiological ionic strength conditions (0.1 M NaCl) at pH 7.4. We anticipate that these results will serve as the foundation for and motivate further study of nanoparticle interaction with compositionally varied lipid rafts.

  17. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C


    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  18. Determination of hair structure and shape. (United States)

    Schlake, Thomas


    The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.

  19. Rich Polymorphic Behavior of Wigner Bilayers (United States)

    Antlanger, Moritz; Kahl, Gerhard; Mazars, Martial; Šamaj, Ladislav; Trizac, Emmanuel


    Self-assembly into target structures is an efficient material design strategy. Combining analytical calculations and computational techniques of evolutionary and Monte Carlo types, we report about a remarkable structural variability of Wigner bilayer ground states, when charges are confined between parallel charged plates. Changing the interlayer separation, or the plate charge asymmetry, a cascade of ordered patterns emerges. At variance with the symmetric case phenomenology, the competition between commensurability features and charge neutralization leads to long range attraction, appearance of macroscopic charges, exotic phases, and nonconventional phase transitions with distinct critical indices, offering the possibility of a subtle, but precise and convenient control over patterns.

  20. Electron Diffraction Determination of Nanoscale Structures

    Energy Technology Data Exchange (ETDEWEB)

    Parks, Joel H


    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  1. Effects of butanol isomers on dipalmitoylphosphatidylcholine bilayer membranes. (United States)

    Reeves, Megan D; Schawel, Adam K; Wang, Weidong; Dea, Phoebe


    Differential scanning calorimetry and (31)P-NMR were used to study the effects of butanol isomers on the thermotropic phase behavior of dipalmitoylphosphatidylcholine (DPPC) bilayers. The threshold concentration for the onset of interdigitation for each isomer was determined by the disappearance of the pretransition and the onset of a large hysteresis between the heating and cooling scans of the gel-to-liquid main transition. The threshold concentration was found to correlate with increased solubility of the isomers in the aqueous phase, led by tert-butanol. However, as the solution concentration of tert-butanol increased, there was an abrupt shrinking of the hysteresis, initially with well-resolved shoulder peaks indicating mixed phases. The eventual disappearance of the shoulder peaks was correlated with a breakdown of the multilamellar structure identified using (31)P-NMR.

  2. Lipid Bilayer Composition Affects Transmembrane Protein Orientation and Function

    Directory of Open Access Journals (Sweden)

    Katie D. Hickey


    Full Text Available Sperm membranes change in structure and composition upon ejaculation to undergo capacitation, a molecular transformation which enables spermatozoa to undergo the acrosome reaction and be capable of fertilization. Changes to the membrane environment including lipid composition, specifically lipid microdomains, may be responsible for enabling capacitation. To study the effect of lipid environment on proteins, liposomes were created using lipids extracted from bull sperm membranes, with or without a protein (Na+ K+-ATPase or -amylase. Protein incorporation, function, and orientation were determined. Fluorescence resonance energy transfer (FRET confirmed protein inclusion in the lipid bilayer, and protein function was confirmed using a colourometric assay of phosphate production from ATP cleavage. In the native lipid liposomes, ATPase was oriented with the subunit facing the outer leaflet, while changing the lipid composition to 50% native lipids and 50% exogenous lipids significantly altered this orientation of Na+ K+-ATPase within the membranes.

  3. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR

    Energy Technology Data Exchange (ETDEWEB)

    Eddy, Matthew T. [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay [Massachusetts Institute of Technology, Department of Chemistry (United States); Wagner, Gerhard [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States); Pintacuda, Guido; Emsley, Lyndon [Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1) (France); Griffin, Robert G., E-mail: [Massachusetts Institute of Technology, Department of Chemistry (United States)


    The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5–0.3 ppm for {sup 13}C line widths and <0.5 ppm {sup 15}N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the

  4. Determination of micro structural corrosion by BN

    Energy Technology Data Exchange (ETDEWEB)

    Zergoug, M.; Kamel, G.; Benchaala, A. [Laboratoire d' Electronique et d' Electrotechnique, Centre de soudage et de controle, Route de Dely Ibrahim, B.P:64, Cheraga (Algeria)


    The quality control of industrial components requires adaptation and the development of new material characterization and particular non destructive testing techniques. To characterize steel, it would be useful to know its chemical composition, physic-chemical constitution, metallurgical state (annealed, hammered) and other parameters (superficial and chemical processing, etc.). The testing method using Barkhausen noise (B.N.) is a particular method, which can be applied on ferromagnetic materials. It is a magnetic non destructive evaluation (NDE) method and can provide very important information about the material microstructure. The work here presented documents the ability to determine the metallurgical state of steel submitted to the corrosive attack by electrochemical process. The samples are characterized by Barkhausen noise as non destructive methods and are compared with methods as metallography, micro hardness measurement, and toughness determination. (authors)

  5. The Determination and Development of Sectoral Structure



    The development over time of sectors in terms of value added and employment has common characteristics in all economies. We develop a simple Ricardian multi-sector general equilibrium model that allows for (i) non-unitary income elasticities, (ii) different paces of technological progress per sector, and (iii) endogenously determined technological progress per sector. A model with these ingredients allows us to replicate the sectoral developments that are found empirically, and which are show...

  6. A systematic investigation and insight into the formation mechanism of bilayers of fatty acid/soap mixtures in aqueous solutions. (United States)

    Xu, Wenlong; Song, Aixin; Dong, Shuli; Chen, Jingfei; Hao, Jingcheng


    Vesicles are the most common form of bilayer structures in fatty acid/soap mixtures in aqueous solutions; however, a peculiar bilayer structure called a "planar sheet" was found for the first time in the mixtures. In the past few decades, considerable research has focused on the formation theory of bilayers in fatty acid/soap mixtures. The hydrogen bond theory has been widely accepted by scientists to explain the formation of bilayers. However, except for the hydrogen bond, no other driving forces were proposed systematically. In this work, three kinds of weak interactions were investigated in detail, which could perfectly demonstrate the formation mechanism of bilayer structures in the fatty acid/soap mixtures in aqueous solutions. (i) The influence of hydrophobic interaction was detected by changing the chain length of fatty acid (C(n)H(2n+1)COOH), in which n = 10 to 18, the phase behavior was investigated, and the phase region was presented. With the help of cryogenic transmission electron microscopy (cryo-TEM) observations, deuterium nuclear magnetic resonance ((2)H NMR), and X-ray diffraction (XRD) measurements, the vesicles and planar sheets were determined. The chain length of C(n)H(2n+1)COOH has an important effect on the physical state of the hydrophobic chain, resulting in an obvious difference in the viscoelasticity of the solution samples. (ii) The existence of hydrogen bonds between fatty acids and their soaps in aqueous solutions was demonstrated by Fourier transform infrared (FT-IR) spectroscopy and molecule dynamical simulation. From the pH measurements, the pH ranges of the bilayer formation were at the pKa values of fatty acids, respectively. (iii) Counterions can be embedded in the stern layer of the bilayers and screen the electrostatic repulsion between the COO(-) anionic headgroups. FT-IR characterization demonstrated a bidentate bridging coordination mode between counterions and carboxylates. The conductivity measurements provided the degree

  7. 铁磁/重金属双层薄膜结构中磁性状态的稳定性分析∗%Stability of magnetization states in a ferromagnet/heavy metal bilayer structure

    Institute of Scientific and Technical Information of China (English)

    王日兴; 贺鹏斌; 肖运昌; 李建英


    The influence of spin Hall effect on magnetization dynamics is one of the hottest topics in spintronics. In this paper, the magnetization dynamics driven by the spin Hall effect-induced torque in a ferromagnet/heavy metal bilayer structure has been investigated theoretically. By linearizing the Landau-Lifshitz-Gilbert equation which includes the spin Hall effect torque term, and taking stability analysis, the phase diagrams in the plane defined by the current density and external magnetic field have been obtained. Under the control of the current density and external magnetic field, several magnetic states, such as in-plane stable state, in-plane precession and bistable states can be realized. With the external magnetic field oriented within a certain range, the magnetization reversal and precession can be realized through adjusting the current density. In addition, the dynamic evolutions of these magnetic states are demonstrated by solving the temporal evolutive equations numerically.

  8. Structural determinants of MALT1 protease activity. (United States)

    Wiesmann, Christian; Leder, Lukas; Blank, Jutta; Bernardi, Anna; Melkko, Samu; Decock, Arnaud; D'Arcy, Allan; Villard, Frederic; Erbel, Paulus; Hughes, Nicola; Freuler, Felix; Nikolay, Rainer; Alves, Juliano; Bornancin, Frederic; Renatus, Martin


    The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.

  9. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice


    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

  10. Determining building interior structures using compressive sensing (United States)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse


    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  11. Structural Determinants of Sleeping Beauty Transposase Activity. (United States)

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán


    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  12. Spatially resolving unconventional interface Landau quantization in a graphene monolayer-bilayer planar junction (United States)

    Yan, Wei; Li, Si-Yu; Yin, Long-Jing; Qiao, Jia-Bin; Nie, Jia-Cai; He, Lin


    Hybrid quantum Hall (QH) junctions have been extensively studied by transport measurements due to their exciting physics and device applications. Here we report on spatially resolving electronic properties of such a junction on the nanoscale. We present a subnanometer-resolved scanning tunneling microscopy (STM) and scanning tunneling spectroscopy study of a monolayer-bilayer graphene planar junction in the QH regime. The atomically well-defined interface of such a junction allows us to spatially resolve the interface electronic properties. Around the interface, we detect Landau quantization of massless Dirac fermions as expected in the graphene monolayer for filled states of the junction, whereas unexpectedly, only Landau quantization of massive Dirac fermions as expected in the graphene bilayer is observed for empty states. The observed unconventional interface Landau quantization arises from the fact that the quantum conductance across the interface is solely determined by the minimum filling factors (number of edge modes) in the graphene monolayer and bilayer regions of the junction. Our finding opens the way to spatially explore the QH effect of different graphene hybrid structures only using a STM.

  13. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.


    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  14. Syntheses and Structure Determinations of Calcium Thiolates. (United States)

    Chadwick, Scott; Englich, Ulrich; Noll, Bruce; Ruhlandt-Senge, Karin


    The exploration of synthetic methodologies toward heavy alkaline-earth chalcogenolates resulted in the preparation and structural characterization of a family of calcium thiolates, including [Ca(SC(6)F(5))(2)(py)(4)], 1 (py = pyridine), the separated ion-triple [Ca(18-crown-6)(NH(3))(3))][SMes](2).2THF, 2 (Mes = 2,4,6-tBu(3)C(6)H(2)), and the contact triple [Ca(18-crown-6)(SMes)(2)].THF, 3. Compound 1 was prepared by treating [Ca(N(SiMe(3))(2))(2)](2) with 4 equiv of HSC(6)F(5) under addition of pyridine. The thiolates 2 and 3 were synthesized by treatment of calcium metal dissolved in dry, liquid NH(3) under addition of 2 equiv of HSMes and crown ether or, alternatively, by the reduction of MesSSMes with calcium metal in dry, liquid ammonia. We also report two reaction products isolated during attempted calcium thiolate syntheses: [CaBr(4)(THF)(2)(&mgr;(2)-Li)(2)(THF)(4)], 4, isolated as the product of a salt elimination reaction between CaBr(2) and 2 equiv of [Li(THF)(n)()S-2,4,6-(i)()Pr(3)C(6)H(2)](m)(). [(NH(4))(py)(SC(6)F(5))], 5, was obtained as the sole product in the reaction of metallic calcium with HSC(6)F(5) in liquid ammonia under addition of pyridine. All compounds were characterized by single-crystal X-ray crystallography in addition to IR and NMR spectroscopy.

  15. Theoretical study on stability of hybrid bilayers (United States)

    Silva, Thiago S.; de Lima Bernardo, Bertúlio; Azevedo, Sèrgio


    Motivated by the recent experimental realization of the hybrid nanostructure of graphene and boron nitride (h-BN) sheet, and studies of gap modulation by strain, we use first principles calculations based on density functional theory to investigate the effects of strain in hybrid bilayers composed of two monolayers of graphene with a nanodomain of {{B}3}{{N}3}. The calculations were made with two different approximations for the functional exchange-correlation, GGA and VDW-DF. We investigate the modification in the electronic structure and structural properties of various configurations of the hybrid bilayers. Among the configurations, those with Bernal stacking are found to be more stable when compared to the others. Studies of the compressive strain influence were made only in the structure that has been shown to be the most stable. We have found that the two approximations used in the calculations exhibit the same results for the electronic properties of all structures. The opening of the energy gap due to strain was possible in the calculations by using the GGA approximation, but the same does not happen in the calculations using the VDW-DF approximation. Our analysis shows that the VDW-DF approximation is better suited for studies involving surfaces.

  16. Determination of Ice Characteristics for Marine Hydroengineering Structures

    Energy Technology Data Exchange (ETDEWEB)

    Kantarzhi, I. G., E-mail: [Moscow State University of Civil Engineering (MSGU) (Russian Federation); Maderich, V. S., E-mail:; Koshebutskii, V. I., E-mail: [Ukrainian Center of Environmental and Water Projects (UTsÉVP) (Ukraine)


    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  17. Giant magnetoresistance in bilayer graphene nanoflakes (United States)

    Farghadan, Rouhollah; Farekiyan, Marzieh


    Coherent spin transport through bilayer graphene (BLG) nanoflakes sandwiched between two electrodes made of single-layer zigzag graphene nanoribbon was investigated by means of Landauer-Buttiker formalism. Application of a magnetic field only on BLG structure as a channel produces a perfect spin polarization in a large energy region. Moreover, the conductance could be strongly modulated by magnetization of the zigzag edge of AB-stacked BLG, and the junction, entirely made of carbon, produces a giant magnetoresistance (GMR) up to 100%. Intestinally, GMR and spin polarization could be tuned by varying BLG width and length. Generally, MR in a AB-stacked BLG strongly increases (decreases) with length (width).

  18. Bilayer avalanche spin-diode logic

    Energy Technology Data Exchange (ETDEWEB)

    Friedman, Joseph S., E-mail:; Querlioz, Damien [Institut d’Electronique Fondamentale, Univ. Paris-Sud, CNRS, 91405 Orsay (France); Fadel, Eric R. [Department of Materials Science, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Wessels, Bruce W. [Department of Electrical Engineering & Computer Science, Northwestern University, Evanston, IL 60208 (United States); Department of Materials Science & Engineering, Northwestern University, Evanston, IL 60208 (United States); Sahakian, Alan V. [Department of Electrical Engineering & Computer Science, Northwestern University, Evanston, IL 60208 (United States); Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 (United States)


    A novel spintronic computing paradigm is proposed and analyzed in which InSb p-n bilayer avalanche spin-diodes are cascaded to efficiently perform complex logic operations. This spin-diode logic family uses control wires to generate magnetic fields that modulate the resistance of the spin-diodes, and currents through these devices control the resistance of cascaded devices. Electromagnetic simulations are performed to demonstrate the cascading mechanism, and guidelines are provided for the development of this innovative computing technology. This cascading scheme permits compact logic circuits with switching speeds determined by electromagnetic wave propagation rather than electron motion, enabling high-performance spintronic computing.

  19. X-Ray Kinematography of Temperature-Jump Relaxation Probes the Elastic Properties of Fluid Bilayers

    CERN Document Server

    Pabst, G; Amenitsch, H; Bernstorff, S; Laggner, P; Pabst, Georg; Rappolt, Michael; Amenitsch, Heinz; Bernstorff, Sigrid; Laggner, Peter


    The response kinetics of liquid crystalline phosphatidylcholine bilayerstacks to rapid, IR-laser induced temperature jumps has been studied bymillisecond time-resolved x-ray diffraction. The system reacts on the fasttemperature change by a discrete bilayer compression normal to its surface anda lateral bilayer expansion. Since water cannot diffuse from the excess phaseinto the interbilayer water region within the 2 ms duration of the laser pulse,the water layer has to follow the bilayer expansion, by an anomalous thinning.Structural analysis of a 20 ms diffraction pattern from the intermediate phaseindicates that the bilayer thickness remains within the limits of isothermalequilibrium values. Both, the intermediate structure and its relaxation intothe original equilibrium L_(alpha)-phase, depend on the visco-elasticproperties of the bilayer/water system. We present an analysis of therelaxation process by an overdamped one-dimensional oscillation model revealingthe concepts of Hooke's law for phospholipid bila...

  20. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row


    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  1. Engineering amorphous-crystalline interfaces in TiO2-x/TiO2-y-based bilayer structures for enhanced resistive switching and synaptic properties (United States)

    Bousoulas, P.; Asenov, P.; Karageorgiou, I.; Sakellaropoulos, D.; Stathopoulos, S.; Tsoukalas, D.


    The operating principle of resistive random access memories (RRAMs) relies on the distribution of ionic species and their influence on the electron transport. Taking into account that formation and annihilation of conducting filaments (CFs) is the driving mechanism for the switching effect, it is very important to control the regions where these filaments will evolve. Thus, homolayers of titanium oxide with different oxygen contents were fabricated in order to tune the local electrical and thermal properties of the CFs and narrow down the potential percolation paths. We show that the oxygen content in the top layer of the TiO2-x/TiO2-y bilayer memristors can directly influence the morphology of the layers which affect the diffusion barrier and consequently the diffusivity and drift velocity of oxygen vacancies, yielding in important enhancement of switching characteristics, in terms of spatial uniformity (σ/μ < 0.2), enlarged switching ratio (˜104), and synaptic learning. In order to address the experimental data, a physical model was applied, divulging the crucial role of temperature, electric potential and oxygen vacancy density on the switching effect and offering physical insights to the SET/RESET transitions and the analog switching. The forming free nature of all the devices in conjunction with the self-rectifying behavior, should also be regarded as important assets towards RRAM device optimization.

  2. Modification of glassy carbon electrode with a bilayer of multiwalled carbon nanotube/tiron-doped polypyrrole: Application to sensitive voltammetric determination of acyclovir

    Energy Technology Data Exchange (ETDEWEB)

    Shahrokhian, Saeed, E-mail: [Department of Chemistry, Sharif University of Technology, Tehran 11155-3516 (Iran, Islamic Republic of); Institute for Nanoscience and Technology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Azimzadeh, Mahnaz [Department of Chemistry, Sharif University of Technology, Tehran 11155-3516 (Iran, Islamic Republic of); Amini, Mohammad K. [Department of Chemistry, Isfahan University, Isfahan (Iran, Islamic Republic of)


    A novel voltammetric sensor based on glassy carbon electrode (GCE) modified with a thin film of multi-walled carbon nanotubes (MWCNTs) coated with an electropolymerized layer of tiron-doped polypyrrole was developed and the resulting electrode was applied for the determination of acyclovir (ACV). The surface morphology and property of the modified electrode were characterized by field emission scanning electron microscopy and electrochemical impedance spectroscopy techniques. The electrochemical performance of the modified electrode was investigated by means of linear sweep voltammetry (LSV). The effect of several experimental variables, such as pH of the supporting electrolyte, drop size of the cast MWCNTssuspension, number of electropolymerization cycles and accumulation time was optimized by monitoring the LSV response of the modified electrode toward ACV. The best response was observed at pH 7.0 after accumulation at open circuit for 160 s. Under the optimized conditions, a significant electrochemical improvement was observed toward the electrooxidation of ACV on the modified electrode surface relative to the bare GCE, resulting in a wide linear dynamic range (0.03–10.0 μM) and a low detection limit (10.0 nM) for ACV. Besides high sensitivity, the sensor represented high stability and good reproducibility for ACV analysis, and provided satisfactory results for the determination of this compound in pharmaceutical and clinical preparations. - Highlights: • A simple method was employed to construct a thin film modified electrode. • Tiron-doped polypyrrole was electropolymerized on MWCNT precast glassy carbon electrode. • Electrode surface characterization was performed by microscopic and spectroscopic techniques. • The modified electrode showed nano-molar detection limit for acyclovir. • The modified electrode was applied for the detection of ACV in pharmaceutical and clinical preparations.

  3. Regulation of sodium channel function by bilayer elasticity: the importance of hydrophobic coupling. Effects of Micelle-forming amphiphiles and cholesterol

    DEFF Research Database (Denmark)

    Lundbæk, Jens August; Birn, Pia; Hansen, Anker J


    Membrane proteins are regulated by the lipid bilayer composition. Specific lipid-protein interactions rarely are involved, which suggests that the regulation is due to changes in some general bilayer property (or properties). The hydrophobic coupling between a membrane-spanning protein...... and the surrounding bilayer means that protein conformational changes may be associated with a reversible, local bilayer deformation. Lipid bilayers are elastic bodies, and the energetic cost of the bilayer deformation contributes to the total energetic cost of the protein conformational change. The energetics...... and kinetics of the protein conformational changes therefore will be regulated by the bilayer elasticity, which is determined by the lipid composition. This hydrophobic coupling mechanism has been studied extensively in gramicidin channels, where the channel-bilayer hydrophobic interactions link...

  4. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Mustafa, Ghulam, E-mail:, E-mail:; Nandekar, Prajwal P.; Yu, Xiaofeng [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Wade, Rebecca C., E-mail:, E-mail: [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120 Heidelberg (Germany); Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120 Heidelberg (Germany)


    An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.

  5. Phospholipid bilayer formation at a bare Si surface

    DEFF Research Database (Denmark)

    Gutberlet, T.; Steitz, R.; Fragneto, G.;


    Neutron reflectivity was applied to monitor in situ the adsorption of small unilamellar phospholipid vesicles on a solid bare hydrophilic Si interface. The obtained reflectivity curves are consistent with the rupture and fusion model for the adsorption of phosphatidylcholine vesicles to solid...... interfaces. The results show details of the adsorbed bilayer system at ångström resolution and indicate the presence of a thin ∼6 Å thick water leaflet that separates the bilayer from the Si surface. The resolved structural details provide the basis for further investigation of processes such as adsorption...

  6. Neutron diffraction studies of amphipathic helices in phospholipid bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Bradshaw, J.P.; Gilchrist, P.J. [Univ. of Edinburgh (United Kingdom); Duff, K.C. [Univ. of Edinburgh Medical School (United Kingdom); Saxena, A.M. [Brookhaven National Laboratory, Upton, NY (United States)


    The structural feature which is thought to facilitate the interaction of many peptides with phospholipid bilayers is the ability to fold into an amphipathic helix. In most cases the exact location and orientation of this helix with respect to the membrane is not known, and may vary with factors such as pH and phospholipid content of the bilayer. The growing interest in this area is stimulated by indications that similar interactions can contribute to the binding of certain hormones to their cell-surface receptors. We have been using the techniques of neutron diffraction from stacked phospholipid bilayers in an attempt to investigate this phenomenon with a number of membrane-active peptides. Here we report some of our findings with three of these: the bee venom melittin; the hormone calcitonin; and a synthetic peptide representing the ion channel fragment of influenza A M2 protein.

  7. Electro-absorption of silicene and bilayer graphene quantum dots (United States)

    Abdelsalam, Hazem; Talaat, Mohamed H.; Lukyanchuk, Igor; Portnoi, M. E.; Saroka, V. A.


    We study numerically the optical properties of low-buckled silicene and AB-stacked bilayer graphene quantum dots subjected to an external electric field, which is normal to their surface. Within the tight-binding model, the optical absorption is calculated for quantum dots, of triangular and hexagonal shapes, with zigzag and armchair edge terminations. We show that in triangular silicene clusters with zigzag edges a rich and widely tunable infrared absorption peak structure originates from transitions involving zero energy states. The edge of absorption in silicene quantum dots undergoes red shift in the external electric field for triangular clusters, whereas blue shift takes place for hexagonal ones. In small clusters of bilayer graphene with zigzag edges the edge of absorption undergoes blue/red shift for triangular/hexagonal geometry. In armchair clusters of silicene blue shift of the absorption edge takes place for both cluster shapes, while red shift is inherent for both shapes of the bilayer graphene quantum dots.

  8. Target selection and determination of function in structural genomics. (United States)

    Watson, James D; Todd, Annabel E; Bray, James; Laskowski, Roman A; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A; Thornton, Janet M


    The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

  9. Equilibrium Configurations of Lipid Bilayer Membranes and Carbon Nanostructures

    Institute of Scientific and Technical Information of China (English)

    Iva(i)lo M.Mladenov; Peter A.Djondjorov; Mariana Ts.Hadzhilazova; Vassil M.Vassilev


    The present article concerns the continuum modelling of the mechanical behaviour and equilibrium shapes of two types of nano-scale objects:fluid lipid bilayer membranes and carbon nanostructures.A unified continuum model is used to handle four different case studies.Two of them consist in representing in analytic form cylindrical and axisymmetric equilibrium configurations of single-wall carbon nanotubes and fluid lipid bilayer membranes subjected to uniform hydrostatic pressure.The third one is concerned with determination of possible shapes of junctions between a single-wall carbon nanotube and a fiat graphene sheet or another single-wall carbon nanotube.The last one deals with the mechanical behaviour of closed fluid lipid bilayer membranes (vesicles) adhering onto a fiat homogeneous rigid substrate subjected to micro-injection and uniform hydrostatic pressure.

  10. Theoretical study on strain induced variations in electronic properties of 2H-MoS{sub 2} bilayer sheets

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Liang; Dongare, Avinash M., E-mail: [Department of Materials Science and Engineering and Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269 (United States); Namburu, Raju R. [Computational and Information Sciences Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); O' Regan, Terrance P.; Dubey, Madan [Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, Adelphi, Maryland 20783 (United States)


    The strain dependence of the electronic properties of bilayer sheets of 2H-MoS{sub 2} is studied using ab initio simulations based on density functional theory. An indirect band gap for bilayer MoS{sub 2} is observed for all variations of strain along the basal plane. Several transitions for the indirect band gap are observed for various strains for the bilayer structure. The variation of the band gap and the carrier effective masses for the holes and the electrons for the bilayer MoS{sub 2} structure under conditions of uniaxial strain, biaxial strain, as well as uniaxial stress is investigated.

  11. Adsorption of beryllium atoms and clusters both on graphene and in a bilayer of graphite investigated by DFT. (United States)

    Ferro, Yves; Fernandez, Nicolas; Allouche, Alain; Linsmeier, Christian


    We herein investigate the interaction of beryllium with a graphene sheet and in a bilayer of graphite by means of periodic DFT calculations. In all cases, we find the beryllium atoms to be more weakly bonded on graphene than in the bilayer. Be(2) forms both magnetic and non-magnetic structures on graphene depending on the geometrical configuration of adsorption. We find that the stability of the Be/bilayer system increases with the size of the beryllium clusters inserted into the bilayer of graphite. We also find a charge transfer from beryllium to the graphite layers. All these results are analysed in terms of electronic structure.

  12. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction. (United States)

    Fromm, S A; Sachse, C


    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method.

  13. Intrinsic magnetism and spontaneous band gap opening in bilayer silicene and germanene. (United States)

    Wang, Xinquan; Wu, Zhigang


    It has been long sought to create magnetism out of simple non-magnetic materials, such as silicon and germanium. Here we show that intrinsic magnetism exists in bilayer silicene and germanene with no need to cut, etch, or dope. Unlike bilayer graphene, strong covalent interlayer bonding formed in bilayer silicene and germanene breaks the original π-bonding network of each layer, leaving the unbonded electrons unpaired and localized to carry magnetic moments. These magnetic moments then couple ferromagnetically within each layer while antiferromagnetically across two layers, giving rise to an infinite magnetic sheet with structural integrity and magnetic homogeneity. Furthermore, this unique magnetic ordering results in fundamental band gaps of 0.55 eV and 0.32 eV for bilayer silicene and germanene, respectively. The integration of intrinsic magnetism and spontaneous band gap opening makes bilayer silicene and germanene attractive for future nanoelectronics as well as spin-based computation and data storage.

  14. Growth and characterization of the ZnO/ZnS bilayer obtained by chemical spray pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, M.C. [Laboratorio de Materiales y Superficie (Unidad Asociada al CSIC), Dptos Fisica Aplicada and Dpto Ingenieria Quimica, Facultad de Ciencias, Universidad de Malaga, E29071 Malaga (Spain); Espinos, J.P. [Instituto de Ciencias de Materiales de Sevilla (CSIC), Avda. Americo Vespucio s/n, E41092 Sevilla (Spain); Leinen, D.; Martin, F. [Laboratorio de Materiales y Superficie (Unidad Asociada al CSIC), Dptos Fisica Aplicada and Dpto Ingenieria Quimica, Facultad de Ciencias, Universidad de Malaga, E29071 Malaga (Spain); Centeno, S.P. [Departamento de Quimica-Fisica, Facultad de Ciencias, Universidad de Malaga, E29071 Malaga (Spain); Romero, R. [Laboratorio de Materiales y Superficie (Unidad Asociada al CSIC), Dptos Fisica Aplicada and Dpto Ingenieria Quimica, Facultad de Ciencias, Universidad de Malaga, E29071 Malaga (Spain); Ramos-Barrado, J.R. [Laboratorio de Materiales y Superficie (Unidad Asociada al CSIC), Dptos Fisica Aplicada and Dpto Ingenieria Quimica, Facultad de Ciencias, Universidad de Malaga, E29071 Malaga (Spain)], E-mail:


    ZnO/ZnS bilayer antireflection coatings have been prepared by spray pyrolysis using aqueous solutions of zinc acetate and thiourea or zinc chloride and thiourea. The structure, surface morphology, chemical composition and optical transmittance of the bilayer have been examined as a function of the composition of the initial solution. X-ray photoelectron spectroscopy analysis and Ar ion-beam sputter etching was carried out to obtain a depth profile of bilayer. Neither carbon nor other by-products, which could alter the optical transmittance of the bilayer were found in either the interface or bulk. The differences between the bilayers arise from the annealing of the ZnS underlayer, as well as the precursor used to prepare it.

  15. Membrane docking geometry of GRP1 PH domain bound to a target lipid bilayer: an EPR site-directed spin-labeling and relaxation study.

    Directory of Open Access Journals (Sweden)

    Huai-Chun Chen

    Full Text Available The second messenger lipid PIP(3 (phosphatidylinositol-3,4,5-trisphosphate is generated by the lipid kinase PI3K (phosphoinositide-3-kinase in the inner leaflet of the plasma membrane, where it regulates a broad array of cell processes by recruiting multiple signaling proteins containing PIP(3-specific pleckstrin homology (PH domains to the membrane surface. Despite the broad importance of PIP(3-specific PH domains, the membrane docking geometry of a PH domain bound to its target PIP(3 lipid on a bilayer surface has not yet been experimentally determined. The present study employs EPR site-directed spin labeling and relaxation methods to elucidate the membrane docking geometry of GRP1 PH domain bound to bilayer-embedded PIP(3. The model target bilayer contains the neutral background lipid PC and both essential targeting lipids: (i PIP(3 target lipid that provides specificity and affinity, and (ii PS facilitator lipid that enhances the PIP(3 on-rate via an electrostatic search mechanism. The EPR approach measures membrane depth parameters for 18 function-retaining spin labels coupled to the PH domain, and for calibration spin labels coupled to phospholipids. The resulting depth parameters, together with the known high resolution structure of the co-complex between GRP1 PH domain and the PIP(3 headgroup, provide sufficient constraints to define an optimized, self-consistent membrane docking geometry. In this optimized geometry the PH domain engulfs the PIP(3 headgroup with minimal bilayer penetration, yielding the shallowest membrane position yet described for a lipid binding domain. This binding interaction displaces the PIP(3 headgroup from its lowest energy position and orientation in the bilayer, but the headgroup remains within its energetically accessible depth and angular ranges. Finally, the optimized docking geometry explains previous biophysical findings including mutations observed to disrupt membrane binding, and the rapid lateral

  16. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes. (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin


    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  17. Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from influenza virus. (United States)

    Victor, Bruno L; Baptista, António M; Soares, Cláudio M


    Membrane fusion is a process involved in a high range of biological functions, going from viral infections to neurotransmitter release. Fusogenic proteins increase the slow rate of fusion by coupling energetically downhill conformational changes of the protein to the kinetically unfavorable fusion of the membrane lipid bilayers. Hemagglutinin is an example of a fusogenic protein, which promotes the fusion of the membrane of the influenza virus with the membrane of the target cell. The N-terminus of the HA2 subunit of this protein contains a fusion domain described to act as a destabilizer of the target membrane bilayers, leading eventually to a full fusion of the two membranes. On the other hand, the C-terminus of the same subunit contains a helical transmembrane domain which was initially described to act as the anchor of the protein to the membrane of the virus. However, in recent years the study of this peptide segment has been gaining more attention since it has also been described to be involved in the membrane fusion process. Yet, the structural characterization of the interaction of such a protein domain with membrane lipids is still very limited. Therefore, in this work, we present a study of this transmembrane peptide domain in the presence of DMPC membrane bilayers, and we evaluate the effect of several mutations, and the effect of peptide oligomerization in this interaction process. Our results allowed us to identify and confirm amino acid residue motifs that seem to regulate the interaction between the segment peptide and membrane bilayers. Besides these sequence requirements, we have also identified length and tilt requirements that ultimately contribute to the hydrophobic matching between the peptide and the membrane. Additionally, we looked at the association of several transmembrane peptide segments and evaluated their direct interaction and stability inside a membrane bilayer. From our results we could conclude that three independent TM peptide

  18. NMRFAM-SDF: a protein structure determination framework

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L., E-mail: [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)


    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( )

  19. Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers

    Indian Academy of Sciences (India)

    Yousef Nademi; Sepideh Amjad Iranagh; Abbas Yousefpour; Seyedeh Zahra Mousavi; Hamid Modarress


    Molecular dynamics (MD) simulations and biased MD simulation were carried out for the neutral form of Paracetamol inserted in fully hydrated dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylcholine (DMPC) lipid bilayers. For comparison, fully hydrated DMPC and DPPC lipid bilayers were also simulated separately without Paracetamol. The simulation time for each system was 50 ns. At two concentrations of Paracetamol, various properties of the lipid bilayer such as area per lipid, order parameter, diffusion coefficient, radial distribution function, electrostatic potential, mass density and hydrogen bonds have been calculated. Also, the convergence in time of the free energy profile of the Paracetamol along a DPPC bilayer normal was calculated by umbrella sampling method. From the obtained results, it can be concluded that neutral form of Paracetamol shows a generally similar behaviour in DPPC and DMPC lipid bilayers. It was shown that the addition of Paracetamol causes a decrease in tail order parameter of both DPPC and DMPC lipid bilayers and the tail of Paracetamol adopts an inward orientation in the lipid bilayers. Also from the free energy profile, the high penetration barrier in the bilayer centre was determined.

  20. High-yield chemical vapor deposition growth of high-quality large-area AB-stacked bilayer graphene. (United States)

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng


    Bernal-stacked (AB-stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electric field. Mechanical exfoliation can be used to produce AB-stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB- and randomly stacked structures. Herein we report a rational approach to produce large-area high-quality AB-stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H(2)/CH(4) ratio in a low-pressure CVD process to enable the continued growth of bilayer graphene. A high-temperature and low-pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90%) and high coverage (up to 99%). The electrical transport studies demonstrate that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB-stacked bilayer graphene with the highest carrier mobility exceeding 4000 cm(2)/V · s at room temperature, comparable to that of the exfoliated bilayer graphene.

  1. China Takes the Lead in the Structural Determination of Lumbrokinase

    Institute of Scientific and Technical Information of China (English)


    @@ After five years of arduous work, CAS scientists re cently succeeded in determining the structure of lumbrokinase (earthworm fibrinolytic enzyme),shedding light on the understanding of this drug at the molecular level and laying a foundation for drug design based on its structure.

  2. Labor Market Structure and Salary Determination among Professional Basketball Players. (United States)

    Wallace, Michael


    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  3. Indole Localization in an Explicit Bilayer Revealed via Molecular Dynamics (United States)

    Norman, Kristen


    It is well known that the amino-acid tryptophan is particularly stable in the interfacial region of biological membranes, and this preference is a property of the tryptophan side-chain. Analogues of this side-chain, such as indole, strongly localize in the interfacial region, especially near the glycerol moiety of the lipids in the bilayer. Using molecular dynamics calculations, we determine the potential of mean force (PMF) for indoles in the bilayer. We compare the calculated PMF for indole with that of benzene to show that exclusion from the center of the lipid bilayer does not occur in all aromatics, but is strong in indoles. We find three minima in the PMF. Indole is most stabilized near the glycerol moiety. A weaker binding location is found near the choline groups of the lipid molecules. An even weaker binding side is found near the center of the lipid hydrocarbon core. Comparisions between uncharged, weakly charged, and highly charged indoles demonstrate that the exclusion is caused by the charge distribution on the indole rather than the ``lipo-phobic'' effect. High temperature simulations are used to determine the relative contribution of enthalpy and entropy to indole localization. The orientation of indole is found to be largely charge independent and is a strong function of depth within the bilayer. We find good agreement between simulated SCD order parameters for indole and experimentally determined order parameters.

  4. The Determinants of Capital Structure: Some Evidence from Banks


    Heider, Florian; Gropp, Reint


    This paper documents that standard cross-sectional determinants of firm leverage also apply to the capital structure of large banks in the United States and Europe. We find a remarkable consistency in sign, significance and economic magnitude. Like non-financial firms, banks appear to have stable capital structures at levels that are specific to each individual bank. The results suggest that capital requirements may only be of second-order importance for banks’ capital structures and confirm ...

  5. Microstructural characterization, optical and photocatalytic properties of bilayered CuO and ZnO based thin films

    Energy Technology Data Exchange (ETDEWEB)

    Sáenz-Trevizo, A.; Amézaga-Madrid, P.; Pizá-Ruiz, P.; Solís-Canto, O.; Ornelas-Gutiérrez, C.; Pérez-García, S.; Miki-Yoshida, M., E-mail:


    Highlights: • High quality bilayered Zn–Cu oxide thin films were deposited by aerosol assisted CVD. • Detailed microstructural characterization was performed by XRD and electron microscopy. • Absorbance of bilayered films shows a shift of absorption edge toward visible region. • Optical band gap or nearly 3.2 and 2 eV was determined for ZnO and Cu oxide. • High photocatalytic activity around 90% was obtained for bilayered samples. - Abstract: In this work, it is presented the synthesis, microstructural characterization and photocatalytic properties of bilayered CuO–ZnO/ZnO thin films onto borosilicate glass and fused silica substrates. The films were deposited by aerosol assisted chemical vapor deposition, using an experimental setup reported elsewhere. Deposition conditions were optimized to get high quality films; i.e. they were structurally uniform, highly transparent, non-light scattering, homogeneous, and well adhered to the substrate. Different Cu/Zn atomic ratios were tried for the upper layer. The microstructure of the films was characterized by grazing incidence X-ray diffraction (GIXRD), scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM) and X-ray photoelectron spectroscopy. GIXRD results indicate the presence of ZnO Wurzite and Cu oxide phases. Results of SEM and HRTEM analysis of the cross sectional microstructure showed that the films were composed of compact and dense layers with no visible evidence of an interfacial boundary or porosity. Optical absorbance of the bilayered films showed a clear shift of the absorption toward the visible range. Optical band gap was determined roughly at 3.2 and 2 eV for ZnO and Cu oxide, respectively. Photocatalytic activity of the samples, for the degradation of a 10{sup −5} mol dm{sup −3} solution of methylene blue (MB), was determined after 120 and 240 min of irradiation with an UV-A source. Around 90% of MB degradation was reached by bilayered films with

  6. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: [University of Cambridge, Department of Biochemistry (United Kingdom)


    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  7. Structural determination of intact proteins using mass spectrometry (United States)

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.


    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  8. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    DEFF Research Database (Denmark)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia


    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present ...... (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3]....

  9. Effect of ionic strength on dynamics of supported phosphatidylcholine lipid bilayer revealed by FRAPP and Langmuir-Blodgett transfer ratios. (United States)

    Harb, Frédéric F; Tinland, Bernard


    To determine how lipid bilayer/support interactions are affected by ionic strength, we carried out lipid diffusion coefficient measurements by fluorescence recovery after patterned photobleaching (FRAPP) and transfer ratio measurements using a Langmuir balance on supported bilayers of phosphatidylcholine lipids. The main effect of increasing ionic strength is shown to be enhanced diffusion of the lipids due to a decrease in the electrostatic interaction between the bilayer and the support. We experimentally confirm that the two main parameters governing bilayer behavior are electrostatic interaction and bilayer/support distance. Both these parameters can therefore be used to vary the potential that acts on the bilayer. Additionally, our findings show that FRAPP is an extremely sensitive tool to study interaction effects: here, variations in diffusion coefficient as well as the presence or absence of leaflet decoupling.

  10. SiBr4--prediction and determination of crystal structures. (United States)

    Wolf, Alexandra K; Glinnemann, Jürgen; Schmidt, Martin U; Tong, Jianwei; Dinnebier, Robert E; Simon, Arndt; Köhler, Jürgen


    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol(-1) above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature beta phase crystallizes in P2(1)/c, the high-temperature alpha phase in Pa3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  11. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, A.; Glinnemann, J; Schmidt, M; Tong, J; Dinnebier, R; Simon, A; Kohler, J


    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol-1 above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature [beta] phase crystallizes in P21/c, the high-temperature [alpha] phase in Pa overline3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  12. Transformation from AA to AB-Stacked Bilayer Graphene on α-SiO2 under an Electric Field

    Institute of Scientific and Technical Information of China (English)

    LIU Yan; AO Zhi-Min; WANG Tao; WANG Wen-Bo; SHENG Kuang; YU Bin


    @@ The energetic and electronic structure of bilayered graphene(BLG) with AA stacking arrangement on a SiO2 substrate is investigated in the presence of an electric field F of different intensities by ab initio density functional calculations.The AA-stacked bilayer graphene is stable on the SiO2 substrate in the absence of an electric field.However, as F increases, the AA-stacked bilayer graphenes are gradually shifted with each other and finally transfers into AB-stacked bilayer graphenes.The bandgap is accordingly changed.

  13. Neutrons in studies of phospholipid bilayers and bilayer–drug interaction. I. Basic principles and neutron diffraction

    Directory of Open Access Journals (Sweden)

    Belička M.


    Full Text Available In our paper, we demonstrate several possibilities of using neutrons in pharmaceutical research with the help of examples of scientific results achieved at our University. In this first part, basic properties of neutrons and elementary principles of elastic scattering of thermal neutrons are described. Results of contrast variation neutron diffraction on oriented phospholipid bilayers with intercalated local anaesthetic or cholesterol demonstrate the potential of this method at determination of their position in bilayers. Diffraction experiments with alkan-1-ols located in the bilayers revealed their influence on bilayer thickness as a function of their alkyl chain length.

  14. Bilayer Effects of Antimalarial Compounds.

    Directory of Open Access Journals (Sweden)

    Nicole B Ramsey

    Full Text Available Because of the perpetual development of resistance to current therapies for malaria, the Medicines for Malaria Venture developed the Malaria Box to facilitate the drug development process. We tested the 80 most potent compounds from the box for bilayer-mediated effects on membrane protein conformational changes (a measure of likely toxicity in a gramicidin-based stopped flow fluorescence assay. Among the Malaria Box compounds tested, four compounds altered membrane properties (p< 0.05; MMV007384 stood out as a potent bilayer-perturbing compound that is toxic in many cell-based assays, suggesting that testing for membrane perturbation could help identify toxic compounds. In any case, MMV007384 should be approached with caution, if at all.

  15. Lepromatous leprosy patients produce antibodies that recognise non-bilayer lipid arrangements containing mycolic acids

    Directory of Open Access Journals (Sweden)

    Isabel Baeza


    Full Text Available Non-bilayer phospholipid arrangements are three-dimensional structures that form when anionic phospholipids with an intermediate structure of the tubular hexagonal phase II are present in a bilayer of lipids. Antibodies that recognise these arrangements have been described in patients with antiphospholipid syndrome and/or systemic lupus erythematosus and in those with preeclampsia; these antibodies have also been documented in an experimental murine model of lupus, in which they are associated with immunopathology. Here, we demonstrate the presence of antibodies against non-bilayer phospholipid arrangements containing mycolic acids in the sera of lepromatous leprosy (LL patients, but not those of healthy volunteers. The presence of antibodies that recognise these non-bilayer lipid arrangements may contribute to the hypergammaglobulinaemia observed in LL patients. We also found IgM and IgG anti-cardiolipin antibodies in 77% of the patients. This positive correlation between the anti-mycolic-non-bilayer arrangements and anti-cardiolipin antibodies suggests that both types of antibodies are produced by a common mechanism, as was demonstrated in the experimental murine model of lupus, in which there was a correlation between the anti-non-bilayer phospholipid arrangements and anti-cardiolipin antibodies. Antibodies to non-bilayer lipid arrangements may represent a previously unrecognised pathogenic mechanism in LL and the detection of these antibodies may be a tool for the early diagnosis of LL patients.

  16. Multi-Stacked Supported Lipid Bilayer Micropatterning through Polymer Stencil Lift-Off

    Directory of Open Access Journals (Sweden)

    Yujie Zhu


    Full Text Available Complex multi-lamellar structures play a critical role in biological systems, where they are present as lamellar bodies, and as part of biological assemblies that control energy transduction processes. Multi-lamellar lipid layers not only provide interesting systems for fundamental research on membrane structure and bilayer-associated polypeptides, but can also serve as components in bioinspired materials or devices. Although the ability to pattern stacked lipid bilayers at the micron scale is of importance for these purposes, limited work has been done in developing such patterning techniques. Here, we present a simple and direct approach to pattern stacked supported lipid bilayers (SLBs using polymer stencil lift-off and the electrostatic interactions between cationic and anionic lipids. Both homogeneous and phase-segregated stacked SLB patterns were produced, demonstrating that the stacked lipid bilayers retain lateral diffusivity. We demonstrate patterned SLB stacks of up to four bilayers, where fluorescence resonance energy transfer (FRET and quenching was used to probe the interactions between lipid bilayers. Furthermore, the study of lipid phase behaviour showed that gel phase domains align between adjacent layers. The proposed stacked SLB pattern platform provides a robust model for studying lipid behaviour with a controlled number of bilayers, and an attractive means towards building functional bioinspired materials or devices.

  17. Role of substrate induced electron-phonon interactions in biased graphitic bilayers (United States)

    Davenport, A. R.; Hague, J. P.


    Bilayers of graphitic materials have potential applications in field effect transistors (FETs). A potential difference applied between certain ionic bilayers made from insulating graphitic materials such as BN, ZnO and AlN could reduce gap sizes, turning them into useful semiconductors. On the other hand, opening of a small semiconducting gap occurs in graphene bilayers under applied field. The aim here is to investigate to what extent substrate induced electron-phonon interactions (EPIs) modify this gap change. We examine EPIs in several lattice configurations of graphitic bilayers, using a perturbative approach. The typical effect of EPIs on the ionic bilayers is an undesirable gap widening. The size of this gap change varies considerably with lattice structure and the magnitude of the bias. When bias is larger than the non-interacting gap size, EPIs have the smallest effect on the bandgap, especially in configurations with A{{A}\\prime} and AB structures. Thus careful selection of substrate, lattice configuration and bias strength to minimise the effects of EPIs could be important for optimising the properties of electronic devices. We use parameters related to BN in this article. In practice, the results presented here are broadly applicable to other graphitic bilayers, and are likely to be qualitatively similar in metal dichalcogenide bilayers such as MoS2, which are already of high interest for their use in FETs.

  18. Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics. (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep


    Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide-lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment.

  19. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Directory of Open Access Journals (Sweden)

    Neni Mariana


    Full Text Available Few researches have been concerned about relation between children’s spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was conducted in Indonesia in which we investigated pre-school children’s (between 2 and 3.5 years old ability in making structured arrangement and their ability to determine the quantities by looking at the arrangements. The result shows us that some of the children were able to make such arrangement. However, the children found difficulties either to determine quantities from those arrangements or to compare some structures to easily recognize number of objects.

  20. In cellulo structure determination of a novel cypovirus polyhedrin

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); Ji, Xiaoyun [University of Oxford, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); University of Oxford, Oxford OX3 7BN (United Kingdom); Sutton, Geoff, E-mail: [University of Oxford, Oxford OX3 7BN (United Kingdom); Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom)


    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.

  1. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations (United States)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  2. Optimizing an emperical scoring function for transmembrane protein structure determination.

    Energy Technology Data Exchange (ETDEWEB)

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson


    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  3. Determinants of Market Structure and the Airline Industry (United States)

    Raduchel, W.


    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  4. Slavnov determinants, Yang-Mills structure constants, and discrete KP

    CERN Document Server

    Foda, O


    Using Slavnov's scalar product of a Bethe eigenstate and a generic state in closed XXZ spin-1/2 chains, with possibly twisted boundary conditions, we obtain determinant expressions for tree-level structure constants in 1-loop conformally-invariant sectors in various planar (super) Yang-Mills theories. When certain rapidity variables are allowed to be free rather than satisfy Bethe equations, these determinants become discrete KP tau-functions.

  5. Horizontal Bilayer for Electrical and Optical Recordings

    Directory of Open Access Journals (Sweden)

    Alf Honigmann


    Full Text Available Artificial bilayer containing reconstituted ion channels, transporters and pumps serve as a well-defined model system for electrophysiological investigations of membrane protein structure–function relationship. Appropriately constructed microchips containing horizontally oriented bilayers with easy solution access to both sides provide, in addition, the possibility to investigate these model bilayer membranes and the membrane proteins therein with high resolution fluorescence techniques up to the single-molecule level. Here, we describe a bilayer microchip system in which long-term stable horizontal free-standing and hydrogel-supported bilayers can be formed and demonstrate its prospects particularly for single-molecule fluorescence spectroscopy and high resolution fluorescence microscopy in probing the physicochemical properties like phase behavior of the bilayer-forming lipids, as well as in functional studies of membrane proteins.

  6. The interaction of new piroxicam analogues with lipid bilayers--a calorimetric and fluorescence spectroscopic study. (United States)

    Maniewska, Jadwiga; Szczęśniak-Sięga, Berenika; Poła, Andrzej; Sroda-Pomianek, Kamila; Malinka, Wiesław; Michalak, Krystyna


    The purpose of the present paper was to assess the ability of new piroxicam analogues to interact with the lipid bilayers. The results of calorimetric and fluorescence spectroscopic experiments of two new synthesized analogues of piroxicam, named PR17 and PR18 on the phase behavior of phospholipid bilayers and fluorescence quenching of fluorescent probes (Laurdan and Prodan), which molecular location within membranes is known with certainty, are shown in present work. The presented results revealed that, depending on the details of chemical structure, the studied compounds penetrated the lipid bilayers.

  7. Finite element modeling of camber evolution during sintering of bi-layers

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Ni, De Wei; Bulatova, Regina;


    The need for understanding the mechanisms and optimization of shape distortions during sintering of bilayers is necessary while producing structures with functionally graded architectures. A finite element model based on the continuum theory of sintering was developed to understand the camber...... and friction as well as the initial geometric parameters of the bilayers were made using optical dilatometry experiments and the model. The developed models were able to capture the observed behaviors of the bilayers’ distortions during sintering. Finally, we present the importance of understanding and hence...... making use of the effect of gravity and friction to minimize the shape distortions during sintering of bilayers....

  8. Failure modes and fracture origins of porcelain veneers on bilayer dental crowns. (United States)

    Liu, Yihong; Liu, Guanghua; Wang, Yong; Shen, James Zhijian; Feng, Hailan


    The aims of this study were to determine the fracture origins and crack paths in the porcelain of clinically failed bilayer ceramic restorations and to reveal the correlation between the porcelain failures and material properties. Three clinically failed crowns of each material (bilayer zirconia crowns, galvano-ceramic crowns, and porcelain-fused-to-metal crowns) were collected and underwent failure analysis. The fractures found in porcelain veneers showed several characteristics including wear, Hertzian cone crack, chipping off, and delamination. The results indicated that the fracture origins and features of the porcelain in bilayer ceramic restorations might be affected by the rigidity of core materials and thickness of copings.

  9. Self-assembly of Asymmetric Dimer Particles in Supported Copolymer Bilayer

    Institute of Scientific and Technical Information of China (English)

    Xiao-chun Qin; Chun-lai Ren


    Using self-consistent field and density functional theories, we investigate the self-assembly behavior of asymmetric dimer particles in a supported AB block copolymer bilayer. Asymmetric dimer particles are amphiphilic molecules composed by two different spheres. One prefers to A block of copolymers and the other likes B block when they are introduced into the copolymer bilayer. The two layer structure of the dimer particles is formed within the bilayer.Due to the presence of the substrate surface, the symmetry of the two leaflets of the bilayer is broken, which may lead to two different layer structures of dimer particles within each leaflet of the bilayer. With the increasing concentration of the asymmetric dimer particles,in-plane structure of the dimer particles undergoes sparse square, hexagonal, dense square, and cylindrical structures. In a further condensed packing, a bending cylindrical structure comes into being. Here we verify that the entropic effect of copolymers, the enthalpy of the system and the steric repulsion of the dimer particles are three important factors determing the self-assembly of dimer particles within the supported copolymer bilayer.

  10. High-resolution protein structure determination by serial femtosecond crystallography. (United States)

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme


    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  11. Inducing morphological changes in lipid bilayer membranes with microfabricated substrates (United States)

    Liu, Fangjie; Collins, Liam F.; Ashkar, Rana; Heberle, Frederick A.; Srijanto, Bernadeta R.; Collier, C. Patrick


    Lateral organization of lipids and proteins into distinct domains and anchoring to a cytoskeleton are two important strategies employed by biological membranes to carry out many cellular functions. However, these interactions are difficult to emulate with model systems. Here we use the physical architecture of substrates consisting of arrays of micropillars to systematically control the behavior of supported lipid bilayers - an important step in engineering model lipid membrane systems with well-defined functionalities. Competition between attractive interactions of supported lipid bilayers with the underlying substrate versus the energy cost associated with membrane bending at pillar edges can be systematically investigated as functions of pillar height and pitch, chemical functionalization of the microstructured substrate, and the type of unilamellar vesicles used for assembling the supported bilayer. Confocal fluorescent imaging and AFM measurements highlight correlations that exist between topological and mechanical properties of lipid bilayers and lateral lipid mobility in these confined environments. This study provides a baseline for future investigations into lipid domain reorganization on structured solid surfaces and scaffolds for cell growth.

  12. Forming lipid bilayer membrane arrays on micropatterned polyelectrolyte film surfaces. (United States)

    Zhang, Ying; Wang, Lei; Wang, Xuejing; Qi, Guodong; Han, Xiaojun


    A novel method of forming lipid bilayer membrane arrays on micropatterned polyelectrolyte film surfaces is introduced. Polyelectrolyte films were fabricated by the layer-by-layer technique on a silicon oxide surface modified with a 3-aminopropyltriethoxysilane (APTES) monolayer. The surface pK(a) value of the APTES monolayer was determined by cyclic voltammetry to be approximately 5.61, on the basis of which a pH value of 2.0 was chosen for layer-by-layer assembly. Micropatterned polyelectrolyte films were obtained by deep-UV (254 nm) photolysis though a mask. Absorbed fluorescent latex beads were used to visualize the patterned surfaces. Lipid bilayer arrays were fabricated on the micropatterned surfaces by immersing the patterned substrates into a solution containing egg phosphatidylcholine vesicles. Fluorescence recovery after photobleaching studies yielded a lateral diffusion coefficient for probe molecules of 1.31±0.17 μm(2) s(-1) in the bilayer region, and migration of the lipid NBD PE in bilayer lipid membrane arrays was observed in an electric field.

  13. Ultra-high vacuum surface analysis study of rhodopsin incorporation into supported lipid bilayers. (United States)

    Michel, Roger; Subramaniam, Varuni; McArthur, Sally L; Bondurant, Bruce; D'Ambruoso, Gemma D; Hall, Henry K; Brown, Michael F; Ross, Eric E; Saavedra, S Scott; Castner, David G


    Planar supported lipid bilayers that are stable under ambient atmospheric and ultra-high-vacuum conditions were prepared by cross-linking polymerization of bis-sorbylphosphatidylcholine (bis-SorbPC). X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were employed to investigate bilayers that were cross-linked using either redox-initiated radical polymerization or ultraviolet photopolymerization. The redox method yields a more structurally intact bilayer; however, the UV method is more compatible with incorporation of transmembrane proteins. UV polymerization was therefore used to prepare cross-linked bilayers with incorporated bovine rhodopsin, a light-activated, G-protein-coupled receptor (GPCR). A previous study (Subramaniam, V.; Alves, I. D.; Salgado, G. F. J.; Lau, P. W.; Wysocki, R. J.; Salamon, Z.; Tollin, G.; Hruby, V. J.; Brown, M. F.; Saavedra, S. S. J. Am. Chem. Soc. 2005, 127, 5320-5321) showed that rhodopsin retains photoactivity after incorporation into UV-polymerized bis-SorbPC, but did not address how the protein is associated with the bilayer. In this study, we show that rhodopsin is retained in supported bilayers of poly(bis-SorbPC) under ultra-high-vacuum conditions, on the basis of the increase in the XPS nitrogen concentration and the presence of characteristic amino acid peaks in the ToF-SIMS data. Angle-resolved XPS data show that the protein is inserted into the bilayer, rather than adsorbed on the bilayer surface. This is the first study to demonstrate the use of ultra-high-vacuum techniques for structural studies of supported proteolipid bilayers.

  14. A large scale molecular dynamics calculation of a lipid bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)


    Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)

  15. Novel genetic algorithm search procedure for LEED surface structure determination. (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E


    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  16. Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake" (United States)

    Kaya, Bastürk; Aladag, Caner


    The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

  17. Synthesis and structure determination of novel hexasubstituted cyclohexadienes

    Institute of Scientific and Technical Information of China (English)

    Hong Mei Qu; Xin Hui Niu; Juan Li; Jun Liu; Li Li Jiang; Jian Ke Tang; Li Shan Zhou


    The linear trienes were obtained in high yields by copper-mediated cycloaddition of 2,5-bis(trimethylsilyl)zirconacyclopentadienes with dimethyl acetylenedicarboxylate (DMAD) which can be quantitatively converted to novel asymmetric hexasubstituted cyclohexadienes with high (E)-stereoselectivity.The structure of cyclohexadienes was determined via X-ray analysis.

  18. A Laboratory Exercise in the Determination of Carbohydrate Structures. (United States)

    White, Bernard J.; Robyt, John F.


    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  19. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities (United States)

    Mariana, Neni


    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  20. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes


    rigorous approach was developed which treats structure determination as a problem of Bayesian inference. In this case, the forcefields are brought in as a prior distribution in the form of a Boltzmann factor. Due to high computational cost, the approach has been only sparsely applied in practice. Here, we...

  1. From bacterial to human dihydrouridine synthase: automated structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Whelan, Fiona, E-mail:; Jenkins, Huw T., E-mail: [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: [The University of York, Heslington, York YO10 5DD (United Kingdom)


    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  2. Combinatorics of giant hexagonal bilayer hemoglobins. (United States)

    Hanin, L G; Vinogradov, S N


    The paper discusses combinatorial and probabilistic models allowing to characterize various aspects of spacial symmetry and structural heterogeneity of the giant hexagonal bilayer hemoglobins (HBL Hb). Linker-dodecamer configurations of HBL are described for two and four linker types (occurring in the two most studied HBL Hb of Arenicola and Lumbricus, respectively), and the most probable configurations are found. It is shown that, for HBL with marked dodecamers, the number of 'normal-marked' pairs of dodecamers in homological position follows a binomial distribution. The group of symmetries of the dodecamer substructure of HBL is identified with the dihedral group D6. Under natural symmetry assumptions, the total dipole moment of the dodecamer substructure of HBL is shown to be zero. Biological implications of the mathematical findings are discussed.

  3. The determinism and boundedness of self-assembling structures

    CERN Document Server

    Tesoro, S


    Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Among the most important of these properties are whether the self-assembly is deterministic or nondeterministic, and whether it is bound or unbound. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph-based approach that can determine, with a few restrictions, whether a set of self-assembly building blocks is deterministic or nondeterministic, and whether it is bound or unbound. We apply this methodology to a previously studied lattice self-assembly model and discuss generalisatio...

  4. Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems (United States)

    Huang, Fong-yin; Chiu, Chi-cheng


    Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.

  5. Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study. (United States)

    Saito, Hiroaki; Shinoda, Wataru


    Water permeability of two different lipid bilayers of dipalmitoylphosphatidylcholine (DPPC) and palmitoylsphingomyelin (PSM) in the absence and presence of cholesterol (0-50 mol %) have been studied by molecular dynamics simulations to elucidate the molecular mechanism of the reduction in water leakage across the membranes by the addition of cholesterol. An enhanced free energy barrier was observed in these membranes with increased cholesterol concentration, and this was explained by the reduced cavity density around the cholesterol in the hydrophobic membrane core. There was an increase of trans conformers in the hydrophobic lipid chains adjacent to the cholesterol, which reduced the cavity density. The enhanced free energy barrier was found to be the main reason to reduce the water permeability with increased cholesterol concentration. At low cholesterol concentrations the PSM bilayer exhibited a higher free energy barrier than the DPPC bilayer for water permeation, while at greater than 30 mol % of cholesterol the difference became minor. This tendency for the PSM and DPPC bilayers to resemble each other at higher cholesterol concentrations was similar to commonly observed trends in several structural properties, such as order parameters, cross-sectional area per molecule, and cavity density profiles in the hydrophobic regions of bilayer membranes. These results demonstrate that DPPC and PSM bilayers with high cholesterol contents possess similar physical properties, which suggests that the solubility of cholesterol in these lipid bilayers has importance for an understanding of multicomponent lipid membranes with cholesterol.

  6. The structure of Sindbis virus produced from vertebrate and invertabrate hosts determined by small angle neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    He, Lilin [ORNL; Piper, Amanda [North Carolina State University; Meilleur, Flora [ORNL; Myles, Dean A A [ORNL; Hernandez, Raquel [North Carolina State University; Brown, Dennis [North Carolina State University; Heller, William T [ORNL


    The complex natural cycle of vectored viruses that transition between host species, such as between insects and mammals, makes understanding the full life cycle of the virus an incredibly complex problem. Sindbis virus, an arbovirus and prototypic alphavirus having an inner protein shell and an outer glycoprotein coat separated by a lipid membrane, is one example of a vectored virus that transitions between vertebrate and insect hosts. While evidence of host-specific differences in Sindbis virus has been observed, no work has been performed to characterize the impact of the host species on the structure of the virus. Here, we report the first study of the structural differences between Sindbis viruses grown in mammalian and insect cells, which were determined by small-angle neutron scattering (SANS), a nondestructive technique that did not decrease the infectivity of the Sindbis virus particles studied. The scattering data and modeling showed that, while the radial position of the lipid bilayer did not change significantly, it was possible to conclude that it did have significantly more cholesterol when the virus was grown in mammalian cells. Additionally, the outer protein coat was found to be more extended in the mammalian Sindbis virus. The SANS data also demonstrated that the RNA and nucleocapsid protein share a closer interaction in the mammalian-cell-grown virus than in the virus from insect cells.

  7. Studying the lateral chain packing in a ceramide bilayer with molecular dynamics simulations (United States)

    Papadimitriou, N. I.; Karozis, S. N.; Kainourgiakis, M. E.; Charalambopoulou, G. Ch


    In this work, we present a novel technique, based on molecular dynamics simulations, that allows the study of the lateral chain packing in a lipid bilayer. It utilizes the radial distribution function of the alkyl chains to determine the arrangement of the chains along the bilayer plane. The positions of the mass centres of the chains are projected onto the bilayer plane and a 2D radial distribution function is calculated for these projections. The proposed technique can be particularly useful for lipid bilayers in the gel (solid) phase where the chains present a limited degree of mobility. As a case study, we have examined a bilayer that consists of ceramide NS 24:0. Ceramide bilayers can be found in the lipid domain of the skin where they have a significant role in its barrier function. The specific bilayer was found (at 300 K) to adopt a strictly hexagonal chain packing with a separation distance between the chains of 0.466 nm, in good agreement with the available experimental data.

  8. LDA + slave-boson approach to the correlated electronic structure of the metamagnetic bilayer ruthenate Sr{sub 3}Ru{sub 2}O{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Piefke, Christoph; Lechermann, Frank [Institut fuer Theoretische Physik, Universitaet Hamburg, 20355 Hamburg (Germany)


    The combination of the local-density approximation (LDA) with the rotationally invariant slave-boson theory (RISB) is used to investigate the realistic correlated electronic structure of Sr{sub 3}Ru{sub 2}O{sub 7}. From Wannier-downfolding the low-energy band structure to a three-band model for the Ru(t{sub 2g}) states, the interacting problem is solved including intra- and inter-orbital Hubbard terms as well as spin-flip and pair-hopping interactions. Therewith it is possible to obtain valuable insight into the orbital occupations, relevant local spin multiplets, and the fermiology with increasing correlation strength. Besides generic correlation-induced band-narrowing and -shifting, an intriguing quasiparticle structure close to the Fermi level is found in the neighborhood of the notorious {gamma}{sub 2} pocket in the Brillouin zone. Along the {gamma}-X direction in k-space, that structure appears very sensitive to electronic self-energy effects. The subtle sensitivity, connected also to its manifest multi-orbital character, may put this very low-energy structure in context with the puzzling metamagnetic properties of the compound. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Overconfidence, Managerial Optimism, and the Determinants of Capital Structure

    Directory of Open Access Journals (Sweden)

    Alexandre di Miceli da Silveira


    Full Text Available This research examines the determinants of the capital structure of firms introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: firms managed by optimistic and/or overconfident people will choose more levered financing structures than others, ceteris paribus. We propose different proxies for optimism/overconfidence, based on the manager’s status as an entrepreneur or non-entrepreneur, an idea that is supported by theories and solid empirical evidence, as well as on the pattern of ownership of the firm’s shares by its manager. The study also includes potential determinants of capital structure used in earlier research. We use a sample of Brazilian firms listed in the Sao Paulo Stock Exchange (Bovespa in the years 1998 to 2003. The empirical analysis suggests that the proxies for the referred cognitive biases are important determinants of capital structure. We also found as relevant explanatory variables: profitability, size, dividend payment and tangibility, as well as some indicators that capture the firms’ corporate governance standards. These results suggest that behavioral approaches based on human psychology research can offer relevant contributions to the understanding of corporate decision making.

  10. Spatial distribution of residual stresses in glass-ZrO2 sphero-cylindrical bilayers. (United States)

    Wendler, Michael; Belli, Renan; Petschelt, Anselm; Lohbauer, Ulrich


    Residual stresses arising from inhomogeneous cooling after sintering have shown to play a preponderant role in the higher incidence of chippings observed for glass-zirconia dental prostheses. Still, current descriptions of their nature and distribution have failed to reconcile with clinical findings. Therefore, an axisymmetric sphero-cylindrical bilayer model was used in this study to determine the effect of the cooling rate on the final spatial distribution of residual stresses. Zirconia frameworks with two different radii (1.6 and 3.2mm) were CAD/CAM fabricated. Subsequent glass overlays with two different thickness ratios (1:1 and 2:1) were generated and heat pressed onto the zirconia substrates. The obtained structures were submitted to a last firing process and fast- (45°C/s) or slow-cooled (0.5°C/s) to room temperature. Unbonded bilayers were produced by firing glass overlays onto boron nitride coated zirconia. Thin sagittal and transversal sections were obtained from the specimens to assess residual stress distribution by means of light birefringence. The applied cooling rates did not affect distribution or magnitude of radial residual stresses (sagittal sections), whereas increased hoop stress magnitudes were measured (transversal sections) in fast-cooled specimens. A distinct stress nature was observed for the hoop stress component of unbonded overlays after fast cooling. Interaction between stress components seems to govern the final stress distribution, highlighting the importance of a multiaxial assessment of this problem in three-dimensional structures.

  11. The effect of tail-length mismatch in binary DMPC/DSPC lipid bilayers (United States)

    Ashkar, Rana; Nagao, Michihiro; Butler, Paul


    Bilayer heterogeneity has been long hypothesized to drive raft formation and promote complex functionality in lipid membranes. The highly dynamic nature of the membrane however is thought to play a critical role in this delicate balance between structure and performance. To probe the effect of lateral heterogeneity on membrane dynamics, we investigate the thermal response of unilamellar-vesicle systems of mixed dimyristoylphosphatidylcholine (DMPC) and distearoylphosphatidylcholine (DSPC) with DMPC/DSPC ratios of 50/50 and 70/30. Both lipids experience a transition from an ordered gel phase, with stiff stretched tails, to a melted fluid phase, with more coiled flexible tails, as they are heated through their melting temperature, Tm(DMPC) ~ 21 °C and Tm(DSPC) ~ 51 °C. The distinct Tm's of the two lipids provide a broad gel-fluid phase with a significant mismatch (~ 20 Å) between the tail-lengths of the DMPC and DSPC molecules. The structural properties of the vesicles were determined by small-angle neutron and x-ray scattering and the collective lipid dynamics in the bilayer were investigated by neutron spin-echo (NSE) spectroscopy on selectively deuterated samples. The NSE results indicate a slowdown of thickness fluctuations in the gel-fluid coexistence phase and an intriguingly strong enhancement in the thickness fluctuation amplitude for T >Tm(DSPC) compared to our previous work on single component vesicles.

  12. Neutron reflectivity studies of single lipid bilayers supported on planar substrates

    Energy Technology Data Exchange (ETDEWEB)

    Krueger, S.; Orts, W.J.; Berk, N.F.; Majkrzak, C.F. [National Inst. of Standards and Technology, Gaithersburg, MD (United States); Koenig, B.W. [National Inst. of Health, Bethesda, MD (United States)


    Neutron reflectivity was used to probe the structure of single phosphatidylcholine (PC) lipid bilayers adsorbed onto a planar silicon surface in an aqueous environment. Fluctuations in the neutron scattering length density profiles perpendicular to the silicon/water interface were determined for different lipids as a function of the hydrocarbon chain length. The lipids were studied in both the gel and liquid crystalline phases by monitoring changes in the specularly-reflected neutron intensity as a function of temperature. Contrast variation of the neutron scattering length density was applied to both the lipid and the solvent. Scattering length density profiles were determined using both model-independent and model-dependent fitting methods. During the reflectivity measurements, a novel experimental set-up was implemented to decrease the incoherent background scattering due to the solvent. Thus, the reflectivity was measured to Q {approx} 0.3{Angstrom}{sup -1}, covering up to seven orders of magnitude in reflected intensity, for PC bilayers in D{sub 2}O and silicon-matched (38% D{sub 2}O/62% H{sub 2}O) water. The kinetics of lipid adsorption at the silicon/water interface were also explored by observing changes in the reflectivity at low Q values under silicon-matched water conditions.

  13. Superdiffusion in supported lipid bilayers

    CERN Document Server

    Campagnola, Grace; Schroder, Bryce W; Peersen, Olve B; Krapf, Diego


    We study the diffusion of membrane-targeting C2 domains using single-molecule tracking in supported lipid bilayers. The ensemble-averaged mean square displacement (MSD) exhibits superdiffusive behavior. However, the time-averaged MSD of individual trajectories is found to be linear with respect to lag time, as in Brownian diffusion. These observations are explained in terms of bulk excursions that introduce jumps with a heavy-tail distribution. Our experimental results are shown to agree with analytical models of bulk-mediated diffusion and with numerical simulations.

  14. Asymmetric bilayer graphene nanoribbon MOSFETs for analog and digital electronics (United States)

    Dinarvand, A.; Ahmadi, V.; Darvish, Gh.


    In this paper, a new structure was proposed for bilayer graphene nanoribbon field-effect transistor (BGNFET) mainly to enhance the electrical characteristics in analog and digital applications. The proposed device uses two metallic gates on the top and bottom of a bilayer graphene nanoribbon, which is surrounded by SiO2 and connected to heavily doped source/drain contacts. Electrical properties of the proposed device were explored using fully self-consistent solution of Poisson and Schrödinger equations based on the nonequilibrium Green's function (NEGF) formalism. Significant improvements in the electrical behavior was seen in the simulation results for gates asymmetrically biased. The comparison with graphene nanoribbon FET showed that the proposed structure benefited from higher intrinsic voltage gain and cut-off frequency and improved switching characteristics such as delay and Ion/Ioff ratio.

  15. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica


    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

  16. A Broadband High-Gain Bi-Layer Log-Periodic Dipole Array (LPDA) for Ultra High Frequency (UHF) Conformal Load Bearing Antenna Structures (CLAS) Applications (United States)


    antenna ,’’ IEEE Trans. Antennas Propag., Vol. 57, pp. 3458-3466, Nov. 2009. [12] A. Calmon, G. Pacheco, M.A.B. Terada, “A novel reconfigurable UWB log...Frequency reconfigurable compact multiband quasi-log periodic dipole array (QLPDA) antenna for wireless communications,’’ 2010 IEEE Antennas and...BEARING ANTENNA STRUCTURES (CLAS) APPLICATIONS Nicholas A. Bishop and Mohammod Ali University of South Carolina Jason Miller, David L. Zeppettella

  17. Pseudocritical Behavior and Unbinding of Phospholipid Bilayers

    DEFF Research Database (Denmark)

    Lemmich, Jesper; Mortensen, Kell; Ipsen, John Hjorth;


    The temperature dependence of the small-angle neutron scattering from fully hydrated multilamellar phospholipid bilayers near the main phase transition is analyzed by means of a simple geometric model which yields both the lamellar repeat distance as well as the hydrophobic thickness of the bilayer...

  18. Structural and electronic properties of epitaxial YBa{sub 2}Cu{sub 3}O{sub 7−δ}–La{sub 0.67}Ca{sub 0.33}MnO{sub 3} bilayers grown on SrTiO{sub 3} (1 1 0) substrates

    Energy Technology Data Exchange (ETDEWEB)

    Mustafa, L.; Driza, N. [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany); Soltan, S. [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany); Faculty of Science, Helwan University, 11795-Cairo (Egypt); Le Tacon, M. [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany); Habermeier, H.-U., E-mail: [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany); Keimer, B. [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany)


    Highlights: • Preparation of (1 1 0) YBCO–LCMO bilayers free of admixtures of (0 0 1) and/or (1 0 3) grains of YBCO. • Structure induced highly anisotropic charge transport and magnetic properties of the film. • New perspectives for the exploration of the interplay between high-temperature superconductivity and ferromagnetism. - Abstract: Epitaxial bilayers of the high-temperature-superconductor YBa{sub 2}Cu{sub 3}O{sub 7−δ} (YBCO) and the ferromagnetic metal La{sub 0.67}Ca{sub 0.33}MnO{sub 3} (LCMO) were prepared by pulsed laser deposition on (1 1 0)-oriented SrTiO{sub 3} substrates, such that the CuO{sub 2} planes of YBCO are perpendicular to the YBCO–LCMO interface. X-ray diffraction and Raman scattering demonstrate complete (1 1 0) orientation of both YBCO and LCMO overlayers. The resistivity and magnetization of the bilayer films are highly anisotropic. The critical temperatures for superconductivity and ferromagnetism as well as the saturation magnetization exhibit modest reductions compared to corresponding bulk values.

  19. Coherence and Optical Emission from Bilayer Exciton Condensates

    Directory of Open Access Journals (Sweden)

    D. W. Snoke


    Full Text Available Experiments aimed at demonstrating Bose-Einstein condensation of excitons in two types of experiments with bilayer structures (coupled quantum wells are reviewed, with an emphasis on the basic effects. Bose-Einstein condensation implies the existence of a macroscopic coherence, also known as off-diagonal long-range order, and proposed tests and past claims for coherence in these excitonic systems are discussed.

  20. Self-assembling bilayers of palladiumthiolates in organic media

    Indian Academy of Sciences (India)

    P John Thomas; A Lavanya; V Sabareesh; G U Kulkarni


    Alkylthiolates of palladium forming a homologous series (butyl to octadecyl) have been prepared and characterized using X-ray diffraction and STM. The thiolates adopt an unusual bilayered lamellar structure, whose thickness is governed by the length of the alkyl chain. These mesophases melt in the temperature range, 60° to 100°C, with the melting point increasing linearly with the thiol chain length. There is evidence to suggest that the alkyl chains are orientationally disordered especially prior to melting.

  1. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)


    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  2. Planar bilayer membranes from photoactivable phospholipids. (United States)

    Borle, F; Sänger, M; Sigrist, H


    Planar bilayer membranes formed from photoactivable phospholipids have been characterized by low frequency voltametry. Cyclic voltametric measurements were applied for simultaneous registration of planar membrane conductivity and capacitance. The procedure has been utilized to characterize the formation and stability of planar bilayer membranes. Bilayer membranes were formed from N'-(1,2-dimyristoyl-sn-glycero-3-phosphoethyl)-N-((m-3- trifluoromethyldiazirine)phenyl)thiourea (C14-PED), a head-group photosensitive phospholipid. In situ photoactivation of C14-PED at wavelengths greater than or equal to 320 nm altered neither the mean conductivity nor the capacitance of the bilayer. Ionophore (valinomycin) and ion channel (gramicidin) activities were not impaired upon photoactivation. In contrast, bilayer membranes formed from 1,2-bis(hexadeca-2,4-dienoyl)-sn- glycero-3-phosphocholine (C16-DENPC) revealed short life times. In situ photopolymerization of the diene fatty acids significantly increased the membrane conductivity or led to membrane rupture.


    Ünlü, Ali; Dettweiler, Ulrich


    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  4. Electron Crystallographic Study on Structure Determination for Minute Crystals

    Institute of Scientific and Technical Information of China (English)

    LI Fanghua; FAN Haifu; WAN Zhenghua; HU Jianjun; TANG Dong


    @@ In the 1970s the development of high-resolution electron microscopy (HREM) provided a new approach to structure determination for minute crystals, which is thoroughly different from the diffraction methods.However, the previous method of trial and error has its own limits, such as some preliminary structural information must be known in advance; the crystals must be sufficient strong under the electron beam irradiation;and not all atoms can be seen in the image. Two ideas were proposed to initiate the present research project:one is to transform an arbitrary image into the crystal structure map, and the other is to enhance the image resolution by combining the information contained in the image and the corresponding electron diffraction pattern. These ideas have been realized via the combination of electron microscopy and diffraction crystallography.

  5. Structure determines medication errors in nursing units: a mechanistic approach. (United States)

    Hung, Chang-Chiao; Lee, Bih-O; Tsai, Shu-Ling; Tseng, Yun Shan; Chang, Chia-Hao


    Medication errors have long been considered critical in global health care systems. However, few studies have been conducted to explore the effects of nursing unit structure on medication errors. The purpose of this study, therefore, was to determine the effects of structural factors on medication errors in nursing units. A total of 977 staff nurses and 62 head nurses participated in this cross-sectional design study. The findings show that professional autonomy (β = .53, t = 6.03, p nursing experts (β = .52, t = 5.99, p medication error rates. This study shows that the structural factors influence medication administration and the mechanistic approach is specifically in relation of low medication error rates. The author suggests that head nurses should consider strategies that require adjustments to unit control mechanisms.

  6. Local magnetic structure determination using polarized neutron holography

    Energy Technology Data Exchange (ETDEWEB)

    Szakál, Alex, E-mail:; Markó, Márton, E-mail:; Cser, László, E-mail: [Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest (Hungary)


    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  7. Anisotropic metal growth on phospholipid nanodiscs via lipid bilayer expansion (United States)

    Oertel, Jana; Keller, Adrian; Prinz, Julia; Schreiber, Benjamin; Hübner, René; Kerbusch, Jochen; Bald, Ilko; Fahmy, Karim


    Self-assembling biomolecules provide attractive templates for the preparation of metallic nanostructures. However, the intuitive transfer of the “outer shape” of the assembled macromolecules to the final metallic particle depends on the intermolecular forces among the biomolecules which compete with interactions between template molecules and the metal during metallization. The shape of the bio-template may thus be more dynamic than generally assumed. Here, we have studied the metallization of phospholipid nanodiscs which are discoidal particles of ~10 nm diameter containing a lipid bilayer ~5 nm thick. Using negatively charged lipids, electrostatic adsorption of amine-coated Au nanoparticles was achieved and followed by electroless gold deposition. Whereas Au nanoparticle adsorption preserves the shape of the bio-template, metallization proceeds via invasion of Au into the hydrophobic core of the nanodisc. Thereby, the lipidic phase induces a lateral growth that increases the diameter but not the original thickness of the template. Infrared spectroscopy reveals lipid expansion and suggests the existence of internal gaps in the metallized nanodiscs, which is confirmed by surface-enhanced Raman scattering from the encapsulated lipids. Interference of metallic growth with non-covalent interactions can thus become itself a shape-determining factor in the metallization of particularly soft and structurally anisotropic biomaterials.

  8. Electrostatic interactions at the microscale modulate dynamics and distribution of lipids in bilayers. (United States)

    Mangiarotti, Agustín; Wilke, Natalia


    For decades, it has been assumed that electrostatic long-range (micron distances) repulsions in lipid bilayers are negligible due to screening from the aqueous milieu. This concept, mostly derived from theoretical calculations, is broadly accepted in the biophysical community. Here we present experimental evidence showing that domain-domain electrostatic repulsions in charged and also in neutral lipid bilayers regulate the diffusion, in-plane structuring and merging of lipid domains in the micron range. All the experiments were performed on both, lipid monolayers and bilayers, and the remarkable similarity in the results found in bilayers compared to monolayers led us to propose that inter-domain repulsions occur mainly within the plane of the membrane. Finally, our results indicate that electrostatic interactions between the species inserted in a cell membrane are not negligible, not only at nanometric but also at larger distances, suggesting another manner for regulating the membrane properties.

  9. Correlation effects in (111) bilayers of perovskite transition-metal oxides

    Energy Technology Data Exchange (ETDEWEB)

    Okamoto, Satoshi [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Zhu, Wenguang [Univ. of Science and Technology of China, Hefei (China); Nomura, Yusuke [Univ. of Tokyo (Japan); Arita, R. [Univ. of Tokyo (Japan); Xiao, Di [Carnegie Mellon Univ., Pittsburgh, PA (United States); Nagaosa, Naoto [Univ. of Tokyo (Japan); RIKEN Center for Emergent Matter Science (CEMS), Saitama (Japan)


    We investigate the correlation-induced Mott, magnetic, and topological phase transitions in artificial (111) bilayers of perovskite transition-metal oxides LaAuO3 and SrIrO3 for which the previous density-functional theory calculations predicted topological insulating states. Using the dynamical-mean-field theory with realistic band structures and Coulomb interactions, LaAuO3 bilayer is shown to be far away from a Mott insulating regime, and a topological-insulating state is robust. On the other hand, SrIrO3 bilayer is on the verge of an orbital-selective topological Mott transition and turns to a trivial insulator by an antiferromagnetic ordering. Oxide bilayers thus provide a novel class of topological materials for which the interplay between the spin-orbit coupling and electron-electron interactions is a fundamental ingredient.

  10. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy. (United States)

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu


    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  11. Camber Evolution and Stress Development of Porous Ceramic Bilayers During Co-Firing

    DEFF Research Database (Denmark)

    Ni, De Wei; Esposito, Vincenzo; Schmidt, Cristine Grings;


    Camber evolution and stress development during co-firing of asymmetric bilayer laminates, consisting of porous Ce0.9Gd0.1O1.95 gadolinium-doped cerium oxide (CGO) and La0.85Sr0.15MnO3 lanthanum strontium manganate (LSM)-CGO were investigated. Individual layer shrinkage was measured by optical...... dilatometer, and the uniaxial viscosities were determined as a function of layer density using a vertical sintering approach. The camber evolution in the bilayer laminates was recorded in situ during co-firing and it was found to correspond well with the one predicted by the theoretical model. The estimated...... sintering mismatch stress in co-fired CGO-LSM/CGO bilayer laminates was significantly lower than general sintering stresses expected for free sintering conditions. As a result, no co-firing defects were observed in the bilayer laminates, illustrating an acceptable sintering compatibility of the ceramic...

  12. Enhanced sensitivity of a microfabricated resonator using a graphene-polystyrene bilayer membrane (United States)

    Yun, Minhyuk; Lee, Eunho; Cho, Kilwon; Jeon, Sangmin


    A graphene layer was synthesized using chemical vapor deposition methods and a polystyrene solution was spin-cast onto the graphene film. The graphene-polystyrene bilayer membrane was attached between the two tines of a microfabricated quartz tuning fork (QTF). The modulus of the graphene-polystyrene bilayer was measured to be twice that of a pristine polystyrene membrane. Exposure of the membrane-coated QTF to ethanol vapor decreased the resonance frequency of the microresonator. The bilayer membrane-coated QTF produced a frequency change that was three times the change obtained using a polystyrene membrane-coated QTF, with a lower degree of degradation in the Q factor. The limit of detection of the bilayer membrane-coated QTF to ethanol vapor was determined to be 20 ppm.

  13. Enhanced sensitivity of a microfabricated resonator using a graphene-polystyrene bilayer membrane

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Minhyuk; Lee, Eunho; Cho, Kilwon; Jeon, Sangmin, E-mail: [Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang (Korea, Republic of)


    A graphene layer was synthesized using chemical vapor deposition methods and a polystyrene solution was spin-cast onto the graphene film. The graphene-polystyrene bilayer membrane was attached between the two tines of a microfabricated quartz tuning fork (QTF). The modulus of the graphene-polystyrene bilayer was measured to be twice that of a pristine polystyrene membrane. Exposure of the membrane-coated QTF to ethanol vapor decreased the resonance frequency of the microresonator. The bilayer membrane-coated QTF produced a frequency change that was three times the change obtained using a polystyrene membrane-coated QTF, with a lower degree of degradation in the Q factor. The limit of detection of the bilayer membrane-coated QTF to ethanol vapor was determined to be 20 ppm.

  14. Effect of Y2O3 stabilized ZrO2 coating with tri-model structure on bi-layered thermally grown oxide evolution in nano thermal barrier coating systems at elevated temperatures

    Institute of Scientific and Technical Information of China (English)

    Mohammadreza Daroonparvar; Muhamad Azizi Mat Yajid; Noordin Mohd Yusof; Hamid Reza Bakhsheshi-Rad; Z Valefi; Esah Hamzah


    Bi-layered thermally grown oxide (TGO) layer plays a major role in the spallation of Y2O3 stabilized ZrO2 (YSZ) layer form the bond coat in the thermal barrier coating (TBC) systems during oxidation. On the other hand, bi-layered TGO formation and growth in the TBC systems with nanostructured YSZ have not been deeply investigated during cyclic oxidation. Hence, Inconel 738/NiCrAlY/normal YSZ and Inconel 738/NiCrAlY/nano YSZ systems were pre-oxidized at 1000 °C and then subjected to cyclic oxidation at 1150 °C. According to microstructural observations, nanostructured YSZ layer over the bond coat should have less mi-cro-cracks and pinholes, due to the compactness of the nanostructure and the presence of nano zones that resulted in lower O infiltration into the nanothermal barrier coating system, formation of thinner and nearly continuous mono-layered thermally grown oxide on the bond coat during pre-oxidation, lower spinels formation at the Al2O3/YSZ interface and finally, reduction of bi-layered thermally grown oxide thickness during cyclic oxidation. It was found that pre-heat treatment and particularly coating microstructure could influence microstructural evolution (bi-layered TGO thickness) and durability of thermal barrier coating systems during cyclic oxidation.

  15. Monolithic multiscale bilayer inverse opal electrodes for dye-sensitized solar cell applications. (United States)

    Lee, Jung Woo; Moon, Jun Hyuk


    Multilayer structures in which the layers are both electrically and physically connected are critical to be used as high-performance electrodes for photovoltaic devices. We present the first multiscale bilayer inverse opal (IO) structures for application as electrodes in dye-sensitized solar cells (DSCs). A bilayer of a mesoscopic IO layer (70 nm pore diameter) and a top macroporous IO layer (215 nm and 250 nm pore diameters) was fabricated as the high-specific-area electrode and the light-harvesting enhancing layer, respectively. The mesoscopic IO layer exhibits a dye-adsorption density, which is approximately 4 times greater than that of the macroporous IO structure because of its small pore size. The macroporous IO layer exhibits a photonic bandgap reflection in the visible-light wavelength range. We incorporated the bilayer IO electrodes into DSCs and compared the effects of the pore sizes of the macroporous layers on the photocurrent densities of the DSCs. We observed that the bilayer IO electrode DSCs that contained a 250 nm IO layer exhibited photocurrent densities greater than those of 215 nm IO DSCs. This enhanced photocurrent density was achieved because the photonic bandgap (PBG) reflection wavelength matches the wavelength range in which the N719 dye has a small light-absorption coefficient. The fabrication of this structurally homogeneous IO bilayer allows a strong contact between the layers, and the resulting bilayer, therefore, exhibits a high photovoltaic performance. We believe that this bilayer structure provides an alternative approach to the development of optimized electrode structures for various devices.

  16. Mechanical properties of electrospun bilayer fibrous membranes as potential scaffolds for tissue engineering. (United States)

    Pu, Juan; Komvopoulos, Kyriakos


    Bilayer fibrous membranes of poly(l-lactic acid) (PLLA) were fabricated by electrospinning, using a parallel-disk mandrel configuration that resulted in the sequential deposition of a layer with fibers aligned across the two parallel disks and a layer with randomly oriented fibers, both layers deposited in a single process step. Membrane structure and fiber alignment were characterized by scanning electron microscopy and two-dimensional fast Fourier transform. Because of the intricacies of the generated electric field, bilayer membranes exhibited higher porosity than single-layer membranes consisting of randomly oriented fibers fabricated with a solid-drum collector. However, despite their higher porosity, bilayer membranes demonstrated generally higher elastic modulus, yield strength and toughness than single-layer membranes with random fibers. Bilayer membrane deformation at relatively high strain rates comprised multiple abrupt microfracture events characterized by discontinuous fiber breakage. Bilayer membrane elongation yielded excessive necking of the layer with random fibers and remarkable fiber stretching (on the order of 400%) in the layer with fibers aligned in the stress direction. In addition, fibers in both layers exhibited multiple localized necking, attributed to the nonuniform distribution of crystalline phases in the fibrillar structure. The high membrane porosity, good mechanical properties, and good biocompatibility and biodegradability of PLLA (demonstrated in previous studies) make the present bilayer membranes good scaffold candidates for a wide range of tissue engineering applications.

  17. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L


    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  18. Bilayer molecular assembly at a solid/liquid interface as triggered by a mild electric field. (United States)

    Zheng, Qing-Na; Liu, Xuan-He; Liu, Xing-Rui; Chen, Ting; Yan, Hui-Juan; Zhong, Yu-Wu; Wang, Dong; Wan, Li-Jun


    The construction of a spatially defined assembly of molecular building blocks, especially in the vertical direction, presents a great challenge for surface molecular engineering. Herein, we demonstrate that an electric field applied between an STM tip and a substrate triggered the formation of a bilayer structure at the solid-liquid interface. In contrast to the typical high electric-field strength (10(9)  V m(-1) ) used to induce structural transitions in supramolecular assemblies, a mild electric field (10(5)  V m(-1) ) triggered the formation of a bilayer structure of a polar molecule on top of a nanoporous network of trimesic acid on graphite. The bilayer structure was transformed into a monolayer kagome structure by changing the polarity of the electric field. This tailored formation and large-scale phase transformation of a molecular assembly in the perpendicular dimension by a mild electric field opens perspectives for the manipulation of surface molecular nanoarchitectures.

  19. Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations (United States)

    Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.


    Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

  20. First-principles modeling hydrogenation of bilayered boron nitride (United States)

    Jing, Wang; Peng, Zhang; Xiang-Mei, Duan


    We have investigated the structural and electronic characteristics of hydrogenated boron-nitride bilayer (H-BNBN-H) using first-principles calculations. The results show that hydrogenation can significantly reduce the energy gap of the BN-BN into the visible-light region. Interestingly, the electric field induced by the interface dipoles helps to promote the formation of well-separated electron-hole pairs, as demonstrated by the charge distribution of the VBM and CBM. Moreover, the applied bias voltage on the vertical direction of the bilayer could modulate the band gap, resulting in transition from semiconductor to metal. We conclude that H-BNBN-H could improve the solar energy conversion efficiency, which may provide a new way for tuning the electronic devices to meet different environments and demands. Project supported by the National Natural Science Foundation of China (Grant No. 11574167).

  1. Biotechnology Applications of Tethered Lipid Bilayer Membranes

    Directory of Open Access Journals (Sweden)

    Joshua A. Jackman


    Full Text Available The importance of cell membranes in biological systems has prompted the development of model membrane platforms that recapitulate fundamental aspects of membrane biology, especially the lipid bilayer environment. Tethered lipid bilayers represent one of the most promising classes of model membranes and are based on the immobilization of a planar lipid bilayer on a solid support that enables characterization by a wide range of surface-sensitive analytical techniques. Moreover, as the result of molecular engineering inspired by biology, tethered bilayers are increasingly able to mimic fundamental properties of natural cell membranes, including fluidity, electrical sealing and hosting transmembrane proteins. At the same time, new methods have been employed to improve the durability of tethered bilayers, with shelf-lives now reaching the order of weeks and months. Taken together, the capabilities of tethered lipid bilayers have opened the door to biotechnology applications in healthcare, environmental monitoring and energy storage. In this review, several examples of such applications are presented. Beyond the particulars of each example, the focus of this review is on the emerging design and characterization strategies that made these applications possible. By drawing connections between these strategies and promising research results, future opportunities for tethered lipid bilayers within the biotechnology field are discussed.

  2. Effect of annealing on the characteristics of Au/Ni50Fe50 bilayer films grown on glass

    Institute of Scientific and Technical Information of China (English)

    Hao Qian; Hong Qiu; Xiaobai Chen; Yue Tian; Ping Wu; Fengping Wang; Liqing Pan


    Sputter-deposited Au/Ni50Fe50 bilayer films were annealed in a vacuum of 5×10-4 Pa at 523 to 723 K for 30 or 90 min. The characteristics of the bilayer films were determined by Auger electron spectroscopy, field emission scanning electron microscopy, X-ray diffractometry, a four-point probe technique, and an alternating gradient magnetometer. When the annealing temperature and time reached 723 K and 90 min, Ni and Fe atoms markedly diffused into the Au layer. The grain size of the Au layer did not change markedly with the annealing condition. As the annealing time was 30 min and the annealing temperature exceeded 573 K, the resistance of the bilayer film increased with increasing the annealing temperature. Furthermore, the resistance of the bilayer film annealed at 723 K for 90 min was lower than that of the bilayer film annealed at 723 K for 30 min. All the bilayer films showed magnetic hysteresis loops. The as-deposited bilayer film showed a hard magnetization. The bilayer film represented an easy magnetization with increasing the annealing temperature. The Au/Ni50Fe50 film that annealed at 723 K for 90 min had the lowest saturation magnetization.

  3. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy (United States)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  4. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)


    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  5. Crystal structure determination of anti-DNA Fab A52. (United States)

    Stanfield, Robyn L; Eilat, Dan


    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  6. Texture of lipid bilayer domains

    DEFF Research Database (Denmark)

    Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov;


    We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain...... are well studied, the possibility of texture in gel domains has so far not been examined. When using polarized light for two-photon excitation of the fluorescent lipid probe Laurdan, the emission intensity is highly sensitive to the angle between the polarization and the tilt orientation of lipid acyl...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method...

  7. Aqueous solutions at the interface with phospholipid bilayers. (United States)

    Berkowitz, Max L; Vácha, Robert


    In a sense, life is defined by membranes, because they delineate the barrier between the living cell and its surroundings. Membranes are also essential for regulating the machinery of life throughout many interfaces within the cell's interior. A large number of experimental, computational, and theoretical studies have demonstrated how the properties of water and ionic aqueous solutions change due to the vicinity of membranes and, in turn, how the properties of membranes depend on the presence of aqueous solutions. Consequently, understanding the character of aqueous solutions at their interface with biological membranes is critical to research progress on many fronts. The importance of incorporating a molecular-level description of water into the study of biomembrane surfaces was demonstrated by an examination of the interaction between phospholipid bilayers that can serve as model biological membranes. The results showed that, in addition to well-known forces, such as van der Waals and screened Coulomb, one has to consider a repulsion force due to the removal of water between surfaces. It was also known that physicochemical properties of biological membranes are strongly influenced by the specific character of the ions in the surrounding aqueous solutions because of the observation that different anions produce different effects on muscle twitch tension. In this Account, we describe the interaction of pure water, and also of aqueous ionic solutions, with model membranes. We show that a symbiosis of experimental and computational work over the past few years has resulted in substantial progress in the field. We now better understand the origin of the hydration force, the structural properties of water at the interface with phospholipid bilayers, and the influence of phospholipid headgroups on the dynamics of water. We also improved our knowledge of the ion-specific effect, which is observed at the interface of the phospholipid bilayer and aqueous solution, and its

  8. Fragmented state of lipid bilayers in water

    DEFF Research Database (Denmark)

    Helfrich, W.; Thimmel, J.; Klösgen, Beate Maria


    The bilayers of some typical biological membrane lipids such as PC and DGDG disintegrate in a large excess of water to form an optically invisible dispersive bilayer phase. `Dark bodies' can be reversibly precipitated from it by raising the temperature. The dispersive phase probably consists...... of `knotted sticks', i.e. very thin nodular tubes of bilayer. After reviewing pertinent experimental and theoretical work we report on the discovery of a lower consolute point near room temperature in DGDG/water systems. Its existence shows that the dispersive phase and the dark bodies belong to the same...

  9. Bilayer-thickness-mediated interactions between integral membrane proteins

    CERN Document Server

    Kahraman, Osman; Klug, William S; Haselwandter, Christoph A


    Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology al...

  10. Simulated microgravity impacts the plant plasmalemma lipid bilayer (United States)

    Nedukha, Olena; Berkovich, Yuliy A.; Vorobyeva, Tamara; Grakhov, Volodimir; Klimenko, Elena; Zhupanov, Ivan; Jadko, Sergiy

    Biological membranes, especially the plasmalemma, and their properties and functions can be considered one of the most sensitive indicators of gravity interaction or alteration of gravity, respectively. Studies on the molecular basis of cellular signal perception and transduction are very important in order to understand signal responses at the cellular and organism level. The plasmalemma lipid bilayer is the boundary between the cell internal and external environment and mediates communication between them. Therefore, we studied the content and composition of lipids, saturated and unsaturated fatty acids, sterols, and microviscosity in the plasmalemma isolated from pea seedling roots and epicotyls grown in the stationary conditions and under slow horizontal clinorotation. In addition, lipid peroxidation intensity of intact roots was also identified. The plasmalemma fraction was isolated by the two-phase aquatic-polymer system optimized for pea using a centrifuge Optima L-90K. Lipid bilayer components were determined by using highly effective liquid chromatography with a system Angilent 1100 (Germany). Spontaneous chemiluminescence intensity was measured with a chemiluminometer ChLMTS-01. The obtained data showed that plasmalemma investigated parameters are sensitive to clinorotation, namely: increasing or decreasing the different lipids content, among which, phospho- and glycolipids were dominated, as well as changes in the content of saturated and unsaturated fatty acids and sterols. A degree of plasmalemma sensitivity to clinorotation was higher for the root plasmalemma than epicocotyl ones. This distinguish may be naturally explained by the differences in the structure, cell types, growth, and specific functions of a root and an epicotyl, those are the most complicated in roots. An index of unsaturation under clinorotation was similar to that in the stationary conditions as a result of the certain balance between changes in the content of saturated and

  11. Topological phase transition in hexagonal boron-nitride bilayers modulated by gate voltage (United States)

    Jin, Guojun; Zhai, Xuechao


    We study the gate-voltage modulated electronic properties of hexagonal boron-nitride bilayers with two different stacking structures in the presence of intrinsic and Rashba spin-orbit interactions. Our analytical results show that there are striking cooperation effects arising from the spin-orbit interactions and the interlayer bias voltage. For realizing topological phase transition, in contrast to a gated graphene bilayer for increasing its energy gap, the energy gap of a boron-nitride bilayer is significantly reduced by an applied gate voltage. For the AA stacking-bilayer which has the inversion symmetry, a strong topological phase is found, and there is an interesting reentrant behavior from a normal phase to a topological phase and then to a normal phase again, characterized by the topological index. Therefore, the gate voltage modulated AA-boron nitride bilayer can be taken as a newcomer of the topological insulator family. For the AB stacking-bilayer which is lack of the inversion symmetry, it is always topologically trivial, but exhibits an unusual quantum Hall phase with four degenerate low-energy states localized at a single edge. It is suggested that these theoretical findings could be verified experimentally in the transport properties of boron-nitride bylayers. This research was supported by the NSFC (Nos. 60876065, 11074108), PAPD, and NBRPC (Nos. 2009CB929504, 2011CB922102).

  12. Dissipative particle dynamics simulation study of the bilayer-vesicle transition

    Institute of Scientific and Technical Information of China (English)


    A bilayer structure is an important immediate for the vesicle formation. However,the mechanism for the bilayer-vesicle transition remains unclear. In this work,a dissipative particle dynamics(DPD) simulation method was employed to study the mechanism of the bilayer-vesicle transition. A coarse-grained model was built based on a lipid molecule termed dimyristoylphosphatidylcholine(DMPC). Simulations were performed from two different initial configurations:a random dispersed solution and a tensionless bilayer. It was found that the bilayer-vesicle transition was driven by the minimization of the water-tail hydrophobic interaction energy,and was accompanied with the increase of the position entropy due to the redistribution of water molecules. The bulk pressure was reduced during the bilayer-vesicle transition,suggesting the evolved vesicle morphology was at the relatively low free energy state. The membrane in the product vesicle was a two-dimensional fluid. It can be concluded that the membrane of a vesicle is not interdigitated and most of the bonds in lipid chains are inclined to orient along the radical axis of the vesicle.

  13. Evaluation and biological characterization of bilayer gelatin/chondroitin-6-sulphate/hyaluronic acid membrane. (United States)

    Wang, Tzu-Wei; Sun, Jui-Sheng; Wu, Hsi-Chin; Huang, Yi-Chau; Lin, Feng-Huei


    A biodegradable polymer scaffold was developed using gelatin, chondroitin-6-sulphate, and hyaluronic acid in the form of bilayer network. The bilayer porous structure of gelatin-chondroitin-6-sulphate-hyaluronic acid (G-C6S-HA) membrane was fabricated using different freezing temperatures followed by lyophilization. 1-Ethyl-3(3-dimethylaminopropyl) carbodiimide was used as crosslinking agent to improve the biological stability of the scaffold. The morphology, physical-chemical properties, and biocompatibility of bilayer G-C6S-HA membrane were evaluated in this study. The functional groups change in crosslinked G-C6S-HA scaffold was characterized by fourier transform infrared spectroscopy. The retention of glycosaminoglycan contents and matrix degradation rate were also examined by p-dimethylamino benzaldehyde and 2,4,6-trinitrobenzene sulphonic acid, respectively. Water absorption capacity was carried out to study G-C6S-HA membrane water containing characteristics. The morphology of the bilayer G-C6S-HA membrane was investigated under scanning electron microscope and light microscopy. In vitro biocompatibility was conducted with MTT test, LDH assay, as well as histological analysis. The results showed that the morphology of bilayer G-C6S-HA membrane was well reserved. The physical-chemical properties were also adequate. With good biocompatibility, this bilayer G-C6S-HA membrane would be suitable as a matrix in the application of tissue engineering.

  14. Functional liposomes and supported lipid bilayers: towards the complexity of biological archetypes. (United States)

    Berti, Debora; Caminati, Gabriella; Baglioni, Piero


    This perspective paper provides some illustrative examples on the interplay between information gathered on planar supported lipid bilayers (SLB) and unilamellar lipid vesicles (ULV) to get an integrated description of phenomena occurring at the nanoscale that involve locally bilayered structures. Similarities and differences are underlined and critically compared in terms of biomimetic fidelity and instrumental accessibility to structural and dynamical parameters, focusing on some recent reports that either explicitly address this comparison or introducing some studies that separately investigate the same process in SLB and lipid vesicles. Despite the structural similarity on the nanoscale, the different topology implies radically different characterization techniques that have evolved in sectorial and separated approaches. The quest for increasing levels of compositional complexity for bilayered systems should not result in a loss of structural and dynamical control: this is the central challenge of future research in this area, where the integrated approach highlighted in this contribution would enable improved levels of understanding.

  15. Formation of individual protein channels in lipid bilayers suspended in nanopores. (United States)

    Studer, André; Han, Xiaojun; Winkler, Fritz K; Tiefenauer, Louis X


    Free-standing lipid bilayers are formed in regularly arranged nanopores of 200, 400 and 800 nm in a 300 nm thin hydrophobic silicon nitride membrane separating two fluid compartments. The extraordinary stability of the lipid bilayers allows us to monitor channel formation of the model peptide melittin and alpha-hemolysin from Staphylococcus aureus using electrochemical impedance spectroscopy and chronoamperometry. We observed that melittin channel formation is voltage-dependent and transient, whereas transmembrane heptameric alpha-hemolysin channels in nano-BLMs persist for hours. The onset of alpha-hemolysin-mediated conduction depends on the applied protein concentration and strongly on the diameter of the nanopores. Heptameric channel formation from adsorbed alpha-hemolysin monomers needs more time in bilayers suspended in 200 nm pores compared to bilayers in pores of 400 and 800 nm diameters. Diffusion of sodium ions across alpha-hemolysin channels present in a sufficiently high number in the bilayers was quantitatively and specifically determined using ion selective electrodes. The results demonstrate that relatively small variations of nano-dimensions have a tremendous effect on observable dynamic biomolecular processes. Such nanopore chips are potentially useful as supports for stable lipid bilayers to establish functional assays of membrane proteins needed in basic research and drug discovery.

  16. Structural determinants of tobacco vein mottling virus protease substrate specificity. (United States)

    Sun, Ping; Austin, Brian P; Tözsér, József; Waugh, David S


    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-Å resolution. As observed in several crystal structures of TEV protease, the C-terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1' position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k(cat) and K(m) for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  17. The Vibration Impact Determination of the Helicopter Structural Components

    Directory of Open Access Journals (Sweden)

    Khaksar Zeinab


    Full Text Available This paper presents the determination of the vibration impact of the helicopter structural components and skin repairs in terms of frequency characteristics. To address this issue, a 3D Finite Element Method (FEM model of 349 Gazelle helicopter has been developed in ABAQUS and the frequency analysis is conducted. The results on the natural frequencies of the full structure reasonably match with the literature giving confidence in the baseline model. The main advantage of this FEM model is that, it can be used to predict the natural frequencies of the full structure, precisely. In addition, the material properties and conditions of the components can be updated based on the applied conditions during the repair and maintenance period. Thus, the model gives a comprehensive design tool for analysing the frequencies of the helicopter with differing components. The effective variations in the frequency changes due to repair are predicted numerically. The discussion of these results helps in developing leads to improved selection of replacement materials and their properties.

  18. Structural and electronic properties of epitaxial YBa2Cu3O7-δ-La0.67Ca0.33MnO3 bilayers grown on SrTiO3 (1 1 0) substrates (United States)

    Mustafa, L.; Driza, N.; Soltan, S.; Le Tacon, M.; Habermeier, H.-U.; Keimer, B.


    Epitaxial bilayers of the high-temperature-superconductor YBa2Cu3O7-δ (YBCO) and the ferromagnetic metal La0.67Ca0.33MnO3 (LCMO) were prepared by pulsed laser deposition on (1 1 0)-oriented SrTiO3 substrates, such that the CuO2 planes of YBCO are perpendicular to the YBCO-LCMO interface. X-ray diffraction and Raman scattering demonstrate complete (1 1 0) orientation of both YBCO and LCMO overlayers. The resistivity and magnetization of the bilayer films are highly anisotropic. The critical temperatures for superconductivity and ferromagnetism as well as the saturation magnetization exhibit modest reductions compared to corresponding bulk values.

  19. Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice (United States)

    Sánchez, M. Alejandra; Kling, Tanja; Ishiyama, Tatsuya; van Zadel, Marc-Jan; Mezger, Markus; Jochum, Mara N.; Cyran, Jenée D.; Smit, Wilbert J.; Bakker, Huib J.; Shultz, Mary Jane; Morita, Akihiro; Donadio, Davide; Nagata, Yuki; Bonn, Mischa; Backus, Ellen H. G.


    On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature. PMID:27956637

  20. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)


    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  1. Multiple quantum oscillation frequencies in YBa{sub 2}Cu{sub 3}O{sub 6+{delta}} and bilayer splitting

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Aldea, David; Chakravarty, Sudip, E-mail: sudip@physics.ucla.ed [Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547 (United States)


    Experiments have revealed multiple quantum oscillation frequencies in underdoped high-temperature superconductor YBa{sub 2}Cu{sub 3}O{sub 6+{delta}}, corresponding to approximately 10% doping, which contains CuO bilayers in the unit cell. These unit cells are further coupled along the c-axis by a tunneling matrix element. A model of the energy dispersion that has its roots in the previously determined electronic structure, combined with twofold commensurate density waves, reveals multiple electron and hole pockets. To the extent that quasiparticles of the reconstructed Fermi surface have finite residues, however small, the formation of Landau levels is the cause of these oscillations, and the bilayer splitting and warping of the electronic dispersion along the direction perpendicular to the CuO-planes are firm consequences. The goal here is to explore this possibility from various directions and provide a better understanding of the rapidly developing experimental situation involving multiple frequencies. An important conclusion is that bilayer splitting is considerably renormalized from the value obtained from band structure calculations. It would be extremely interesting to perform these experiments for higher values of doping. We roughly expect the splitting of the frequencies to increase with doping, but the full picture may be more complex because the density wave order parameter is also expected to decrease with doping, vanishing around the middle of the superconducting dome.

  2. The effects of residual stress, viscoelastic and thermodynamic parameters on apparent fracture toughness of dental bilayer ceramic composites (United States)

    Taskonak, Burak

    Bilayer dental ceramic composites used for fixed partial dentures are becoming more widely used in dental practices because of their biocompatibility, aesthetic properties, and chemical durability. However, large statistical variations in the strength of ceramics are associated with the structural flaws as a result of processing and complex stress states within the surfaces of the materials because of thermal properties of each layer. In addition, partial delaminations of the veneer layer and connector fractures of bilayer ceramic fixed partial dentures (FPDs) have been observed in a clinical study which is a part of this dissertation. Analysis of fracture surfaces of failed FPDs reveals that such fractures of the veneering ceramic are most likely caused by lateral crack growth. Global residual stresses associated with the coefficient of thermal expansion differences between core and veneering ceramics can cause lateral crack initiation. Also, rapid cooling of bilayer ceramics from the sintering temperature of the glass veneer may not allow the interfacial stresses in the viscoelastic glass to relax to equilibrium values. This can further contribute to the propagation of lateral cracks. Furthermore, local residual stresses that develop in the plastic deformation zone below sharp contact areas on the occlusal surface are another contributor to lateral crack growth. Superposition of global residual stresses and a Boussinesq stress field can incrementally increase the possibility of lateral crack growth. The long-range goals of this study are to critically analyze the lateral crack growth mechanisms associated with residual stresses, to modify residual tensile stress distributions by controlled heat treatment, and to minimize the probability of veneering ceramic fractures. Four approaches were used to accomplish these goals: (1) clinical evaluation of a bilayer ceramic fixed partial denture system; (2) fracture surface analysis of clinically failed FPDs; (3

  3. Nanoscale structural features determined by AFM for single virus particles. (United States)

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc


    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  4. Dynamic Morphologies of Microscale Droplet Interface Bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Mruetusatorn, Prachya [ORNL; Boreyko, Jonathan B [ORNL; Sarles, Stephen A [ORNL; Venkatesan, Guru [The University of Tennessee; Hayes, Douglas G [ORNL; Collier, Pat [ORNL


    Droplet interface bilayers (DIBs) are a powerful platform for studying the dynamics of synthetic cellular membranes; however, very little has been done to exploit the unique dynamical features of DIBs. Here, we generate microscale droplet interface bilayers ( DIBs) by bringing together femtoliter-volume water droplets in a microfluidic oil channel, and characterize morphological changes of the DIBs as the droplets shrink due to evaporation. By varying the initial conditions of the system, we identify three distinct classes of dynamic morphology. (1) Buckling and Fission: When forming DIBs using the lipid-out method (lipids in oil phase), lipids in the shrinking monolayers continually pair together and slide into the bilayer to conserve their mass. As the bilayer continues to grow, it becomes confined, buckles, and eventually fissions one or more vesicles. (2) Uniform Shrinking: When using the lipid-in method (lipids in water phase) to form DIBs, lipids uniformly transfer from the monolayers and bilayer into vesicles contained inside the water droplets. (3) Stretching and Unzipping: Finally, when the droplets are pinned to the wall(s) of the microfluidic channel, the droplets become stretched during evaporation, culminating in the unzipping of the bilayer and droplet separation. These findings offer a better understanding of the dynamics of coupled lipid interfaces.

  5. Photoinduced electron transfer of chlorophyll in lipid bilayer system

    Indian Academy of Sciences (India)

    D K Lee; K W Seo; Y S Kang


    Photoinduced electron transfer from chlorophyll- through the interface of dipalmitoylphosphatidylcholine (DPPC) headgroup of the lipid bilayers was studied with electron magnetic resonance (EMR). The photoproduced radicals were identified with electron spin resonance (ESR) and radical yields of chlorophyll- were determined by double integration ESR spectra. The formation of vesicles was identified by changes in measured max values from diethyl ether solutions to vesicles solutions indirectly, and observed directly with SEM and TEM images. The efficiency of photosynthesis in model system was determined by measuring the amount of chlorophyll-a radical yields which were obtained from integration of ESR spectra.

  6. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)


    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  7. Magnetostriction of FM/TbFe (FM=Fe, Py-permalloy, FeCo) coupled bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Li Jianjun, E-mail: [National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Harbin Institute of Technology, Harbin150080 (China); Laboratoire de Magnetisme de Bretagne-CNRS FRE 3117, Universite de Bretagne Occidentale, 6, Avenue le Gorgeu C.S. 93837, 29238 Brest Cedex 3 (France)


    Choosing TbFe as the magnetostrictive layer and using soft ferromagnetic materials (FM=Fe, Py-permalloy, FeCo) as the inductive layer, we report the magnetization and magnetostriction of the S/FM(10 nm)/TbFe(10 nm) coupled bilayer (S-glass substrate). The magnetization of the coupled bilayer is attributed to the soft ferromagnetic layer and there is no contribution from the TbFe layer. Interfacial exchange interaction plays an important role in determining the magnetostriction of the coupled bilayer. The effect coming from the deposition Argon pressure on the magnetostriction of the coupled bilayer was also investigated. - Highlights: Black-Right-Pointing-Pointer Choosing TbFe as magnetostrictive layer and with soft ferromagnetic material (FM=Fe, Py-permalloy, FeCo) as inductive layer. Black-Right-Pointing-Pointer We report the magnetization and magnetostriction of the S/FM(10 nm)/TbFe(10 nm) coupled bilayer (S-glass substrate). Black-Right-Pointing-Pointer The magnetization of coupled bilayer is attributed to soft ferromagnetic layer and there is no contribution from TbFe layer. Black-Right-Pointing-Pointer Interfacial exchange interaction plays an important role in determining the magnetostriction of the coupled bilayer.

  8. Modulation of bandgap in bilayer armchair graphene ribbons by tuning vertical and transverse electric fields (United States)

    Vu, Thanh-Tra; Nguyen, Thi-Kim-Quyen; Huynh, Anh-Huy; Phan, Thi-Kim-Loan; Tran, Van-Truong


    We investigate the effects of external electric fields on the electronic properties of bilayer armchair graphene nano-ribbons. Using atomistic simulations with Tight Binding calculations and the Non-equilibrium Green's function formalism, we demonstrate that (i) in semi-metallic structures, vertical fields impact more effectively than transverse fields in terms of opening larger bandgap, showing a contrary phenomenon compared to that demonstrated in previous studies in bilayer zigzag graphene nano-ribbons; (ii) in some semiconducting structures, if transverse fields just show usual effects as in single layer armchair graphene nano-ribbons where the bandgap is suppressed when varying the applied potential, vertical fields exhibit an anomalous phenomenon that the bandgap can be enlarged, i.e., for a structure of width of 16 dimer lines, the bandgap increases from 0.255 eV to the maximum value of 0.40 eV when a vertical bias equates 0.96 V applied. Although the combined effect of two fields does not enlarge the bandgap as found in bilayer zigzag graphene nano-ribbons, it shows that the mutual effect can be useful to reduce faster the bandgap in semiconducting bilayer armchair graphene nano-ribbons. These results are important to fully understand the effects of electric fields on bilayer graphene nano-ribbons (AB stacking) and also suggest appropriate uses of electric gates with different edge orientations.

  9. Determinants of capital structure: New evidence from Portuguese small firms

    Directory of Open Access Journals (Sweden)

    Zélia Serrasqueiro


    Full Text Available This paper studies the determinants of capital structure of 2,329 Portuguese small firms, decomposing total liabilities in long and short-term debt. The results of 2007-2011 panel data suggest that information asymmetry and agency problems seem to be important for small firms in accessing long-term debt. Greater size and a higher level of collateral are quite important in accessing long-term debt. Liquidity is positively associated with long-term debt, although it is negatively related to short-term debt. Higher profitability is related to lower levels of debt. When internal finance is insufficient, these firms seem to be strongly dependent on short-term debt, due to the difficulties in accessing long-term. The main conclusion of the current study is that the predicitons of POT and TOT are followed by small firms in their capital structure, which is in accordance with the results of previous studies focusing on SMEs.

  10. The determinants of capital structure choice: Evidence from Western Europe

    Directory of Open Access Journals (Sweden)

    Ana Mugosa


    Full Text Available This paper examines corporate leverage and its determinants on panel of 921 large Western European companies from 2003 to 2010. The results proved a substantial influence of estimated variables on changes in target debt or leverage ratio. Apart of the determinants from the “core” model, I test the influence of stock price variations on changes in capital structure to conclude if companies “time” the market. The estimation procedure of target debt ratio was performed using Fixed-Effect and FGLS methods. The results were compared to the results of often used methodology in previous research – OLS and Tobit regression. I found statistically significant and negative correlation between target leverage ratio and tangibility, market to book, profitability, product uniqueness and total return (average stock return and statistically significant and positive correlation between target leverage ratio and size. The results suggest the mix of trade-off and pecking order theory predictions and are consistent with findings of previous studies. Future research should focus on impact of leverage deficit (deviations from target leverage ratio on corporate decisions in Europe.

  11. Formation of cholesterol bilayer domains precedes formation of cholesterol crystals in cholesterol/dimyristoylphosphatidylcholine membranes: EPR and DSC studies. (United States)

    Mainali, Laxman; Raguz, Marija; Subczynski, Witold K


    Saturation-recovery EPR along with DSC were used to determine the cholesterol content at which pure cholesterol bilayer domains (CBDs) and cholesterol crystals begin to form in dimyristoylphosphatidylcholine (DMPC) membranes. To preserve compositional homogeneity throughout the membrane suspension, lipid multilamellar dispersions were prepared using a rapid solvent exchange method. The cholesterol content increased from 0 to 75 mol %. With spin-labeled cholesterol analogues, it was shown that the CBDs begin to form at ~50 mol % cholesterol. It was confirmed by DSC that the cholesterol solubility threshold for DMPC membranes is detected at ~66 mol % cholesterol. At levels above this cholesterol content, monohydrate cholesterol crystals start to form. The major finding is that the formation of CBDs precedes formation of cholesterol crystals. The region of the phase diagram for cholesterol contents between 50 and 66 mol % is described as a structured one-phase region in which CBDs have to be supported by the surrounding DMPC bilayer saturated with cholesterol. Thus, the phase boundary located at 66 mol % cholesterol separates the structured one-phase region (liquid-ordered phase of DMPC with CBDs) from the two-phase region where the structured liquid-ordered phase of DMPC coexists with cholesterol crystals. It is likely that CBDs are precursors of monohydrate cholesterol crystals.

  12. The Detection of Structural Deformation Errors in Attitude Determination

    Institute of Scientific and Technical Information of China (English)

    M. J. Moore; C. Rizos; J. Wang


    In the determination of the attitude parameters from a multi-antenna GPS array, one of the major assumptions is that the body frame is rigid at all times. If this assumption is not true then the derived attitude parameters will be in error. It is well known that in airborne platforms the wings often experience some displacement during flight, especially during periods of initializing maneouvres, such as taking off, landing,and banking. Often it is at these points in time that it is most critical to have the most precise attitude parameters.There are a number of techniques available for the detection of modeling errors.The CUSUM algorithm has successfully been implemented in the past to detect small persistent changes. In this paper the authors investigate different methods of generating the residuals, to be tested by the CUSUM algorithm, in an effort to determine which technique is best suited for the detection of structural deformation of an airborne platform. The methods investigated include monitoring the mean of the residuals generated from the difference between the known body frame coordinates, and those calculated from the derived attitude parameters. The generated residuals are then passed to a CUSUM algorithm to detect any small persistent changes. An alternative method involves transforming the generated residuals into the frequency domain through the use of the Fast Fourier Transform. The CUSUM algorithm is then used to detect any frequency changes. The final technique investigated involves transforming the generated residuals using the Haar wavelet. The wavelet coefficients are then monitored by the CUSUM algorithm in order to detect any significant change to the rigidity of the body frame.Detecting structural deformation, and quantifying the degree of deformation, during flight will ensure that these effects can be removed from the system, thus ensuring the most precise and reliable attitude parameter solutions. This paper, through a series

  13. Atomic force microscope visualization of lipid bilayer degradation due to action of phospholipase A(2) and Humicola lanuginosa lipase

    DEFF Research Database (Denmark)

    Balashev, Konstantin; DiNardo, N. John; Callisen, Thomas H.;


    at the surface of a supported lipid bilayer. In particular, the time course of the degradation of lipid bilayers by Phospholipase A(2) (PLA(2)) and Humicola Lanuginosa Lipase (HLL) has been investigated. Contact mode imaging allows visualization of enzyme activity on the substrate with high lateral resolution....... Lipid bilayers were prepared by the Langmuir-Blodgett technique and transferred to an AFM liquid cell. Following injection of the enzyme into the liquid cell, a sequence of images was acquired at regular time intervals to allow the identification of substrate structure, preferred sites of enzyme...

  14. RKKY interaction in bilayer graphene (United States)

    Mohammadi, Yawar; Moradian, Rostam


    We study the RKKY interaction between two magnetic impurities located on the same layer (intralayer case) or on different layers (interlayer case) in undoped bilayer graphene (BLG) in the four-bands model, by directly calculating the Green functions in the eigenvalues and eigenvectors representation. Our results show that both intra- and interlayer RKKY interactions between two magnetic impurities located on the same (opposite) sublattice are always ferromagnetic (antiferromagnetic). Furthermore we find unusual long-distance decay of the RKKY interaction in BLG. The intralyer RKKY interactions between two magnetic impurities located on the same sublattice, J AnAn(R) and J BnBn(R), decay closely as 1 /R6 and 1 /R2 at large impurity distances respectively, but when they are located on opposite sublattices the RKKY interactions exhibit 1 /R4 decays approximately. In the interlayer case, the RKKY interactions between two magnetic impurities located on the same sublattice show a decay close to 1 /R4 at large impurity distances, but if two magnetic impurities be on opposite sublattices the RKKY interactions, J A1B2(R) and J B1A2(R), decay closely as 1 /R6 and 1 /R2 respectively. Both intra- and interlayer RKKY interactions have anisotropic oscillatory factors which for intralayer case is equal to that for single layer graphene (SLG). Our results at weak and strong interlayer coupling limits reduce to the RKKY interaction of SLG and that of BLG in the two-bands approximation respectively.

  15. Automatic Structure Determination of Organic Molecules: Principle and Implementation of the LSD Program

    Institute of Scientific and Technical Information of China (English)



    The LSD (Logic for Structure Determination) program generates organic molecular structures from 1D and 2D NMR data without resorting to chemical shift databases. Its use in the resolution of natural product structure determination problems has been already reported in the literature. This paper describes how data and structures are internally represented and processed by LSD to build solution structures.

  16. Importance of phospholipid bilayer integrity in the analysis of protein–lipid interactions

    Energy Technology Data Exchange (ETDEWEB)

    Drücker, Patrick [Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster (Germany); Gerke, Volker [Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster (Germany); Galla, Hans-Joachim, E-mail: [Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster (Germany)


    Highlights: • We show long-term mechanical stabilization of solid supported bilayers. • Bilayer integrity is essential for the investigation of protein–lipid interactions. • Protein adsorption to a bilayer containing defects causes membrane destruction. - Abstract: The integrity of supported phospholipid bilayer membranes is of crucial importance for the investigation of lipid–protein interactions. Therefore we recorded the formation of supported membranes on SiO{sub 2} and mica by quartz crystal microbalance and controlled the integrity by atomic force microscopy. This study aims to analyze how membrane defects affect protein–lipid interactions. The experiments focused on a lipid mixture of POPC/DOPC/Chol/POPS/PI(4,5)P{sub 2} (37:20:20:20:3) and the binding of the peripheral membrane associated protein annexin A2. We found that formation of a continuous undisturbed bilayer is an indispensable precondition for a reliable determination and quantification of lipid–protein-interactions. If membrane defects were present, protein adsorption causes membrane disruption and lipid detachment on a support thus leading to false determination of binding constants. Our results obtained for PI(4,5)P{sub 2} and cholesterol containing supported membranes yield new knowledge to construct functional surfaces that may cover nanoporous substrates, form free standing membranes or may be used for lab-on-a-chip applications.

  17. Absorption and fluorescence of PRODAN in phospholipid bilayers: a combined quantum mechanics and classical molecular dynamics study. (United States)

    Cwiklik, Lukasz; Aquino, Adelia J A; Vazdar, Mario; Jurkiewicz, Piotr; Pittner, Jiří; Hof, Martin; Lischka, Hans


    Absorption and fluorescence spectra of PRODAN (6-propionyl-2-dimethylaminonaphthalene) were studied by means of the time-dependent density functional theory and the algebraic diagrammatic construction method. The influence of environment, a phosphatidylcholine lipid bilayer and water, was taken into account employing a combination of quantum chemical calculations with empirical force-field molecular dynamics simulations. Additionally, experimental absorption and emission spectra of PRODAN were measured in cyclohexane, water, and lipid vesicles. Both planar and twisted configurations of the first excited state of PRODAN were taken into account. The twisted structure is stabilized in both water and a lipid bilayer, and should be considered as an emitting state in polar environments. Orientation of the excited dye in the lipid bilayer significantly depends on configuration. In the bilayer, the fluorescence spectrum can be regarded as a combination of emission from both planar and twisted structures.

  18. Interlayer couplings, Moiré patterns, and 2D electronic superlattices in MoS2/WSe2 hetero-bilayers (United States)

    Zhang, Chendong; Chuu, Chih-Piao; Ren, Xibiao; Li, Ming-Yang; Li, Lain-Jong; Jin, Chuanhong; Chou, Mei-Yin; Shih, Chih-Kang


    By using direct growth, we create a rotationally aligned MoS2/WSe2 hetero-bilayer as a designer van der Waals heterostructure. With rotational alignment, the lattice mismatch leads to a periodic variation of atomic registry between individual van der Waals layers, exhibiting a Moiré pattern with a well-defined periodicity. By combining scanning tunneling microscopy/spectroscopy, transmission electron microscopy, and first-principles calculations, we investigate interlayer coupling as a function of atomic registry. We quantitatively determine the influence of interlayer coupling on the electronic structure of the hetero-bilayer at different critical points. We show that the direct gap semiconductor concept is retained in the bilayer although the valence and conduction band edges are located at different layers. We further show that the local bandgap is periodically modulated in the X-Y direction with an amplitude of ~0.15 eV, leading to the formation of a two-dimensional electronic superlattice. PMID:28070558

  19. Interlayer couplings, Moiré patterns, and 2D electronic superlattices in MoS 2 /WSe 2 hetero-bilayers

    KAUST Repository

    Zhang, Chendong


    By using direct growth, we create a rotationally aligned MoS2/WSe2 hetero-bilayer as a designer van der Waals heterostructure. With rotational alignment, the lattice mismatch leads to a periodic variation of atomic registry between individual van der Waals layers, exhibiting a Moiré pattern with a well-defined periodicity. By combining scanning tunneling microscopy/spectroscopy, transmission electron microscopy, and first-principles calculations, we investigate interlayer coupling as a function of atomic registry. We quantitatively determine the influence of interlayer coupling on the electronic structure of the hetero-bilayer at different critical points. We show that the direct gap semiconductor concept is retained in the bilayer although the valence and conduction band edges are located at different layers. We further show that the local bandgap is periodically modulated in the X-Y direction with an amplitude of ~0.15 eV, leading to the formation of a two-dimensional electronic superlattice.

  20. Piezoelectricity in asymmetrically strained bilayer graphene (United States)

    Van der Donck, M.; De Beule, C.; Partoens, B.; Peeters, F. M.; Van Duppen, B.


    We study the electronic properties of commensurate faulted bilayer graphene by diagonalizing the one-particle Hamiltonian of the bilayer system in a complete basis of Bloch states of the individual graphene layers. Our novel approach is very general and can be easily extended to any commensurate graphene-based heterostructure. Here, we consider three cases: (i) twisted bilayer graphene, (ii) bilayer graphene where triaxial stress is applied to one layer and (iii) bilayer graphene where uniaxial stress is applied to one layer. We show that the resulting superstructures can be divided into distinct classes, depending on the twist angle or the magnitude of the induced strain. The different classes are distinguished from each other by the interlayer coupling mechanism, resulting in fundamentally different low-energy physics. For the cases of triaxial and uniaxial stress, the individual graphene layers tend to decouple and we find significant charge transfer between the layers. In addition, this piezoelectric effect can be tuned by applying a perpendicular electric field. Finally, we show how our approach can be generalized to multilayer systems.

  1. Magnetoacoustic resonance in magnetoelectric bilayers (United States)

    Filippov, D. A.; Bichurin, M. I.; Petrov, V. M.; Srinivasan, G.


    Layered composites of ferrite and ferroelectric single crystal thin films are of interest for studies on magnetoelectric interactions [1,2]. Such interactions result in unique and novel effects that are absent in single phase materials. For example, in a single crystal composite it is possible to control the ferromagnetic resonance (FMR) parameters for the ferrite by means of hypersonic oscillations induced in the ferroelectric phase. The absorption of acoustic oscillations by the ferrite results in variation in FMR line shape and power absorbed. One anticipates resonance absorption of elastic waves when the frequency of elastic waves coincides with the precession frequency of magnetization vector. This work is concerned with the nature of FMR under the influence of acoustic oscillations with the same frequency as FMR. Bilayers of ferrite and piezoelectric single crystals are considered. Hypersonic waves induced in the piezoelectric phase transmit acoustic power into ferrite due to mechanical connectivity between the phases. That transmission depends strongly on interface coupling [3]. We estimate the resulting variations in ferromagnetic resonance line shape. Estimates of magnetoelectric effect at magnetoacoustic resonance are also given. In addition, dependence of absorption of acoustic power on sample dimensions and compliances, electric and magnetic susceptibilities, piezoelectric and magnetostriction coefficients is discussed. The theory provided here is important for an understanding of interface coupling and the nature of magnetoelastic interactions in the composites. 1. M. I. Bichurin and V. M. Petrov, Zh. Tekh. Fiz. 58, 2277 (1988) [Sov. Phys. Tech. Phys. 33, 1389 (1988)]. 2. M.I. Bichurin, I. A. Kornev, V. M. Petrov, A. S. Tatarenko, Yu. V. Kiliba, and G. Srinivasan. Phys. Rev. B 64, 094409 (2001). 3. M. I. Bichurin, V. M. Petrov, and G. Srinivasan, J. Appl. Phys. 92, 7681 (2002). This work was supported by grants from the Russian Ministry of Education (

  2. Crystal and molecular structures of some organophosphorus insecticides and computer methods for structure determination. [Dissertation

    Energy Technology Data Exchange (ETDEWEB)

    Lapp, R.L.


    Molecular structure investigations of a set of organophosphorus insecticides have been carried out in order to acquire the data base to develop correlations between such parameters and their toxicities. The crystal and molecular structures of dimethoate (LD/sub 50/ (rats) = 600 mg/kg), IPAT, and leptophos (LD/sub 50/ (rats) = 90 mg/kg) have been determined via three-dimensional x-ray analysis. The crystal and molecular structure of (-)-..cap alpha..-phenylethylammonium (-)-0-methyl-phenylphosphonothioate was solved by conventional Patterson and Fourier techniques to a final R value of 0.057. The crystal and molecular structures of two crystalline forms of calcium formate were determined. A new least-squares refinement program was written which is much more general and efficient than any previous program. In particular, a new block-diagonal approximation has been devised which is much more economical than full-matrix refinement and appears to work much better than previous block-diagonal methods. A Howells, Phillips and Rogers test for a center of symmetry and a Wilson plot have been programmed into the data collection algorithm. Some approximations and special problems are discussed relative to implementing these routines in a real-time mode on a minicomputer. A mathematical background and program description are included for each program.

  3. Assessing the amorphousness and periodicity of common domain boundaries in silica bilayers on Ru(0 0 0 1) (United States)

    Burson, Kristen M.; Büchner, Christin; Heyde, Markus; Freund, Hans-Joachim


    Domain boundaries are hypothesized to play a role in the crystalline to amorphous transition. Here we examine domain boundary structures in comparison to crystalline and amorphous structures in bilayer silica grown on Ru(0 0 0 1). Atomically resolved scanning probe microscopy data of boundaries in crystalline bilayer films are analyzed to determine structural motifs. A rich variety of boundary structures including rotational, closed-loop, antiphase, and complex boundaries are identified. Repeating units with ring sizes of 558 and 57 form the two most common domain boundary types. Quantitative metrics are utilized to assess the structural composition and degree of order for the chemically equivalent crystalline, domain boundary, and amorphous structures. It is found that domain boundaries in the crystalline phase show similarities to the amorphous phase in their ring statistics and, in some cases, in terms of the observed ring neighborhoods. However, by assessing order and periodicity, domain boundaries are shown to be distinct from the glassy state. The role of the Ru(0 0 0 1) substrate in influencing grain boundary structure is also discussed.

  4. Structure-dependent charge density as a determinant of antimicrobial activity of peptide analogues of defensin. (United States)

    Bai, Yang; Liu, Shouping; Jiang, Ping; Zhou, Lei; Li, Jing; Tang, Charles; Verma, Chandra; Mu, Yuguang; Beuerman, Roger W; Pervushin, Konstantin


    Defensins are small (3-5 kDa) cysteine-rich cationic proteins found in both vertebrates and invertebrates constituting the front line of host innate immunity. Despite intensive research, bactericidal and cytotoxic mechanisms of defensins are still largely unknown. Moreover, we recently demonstrated that small peptides derived from defensins are even more potent bactericidal agents with less toxicity toward host cells. In this paper, structures of three C-terminal (R36-K45) analogues of human beta-defensin-3 were studied by 1H NMR spectroscopy and extensive molecular dynamics simulations. Because of indications that these peptides might target the inner bacterial membrane, they were reconstituted in dodecylphosphocholine or dodecylphosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] mixed micelles, and lipid bicelles mimicking the phospholipid-constituted bilayer membrane of mammalian and bacterial cells. The results show that the binding affinity and partitioning into the lipid phase and the ability to dimerize and accrete well-defined structures upon interactions with lipid membranes contribute to compactization of positive charges within peptide oligomers. The peptide charge density, mediated by corresponding three-dimensional structures, was found to directly correlate with the antimicrobial activity. These novel observations may provide a new rationale for the design of improved antimicrobial agents.

  5. Spontaneous Formation of Two-Dimensional and Three-Dimensional Cholesterol Crystals in Single Hydrated Lipid Bilayers



    Grazing incidence x-ray diffraction measurements were performed on single hydrated bilayers and monolayers of Ceramide/Cholesterol/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocyholine at varying concentrations. There are substantial differences in the phase and structure behavior of the crystalline domains formed within the bilayers relative to the corresponding monolayers, due to interactions between the opposing lipid leaflets. Depending on the lipid composition, these interactions lead to pha...

  6. Phase Diagram of Antiferromagnetically Exchange-Coupled Bilayer

    Institute of Scientific and Technical Information of China (English)

    GUO Guang-Hua; ZHANG Guang-Fu; SUN Li-Yuan; Peter A. J. de Groot


    Magnetic hysteresis properties of antiferromagnetically exchange-coupled bilayer structures, in which the two magnetic layers have different magnetic parameters and thicknesses, are studied within the framework of the Stoner-Wohifarth model. Analytical expressions for the switching fields corresponding to the linear magnetic states are obtained. By adjusting the magnetic parameters or thicknesses of layers, nine different types of easyaxis hysteresis loops may exist. The phase diagram of easy-axis hysteresis loops is mapped in the k,1 and k,2 plane, where k,1 and k,2 are the ratios of magnetic anisotropy to the interlayer exchange coupling of the two magnetic layers, respectively.

  7. Ultraviolet-induced erasable photochromism in bilayer metal oxide films (United States)

    Terakado, Nobuaki; Tanaka, Keiji; Nakazawa, Akira


    We demonstrate that the optical transmittance of bilayer samples consisting of pyrolytically coated amorphous Mg-Sn-O and metal oxide films such as In 2O 3 and SnO 2 decreases upon ultraviolet illumination, but can be recovered by annealing in air at ˜300 ∘C. Spectral, structural, and compositional studies suggest that this photochromic phenomenon is induced by photoelectronic excitation in the Mg-Sn-O film, electron injection into the metal oxide, which becomes negatively charged, and subsequent formation of metallic particles, which absorb and/or scatter visible light.

  8. Monte Carlo simulation of charge mediated magnetoelectricity in multiferroic bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz-Álvarez, H.H. [Universidad de Caldas, Manizales (Colombia); Universidad Nacional de Colombia Sede Manizales, Manizales, Caldas (Colombia); Bedoya-Hincapié, C.M. [Universidad Nacional de Colombia Sede Manizales, Manizales, Caldas (Colombia); Universidad Santo Tomás, Bogotá (Colombia); Restrepo-Parra, E., E-mail: [Universidad Nacional de Colombia Sede Manizales, Manizales, Caldas (Colombia)


    Simulations of a bilayer ferroelectric/ferromagnetic multiferroic system were carried out, based on the Monte Carlo method and Metropolis dynamics. A generic model was implemented with a Janssen-like Hamiltonian, taking into account magnetoelectric interactions due to charge accumulation at the interface. Two different magnetic exchange constants were considered for accumulation and depletion states. Several screening lengths were also included. Simulations exhibit considerable magnetoelectric effects not only at low temperature, but also at temperature near to the transition point of the ferromagnetic layer. The results match experimental observations for this kind of structure and mechanism.

  9. Multicritical point in a diluted bilayer Heisenberg quantum antiferromagnet. (United States)

    Sandvik, Anders W


    The S=1/2 Heisenberg bilayer antiferromagnet with randomly removed interlayer dimers is studied using quantum Monte Carlo simulations. A zero-temperature multicritical point (p(*),g(*)) at the classical percolation density p=p(*) and interlayer coupling g(*) approximately equal 0.16 is demonstrated. The quantum critical exponents of the percolating cluster are determined using finite-size scaling. It is argued that the associated finite-temperature quantum critical regime extends to zero interlayer coupling and could be relevant for antiferromagnetic cuprates doped with nonmagnetic impurities.

  10. Possible mechanism of adhesion in a mica supported phospholipid bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Pertsin, Alexander, E-mail: [Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg (Germany); Institute of Organo-Element Compounds, Russian Academy of Sciences, Vavilov Str. 28, 117991 Moscow (Russian Federation); Grunze, Michael [Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg (Germany); Institute for Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)


    Phospholipid bilayers supported on hydrophilic solids like silica and mica play a substantial role in fundamental studies and technological applications of phospholipid membranes. In both cases the molecular mechanism of adhesion between the bilayer and the support is of primary interest. Since the possibilities of experimental methods in this specific area are rather limited, the methods of computer simulation acquire great importance. In this paper we use the grand canonical Monte Carlo technique and an atomistic force field to simulate the behavior of a mica supported phospholipid bilayer in pure water as a function of the distance between the bilayer and the support. The simulation reveals a possible adhesion mechanism, where the adhesion is due to individual lipid molecules that protrude from the bilayer and form widely spaced links with the support. Simultaneously, the bilayer remains separated from the bilayer by a thin water interlayer which maintains the bilayer fluidity.

  11. Ionic motion in PEDOT and PPy conducting polymer bilayers

    DEFF Research Database (Denmark)

    Zainudeen, Umer L.; Skaarup, Steen


    Conducting polymer bilayers with poly(3,4-ethylenedioxythiophene) (PEDOT) and polypyrrole (PPy), each containing dodecyl benzenesulfonate (DBS) as immobile dopant species, were synthesized galvanostatically. The electrochemical behaviour of the bilayers was investigated using cyclic voltammetry...

  12. Capacitance Variation of Electrolyte-Gated Bilayer Graphene Based Transistors


    Hediyeh Karimi; Rubiyah Yusof; Mohammad Taghi Ahmadi; Mehdi Saeidmanesh; Meisam Rahmani; Elnaz Akbari; Wong King Kiat


    Quantum capacitance of electrolyte-gated bilayer graphene field-effect transistors is investigated in this paper. Bilayer graphene has received huge attention due to the fact that an energy gap could be opened by chemical doping or by applying external perpendicular electric field. So, this extraordinary property can be exploited to use bilayer graphene as a channel in electrolyte-gated field-effect transistors. The quantum capacitance of bi-layer graphene with an equivalent circuit is presen...

  13. Temperature-induced strain and doping in monolayer and bilayer isotopically labeled graphene (United States)

    Verhagen, T. G. A.; Drogowska, K.; Kalbac, M.; Vejpravova, J.


    The electronic band structure of graphene is strongly dependent on the amount of strain and/or doping present. We performed a comprehensive study of temperature-dependent strain and doping in isotopically labeled graphene mono- and bilayers on a SiO2/Si substrate by Raman spectral mapping at well-defined temperatures between 300 and 10 K. The principal Raman active modes of the graphene (G, 2D) were subjected to correlation analysis, which enabled reliable separation of the strain and doping contributions. The influence of strain on the monolayer and top and bottom layers of the bilayer graphene is large and shows a pronounced temperature-dependent variation. A clear difference is observed in local strain fluctuations on length scales much smaller than the laser spot. In both the monolayer and the bottom layer of the bilayer, which are in contact with the substrate, a significant amount of local strain is induced when the temperature is varied. In contrast, the influence of local strain on the top layer of the bilayer is much smaller. Temperature dependence of the doping is clearly present in both layers, suggesting equalization of the captured charge in the bilayer down to low temperatures.

  14. Feeling the hidden mechanical forces in lipid bilayer is an original sense. (United States)

    Anishkin, Andriy; Loukin, Stephen H; Teng, Jinfeng; Kung, Ching


    Life's origin entails enclosing a compartment to hoard material, energy, and information. The envelope necessarily comprises amphipaths, such as prebiotic fatty acids, to partition the two aqueous domains. The self-assembled lipid bilayer comes with a set of properties including its strong anisotropic internal forces that are chemically or physically malleable. Added bilayer stretch can alter force vectors on embedded proteins to effect conformational change. The force-from-lipid principle was demonstrated 25 y ago when stretches opened purified Escherichia coli MscL channels reconstituted into artificial bilayers. This reductionistic exercise has rigorously been recapitulated recently with two vertebrate mechanosensitive K(+) channels (TREK1 and TRAAK). Membrane stretches have also been known to activate various voltage-, ligand-, or Ca(2+)-gated channels. Careful analyses showed that Kv, the canonical voltage-gated channel, is in fact exquisitely sensitive even to very small tension. In an unexpected context, the canonical transient-receptor-potential channels in the Drosophila eye, long presumed to open by ligand binding, is apparently opened by membrane force due to PIP2 hydrolysis-induced changes in bilayer strain. Being the intimate medium, lipids govern membrane proteins by physics as well as chemistry. This principle should not be a surprise because it parallels water's paramount role in the structure and function of soluble proteins. Today, overt or covert mechanical forces govern cell biological processes and produce sensations. At the genesis, a bilayer's response to osmotic force is likely among the first senses to deal with the capricious primordial sea.

  15. Two-photon absorption in gapped bilayer graphene with a tunable chemical potential (United States)

    Brinkley, M. K.; Abergel, D. S. L.; Clader, B. D.


    Despite the now vast body of two-dimensional materials under study, bilayer graphene remains unique in two ways: it hosts a simultaneously tunable band gap and electron density; and stems from simple fabrication methods. These two advantages underscore why bilayer graphene is critical as a material for optoelectronic applications. In the work that follows, we calculate the one- and two-photon absorption coefficients for degenerate interband absorption in a graphene bilayer hosting an asymmetry gap and adjustable chemical potential—all at finite temperature. Our analysis is comprehensive, characterizing one- and two-photon absorptive behavior over wide ranges of photon energy, gap, chemical potential, and thermal broadening. The two-photon absorption coefficient for bilayer graphene displays a rich structure as a function of photon energy and band gap due to the existence of multiple absorption pathways and the nontrivial dispersion of the low energy bands. This systematic work will prove integral to the design of bilayer-graphene-based nonlinear optical devices.

  16. The Effect of Bilayer Graphene Nanoribbon Geometry on Schottky-Barrier Diode Performance

    Directory of Open Access Journals (Sweden)

    Meisam Rahmani


    Full Text Available Bilayer graphene nanoribbon is a promising material with outstanding physical and electrical properties that offers a wide range of opportunities for advanced applications in future nanoelectronics. In this study, the application of bilayer graphene nanoribbon in schottky-barrier diode is explored due to its different stacking arrangements. In other words, bilayer graphene nanoribbon schottky-barrier diode is proposed as a result of contact between a semiconductor (AB stacking and metal (AA stacking layers. To this end, an analytical model joint with numerical solution of carrier concentration for bilayer graphene nanoribbon in the degenerate and nondegenerate regimes is presented. Moreover, to determine the proposed diode performance, the carrier concentration model is adopted to derive the current-voltage characteristic of the device. The simulated results indicate a strong bilayer graphene nanoribbon geometry and temperature dependence of current-voltage characteristic showing that the forward current of the diode rises by increasing of width. In addition, the lower value of turn-on voltage appears as the more temperature increases. Finally, comparative study indicates that the proposed diode has a better performance compared to the silicon schottky diode, graphene nanoribbon homo-junction contact, and graphene-silicon schottky diode in terms of electrical parameters such as turn-on voltage and forward current.

  17. Wear and corrosion behavior of W/WC bilayers deposited by magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, N.A. de [Excellence Center for Novel Materials, Universidad del Valle, Cali (Colombia); Jaramillo, H.E. [Science and Engineering of Materials Group, Department of Basic Science of Engineering, Universidad Autonoma de Occidente, Cali (Colombia); Department of Energetic and Mechanic, Universidad Autonoma de Occidente, Cali (Colombia); Bejarano, G. [Excellence Center for Novel Materials, Universidad del Valle, Cali (Colombia); Group for Engineering and Materials Development, CDT ASTIN-SENA, Cali (Colombia); Group of Corrosion and Protection, Antioquia University, Medellin (Colombia); Villamil, B.E.; Teran, G. [Richer Young, COLCIENCIAS, Cali (Colombia)


    WC/W coatings were deposited by reactive magnetron sputtering using 40%, 60% and 80% methane CH{sub 4} in the gas mixture. The bilayers were grown on to AISI 420 stainless-steel substrates in order to study the wear and corrosion behavior. Before growing the bilayers, one Ti monolayer was grown to improve the adherence of the coatings to the substrate. The wear resistance and the friction coefficient of the coatings were determined using a pin-on-disk tribometer. All coatings had a friction coefficient of about 0.5. The measured weight lost of the bilayers from each probe allowed the qualitative analysis of wear behavior all coatings. The bilayers grown with 80% methane showed the best abrasive wear resistance and adhesion without failure through the coating in the wear track for dry pin-on-disk sliding. Electrochemical corrosion test showed that the bilayers grown with 80% methane were more resistant to corrosion than the ones uncoated. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  18. Temperature effect on plasmons in bilayer graphene

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Digish K., E-mail:; Sharma, A. C. [Physics Department, Faculty of Science, The M.S. University of Baroda, Vadodara-390002, Gujarat (India); Ashraf, S. S. Z. [Physics Department, Faculty of Science, Aligarh Muslim University, Aligarh-202002, Uttar Pradesh (India); Ambavale, S. K. [Vishwakarma Government Engineering College Chandkheda, Ahmedabad-382424, Gujarat (India)


    We have theoretically investigated the plasmon dispersion and damping rate of doped bilayer graphene (BLG) at finite temperatures within the random phase approximation. Our computed results on plasmon dispersion show that plasmon frequency enhances with increasing temperatures in contrast to single layer graphene where it is suppressed. This can be attributed to the fact that the dynamic response of the electron gas or screening in bilayer graphene is different from that of single layer graphene. Further the temperature effect on damping rate is also discussed.

  19. Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). (United States)

    Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen


    The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

  20. Bilayers at High pH in the Fatty Acid Soap Systems and the Applications for the Formation of Foams and Emulsions. (United States)

    Xu, Wenlong; Zhang, Heng; Zhong, Yingping; Jiang, Liwen; Xu, Mengxin; Zhu, Xionglu; Hao, Jingcheng


    In our previous work, we reported bilayers at high pH in the stearic acid/CsOH/H2O system, which was against the traditional viewpoint that fatty acid (FA) bilayers must be formed at the pKa of the fatty acid. Herein, the microstructures at high pH of several fatty acid soap systems were investigated systematically. We found that palmitic acid/KOH/H2O, palmitic acid/CsOH/H2O, stearic acid/KOH/H2O, and stearic acid/CsOH/H2O systems can form bilayers at high pH. The bilayer structure was demonstrated by cryogenic transmission electron microscopy (cryo-TEM) and deuterium nuclear magnetic resonance ((2)H NMR), and molecular dynamics simulation was used to confirm the formation of bilayers. The influence of fatty acids with different chain lengths (n = 10, 12, 14, 16, and 18) and different counterions including Li(+), Na(+), K(+), Cs(+), (CH3)4N(+), (C2H5)4N(+), (C3H7)4N(+), and (C4H9)4N(+) on the formation of bilayers was discussed. The stability of foam and emulsification properties were compared between bilayers and micelles, drawing the conclusion that bilayer structures possess a much stronger ability to foam and stronger emulsification properties than micelles do.

  1. Market power versus capital structure determinants: Do they impact leverage?

    Directory of Open Access Journals (Sweden)

    Agha Jahanzeb


    Full Text Available The purpose of this study is to investigate the association between market power and capital structure. This study will further provide a logical explanation towards the factors affecting capital structure. This study analysed 176 non-financial Pakistani companies listed on Karachi Stock Exchange over the period of 2003–2012. Capital structure has been tried to investigate with a different perspective by investigating its association with market power. It has been seen that there is a significant and positive relation between market power and capital structure. Size and liquidity remained significantly negative with capital structure, whereas profitability and dividend payout remained significantly positive with capital structure. To the best of authors’ knowledge, this is the first study that investigates the relationship between market power and capital structure in any developing economy by employing the data of non-financial Pakistani firms.

  2. Low Resolution Structure and Dynamics of a Colicin-Receptor Complex Determined by Neutron Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Clifton, Luke A [ORNL; Johnson, Christopher L [ORNL; Solovyova, Alexandra [University of Newcastle upon Tyne; Callow, Phil [Institut Laue-Langevin (ILL); Weiss, Kevin L [ORNL; Ridley, Helen [University of Newcastle upon Tyne; Le Brun, Anton P [ORNL; Kinane, Christian [ISIS Facility, Rutherford Appleton Laboratory; Webster, John [ISIS Facility, Rutherford Appleton Laboratory; Holt, Stephen A [ORNL; Lakey, Jeremy H [ORNL


    Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.

  3. Boundary conditions at closed edge of bilayer graphene and energy bands of collapsed nanotubes (United States)

    Nakanishi, Takeshi; Ando, Tsuneya


    Band structure is systematically studied in an effective-mass scheme in collapsed armchair and zigzag nanotubes based on the model in which collapsed tubes are regarded as bilayer ribbons with closed edges. Boundary conditions at closed edges, describing the connection of the envelope wave functions between the bottom and top layers, are derived. Among electronic states in bilayers, which change sensitively depending on the relative displacement of two layers, those having wave functions matching well with the obtained boundary conditions, i.e., unaffected by the presence of closed edges, constitute important states near the Fermi level in collapsed nanotubes.

  4. Process Characterization of 32nm Semi Analytical Bilayer Graphene-based MOSFET


    Noor Faizah Z. A.; Ahmad Ibrahim; Ker P.J.; Menon P. S.


    This paper presents an inclusive study and analysis of graphene-based MOSFET device at 32nm gate length. The analysis was based on top-gated structure which utilized Hafnium Dioxide (HfO2) dielectrics and metal gate. The same conventional process flows of a transistor were applied except the deposition of bilayer graphene as a channel. The analytical expression of the channel potential includes all relevant physics of bilayer graphene and by assuming that this device displays an ideal ohmic c...

  5. The concept of a bilayer hydrosphere: From the origins to the methodological approaches (United States)

    Shaporenko, S. I.


    This paper considers the results of development of the bilayer hydrosphere concept of the Earth offered by the author in 2000. The bilayering concept is logically based on the classical works in the field of geochemistry and is in the context of mid-twentieth century studies on the structure of the biosphere. The research methods based on this concept are interdisciplinary in nature and make it possible to unify and thereby to facilitate the solution of many problems in the field of oceanology, hydrology and other geographic sciences related to geochemistry.

  6. Nonlinear interaction of two trapped-mode resonances in a bilayer "fish-scale" metamaterial

    CERN Document Server

    Tuz, Vladimir R; Mladyonov, Pavel L; Prosvirnin, Sergey L; Novitsky, Andrey V


    We report on a bistable light transmission through a bilayer "fish-scale" (meander-line) metamaterial. It is demonstrated that an all-optical switching may be achieved nearly the frequency of the high-quality-factor Fano-shaped trapped-mode resonance excitation. The nonlinear interaction of two closely spaced trapped-mode resonances in the bilayer structure composed with a Kerr-type nonlinear dielectric slab is analyzed in both frequency and time domains. It is demonstrated that these two resonances react differently on the applied intense light which leads to destination of a multistable transmission.

  7. Combined effect of the transition layer and interfacial coupling on the properties of ferroelectric bilayer film

    Institute of Scientific and Technical Information of China (English)

    Sun Pu-Nan; Cui Lian; Lü Tian-Quan


    Within the framework of modified Ginzburg-Landau-Devonshire phenomenological theory,a ferroelectric bilayer film with a transition layer within each constituent film and an interfacial coupling between two materials has been studied.Properties including the Curie temperature and the spontaneous polarization of a bilayer film composed of two equally thick ferroelectric constituent films are discussed.The results show that the combined effect of the transition layer and the interfacial coupling plays an important role in explaining the interesting behaviour of ferroelectric multilayer structures consisting of two ferroelectric materials.

  8. Manipulating effective spin orbit coupling based on proximity effect in magnetic bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y. Q.; Sun, N. Y.; Che, W. R.; Zhang, J. W.; Shan, R., E-mail: [School of Physics Science and Engineering, Tongji University, Shanghai 200092 (China); Li, X. L. [Shanghai Synchrotron Radiation Facility (SSRF), Shanghai 201204 (China); Zhu, Z. G., E-mail:; Su, G., E-mail: [School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049 (China); Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, College of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049 (China)


    A proximity effect of spin orbit coupling (SOC) is proposed in nonmagnetic metal/ferromagnet (NM/FM) bilayers by extending the Crépieux-Bruno (CB) theory. We demonstrate that over 1000% enhancement of the SOC strength can be realized based on this effect (Pt/FM bilayers) and it brings greatly enhanced anomalous Hall effect and anomalous Nernst effect. This work could help maximize the performance of magnetic transport property for the spintronics device using NM/FM as the key structure.

  9. Molecular dynamics simulation of the transmembrane subunit of BtuCD in the lipid bilayer

    Institute of Scientific and Technical Information of China (English)


    Based on the crystal structure of the vitamin B12 transporter protein of Escherichia coli(BtuCD) a system consisting of the BtuCD transmembrane domain(BtuC) and the palmitoyloleoyl phosphatidylcholine(POPC) lipid bilayer was constructed in silica,and a more-than-57-nanosecond molecular dynamics(MD) simulation was performed on it to reveal the intrinsic functional motions of BtuC.The results showed that a stable protein-lipid bilayer was obtained and the POPC lipid bilayer was able to adjust its thickness to match the embedded BtuC which underwent relatively complicated motions.These results may help to understand the mechanism of transmembrane substrate transport at the atomic level.

  10. Unusual Charge Transport and Spin Response of Doped Bilayer Triangular Antiferromagnets

    Institute of Scientific and Technical Information of China (English)

    LIANG Ying; MA Tian-Xing; FENG Shi-Ping


    Within the t-J model, the charge transport and spin response of the doped bilayer triangular antiferromagnetare studied by considering the bilayer interaction. Although the bilayer interaction leads to the band splitting in theelectronic structure, the qualitative behaviors of the physical properties are the same as in the single layer case. Theconductivity spectrum shows the low-energy peak and unusual midinfrared band, the temperature-dependent resistivityis characterized by the nonlinearity metallic-like behavior in the higher temperature range and the deviation from themetallic-like behavior in the lower temperature range and the commensurate neutron scattering peak near the half-fillingis split into six incommensurate peaks in the underdoped regime, with the incommensurability increasing with the holeconcentration at lower dopings, and saturating at higher dopings.

  11. Transfer matrix theory of monolayer graphene/bilayer graphene heterostructure superlattice

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yu, E-mail: [Department of Physics, Faculty of Science, Kunming University of Science and Technology, Kunming 650500 (China)


    We have formulated a transfer matrix method to investigate electronic properties of graphene heterostructure consisting of monolayer graphene and bilayer counterpart. By evaluating transmission, conductance, and band dispersion, we show that, irrespective of the different carrier chiralities in monolayer graphene and bilayer graphene, superlattice consisting of biased bilayer graphene barrier and monolayer graphene well can mimic the electronic properties of conventional semiconductor superlattice, displaying the extended subbands in the quantum tunneling regime and producing anisotropic minigaps for the classically allowed transport. Due to the lateral confinement, the lowest mode has shifted away from the charge neutral point of monolayer graphene component, opening a sizeable gap in concerned structure. Following the gate-field and geometry modulation, all electronic states and gaps between them can be externally engineered in an electric-controllable strategy.

  12. Transfer matrix theory of monolayer graphene/bilayer graphene heterostructure superlattice (United States)

    Wang, Yu


    We have formulated a transfer matrix method to investigate electronic properties of graphene heterostructure consisting of monolayer graphene and bilayer counterpart. By evaluating transmission, conductance, and band dispersion, we show that, irrespective of the different carrier chiralities in monolayer graphene and bilayer graphene, superlattice consisting of biased bilayer graphene barrier and monolayer graphene well can mimic the electronic properties of conventional semiconductor superlattice, displaying the extended subbands in the quantum tunneling regime and producing anisotropic minigaps for the classically allowed transport. Due to the lateral confinement, the lowest mode has shifted away from the charge neutral point of monolayer graphene component, opening a sizeable gap in concerned structure. Following the gate-field and geometry modulation, all electronic states and gaps between them can be externally engineered in an electric-controllable strategy.

  13. Layer-resolved photoemission tomography: The p -sexiphenyl bilayer upon Cs doping (United States)

    Reinisch, E. M.; Puschnig, P.; Ules, T.; Ramsey, M. G.; Koller, G.


    The buried interface between a molecular thin film and the metal substrate is generally not accessible to the photoemission experiment. With the example of a sexiphenyl (6 P ) bilayer on Cu we show that photoemission tomography can be used to study the electronic level alignment and geometric structure, where it was possible to assign the observed orbital emissions to the individual layers. We further study the Cs doping of this bilayer. Initial Cs exposure leads to a doping of only the first interface layer, leaving the second layer unaffected except for a large energy shift. This result shows that it is in principle possible to chemically modify just the interface, which is important to issues like tuning of the energy level alignment and charge transfer to the interface layer. Upon saturating the film with Cs, photoemission tomography shows a complete doping (6 p4 - ) of the bilayer, with the molecular geometry changing such that the spectra become dominated by σ -orbital emissions.

  14. P-type Cu2O/SnO bilayer thin film transistors processed at low temperatures

    KAUST Repository

    Al-Jawhari, Hala A.


    P-type Cu2O/SnO bilayer thin film transistors (TFTs) with tunable performance were fabricated using room temperature sputtered copper and tin oxides. Using Cu2O film as capping layer on top of a SnO film to control its stoichiometry, we have optimized the performance of the resulting bilayer transistor. A transistor with 10 nm/15 nm Cu2O to SnO thickness ratio (25 nm total thickness) showed the best performance using a maximum process temperature of 170 C. The bilayer transistor exhibited p-type behavior with field-effect mobility, on-to-off current ratio, and threshold voltage of 0.66 cm2 V-1 s-1, 1.5×10 2, and -5.2 V, respectively. The advantages of the bilayer structure relative to single layer transistor are discussed. © 2013 American Chemical Society.

  15. A new approach to study the effect of generation rate on drain-source current of bilayer graphene transistors (United States)

    Ahmad, H.; Ghadiry, M.; AbdManaf, A.


    This paper presents a new approach to study the effect of impact ionization on the current of bilayer graphene field effect transistors. Analytical models for surface potential and current together with a Monte Carlo approach which include the edge effect scattering are used to calculate the current and generation rate in bilayer graphene transistors due to ionization. FlexPDE simulation is also employed for verification of surface potential modeling. Using the approach, the profile of generation rate, surface potential and current are plotted with respect to several structural parameters. We have shown that ignoring this effect in the modeling will result in an error of up to 10 % for a typical 30 nm bilayer graphene field effect transistor. As a result, we conclude that any analytical study ignoring the ionization is incomplete for bilayer graphene field effect transistors. The model presented here can be applied in optimization of photo detectors based on graphene.

  16. Thickness dependence of spin Hall magnetoresistance in FeMn/Pt bilayers

    Directory of Open Access Journals (Sweden)

    Yumeng Yang


    Full Text Available We investigated spin Hall magnetoresistance in FeMn/Pt bilayers, which was found to be one order of magnitude larger than that of heavy metal and insulating ferromagnet or antiferromagnet bilayer systems, and comparable to that of NiFe/Pt bilayers. The spin Hall magnetoresistance shows a non-monotonic dependence on the thicknesses of both FeMn and Pt. The former can be accounted for by the thickness dependence of net magnetization in FeMn thin films, whereas the latter is mainly due to spin accumulation and diffusion in Pt. Through analysis of the Pt thickness dependence, the spin Hall angle, spin diffusion length of Pt and the real part of spin mixing conductance were determined to be 0.2, 1.1 nm, and 5.5 × 1014 Ω−1m−2, respectively. The results corroborate the spin orbit torque effect observed in this system recently.

  17. Specific volume and compressibility of bilayer lipid membranes with incorporated Na,K-ATPase. (United States)

    Hianik, Tibor; Rybár, Peter; Krivánek, Roland; Petríková, Mária; Roudna, Milena; Apell, Hans Jürgen


    Ultrasound velocimetry and densitometry methods were used to study the interactions of the Na,K-ATPase with the lipid bilayer in large unilamellar liposomes composed of dioleoyl phosphatidylcholine (DOPC). The ultrasound velocity increased and the specific volume of the phospholipids decreased with increasing concentrations of protein. These experiments allowed us to determine the reduced specific apparent compressibility of the lipid bilayer, which decreased by approx. 11% with increasing concentrations of the Na,K-ATPase up to an ATPase/DOPC molar ratio = 2 × 10⁻⁴. Assuming that ATPase induces rigidization of the surrounding lipid molecules one can obtain from the compressibility data that 3.7 to 100 times more lipid molecules are affected by the protein in comparison with annular lipids. However, this is in contradiction with the current theories of the phase transitions in lipid bilayers. It is suggested that another physical mechanisms should be involved for explanation of observed effect.

  18. Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: methodological issues

    DEFF Research Database (Denmark)

    Gurtovenko, Andrey A; Vattulainen, Ilpo


    of the sides of a simulation box and (ii) an alternative form, when the potential is set to be the same on the opposite sides of a simulation box. Both forms differ by a position-dependent correction term, which has been shown to be proportional to the overall dipole moment of a bilayer system (for neutral......, for asymmetric lipid bilayers, the second approach is no longer appropriate due to a nonzero net dipole moment across a simulation box with a single asymmetric bilayer. We demonstrate that in this case the electrostatic potential can adequately be described by the classical form of Poisson equation, provided...... to the conventional periodic boundaries, but accurate determination of the transmembrane potential difference is then hindered due to detachment of some water dipoles from bulk aqueous solution to vacuum....

  19. Synthesis and structure determination of uranyl peroxide nanospheres in the presence of organic structure directing agents (United States)

    Forbes, T. Z.; Burns, P. C.


    Recently, actinyl peroxide nanoclusters containing 20, 24, 28, or 32 actinyl polyhedra have been synthesized and their structures identified with single crystal X-ray diffraction [1]. Most nanomaterials are composed of main group elements or transition metals, therefore, these actinyl nanospheres may display vastly different chemical and physical properties due to the presence of filled f-orbitals. A major goal of our research group is to create novel actinyl materials, focusing on nano- and mesoporous materials. The original nanosphere syntheses were limited to inorganic crystallization agents, such as monovalent cations. Over the last decade, the use of organic compounds and surfactants have received increased attention as structure-directing agents for the generation of novel inorganic materials. Using structure-directing organic amines we have successfully synthesized and determined the structures of uranyl nanospheres containing 40 and 50 uranyl polyhedra. The topology of the skeletal U-50 nanosphere is identical to the C50Cl10 fullerene [2]. The topographical relationship between the actinyl nanospheres and fullerene or fullerene-like material may provide additional insight into stable configurations for lower fullerenes. [1] Burns et al., Actinyl peroxide nanospheres. Angewandte Chemie, International Edition, 2005. 44(14): p. 2135. [2] Xie et al., Capturing the Labile Fullerene[50] as C50Cl10. Science, (2004) 305(5671): p. 699.

  20. Small-angle neutron scattering from multilamellar lipid bilayers: Theory, model, and experiment

    DEFF Research Database (Denmark)

    Lemmich, Jesper; Mortensen, Kell; Ipsen, John Hjorth;


    of temperature for the lamellar repeat distance, the hydrophobic bilayer thickness, as well as the thickness of the aqueous and polar head group region. In addition to these geometric parameters the analysis permits determination of molecular cross-sectional area, number of interlamellar water molecules, as well...

  1. Multiscale modeling of droplet interface bilayer membrane networks. (United States)

    Freeman, Eric C; Farimani, Amir B; Aluru, Narayana R; Philen, Michael K


    Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks.

  2. Reversible Polarization Rotation in Epitaxial Ferroelectric Bilayers

    DEFF Research Database (Denmark)

    Liu, Guangqing; Zhang, Qi; Huang, Hsin-Hui


    large-scale polarization rotation switching (≈60 μC cm−2) and an effective d 33 response 500% (≈250 pm V−1) larger than the PZT-R layer alone. Furthermore, this enhancement is stable for more than 107 electrical switching cycles. These bilayers present a simple and highly controllable means to design...

  3. Localized plasmons in bilayer graphene nanodisks

    DEFF Research Database (Denmark)

    Wang, Weihua; Xiao, Sanshui; Mortensen, N. Asger


    We study localized plasmonic excitations in bilayer graphene (BLG) nanodisks, comparing AA-stacked and AB-stacked BLG and contrasting the results to the case of two monolayers without electronic hybridization. The electrodynamic response of the BLG electron gas is described in terms of a spatially...

  4. Capillary wrinkling of thin bilayer polymeric sheets (United States)

    Chang, Jooyoung; Menon, Narayanan; Russell, Thomas

    We have investigated capillary force induced wrinkling on a floated polymeric bilayer thin sheet. The origin of the wrinkle pattern is compressional hoop stress caused by the capillary force of a water droplet placed on the floated polymeric thin sheet afore investigated. Herein, we study the effect of the differences of surface energy arising from the hydrophobicity of Polystyrene (PS Mw: 97 K, Contact Angle: 88 º) and the hydrophilicity of Poly(methylmethacrylate) (PMMA Mw: 99K, Contact Angle: 68 º) on two sides of a bilayer film. We measure the number and the length of the wrinkles by broadly varying the range of thicknesses of top (9 nm to 550 nm) and bottom layer (25 nm to 330 nm). At the same, there is only a small contrast in mechanical properties of the two layers (PS E = 3.4 GPa, and PMMA E = 3 GPa). The number of the wrinkles is not strongly affected by the composition (PS(Top)/PMMA(Bottom) or PMMA(Top)/PS(Bottom)) and the thickness of each and overall bilayer system. However, the length of the wrinkle is governed by the contact angle of the drop on the top layer of bilayer system. We also compare this to the wrinkle pattern obtained in monolayer systems over a wide range of thickness from PS and PMMA (7 nm to 1 μm). W.M. Keck Foundation.

  5. Bilayer Tablet via Microsphere: A Review

    Directory of Open Access Journals (Sweden)

    Piyushkumar Vinubhai Gundaraniya


    Full Text Available The aim of the present work is to develop bilayer tablets containing sustained release microspheres as one layer and immediate release as another layer. The proposed dosage form is intended to decrease the dosing frequency and the combined administration of an anti-diabetic agent. Several pharmaceutical companies are currently developing bi-layer tablets, for a variety of reasons: patent extension, therapeutic, marketing to name a few. To reduce capital investment, quite often existing but modified tablet presses are used to develop and produce such tablets. One such approach is using microspheres as carriers for drugs also known as micro particles. It is the reliable means to deliver the drug to the target site with specificity, if modified, and to maintain the desired concentration at the site of interest. Microspheres received much attention not only for prolonged release, but also for targeting of anti-diabetic drugs. Bilayer tablet via microsphere is new era for the successful development of controlled release formulation along with various features to provide a way of successful drug delivery system. Especially when in addition high production output is required. An attempt has been made in this review article to introduce the society to the current technological developments in bilayer and floating drug delivery system.

  6. Confinement of charge carriers in bilayer graphene

    NARCIS (Netherlands)

    Goossens, A.M.


    In this thesis we investigate the fundamental properties of electronic transport in bilayer graphene. We do this by confining electrons to narrow constrictions and small islands. Our key result is the fabrication and measurement of nanoscale devices that permit confinement with electric fields in b

  7. Electronic properties of a biased graphene bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Castro, Eduardo V; Lopes dos Santos, J M B [CFP and Departamento de Fisica, Faculdade de Ciencias Universidade do Porto, P-4169-007 Porto (Portugal); Novoselov, K S; Morozov, S V; Geim, A K [Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL (United Kingdom); Peres, N M R [Centre of Physics and Departamento de Fisica, Universidade do Minho, P-4710-057 Braga (Portugal); Nilsson, Johan; Castro Neto, A H [Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215 (United States); Guinea, F [Instituto de Ciencia de Materiales de Madrid, CSIC, Cantoblanco, E-28049 Madrid (Spain)


    We study, within the tight-binding approximation, the electronic properties of a graphene bilayer in the presence of an external electric field applied perpendicular to the system-a biased bilayer. The effect of the perpendicular electric field is included through a parallel plate capacitor model, with screening correction at the Hartree level. The full tight-binding description is compared with its four-band and two-band continuum approximations, and the four-band model is shown to always be a suitable approximation for the conditions realized in experiments. The model is applied to real biased bilayer devices, made out of either SiC or exfoliated graphene, and good agreement with experimental results is found, indicating that the model is capturing the key ingredients, and that a finite gap is effectively being controlled externally. Analysis of experimental results regarding the electrical noise and cyclotron resonance further suggests that the model can be seen as a good starting point for understanding the electronic properties of graphene bilayer. Also, we study the effect of electron-hole asymmetry terms, such as the second-nearest-neighbour hopping energies t' (in-plane) and {gamma}{sub 4} (inter-layer), and the on-site energy {Delta}.

  8. Electronic properties of a biased graphene bilayer. (United States)

    Castro, Eduardo V; Novoselov, K S; Morozov, S V; Peres, N M R; Lopes dos Santos, J M B; Nilsson, Johan; Guinea, F; Geim, A K; Castro Neto, A H


    We study, within the tight-binding approximation, the electronic properties of a graphene bilayer in the presence of an external electric field applied perpendicular to the system-a biased bilayer. The effect of the perpendicular electric field is included through a parallel plate capacitor model, with screening correction at the Hartree level. The full tight-binding description is compared with its four-band and two-band continuum approximations, and the four-band model is shown to always be a suitable approximation for the conditions realized in experiments. The model is applied to real biased bilayer devices, made out of either SiC or exfoliated graphene, and good agreement with experimental results is found, indicating that the model is capturing the key ingredients, and that a finite gap is effectively being controlled externally. Analysis of experimental results regarding the electrical noise and cyclotron resonance further suggests that the model can be seen as a good starting point for understanding the electronic properties of graphene bilayer. Also, we study the effect of electron-hole asymmetry terms, such as the second-nearest-neighbour hopping energies t' (in-plane) and γ(4) (inter-layer), and the on-site energy Δ.

  9. Electronic properties of graphene-based bilayer systems

    Energy Technology Data Exchange (ETDEWEB)

    Rozhkov, A.V., E-mail: [CEMS, RIKEN, Saitama 351-0198 (Japan); Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, 125412 Moscow (Russian Federation); Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700 (Russian Federation); Sboychakov, A.O. [CEMS, RIKEN, Saitama 351-0198 (Japan); Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, 125412 Moscow (Russian Federation); Rakhmanov, A.L. [CEMS, RIKEN, Saitama 351-0198 (Japan); Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, 125412 Moscow (Russian Federation); Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700 (Russian Federation); All-Russia Research Institute of Automatics, Moscow, 127055 (Russian Federation); Nori, Franco, E-mail: [CEMS, RIKEN, Saitama 351-0198 (Japan); Physics Department, The University of Michigan, Ann Arbor, MI 48109-1040 (United States)


    This article reviews the theoretical and experimental work related to the electronic properties of bilayer graphene systems. Three types of bilayer stackings are discussed: the AA, AB, and twisted bilayer graphene. This review covers single-electron properties, effects of static electric and magnetic fields, bilayer-based mesoscopic systems, spin–orbit coupling, dc transport and optical response, as well as spontaneous symmetry violation and other interaction effects. The selection of the material aims to introduce the reader to the most commonly studied topics of theoretical and experimental research in bilayer graphene.

  10. Electronic properties of graphene-based bilayer systems (United States)

    Rozhkov, A. V.; Sboychakov, A. O.; Rakhmanov, A. L.; Nori, Franco


    This article reviews the theoretical and experimental work related to the electronic properties of bilayer graphene systems. Three types of bilayer stackings are discussed: the AA, AB, and twisted bilayer graphene. This review covers single-electron properties, effects of static electric and magnetic fields, bilayer-based mesoscopic systems, spin-orbit coupling, dc transport and optical response, as well as spontaneous symmetry violation and other interaction effects. The selection of the material aims to introduce the reader to the most commonly studied topics of theoretical and experimental research in bilayer graphene.

  11. Interaction of curcumin with lipid monolayers and liposomal bilayers. (United States)

    Karewicz, Anna; Bielska, Dorota; Gzyl-Malcher, Barbara; Kepczynski, Mariusz; Lach, Radosław; Nowakowska, Maria


    Curcumin shows huge potential as an anticancer and anti-inflammatory agent. However, to achieve a satisfactory bioavailability and stability of this compound, its liposomal form is preferable. Our detailed studies on the curcumin interaction with lipid membranes are aimed to obtain better understanding of the mechanism and eventually to improve the efficiency of curcumin delivery to cells. Egg yolk phosphatidylcholine (EYPC) one-component monolayers and bilayers, as well as mixed systems containing additionally dihexadecyl phosphate (DHP) and cholesterol, were studied. Curcumin binding constant to EYPC liposomes was determined based on two different methods: UV/Vis absorption and fluorescence measurements to be 4.26×10(4)M(-1) and 3.79×10(4)M(-1), respectively. The fluorescence quenching experiment revealed that curcumin locates in the hydrophobic region of EYPC liposomal bilayer. It was shown that curcumin impacts the size and stability of the liposomal carriers significantly. Loaded into the EYPC/DPH/cholesterol liposomal bilayer curcumin stabilizes the system proportionally to its content, while the EYPC/DPH system is destabilized upon drug loading. The three-component lipid composition of the liposome seems to be the most promising system for curcumin delivery. An interaction of free and liposomal curcumin with EYPC and mixed monolayers was also studied using Langmuir balance measurements. Monolayer systems were treated as a simple model of cell membrane. Condensing effect of curcumin on EYPC and EYPC/DHP monolayers and loosening influence on EYPC/DHP/chol ones were observed. It was also demonstrated that curcumin-loaded EYPC liposomes are more stable upon interaction with the model lipid membrane than the unloaded ones.

  12. Lipid asymmetry in DLPC/DSPC supported lipid bilayers, a combined AFM and fluorescence microscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Lin, W; Blanchette, C D; Ratto, T V; Longo, M L


    A fundamental attribute of cell membranes is transmembrane asymmetry, specifically the formation of ordered phase domains in one leaflet that are compositionally different from the opposing leaflet of the bilayer. Using model membrane systems, many previous studies have demonstrated the formation of ordered phase domains that display complete transmembrane symmetry but there have been few reports on the more biologically relevant asymmetric membrane structures. Here we report on a combined atomic force microscopy (AFM) and fluorescence microscopy study whereby we observe three different states of transmembrane symmetry in phase-separated supported bilayers formed by vesicle fusion. We find that if the leaflets differ in gel-phase area fraction, then the smaller domains in one leaflet are in registry with the larger domains in the other leaflet and the system is dynamic. In a presumed lipid flip-flop process similar to Ostwald Ripening, the smaller domains in one leaflet erode away while the large domains in the other leaflet grow until complete compositional asymmetry is reached and remains stable. We have quantified this evolution and determined that the lipid flip-flop event happens most frequently at the interface between symmetric and asymmetric DSPC domains. If both leaflets have nearly identical area fraction of gel-phase, gel-phase domains are in registry and are static in comparison to the first state. The stability of these three DSPC domain distributions, the degree of registry observed, and the domain immobility have direct biological significance with regards to maintenance of lipid asymmetry in living cell membranes, communication between inner leaflet and outer leaflet, membrane adhesion, and raft mobility.

  13. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts. (United States)

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas


    Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs.

  14. Neutron scattering from myelin revisited: bilayer asymmetry and water-exchange kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Denninger, Andrew R. [Boston College, Chestnut Hill, MA 02467 (United States); Demé, Bruno; Cristiglio, Viviana [Institut Laue–Langevin (ILL), CS 20156, F-38042 Grenoble CEDEX 9 (France); LeDuc, Géraldine [European Synchrotron Radiation Facility (ESRF), CS 40220, F-38043 Grenoble CEDEX 9 (France); Feller, W. Bruce [NOVA Scientific Inc., Sturbridge, MA 01566 (United States); Kirschner, Daniel A., E-mail: [Boston College, Chestnut Hill, MA 02467 (United States)


    The structure of internodal myelin in the rodent central and peripheral nervous systems has been determined using neutron diffraction. The kinetics of water exchange in these tissues is also described. Rapid nerve conduction in the central and peripheral nervous systems (CNS and PNS, respectively) of higher vertebrates is brought about by the ensheathment of axons with myelin, a lipid-rich, multilamellar assembly of membranes. The ability of myelin to electrically insulate depends on the regular stacking of these plasma membranes and on the presence of a number of specialized membrane-protein assemblies in the sheath, including the radial component, Schmidt–Lanterman incisures and the axo–glial junctions of the paranodal loops. The disruption of this fine-structure is the basis for many demyelinating neuropathies in the CNS and PNS. Understanding the processes that govern myelin biogenesis, maintenance and destabilization requires knowledge of myelin structure; however, the tight packing of internodal myelin and the complexity of its junctional specializations make myelin a challenging target for comprehensive structural analysis. This paper describes an examination of myelin from the CNS and PNS using neutron diffraction. This investigation revealed the dimensions of the bilayers and aqueous spaces of myelin, asymmetry between the cytoplasmic and extracellular leaflets of the membrane, and the distribution of water and exchangeable hydrogen in internodal multilamellar myelin. It also uncovered differences between CNS and PNS myelin in their water-exchange kinetics.

  15. Facile fabrication of PEDOT:PSS/polythiophenes bilayered nanofilms on pure organic electrodes and their thermoelectric performance. (United States)

    Shi, Hui; Liu, Congcong; Xu, Jingkun; Song, Haijun; Lu, Baoyang; Jiang, Fengxing; Zhou, Weiqiang; Zhang, Ge; Jiang, Qinglin


    A pure organic PEDOT:PSS nanofilm was used as a working electrode for the first time to electrodeposit polymer films of polythiophene (PTh) and its derivatives in a boron trifluoride diethyl ether (BFEE) solution, fabricating a novel generation of bilayered nanofilms. Cyclic voltammetry (CV) demonstrated good electrochemical stability of the as-formed films. Structures and surface morphologies were systematically investigated by the characterizations of cross-section SEM, FT-IR, UV-vis, SEM, and AFM. The resulting films revealed stable and enhanced thermoelectric (TE) performances. The electrical conductivity values of PEDOT:PSS/PTh, PEDOT:PSS/P3MeT, and PEDOT:PSS/P3HT nanofilms were determined to be 123.9, 136.5, and 200.5 S cm(-1), respectively. The power factor reached up to be a maximum value of 5.79 μW m(-1) k(-2). Thus, this technique offers a facile approach to a class of bilayered nanofilms, and it may provide a general strategy for fabricating a new generation of conducting polymers for more practical applications.

  16. The influence of interface on spin pumping effect in Ni80Fe20 /Tb bilayer

    Directory of Open Access Journals (Sweden)

    Jinjin Yue


    Full Text Available Focusing on the interface effect of the Ni80Fe20 (Py/terbium (Tb bilayer, the influence of interface on the magnetization dynamic damping is investigated systematically. Two series of Py (12 nm/Tb (d nm films with and without copper (Cu (1 nm interlayer are deposited on silicon (Si substrates by DC magnetron sputtering at room temperature. From vibrating sample magnetometer (VSM measurements, the saturation magnetization (Ms decreases with increasing Tb thickness in Py/Tb bilayer while the decrease of Ms is suppressed efficiently by inserting a Cu layer with even 1 nm of thickness. From the frequency dependence of ferromagnetic resonance (FMR linewidth, we can obtain the Gilbert damping coefficient (α, α is found to exhibit an extreme enhancement in comparison to the single Py layer and shows an increasing trend with increasing Tb thickness. By inserting the Cu layer, α decreases significantly. From theoretical fitting, the spin diffusion length (λSD and spin mixing conductance (g↑↓ are determined. It shows that the interface structure influences the spin mixing conductance but not the spin diffusion length.


    Directory of Open Access Journals (Sweden)

    Floriniţa Duca


    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  18. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex Ⅱ Determined

    Institute of Scientific and Technical Information of China (English)


    @@ Scientists at the CAS Institute of Biophysics (IBP) and Tsinghua University have gained new insights into the mechanism of mitochondria, the subcellular structures which generate energy for living cells.

  19. Structural determinants of Smad function in TGF-β signaling. (United States)

    Macias, Maria J; Martin-Malpartida, Pau; Massagué, Joan


    Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the transforming growth factor β (TGF-β) superfamily of cytokines in metazoan embryo development as well as in adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphisms, and cancer. Structural studies of Smads bound to partner proteins and target DNA provide a framework for understanding the significance of these evolutionary and pathologic sequence variations. We synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. We also present a web application that compares Smad sequences and displays Smad protein structures and their disease-associated variants.

  20. Interaction of myelin basic protein isoforms with lipid bilayers studied by FTIR spectroscopy (United States)

    Jackson, Michael; Choo, Lin-P'ing; Boulias, Christopher; Moscarello, Mario A.; Mantsch, Henry H.


    The secondary structure of the naturally occurring isoforms of myelin basic protein (MBP1-8) from human myelin was studied by Fourier transform infrared spectroscopy under a variety of experimental conditions. In aqueous solution each isoform was found to be unstructured. In the presence of negatively charged liquid bilayers MBP1-4 were shown to exhibit an amide I band maximum indicative of the adoption of (alpha) -helical secondary structures. A detailed analysis revealed that significant proportions of (beta) -sheet secondary structure were also present. MBP5 and MBP8, which have significantly less cationic charge than MBP1-4, exhibited an amide I maximum identical to that seen in solution, suggesting that no interaction with the bilayer occurred. Analysis of the lipid CH2 and C equals O stretching vibrations also pointed towards significant interaction of MBP1-4 with the bilayer. The changes in intensity and frequency of these bands which typically accompany the phase transition in the pure bilayer were abolished by addition of the proteins. No such effect was seen for MBP5 and 8, the normal lipid phase transition being apparent. The implications of these results in the aetiology of multiple sclerosis is discussed.

  1. Tailored sequential drug release from bilayered calcium sulfate composites

    Energy Technology Data Exchange (ETDEWEB)

    Orellana, Bryan R.; Puleo, David A., E-mail:


    The current standard for treating infected bony defects, such as those caused by periodontal disease, requires multiple time-consuming steps and often multiple procedures to fight the infection and recover lost tissue. Releasing an antibiotic followed by an osteogenic agent from a synthetic bone graft substitute could allow for a streamlined treatment, reducing the need for multiple surgeries and thereby shortening recovery time. Tailorable bilayered calcium sulfate (CS) bone graft substitutes were developed with the ability to sequentially release multiple therapeutic agents. Bilayered composite samples having a shell and core geometry were fabricated with varying amounts (1 or 10 wt.%) of metronidazole-loaded poly(lactic-co-glycolic acid) (PLGA) particles embedded in the shell and simvastatin directly loaded into either the shell, core, or both. Microcomputed tomography showed the overall layered geometry as well as the uniform distribution of PLGA within the shells. Dissolution studies demonstrated that the amount of PLGA particles (i.e., 1 vs. 10 wt.%) had a small but significant effect on the erosion rate (3% vs. 3.4%/d). Mechanical testing determined that introducing a layered geometry had a significant effect on the compressive strength, with an average reduction of 35%, but properties were comparable to those of mandibular trabecular bone. Sustained release of simvastatin directly loaded into CS demonstrated that changing the shell to core volume ratio dictates the duration of drug release from each layer. When loaded together in the shell or in separate layers, sequential release of metronidazole and simvastatin was achieved. By introducing a tunable, layered geometry capable of releasing multiple drugs, CS-based bone graft substitutes could be tailored in order to help streamline the multiple steps needed to regenerate tissue in infected defects. - Highlights: • Bilayered CS composites were fabricated as potential bone graft substitutes. • The shell

  2. Structural Determinants of Cadherin-23 Function in Hearing and Deafness

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P. (Harvard-Med); (Harvard)


    The hair-cell tip link, a fine filament directly conveying force to mechanosensitive transduction channels, is composed of two proteins, protocadherin-15 and cadherin-23, whose mutation causes deafness. However, their molecular structure, elasticity, and deafness-related structural defects are unknown. We present crystal structures of the first and second extracellular cadherin repeats of cadherin-23. Overall, structures show typical cadherin folds, but reveal an elongated N terminus that precludes classical cadherin interactions and contributes to an N-terminal Ca{sup 2+}-binding site. The deafness mutation D101G, in the linker region between the repeats, causes a slight bend between repeats and decreases Ca{sup 2+} affinity. Molecular dynamics simulations suggest that cadherin-23 repeats are stiff and that either removing Ca{sup 2+} or mutating Ca{sup 2+}-binding residues reduces rigidity and unfolding strength. The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadherin-23 may bind with itself and with protocadherin-15 to form the tip link.

  3. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.


    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  4. Hematite/silver nanoparticle bilayers on mica--AFM, SEM and streaming potential studies. (United States)

    Morga, Maria; Adamczyk, Zbigniew; Oćwieja, Magdalena; Bielańska, Elżbieta


    Bilayers of hematite/silver nanoparticles were obtained in the self-assembly process and thoroughly characterized using scanning electron microscopy (SEM), atomic force microscopy (AFM), and in situ streaming potential measurements. The hematite nanoparticles, forming a supporting layer, were 22 nm in diameter, exhibiting an isoelectric point at pH 8.9. The silver nanoparticles, used to obtain an external layer, were 29 nm in diameter, and remained negative within the pH range 3 to 11. In order to investigate the particle deposition, mica sheets were used as a model solid substrate. The coverage of the supporting layer was adjusted by changing the bulk concentration of the hematite suspension and the deposition time. Afterward, silver nanoparticle monolayers of controlled coverage were deposited under the diffusion-controlled transport. The coverage of bilayers was determined by a direct enumeration of deposited particles from SEM micrographs and AFM images. Additionally, the formation of the hematite/silver bilayers was investigated by streaming potential measurements carried out under in situ conditions. The effect of the mica substrate and the coverage of a supporting layer on the zeta potential of bilayers was systematically studied. It was established that for the coverage exceeding 0.20, the zeta potential of bilayers was independent on the substrate and the supporting layer coverage. This behavior was theoretically interpreted in terms of the 3D electrokinetic model. Beside significance for basic sciences, these measurements allowed to develop a robust method of preparing nanoparticle bilayers of controlled properties, having potential applications in catalytic processes.

  5. Structure determination of T-cell protein-tyrosine phosphatase

    DEFF Research Database (Denmark)

    Iversen, L.F.; Møller, K. B.; Pedersen, A.K.;


    homologous T cell protein-tyrosine phosphatase (TC-PTP) has received much less attention, and no x-ray structure has been provided. We have previously co-crystallized PTP1B with a number of low molecular weight inhibitors that inhibit TC-PTP with similar efficiency. Unexpectedly, we were not able to co...... the high degree of functional and structural similarity between TC-PTP and PTP1B, we have been able to identify areas close to the active site that might be addressed to develop selective inhibitors of each enzyme....

  6. First-principles determination of the structure of magnesium borohydride. (United States)

    Zhou, Xiang-Feng; Oganov, Artem R; Qian, Guang-Rui; Zhu, Qiang


    The energy landscape of Mg(BH(4))(2) under pressure is explored by ab initio evolutionary calculations. Two new tetragonal structures, with space groups P4 and I4(1)/acd, are predicted to be lower in enthalpy by 15.4 and 21.2 kJ/mol, respectively, than the earlier proposed P4(2)nm phase. We have simulated x-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and simulated x-ray diffraction patterns of I4(1)/acd and P4 structures are in excellent agreement with the experimental results.

  7. Unified approach for determining tetragonal tungsten bronze crystal structures. (United States)

    Smirnov, M; Saint-Grégoire, P


    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions.

  8. Corrosion resistance of sintered NdFeB coated with SiC/Al bilayer thin films by magnetron sputtering (United States)

    Huang, Yiqin; Li, Heqin; Zuo, Min; Tao, Lei; Wang, Wei; Zhang, Jing; Tang, Qiong; Bai, Peiwen


    The poor corrosion resistance of sintered NdFeB imposes a great challenge in industrial applications. In this work, the SiC/Al bilayer thin films with the thickness of 510 nm were deposited on sintered NdFeB by magnetron sputtering to improve the corrosion resistance. A 100 nm Al buffer film was used to reduce the internal stress between SiC and NdFeB and improve the surface roughness of the SiC thin film. The morphologies and structures of SiC/Al bilayer thin films and SiC monolayer film were investigated with FESEM, AFM and X-ray diffraction. The corrosion behaviors of sintered NdFeB coated with SiC monolayer film and SiC/Al bilayer thin films were analyzed by polarization curves. The magnetic properties were measured with an ultra-high coercivity permanent magnet pulse tester. The results show that the surface of SiC/Al bilayer thin films is more compact and uniform than that of SiC monolayer film. The corrosion current densities of SiC/Al bilayer films coated on NdFeB in acid, alkali and salt solutions are much lower than that of SiC monolayer film. The SiC/Al bilayer thin films have little influence to the magnetic properties of NdFeB.

  9. First principles study and empirical parametrization of twisted bilayer MoS2 based on band-unfolding (United States)

    Tan, Yaohua; Chen, Fan W.; Ghosh, Avik W.


    We explore the band structure and ballistic electron transport in twisted bilayer MoS2 using the density functional theory. The sphagetti like bands are unfolded to generate band structures in the primitive unit cell of the original 2H MoS2 bilayer and projected onto the original bands of an individual layer. The corresponding twist angle dependent bandedges are extracted from the unfolded band structures. Based on a comparison within the same primitive unit cell, an efficient two band effective mass model for indirect ΓV and ΛC valleys is created and parametrized by fitting to the unfolded band structures. With the two band effective mass model, we calculate transport properties—specifically, the ballistic transmission in arbitrarily twisted bilayer MoS2 .

  10. First principles study and empirical parametrization of twisted bilayer MoS2 based on band-unfolding

    CERN Document Server

    Tan, Yaohua; Ghosh, Avik


    We explore the band structure and ballistic electron transport in twisted bilayer $\\textrm{MoS}_2$ using Density Functional Theory (DFT). The sphagetti like bands are unfolded to generate band structures in the primitive unit cell of the original un-twisted $\\textrm{MoS}_2$ bilayer and projected onto an individual layer. The corresponding twist angle dependent indirect bandedges are extracted from the unfolded band structures. Based on a comparison within the same primitive unit cell, an efficient two band effective mass model for indirect conduction and valence valleys is created and parameterized by fitting the unfolded band structures. With the two band effective mass model, transport properties - specifically, we calculate the ballistic transmission in arbitrarily twisted bilayer $\\textrm{MoS}_2$.

  11. Phospholipid bilayer relaxation dynamics as revealed by the pulsed electron-electron double resonance of spin labels (United States)

    Syryamina, V. N.; Dzuba, S. A.


    Electron paramagnetic resonance (EPR) spectroscopy in the form of pulsed electron-electron double resonance (ELDOR) was applied to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers containing lipids that were spin-labeled at different carbon positions along the lipid acyl chain. Pulsed ELDOR detects motionally induced spin flips of nitrogen nuclei in the nitroxide spin labels, which manifests itself as magnetization transfer (MT) in the nitroxide EPR spectrum. The MT effect was observed over a wide temperature range (100-225 K) on a microsecond time scale. In line with a previous study on molecular glasses [N. P. Isaev and S. A. Dzuba, J. Chem. Phys. 135, 094508 (2011), 10.1063/1.3633241], the motions that induce MT effect were suggested to have the same nature as those in dielectric secondary (β) Johari-Goldstein fast relaxation. The results were compared with literature dielectric relaxation data for POPC bilayers, revealing some common features. Molecular motions resulting in MT are faster for deeper spin labels in the membrane interior. The addition of cholesterol to the bilayer suppresses the lipid motions near the steroid nucleus and accelerates the lipid motions beyond the steroid nucleus, in the bilayer interior. This finding was attributed to the lipid acyl chains being more ordered near the steroid nucleus and less ordered in the bilayer interior. The motions are absent in dry lipids, indicating that the motions are determined by intermolecular interactions in the bilayer.

  12. Compressed Sensing Electron Tomography for Determining Biological Structure (United States)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.


    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  13. Structural Determinants of Intergroup Association: Interracial Marriage and Crime. (United States)

    South, Scott J.; Messner, Steven F.


    Using data from a sample of 25 U. S. metropolitan cities, this study investigates the relationship between interracial marriage and violent interracial crime. Results show a positive relationship, one which was predicted by Blau's macrosociological theory of social structure. (Author/JDH)

  14. Some structural determinants of Pavlovian conditioning in artificial neural networks

    NARCIS (Netherlands)

    Sanchez, Jose M.; Galeazzi, Juan M.; Burgos, Jose E.


    This paper investigates the possible role of neuroanatomical features in Pavlovian conditioning, via computer simulations with layered, feedforward artificial neural networks. The networks' structure and functioning are described by a strongly bottom-up model that takes into account the roles of hip

  15. Novel test structures for dedicated temperature budget determination

    NARCIS (Netherlands)

    Faber, Erik J.; Wolters, Rob A.M.; Schmitz, Jurriaan


    We present a novel method for determining the temperature budget of the process side of silicon substrates and chips, based on well-known silicide formation reactions of metal–Si systems and (four-point probe) resistance measurements. In this paper, we focus on the Pd–Si system that is most temperat

  16. Fractal structure and fractal dimension determination at nanometer scale

    Institute of Scientific and Technical Information of China (English)

    张跃; 李启楷; 褚武扬; 王琛; 白春礼


    Three-dimensional fractures of different fractal dimensions have been constructed with successive random addition algorithm, the applicability of various dimension determination methods at nanometer scale has been studied. As to the metallic fractures, owing to the limited number of slit islands in a slit plane or limited datum number at nanometer scale, it is difficult to use the area-perimeter method or power spectrum method to determine the fractal dimension. Simulation indicates that box-counting method can be used to determine the fractal dimension at nanometer scale. The dimensions of fractures of valve steel 5Cr21Mn9Ni4N have been determined with STM. Results confirmed that fractal dimension varies with direction at nanometer scale. Our study revealed that, as to theoretical profiles, the dependence of fractal dimension with direction is simply owing to the limited data set number, i.e. the effect of boundaries. However, the dependence of fractal dimension with direction at nanometer scale in rea

  17. One-dimensional Topological Edge States of Bismuth Bilayers (United States)

    Drozdov, Ilya; Alexandradinata, Aris; Jeon, Sangjun; Nadj-Perge, Stevan; Ji, Huiwen; Cava, Robert; Bernevig, B. Andrei; Yazdani, Ali


    The hallmark of a time-reversal symmetry protected topologically insulating state of matter in two-dimensions (2D) is the existence of chiral edge modes propagating along the perimeter of the sample. Bilayers of bismuth (Bi), an elemental system theoretically predicted to be a Quantum Spin Hall (QSH) insulator1, has been studied with Scanning Tunneling Microscopy (STM) and the electronic structure of its bulk and edge modes has been experimentally investigated. Spectroscopic mapping with STM reveals the presence of the state bound to the edges of the Bi-bilayer. By visualizing quantum interference of the edge state quasi-particles in confined geometries we characterize their dispersion and demonstrate that their properties are consistent with the absence of backscattering. Hybridization of the edge modes to the underlying substrate will be discussed. [1] Shuichi Murakami, Phys. Rev. Lett. 97, 236805 (2006). The work at Princeton and the Princeton Nanoscale Microscopy Laboratory was supported by ARO MURI program W911NF-12-1-0461, DARPA-SPWAR Meso program N6601-11-1-4110, NSF-DMR1104612, and NSF-MRSEC programs through the Princeton Center for Complex Materials (DMR-0819860)

  18. Unexpected bilayer formation in Langmuir films of nucleolipids. (United States)

    Desbat, Bernard; Arazam, Nessim; Khiati, Salim; Tonelli, Giovanni; Neri, Wilfrid; Barthélémy, Philippe; Navailles, Laurence


    Langmuir monolayers have been extensively investigated by various experimental techniques. These studies allowed an in-depth understanding of the molecular conformation in the layer, phase transitions, and the structure of the multilayer. As the monolayer is compressed and the surface pressure is increased beyond a critical value, usually occurring in the minimal closely packed molecular area, the monolayer fractures and/or folds, forming multilayers in a process referred to as collapse. Various mechanisms for monolayer collapse and the resulting reorganization of the film have been proposed, and only a few studies have demonstrated the formation of a bilayer after collapse and with the use of a Ca(2+) solution. In this work, Langmuir isotherms coupled with imaging ellipsometry and polarization modulation infrared reflection absorption spectroscopy were recorded to investigate the air-water interface properties of Langmuir films of anionic nucleolipids. We report for these new molecules the formation of a quasi-hexagonal packing of bilayer domains at a low compression rate, a singular behavior for lipids at the air-water interface that has not yet been documented.

  19. Nonlocal Drag of Magnons in a Ferromagnetic Bilayer (United States)

    Liu, Tianyu; Vignale, G.; Flatté, Michael E.


    Quantized spin waves, or magnons, in a magnetic insulator are assumed to interact weakly with the surroundings, and to flow with little dissipation or drag, producing exceptionally long diffusion lengths and relaxation times. In analogy to Coulomb drag in bilayer two-dimensional electron gases, in which the contribution of the Coulomb interaction to the electric resistivity is studied by measuring the interlayer resistivity (transresistivity), we predict a nonlocal drag of magnons in a ferromagnetic bilayer structure based on semiclassical Boltzmann equations. Nonlocal magnon drag depends on magnetic dipolar interactions between the layers and manifests in the magnon current transresistivity and the magnon thermal transresistivity, whereby a magnon current in one layer induces a chemical potential gradient and/or a temperature gradient in the other layer. The largest drag effect occurs when the magnon current flows parallel to the magnetization; however, for oblique magnon currents a large transverse current of magnons emerges. We examine the effect for practical parameters, and find that the predicted induced temperature gradient is readily observable.

  20. Iron phosphate glasses: Structure determination and radiation tolerance (United States)

    Jolley, Kenny; Smith, Roger


    Iron phosphate glass (IPG) has gained recent interest for use in encapsulating radioactive waste for long term storage. In this work, we investigate 5 different compositions of iron phosphate glass. We consider amorphous structures of 3 known crystalline phases: Fe2+ Fe23+ (P2O7)2, Fe43 + (P2O7)3 and Fe3+(PO3)3, and structures of IPG (40 mol% Fe2O3 and 60 mol% P2O5), with 4% and 17% Fe2+ ion concentrations. Using constant volume molecular dynamics (MD), we quench a set of structures for each glass composition, to find the optimal density structure. We found that the lowest energy structures of IPG with 4% and 17% concentration of Fe2+, have a density of 3.25 and 3.28 g/cm3 respectively. This is slightly higher than the experimentally measured values of 2.9 and 2.95 g/cm3 respectively. We also estimate an upper and lower bound on the melting temperatures of each glass, then for each glass, we simulate radiation damage cascades at 4 keV. The cascade structures can be in the form of either a concentrated thermal spike or more diffuse with sub-cascade branching. We found that the glass compositions with a higher Fe/P atomic ratio, contained a greater number of displacements after the cascade. We also found that the IPG with 4% Fe2+, contained slightly fewer displacements than the IPG with 17% Fe2+. This is consistent with our previous work, which showed that the threshold displacement energies are lower for glasses with a lower Fe2+ content. In all the simulations, many PO4 polyhedra are destroyed during the early stages of irradiation, but recover strongly over a time scale of picoseconds, leaving very few over or under co-ordinated P atoms at the end of the ballistic phase. This is in contrast to recent work in apatite. The strong recovery indicates that phosphate glasses with a low Fe2+ content could be good materials for waste encapsulation.

  1. Solid-state NMR structures of integral membrane proteins. (United States)

    Patching, Simon G


    Solid-state NMR is unique for its ability to obtain three-dimensional structures and to measure atomic-resolution structural and dynamic information for membrane proteins in native lipid bilayers. An increasing number and complexity of integral membrane protein structures have been determined by solid-state NMR using two main methods. Oriented sample solid-state NMR uses macroscopically aligned lipid bilayers to obtain orientational restraints that define secondary structure and global fold of embedded peptides and proteins and their orientation and topology in lipid bilayers. Magic angle spinning (MAS) solid-state NMR uses unoriented rapidly spinning samples to obtain distance and torsion angle restraints that define tertiary structure and helix packing arrangements. Details of all current protein structures are described, highlighting developments in experimental strategy and other technological advancements. Some structures originate from combining solid- and solution-state NMR information and some have used solid-state NMR to refine X-ray crystal structures. Solid-state NMR has also validated the structures of proteins determined in different membrane mimetics by solution-state NMR and X-ray crystallography and is therefore complementary to other structural biology techniques. By continuing efforts in identifying membrane protein targets and developing expression, isotope labelling and sample preparation strategies, probe technology, NMR experiments, calculation and modelling methods and combination with other techniques, it should be feasible to determine the structures of many more membrane proteins of biological and biomedical importance using solid-state NMR. This will provide three-dimensional structures and atomic-resolution structural information for characterising ligand and drug interactions, dynamics and molecular mechanisms of membrane proteins under physiological lipid bilayer conditions.

  2. Spectroscopic infrared ellipsometry to determine the structure of layered samples

    Energy Technology Data Exchange (ETDEWEB)

    Korte, Ernst-Heiner; Hinrichs, Karsten; Roeseler, Arnulf


    This contribution outlines investigations in our laboratory in the course of developing spectroscopic infrared ellipsometry into an analytical tool for structure elucidation of a given solid sample with one single experimental technique. The term 'structure' is meant here to comprise the layer or stack geometry of a sample along with the thicknesses, as well as the optical properties of the individual layers. The latter ones--expressed as optical constants--serve as a basis to characterize the layer material, from the identity of the compound to specific molecular interactions and order. There are no general restrictions as to the physical properties of the materials; the individual layers or films should advantageously be thin enough to transmit infrared radiation at least within spectral windows. The sensitivity of infrared ellipsometry to films as thin as a few nanometers or less is illustrated by experimental examples.

  3. Determination of channeling perspectives for complex crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Allen, W.R.


    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  4. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    DEFF Research Database (Denmark)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M;


    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a ...... to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted....

  5. Determination of the pion and kaon structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Aitkenhead, W.; Barton, D.S.; Brandenburg, G.W.; Busza, W.; Dobrowolski, T.; Friedman, J.I.; Kendall, H.W.; Lyons, T.; Nelson, B.; Rosenson, L.; Toy, W.; Verdier, R.; Votta, L.; Chiaradia, M.T.; DeMarzo, C.; Favuzzi, C.; Germinario, G.; Guerriero, L.; LaVopa, P.; Maggi, G.; Posa, F.; Selvaggi, G.; Spinelli, P.; Waldner, F.; Brenner, A.E.; Carey, D.C.; Elias, J.E.; Garbincius, P.H.; Mikenberg, G.; Polychronakos, V.A.; Meunier, R.; Cutts, D.; Dulude, R.S.; Lanou, R.E. Jr.; Massimo, J.T.


    Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup ..pi../=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5.

  6. Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity. (United States)

    Berndt, Andre; Lee, Soo Yeun; Wietek, Jonas; Ramakrishnan, Charu; Steinberg, Elizabeth E; Rashid, Asim J; Kim, Hoseok; Park, Sungmo; Santoro, Adam; Frankland, Paul W; Iyer, Shrivats M; Pak, Sally; Ährlund-Richter, Sofie; Delp, Scott L; Malenka, Robert C; Josselyn, Sheena A; Carlén, Marie; Hegemann, Peter; Deisseroth, Karl


    The structure-guided design of chloride-conducting channelrhodopsins has illuminated mechanisms underlying ion selectivity of this remarkable family of light-activated ion channels. The first generation of chloride-conducting channelrhodopsins, guided in part by development of a structure-informed electrostatic model for pore selectivity, included both the introduction of amino acids with positively charged side chains into the ion conduction pathway and the removal of residues hypothesized to support negatively charged binding sites for cations. Engineered channels indeed became chloride selective, reversing near -65 mV and enabling a new kind of optogenetic inhibition; however, these first-generation chloride-conducting channels displayed small photocurrents and were not tested for optogenetic inhibition of behavior. Here we report the validation and further development of the channelrhodopsin pore model via crystal structure-guided engineering of next-generation light-activated chloride channels (iC++) and a bistable variant (SwiChR++) with net photocurrents increased more than 15-fold under physiological conditions, reversal potential further decreased by another ∼ 15 mV, inhibition of spiking faithfully tracking chloride gradients and intrinsic cell properties, strong expression in vivo, and the initial microbial opsin channel-inhibitor-based control of freely moving behavior. We further show that inhibition by light-gated chloride channels is mediated mainly by shunting effects, which exert optogenetic control much more efficiently than the hyperpolarization induced by light-activated chloride pumps. The design and functional features of these next-generation chloride-conducting channelrhodopsins provide both chronic and acute timescale tools for reversible optogenetic inhibition, confirm fundamental predictions of the ion selectivity model, and further elucidate electrostatic and steric structure-function relationships of the light-gated pore.

  7. Xenon-ion-induced and thermal mixing of Co/Si bilayers and their interplay (United States)

    Novaković, M.; Zhang, K.; Popović, M.; Bibić, N.; Hofsäss, H.; Lieb, K. P.


    Studies on ion-irradiated transition-metal/silicon bilayers demonstrate that interface mixing and silicide phase formation depend sensitively on the ion and film parameters, including the structure of the metal/Si interface. Thin Co layers e-gun evaporated to a thickness of 50 nm on Si(1 0 0) wafers were bombarded at room temperature with 400-keV Xe + ions at fluences of up to 3 × 10 16 cm -2. We used either crystalline or pre-amorphized Si wafers the latter ones prepared by 1.0-keV Ar-ion implantation. The as-deposited or Xe-ion-irradiated samples were then isochronally annealed at temperatures up to 700 °C. Changes of the bilayer structures induced by ion irradiation and/or annealing were investigated with RBS, XRD and HRTEM. The mixing rate for the Co/c-Si couples, Δ σ2/ Φ = 3.0(4) nm 4, is higher than the value expected for ballistic mixing and about half the value typical for spike mixing. Mixing of pre-amorphized Si is much weaker relative to crystalline Si wafers, contrary to previous results obtained for Fe/Si bilayers. Annealing of irradiated samples produces very similar interdiffusion and phase formation patterns above 400 °C as in the non-irradiated Co/Si bilayers: the phase evolution follows the sequence Co 2Si → CoSi → CoSi 2.

  8. Tuning the energy gap of bilayer α-graphyne by applying strain and electric field (United States)

    Yang, Hang; Wu, Wen-Zhi; Jin, Yu; Wan-Lin, Guo


    Our density functional theory calculations show that the energy gap of bilayer α-graphyne can be modulated by a vertically applied electric field and interlayer strain. Like bilayer graphene, the bilayer α-graphyne has electronic properties that are hardly changed under purely mechanical strain, while an external electric field can open the gap up to 120 meV. It is of special interest that compressive strain can further enlarge the field induced gap up to 160 meV, while tensile strain reduces the gap. We attribute the gap variation to the novel interlayer charge redistribution between bilayer α-graphynes. These findings shed light on the modulation of Dirac cone structures and potential applications of graphyne in mechanical-electric devices. Project supported by the National Key Basic Research Program of China (Grant Nos. 2013CB932604 and 2012CB933403), the National Natural Science Foundation of China (Grant Nos. 51472117 and 51535005), the Research Fund of State Key Laboratory of Mechanics and Control of Mechanical Structures, China (Grant No. 0414K01), the Nanjing University of Aeronautics and Astronautics (NUAA) Fundamental Research Funds, China (Grant No. NP2015203), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.

  9. Self-consistent mean-field model for palmitoyloleoylphosphatidylcholine-palmitoyl sphingomyelin-cholesterol lipid bilayers (United States)

    Tumaneng, Paul W.; Pandit, Sagar A.; Zhao, Guijun; Scott, H. L.


    The connection between membrane inhomogeneity and the structural basis of lipid rafts has sparked interest in the lateral organization of model lipid bilayers of two and three components. In an effort to investigate anisotropic lipid distribution in mixed bilayers, a self-consistent mean-field theoretical model is applied to palmitoyloleoylphosphatidylcholine (POPC)-palmitoyl sphingomyelin (PSM)-cholesterol mixtures. The compositional dependence of lateral organization in these mixtures is mapped onto a ternary plot. The model utilizes molecular dynamics simulations to estimate interaction parameters and to construct chain conformation libraries. We find that at some concentration ratios the bilayers separate spatially into regions of higher and lower chain order coinciding with areas enriched with PSM and POPC, respectively. To examine the effect of the asymmetric chain structure of POPC on bilayer lateral inhomogeneity, we consider POPC-lipid interactions with and without angular dependence. Results are compared with experimental data and with results from a similar model for mixtures of dioleoylphosphatidylcholine, steroyl sphingomyelin, and cholesterol.

  10. Raman Spectroscopy of DLC/a-Si Bilayer Film Prepared by Pulsed Filtered Cathodic Arc

    Directory of Open Access Journals (Sweden)

    C. Srisang


    Full Text Available DLC/a-Si bilayer film was deposited on germanium substrate. The a-Si layer, a seed layer, was firstly deposited on the substrate using DC magnetron sputtering and DLC layer was then deposited on the a-Si layer using pulsed filtered cathodic arc method. The bilayer films were deposited with different DLC/a-Si thickness ratios, including 2/2, 2/6, 4/4, 6/2, and 9/6. The effect of DLC/a-Si thickness ratios on the sp3 content of DLC was analyzed by Raman spectroscopy. The results show that a-Si layer has no effect on the structure of DLC film. Furthermore, the upper shift in G wavenumber and the decrease in ID/IG inform that sp3 content of the film is directly proportional to DLC thickness. The plot modified from the three-stage model informed that the structural characteristics of DLC/a-Si bilayer films are located close to the tetrahedral amorphous carbon. This information may be important for analyzing and developing bilayer protective films for future hard disk drive.

  11. Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers (United States)

    Zhu, Wei; Xiong, Le; Peng, Jinming; Deng, Xiangyi; Gao, Jun; Li, Chun-Mei


    Experimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers. The gallated PA dimers penetrated deeper into the bilayer and formed more hydrogen bonds (H-bonds) with bilayer oxygen atoms, especially the deeper oxygen atoms of the lipids simultaneously, thus inducing stronger lateral expansion of the membrane and lipid tails disorder. The present results provided molecular insights into the interactions between PA dimers and bio-membranes and agreed with our experimental results well. These molecular interactions helped to elucidate the structure-function relationship of the PA dimers and provided a foundation for a better understanding of the underlying mechanisms of the bioactivities of PA oligomers.

  12. Music structure determines heart rate variability of singers (United States)

    Vickhoff, Björn; Malmgren, Helge; Åström, Rickard; Nyberg, Gunnar; Ekström, Seth-Reino; Engwall, Mathias; Snygg, Johan; Nilsson, Michael; Jörnsten, Rebecka


    Choir singing is known to promote wellbeing. One reason for this may be that singing demands a slower than normal respiration, which may in turn affect heart activity. Coupling of heart rate variability (HRV) to respiration is called Respiratory sinus arrhythmia (RSA). This coupling has a subjective as well as a biologically soothing effect, and it is beneficial for cardiovascular function. RSA is seen to be more marked during slow-paced breathing and at lower respiration rates (0.1 Hz and below). In this study, we investigate how singing, which is a form of guided breathing, affects HRV and RSA. The study comprises a group of healthy 18 year olds of mixed gender. The subjects are asked to; (1) hum a single tone and breathe whenever they need to; (2) sing a hymn with free, unguided breathing; and (3) sing a slow mantra and breathe solely between phrases. Heart rate (HR) is measured continuously during the study. The study design makes it possible to compare above three levels of song structure. In a separate case study, we examine five individuals performing singing tasks (1–3). We collect data with more advanced equipment, simultaneously recording HR, respiration, skin conductance and finger temperature. We show how song structure, respiration and HR are connected. Unison singing of regular song structures makes the hearts of the singers accelerate and decelerate simultaneously. Implications concerning the effect on wellbeing and health are discussed as well as the question how this inner entrainment may affect perception and behavior. PMID:23847555

  13. A generic tight-binding model for monolayer, bilayer and bulk MoS2

    Directory of Open Access Journals (Sweden)

    Ferdows Zahid


    Full Text Available Molybdenum disulfide (MoS2 is a layered semiconductor which has become very important recently as an emerging electronic device material. Being an intrinsic semiconductor the two-dimensional MoS2 has major advantages as the channel material in field-effect transistors. In this work we determine the electronic structures of MoS2 with the highly accurate screened hybrid functional within the density functional theory (DFT including the spin-orbit coupling. Using the DFT electronic structures as target, we have developed a single generic tight-binding (TB model that accurately produces the electronic structures for three different forms of MoS2 - bulk, bilayer and monolayer. Our TB model is based on the Slater-Koster method with non-orthogonal sp3d5 orbitals, nearest-neighbor interactions and spin-orbit coupling. The TB model is useful for atomistic modeling of quantum transport in MoS2 based electronic devices.

  14. Stacking transition in bilayer graphene caused by thermally activated rotation (United States)

    Zhu, Mengjian; Ghazaryan, Davit; Son, Seok-Kyun; Woods, Colin R.; Misra, Abhishek; He, Lin; Taniguchi, Takashi; Watanabe, Kenji; Novoselov, Kostya S.; Cao, Yang; Mishchenko, Artem


    Crystallographic alignment between two-dimensional crystals in van der Waals heterostructures brought a number of profound physical phenomena, including observation of Hofstadter butterfly and topological currents, and promising novel applications, such as resonant tunnelling transistors. Here, by probing the electronic density of states in graphene using graphene-hexagonal boron nitride-graphene tunnelling transistors, we demonstrate a structural transition of bilayer graphene from incommensurate twisted stacking state into a commensurate AB stacking due to a macroscopic graphene self-rotation. This structural transition is accompanied by a topological transition in the reciprocal space and by pseudospin texturing. The stacking transition is driven by van der Waals interaction energy of the two graphene layers and is thermally activated by unpinning the microscopic chemical adsorbents which are then removed by the self-cleaning of graphene.

  15. One GHz leaky SAW velocity of metal layers and bilayers evaporated onto fused quartz (United States)

    Walikainen, Dale


    An acoustic microscope operating at 1 GHz was used to determine the surface acoustic wave velocities v of thin film metal layers and metal bilayers deposited onto fused quartz. V(0)'s influence was reduced by gating. This produced a calibrated accuracy of 3 percent. A program was constructed from the explicitly solved 6 x 6 theoretical determinant. Single film thicknesses were decided upon by using this theory to produce a v equal to a standard. Since the single film v's were linear with respect to their thickness, half the single film thicknesses were used for the bilayered films. The velocities for these bilayered films agreed with theory. This experimentally confirms the theoretical technique used here to examine bilayered systems, or a prototype composite interphase. No discrepancy was seen for gold films as others have reported. V(z) seemed insensitive to the formation of intermetallics or CuO. Some annealed and unannealed platinum films did not change the v from that of fused quartz. Two platinum films whose v's were in agreement with theory peeled off with the tape test.

  16. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project (United States)

    National Aeronautics and Space Administration — We propose a dual objective innovation that has valuable NASA applicability and tremendous commercial potential. The first innovation is the structure determination...

  17. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  18. 双层单负材料结构的古斯-亨兴位移调控%Control of Goos-Hanchen Displacement on Bilayer Structure Composed of Single Negative Materials

    Institute of Scientific and Technical Information of China (English)

    张曦; 许静平; 羊亚平


    运用反射相位法和高斯光束峰值位移判断法研究了由电单负材料(ENM)和磁单负材料(MNM)组成的双层结构的古斯-亨兴位移现象.首先利用传输矩阵计算结构的反射系数,通过对反射系数的相位分析,发现对于单层的电单负材料和单层的磁单负材料,反射高斯光束的古斯-亨兴位移方向相反,同时位移的大小与材料厚度存在一定的联系.进一步对双层材料传输矩阵进行解析分析,发现由电磁参数互为相反数的电单负材料和磁单负材料组合而成的双层材料,可以便捷地通过改变某一层材料的厚度来调控古斯-亨兴位移的大小和方向.%Goos-Hcinchen effect which occurs on the surface of bilayer composed of electric-negative-material (ENM) slab and magnetic-negative-material (MNM) slab is analyzed by using the reflective-phase method and the Gaussianbeam peak-shift criterion. And by using the transfer matrix, it is found that the directions of Goos-Hanchendisplacement are different between the situation when the beams reflect from the ENM and the situation that happen on MNM. It also shows that the Goos-H(a)nchen displacement of such bilayer can be controlled expediently by adjusting the thickness of one layer as the indices of ENM slab are opposite to those of MNM slab.

  19. Determining the Spectral Signature of Spatial Coherent Structures

    CERN Document Server

    Pastur, L R; Fraigneau, Y; Podvin, B


    We applied to an open flow a proper orthogonal decomposition (pod) technique, on 2D snapshots of the instantaneous velocity field, to reveal the spatial coherent structures responsible of the self-sustained oscillations observed in the spectral distribution of time series. We applied the technique to 2D planes out of 3D direct numerical simulations on an open cavity flow. The process can easily be implemented on usual personal computers, and might bring deep insights on the relation between spatial events and temporal signature in (both numerical or experimental) open flows.

  20. Fabrication and characterization of nano-fibrous bilayer composite for skin regeneration application. (United States)

    Arasteh, Shaghayegh; Kazemnejad, Somaieh; Khanjani, Sayeh; Heidari-Vala, Hamed; Akhondi, Mohammad Mehdi; Mobini, Sahba


    Full thickness wound healing with minimal scarring and complete restoration of normal skin properties still remains as a clinical challenge. In this study, a bilayer skin substitute has been fabricated to biomimic the microstructure of natural extracellular matrix of the skin. Human amniotic membrane (HAM) and silk fibroin nano-fibers were combined to produce bilayer construct, which was further treated and characterized. HAM was obtained from healthy mothers and de-epithelized by means of fine enzymatic method to preserve the extracellular structure. Fibroin protein was extracted from fresh Bombyx mori cocoons and transformed to uniform nano-fiberous structure, which was used as a coating layer on the de-epithelized membrane. Surface modification through oxygen plasma treatment was attempted to further induce hydrophilicity. Subsequently, scaffolds were fully characterized in terms of morphology, mechanical properties, hydrophilicity and cell culture response. Histological and immunohistological staining demonstrated localization of fibronectin, cell denudation and structural integrity of HAM after de-epithelization. Scanning electron microscopy images showed bead-free silk fibroin nano-fibers with the average diameter of 250nm. Water contact angle of bilayer scaffolds reduced dramatically to 26.34° after oxygen plasma treatment, which is correlated with more hydrophilic surface. Due to fibroin nano-fiber coating, mechanical properties of HAM improved significantly. Tensile Young's modulus and tensile strength increased from 16.14MPa and 68.46MPa to 25.69MPa and 108.03MPa, respectively. 14days in vitro cultivation of mouse embryonic fibroblasts on the scaffolds revealed that bilayer scaffolds are able to support cell attachment and proliferation. Plasma-etched scaffolds provided the best niche for cell-matrix crosstalk by allowing cells to penetrate beneath the pores and to integrate in fibers direction. The obtained results suggest that the presented nano

  1. Electric Octupole Order in Bilayer Rashba System (United States)

    Hitomi, Takanori; Yanase, Youichi


    The odd-parity multipole is an emergent degree of freedom, leading to spontaneous inversion symmetry breaking. The odd-parity multipole order may occur by forming staggered even-parity multipoles in a unit cell. We focus on a locally noncentrosymmetric bilayer Rashba system, and study an odd-parity electric octupole order caused by the antiferro stacking of local electric quadrupoles. Analyzing the forward scattering model, we show that the electric octupole order is stabilized by a layer-dependent Rashba spin-orbit coupling. The roles of the spin-orbit coupling are clarified on the basis of the analytic formula of multipole susceptibility. The spin texture allowed in the D2d point group symmetry and its magnetic response are revealed. Furthermore, we show that the parity-breaking quantum critical point appears in the magnetic field. The possible realization of the electric octupole order in bilayer high-Tc cuprate superconductors is discussed.

  2. Understanding chlorophylls: central magnesium ion and phytyl as structural determinants. (United States)

    Fiedor, Leszek; Kania, Agnieszka; Myśliwa-Kurdziel, Beata; Orzeł, Łukasz; Stochel, Grazyna


    Phytol, a C20 alcohol esterifying the C-17(3) propionate, and Mg2+ ion chelated in the central cavity, are conservative structural constituents of chlorophylls. To evaluate their intramolecular structural effects we prepared a series of metal- and phytyl-free derivatives of bacteriochlorophyll a and applied them as model chlorophylls. A detailed spectroscopic study on the model pigments reveals meaningful differences in the spectral characteristics of the phytylated and non-phytylated pigments. Their analysis in terms of solvatochromism and axial coordination shows how the central Mg and phytyl residue shape the properties of the pigment. Surprisingly, the presence/absence of the central Mg has no effect on the solvatochromism of (bacterio)chlorophyll pi-electron system and the hydrophobicity of phytyl does not interfere with the first solvation shell of the chromophore. However, both residues significantly influence the conformation of the pigment macrocycle and the removal of either residue increases the macrocycle flexibility. The chelation of Mg has a flattening effect on the macrocycle whereas bulky phytyl residue seems to control the conformation of the chromophore via steric interactions with ring V and its substituents. The analysis of spectroscopic properties of bacteriochlorophyllide (free acid) shows that esterification of the C-17(3) propionate is necessary in chlorophylls because the carboxyl group may act as a strong chelator of the central Mg. These observations imply that the truncated chlorophylls used in theoretical studies are not adequate as models of native chromophores, especially when fine effects are to be modeled.

  3. Molecular Determinants of Staphylococcal Biofilm Dispersal and Structuring

    Directory of Open Access Journals (Sweden)

    Katherine Y Le


    Full Text Available Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: 1 attachment, 2 proliferation/structuring, and 3 detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs have been consistently demonstrated to serve in this role under both in-vitro and in-vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets.

  4. Using Dust as Probes to Determine Sheath Extent and Structure

    CERN Document Server

    Douglass, Angela; Qiao, Ke; Matthews, Lorin; Hyde, Truell


    Two in-situ experimental methods are presented in which dust particles are used to determine the extent of the sheath and gain information about the time-averaged electric force profile within a RF plasma sheath. These methods are advantageous because they are not only simple and quick to carry out, but they also can be performed using standard dusty plasma experimental equipment. In the first method, dust particles are tracked as they fall through the plasma toward the lower electrode. These trajectories are then used to determine the electric force on the particle as a function of height as well as the extent of the sheath. In the second method, dust particle levitation height is measured across a wide range of RF voltages. Similarities were observed between the two experiments, but in order to understand the underlying physics behind these observations, the same conditions were replicated using a self-consistent fluid model. Through comparison of the fluid model and experimental results, it is shown that t...

  5. Ion beam mixing isotopic metal bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Fell, C.J. [Newcastle Univ., NSW (Australia). Dept. of Physics; Kenny, M.J. [CSIRO, Lindfield, NSW (Australia). Div. of Applied Physics


    In order to obtain an insight into the mechanisms of ion-solid interactions, bilayer targets can be prepared from two different isotopes. A mixing study SIMS is to be carried out using specially grown monocrystalline bilayers of {sup 58}Ni / {sup 60}Ni. An important aspect of the work is the preparation of high quality single-crystal thin films. The Ni layers will be grown on the (110) surface of pure Ni and verified for crystallinity using Reflection High-Energy Electron Diffraction and Rutherford Backscattering channelling analysis. The Pd bilayers will be grown on a Pd (100) surface. RHEED will be used to confirm the two-dimensional crystallinity of the surface before and after deposition of each layer, and channelling used to confirm bulk film crystallinity. Single crystal substrates are currently being prepared. Analysis of the Ni (110) surface using RHEED at 9 kV shows a streak spacing which corresponds to a lattice spacing of 2.47 {+-} 0.09 Angstroms. 9 refs., 1 fig.

  6. Electron Crystallography Novel Approaches for Structure Determination of Nanosized Materials

    CERN Document Server

    Weirich, Thomas E; Zou, Xiaodong


    During the last decade we have been witness to several exciting achievements in electron crystallography. This includes structural and charge density studies on organic molecules complicated inorganic and metallic materials in the amorphous, nano-, meso- and quasi-crystalline state and also development of new software, tailor-made for the special needs of electron crystallography. Moreover, these developments have been accompanied by a now available new generation of computer controlled electron microscopes equipped with high-coherent field-emission sources, cryo-specimen holders, ultra-fast CCD cameras, imaging plates, energy filters and even correctors for electron optical distortions. Thus, a fast and semi-automatic data acquisition from small sample areas, similar to what we today know from imaging plates diffraction systems in X-ray crystallography, can be envisioned for the very near future. This progress clearly shows that the contribution of electron crystallography is quite unique, as it enables to r...

  7. Extracellular matrix structure and nano-mechanics determine megakaryocyte function. (United States)

    Malara, Alessandro; Gruppi, Cristian; Pallotta, Isabella; Spedden, Elise; Tenni, Ruggero; Raspanti, Mario; Kaplan, David; Tira, Maria Enrica; Staii, Cristian; Balduini, Alessandra


    Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1-dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.

  8. Method of fabricating lipid bilayer membranes on solid supports (United States)

    Cho, Nam-Joon (Inventor); Frank, Curtis W. (Inventor); Glenn, Jeffrey S. (Inventor); Cheong, Kwang Ho (Inventor)


    The present invention provides a method of producing a planar lipid bilayer on a solid support. With this method, a solution of lipid vesicles is first deposited on the solid support. Next, the lipid vesicles are destabilized by adding an amphipathic peptide solution to the lipid vesicle solution. This destabilization leads to production of a planar lipid bilayer on the solid support. The present invention also provides a supported planar lipid bilayer, where the planar lipid bilayer is made of naturally occurring lipids and the solid support is made of unmodified gold or titanium oxide. Preferably, the supported planar lipid bilayer is continuous. The planar lipid bilayer may be made of any naturally occurring lipid or mixture of lipids, including, but not limited to phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinsitol, cardiolipin, cholesterol, and sphingomyelin.

  9. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei [Institute of High Performance Computing, A*STAR, 138632 (Singapore)


    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  10. Synthesis of mono- and bi-layer MFI zeolite films on macroporous alumina tubular supports: Application to nanofiltration (United States)

    Said, Ali; Limousy, Lionel; Nouali, Habiba; Michelin, Laure; Halawani, Jalal; Toufaily, Joumana; Hamieh, Tayssir; Dutournié, Patrick; Daou, T. Jean


    This work is dedicated to the development of MFI-type structure zeolite films (single-layer or bilayer) on the internal layer of a specific macroporous alumina tubular support for nanofiltration applications. The bottom MFI layer was obtained by direct hydrothermal synthesis while a secondary growth method was used for the top MFI layer. A complete characterization of the obtained MFI membranes (single-layer or bilayer) is proposed using various techniques, such as X-ray diffraction, scanning electron microscopy, mercury porosimetry and nitrogen sorption measurements. Dense and highly crystallized films of MFI-type structure zeolite were obtained for both single-layer and bilayer MFI films. The total film thickness were around 7.1±0.5 μm and 14.5±1 μm for single-layer and bilayer MFI films respectively. The Si/Al molar ratio of the MFI films varied between 185 and 305 for single-layer and bilayer MFI films respectively. The hydraulic permeability of the tubular MFI membrane was achieved by the filtration of pure water. The hydraulic permeability of the single-layer and bilayer MFI membranes decreased rapidly at the beginning of the conditioning process, and stabilized at 1.08×10-14 m3 m-2 and 1.02×10-15 m3 m-2 after 15 h and the rejection rates of neutral solute (Vb 12) are 10% and 50% for the single-layer and bilayer MFI films respectively.

  11. Edge effects on band gap energy in bilayer 2H-MoS{sub 2} under uniaxial strain

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Liang; Wang, Jin; Dongare, Avinash M., E-mail: [Department of Materials Science and Engineering and Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269 (United States); Namburu, Raju [Computational and Information Sciences Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); O' Regan, Terrance P.; Dubey, Madan [Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, Adelphi, Maryland 20783 (United States)


    The potential of ultrathin MoS{sub 2} nanostructures for applications in electronic and optoelectronic devices requires a fundamental understanding in their electronic structure as a function of strain. Previous experimental and theoretical studies assume that an identical strain and/or stress state is always maintained in the top and bottom layers of a bilayer MoS{sub 2} film. In this study, a bilayer MoS{sub 2} supercell is constructed differently from the prototypical unit cell in order to investigate the layer-dependent electronic band gap energy in a bilayer MoS{sub 2} film under uniaxial mechanical deformations. The supercell contains an MoS{sub 2} bottom layer and a relatively narrower top layer (nanoribbon with free edges) as a simplified model to simulate the as-grown bilayer MoS{sub 2} flakes with free edges observed experimentally. Our results show that the two layers have different band gap energies under a tensile uniaxial strain, although they remain mutually interacting by van der Waals interactions. The deviation in their band gap energies grows from 0 to 0.42 eV as the uniaxial strain increases from 0% to 6% under both uniaxial strain and stress conditions. The deviation, however, disappears if a compressive uniaxial strain is applied. These results demonstrate that tensile uniaxial strains applied to bilayer MoS{sub 2} films can result in distinct band gap energies in the bilayer structures. Such variations need to be accounted for when analyzing strain effects on electronic properties of bilayer or multilayered 2D materials using experimental methods or in continuum models.

  12. Boundary potential of lipid bilayers: methods and interpretations (United States)

    Ermakov, Yu A.; Nesterenko, A. M.


    The electric field distribution at the boundaries of cell membrane consists of diffuse part of the electrical double layer and the potential drop over polar area inside the membrane itself. The latter is generally attributed to the dipole effect, which depends on the lipid hydration and phase state. This report focuses on the experimental approaches developed to detect the relation between dipole effects and the bilayer structure, and to study their molecular nature. The total boundary potential (BP) of planar bilayer lipid membranes (BLM) can be controlled by Intramembranous Field Compensation (IFC) method developed in our laboratory. When combined with electrokinetic measurements in liposome suspension it allows detecting the changes of the dipole potential due to adsorption of inorganic cations and charged molecules. Multivalent inorganic cations increase the dipole potential up to 100-150 mV and make the membrane rigid. Most of these observations were simulated by Molecular Dynamics (MD) in order to visualize the relationship of electric field with the different structural factors (lipid structure, water orientation, ion adsorption etc.) responsible for its dipole component. Two principal contributors to BP – water and lipid molecules – create the opposite effects. The negative contribution with respect to the bulk is due to lipid itself and the inorganic cation penetration into the polar area of membrane. The positive contribution is caused by water orientation. Particularly, in the case of lysine adsorption, the contribution of water includes the rearrangement of H-bonds with the lipid phosphate group. This fact explains well the unusual kinetic phenomena registered by IFC in the case of polylysine adsorption at the BLM surface.

  13. Surface structure determination of group 11 metals adsorbed on a rhenium(10 anti 10) surface by low-energy electron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Messahel, Lyria


    This thesis deals with the computational surface determination of various long-range ordered phases formed by thin films of copper, silver, and gold adsorbed on the rhenium- (10 anti 10) surface. It is based upon LEED-I,V curves for these phases that were recorded in the course of detailed experimental investigations of the respective films carried out in our group (using techniques such as LEED, MEED, and TPD). In order to solve the intricate puzzle of surface structural analysis, the electron elastic scattering behaviour of the investigated coinage metal phases was calculated using the Erlangen TensErLEED program package. Thereby first a set of theoretical LEED-I,V curves is derived for a guessed reference structure. Subsequently its structural input parameters are varied in a trial-and-error procedure until optimal agreement between experiment and theory is attained. The (1 x 1) phases formed by the deposited metals were tackled first to establish an absolute coverage calibration and to elucidate the respective growth modes on the Re(10 anti 10) surface. In all three cases the (1 x 1) structure is developed best at a coverage {Theta}{sub Cu,Ag,Au}=2 ML=1 BL. Extension of the investigation to experimental I,V curves for higher Cu coverages revealed that this element continues to grow bilayerwise, thereby retaining the Re hcp morphology. Ag, in contrast to Cu and Au, happens not to grow as homogeneously, and the TPD data suggest that Ag films exhibit the so-called simultaneous-multilayer (SM) growth mode. The following analysis of the sub-bilayer coverage range shows that the three systems exhibit considerable differences. While Cu, having a negative lattice misfit compared to Re, shows no long-range ordered superstructures, Ag and Au with a similar positive misfit form a couple of such phases. Ag features both a (1 x 4) phase, stable at ambient temperatures, that upon heating transforms into a c(2 x 2) phase that only exists at elevated temperatures. The

  14. Mesopore quality determines the lifetime of hierarchically structured zeolite catalysts (United States)

    Milina, Maria; Mitchell, Sharon; Crivelli, Paolo; Cooke, David; Pérez-Ramírez, Javier


    Deactivation due to coking limits the lifetime of zeolite catalysts in the production of chemicals and fuels. Superior performance can be achieved through hierarchically structuring the zeolite porosity, yet no relation has been established between the mesopore architecture and the catalyst lifetime. Here we introduce a top-down demetallation strategy to locate mesopores in different regions of MFI-type crystals with identical bulk porous and acidic properties. In contrast, well-established bottom-up strategies as carbon templating and seed silanization fail to yield materials with matching characteristics. Advanced characterization tools capable of accurately discriminating the mesopore size, distribution and connectivity are applied to corroborate the concept of mesopore quality. Positron annihilation lifetime spectroscopy proves powerful to quantify the global connectivity of the intracrystalline pore network, which, as demonstrated in the conversions of methanol or of propanal to hydrocarbons, is closely linked to the lifetime of zeolite catalysts. The findings emphasize the need to aptly tailor hierarchical materials for maximal catalytic advantage.

  15. Structural determinants allowing endolysosomal sorting and degradation of endosomal GTPases. (United States)

    Valero, Ruth A; Oeste, Clara L; Stamatakis, Konstantinos; Ramos, Irene; Herrera, Mónica; Boya, Patricia; Pérez-Sala, Dolores


    Rapid control of protein degradation is usually achieved through the ubiquitin-proteasome pathway. We recently found that the short-lived GTPase RhoB is degraded in lysosomes. Moreover, the fusion of the RhoB C-terminal sequence CINCCKVL, containing the isoprenylation and palmitoylation sites, to other proteins directs their sorting into multivesicular bodies (MVBs) and rapid lysosomal degradation. Here, we show that this process is highly specific for RhoB. Alteration of late endosome lipid dynamics produced the accumulation of RhoB, but not of other endosomal GTPases, including Rab5, Rab7, Rab9 or Rab11, into enlarged MVB. Other isoprenylated and bipalmitoylated GTPases, such as H-Ras, Rap2A, Rap2B and TC10, were not accumulated into MVB and were stable. Remarkably, although TC10, which is highly homologous to RhoB, was stable, a sequence derived from its C-terminus (CINCCLIT) elicited MVB sorting and degradation of a green fluorescent protein (GFP)-chimeric protein. This led us to identify a cluster of basic amino acids (KKH) in the TC10 hypervariable region, constituting a secondary signal potentially involved in electrostatic interactions with membrane lipids. Mutation of this cluster allowed TC10 MVB sorting and degradation, whereas inserting it into RhoB hypervariable region rescued this protein from its lysosomal degradation pathway. These findings define a highly specific structural module for entering the MVB pathway and rapid lysosomal degradation.

  16. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar


    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  17. Genetic and perinatal determinants of structural brain deficits in schizophrenia. (United States)

    Cannon, T D; Mednick, S A; Parnas, J


    Using a subsample from the Copenhagen schizophrenia high-risk project, we examined the contributions of schizophrenic genetic liability and perinatal complications to computed tomographic (CT) measurements of ventricular enlargement and cortical and cerebellar abnormalities. A factor analysis of six CT measurements yielded two significant factors. One factor reflected multisite neural deficits as evidenced by abnormality of the cerebellar vermis and widening of the sylvian and interhemispheric fissures and cortical sulci. The other factor reflected periventricular damage as evidenced by enlargement of the third and lateral ventricles. Because all of the subjects had schizophrenic mothers, the major source of genetic variation is contributed by the diagnostic status of their fathers. In a stepwise multiple-regression analysis, it was determined that the multisite neural deficits factor was significantly related to genetic risk for schizophrenia (as measured by schizophrenia spectrum illness in the subjects' fathers) but was unrelated to pregnancy or delivery complications or to weight at birth. Periventricular damage was highly and significantly correlated with the number of complications suffered at delivery, but only among subjects with an elevated genetic risk. Although limited by a small sample size, these results suggest that the two types of CT abnormalities in schizophrenia may reflect partially independent processes based on different combinations of genetic and perinatal influences.

  18. Determination of pair-structure factor of scattering potential of a collection of particles. (United States)

    Wang, Tao; Zhao, Daomu


    The method of determination of the pair-structure factor of a collection of particles has been discussed. It is shown that the pair-structure factor of scattering potential of the collection of particles can be determined from the cross-spectral density function of the scattered field.

  19. Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field. (United States)

    Miguel, Virginia; Perillo, Maria A; Villarreal, Marcos A


    Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the Lα phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.

  20. Growth of Single- and Bilayer ZnO on Au(111) and Interaction with Copper

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Xingyi; Yao, Kun; Sun, Keju; Li, Wei-Xue; Lee, Junseok; Matranga, Christopher


    The stoichiometric single- and bi-layer ZnO(0001) have been prepared by reactive deposition of Zn on Au(111) and studied in detail with X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations. Both single- and bi-layer ZnO(0001) adopt a planar, graphite-like structure similar to freestanding ZnO(0001) due to the weak van der Waals interactions dominating their adhesion with the Au(111) substrate. At higher temperature, the single-layer ZnO(0001) converts gradually to bi-layer ZnO(0001) due to the twice stronger interaction between two ZnO layers than the interfacial adhesion of ZnO with Au substrate. It is found that Cu atoms on the surface of bi-layer ZnO(0001) are mobile with a diffusion barrier of 0.31 eV, and likely to agglomerate and form nanosized particles at low coverages; while Cu atoms tend to penetrate a single layer of ZnO(0001) with a barrier of 0.10 eV, resulting in a Cu free surface.