Plasmon-polaritons on graphene-metal surface and their use in biosensors

Cataloged from PDF version of article.We studied excitation of surface plasmon-polaritons on graphene-metal surface. The metal surface is functionalized by transfer printing of graphene grown by chemical vapor deposition on copper foils. Surface plasmon resonance characteristics of monolayer and multilayer graphene on the metal surface are presented. We were able to obtain the dispersion relation of graphene-metal surface which reveals the essential feature of the plasmon-polaritons. As an application, we fabricated a surface plasmon resonance sensor integrated with a microfluidic device to study nonspecific physical interaction between graphene layer and proteins. (C) 2012 American Institute of Physics

Nutrient exchange fluxes between the Aegean and Black Seas through the Marmara Sea

Long-term data obtained in the Turkish Strait System (TSS) including the Sea of Marmara, the Dardanelles and Bosphorus straits, during 1990-2000, have permitted us to calculate seasonal and annual fluxes of water and nutrients (nitrate, phosphate) exchanged between the Aegean and Black Seas through the TSS. Two-layer flow regimes in the TSS introduce the brackish waters of the Black Sea into the Aegean basin of the northeastern Mediterranean throughout the year. A counter flow in the TSS carries the salty Mediterranean water into the Black Sea via the Marmara deep basin. The annual volume influx from the Black Sea to the Marmara upper layer is nearly two-fold the salty water exported from the Marmara to the Black Sea via the Bosphorus underflow. The brackish Black Sea inflow is relatively rich in nitrate and phosphate in winter, decreasing to the lowest levels in late summer and autumn. Biologically labile nutrients of Black Sea origin are utilized in photosynthetic processes in the Marmara Sea and are partly exported to the Marmara lower layer. Eventually, the brackish Black Sea waters reach the Dardanelles Strait, with modified bio-chemical properties. On the other hand, the salty Mediterranean waters with low concentrations of nutrients enter the Marmara deep basin. During threir 6-7 year sojourn in the Marmara basin, the salty waters become enriched in nitrate (DIN) and phosphate (DIP), due to oxidation of planktonic particles sinking from the Marmara surface layer. The annual nutrient inputs from the Black Sea to the Marmara basin were estimated as 8.17x108 moles of DIN and 4.25x107 moles of DIP, which are much less than the importation from the Marmara lower layer via the Bosphorus undercurrent. The salty Aegean water introduces nearly 6.13x108 moles of DIN and 2.79x107 moles of DIP into the Marmara lower layer. The estimated DIP outflux from the Aegean Sea is nearly 2 times less than the importation from the Marmara Sea via the Dardanelles Strait

Palgol: A High-Level DSL for Vertex-Centric Graph Processing with Remote Data Access

Pregel is a popular distributed computing model for dealing with large-scale graphs. However, it can be tricky to implement graph algorithms correctly and efficiently in Pregel's vertex-centric model, especially when the algorithm has multiple computation stages, complicated data dependencies, or even communication over dynamic internal data structures. Some domain-specific languages (DSLs) have been proposed to provide more intuitive ways to implement graph algorithms, but due to the lack of support for remote access --- reading or writing attributes of other vertices through references --- they cannot handle the above mentioned dynamic communication, causing a class of Pregel algorithms with fast convergence impossible to implement. To address this problem, we design and implement Palgol, a more declarative and powerful DSL which supports remote access. In particular, programmers can use a more declarative syntax called chain access to naturally specify dynamic communication as if directly reading data on arbitrary remote vertices. By analyzing the logic patterns of chain access, we provide a novel algorithm for compiling Palgol programs to efficient Pregel code. We demonstrate the power of Palgol by using it to implement several practical Pregel algorithms, and the evaluation result shows that the efficiency of Palgol is comparable with that of hand-written code.Comment: 12 pages, 10 figures, extended version of APLAS 2017 pape

EwE-F 1.0: an implementation of Ecopath with Ecosim in Fortran 95/2003 for coupling and integration with other models

Abstract. Societal and scientific challenges foster the implementation of the ecosystem approach to marine ecosystem analysis and management, which is a comprehensive means of integrating the direct and indirect effects of multiple stressors on the different components of ecosystems, from physical to chemical and biological and from viruses to fishes and marine mammals. Ecopath with Ecosim (EwE) is a widely used software package, which offers capability for a dynamic description of the multiple interactions occurring within a food web, and, potentially, a crucial component of an integrated platform supporting the ecosystem approach. However, being written for the Microsoft .NET framework, seamless integration of this code with Fortran-based physical and/or biogeochemical oceanographic models is technically not straightforward. In this work we release a re-coding of EwE in Fortran (EwE-F). We believe that the availability of a Fortran version of EwE is an important step towards setting up coupled/integrated modelling schemes utilising this widely adopted software because it (i) increases portability of the EwE models and (ii) provides additional flexibility towards integrating EwE with Fortran-based modelling schemes. Furthermore, EwE-F might help modellers using the Fortran programming language to get close to the EwE approach. In the present work, first fundamentals of EwE-F are introduced, followed by validation of EwE-F against standard EwE utilising sample models. Afterwards, an end-to-end (E2E) ecological representation of the Gulf of Trieste (northern Adriatic Sea) ecosystem is presented as an example of online two-way coupling between an EwE-F food web model and a biogeochemical model. Finally, the possibilities that having EwE-F opens up are discussed

Climatic controls on biophysical interactions in the Black Sea under present day conditions and a potential future (A1B) climate scenario

A dynamical downscaling approach has been applied to investigate climatic controls on biophysical interactions and lower trophic level dynamics in the Black Sea. Simulations were performed under present day conditions (1980–1999) and a potential future (2080–2099) climate scenario, based on the Intergovernmental Panel for Climate Change A1B greenhouse gas emission scenario. Simulations project a 3.7 °C increase in SST, a 25% increase in the stability of the seasonal thermocline and a 37 day increase in the duration of seasonal stratification. Increased winter temperatures inhibited the formation of Cold Intermediate Layer (CIL) waters resulting in near complete erosion of the CIL, with implications for the ventilation of intermediate water masses and the subduction of riverine nutrients. A 4% increase in nitrate availability within the upper 30 m of the water column reflected an increase in the retention time of river water within the surface mixed-layer. Changes in thermohaline structure, combined with a 27% reduction in positive wind stress curl, forced a distinct change in the structure of the basin-scale circulation. The predominantly cyclonic circulation characteristic of contemporary conditions was reversed within the southern and eastern regions of the basin, where under A1B climatic conditions, anticyclonic circulation prevailed. The change in circulation structure significantly altered the horizontal advection and dispersion of high nutrient river waters originating on the NW self. Net primary production increased by 5% on average, with much spatial variability in the response, linked to advective processes. Phytoplankton biomass also increased by 5% and the higher nutrient environment of the future scenario caused a shift in species composition in favour of larger phytoplankton. No significant change in zooplankton biomass was projected. These results constitute one of many possible future scenarios for the Black Sea, being dependent on the modelling systems employed in addition to the choice of emission scenario. Our results emphasise in particular the sensitivity of dynamical downscaling studies to the regional wind forcing fields extracted from global models (these being typically model dependent). As atmospheric warming is projected with a high degree of confidence warming of the Black Sea upper layer, increased water column stability, and erosion of the CIL are believed to be robust results of this study

Graphene as a Reversible and Spectrally Selective Fluorescence Quencher

We report reversible and spectrally selective fluorescence quenching of quantum dots (QDs) placed in close proximity to graphene. Controlling interband electronic transitions of graphene via electrostatic gating greatly modifies the fluorescence lifetime and intensity of nearby QDs via blocking of the nonradiative energy transfer between QDs and graphene. Using ionic liquid (IL) based electrolyte gating, we are able to control Fermi energy of graphene in the order of 1 eV, which yields electrically controllable fluorescence quenching of QDs in the visible spectrum. Indeed, our technique enables us to perform voltage controllable spectral selectivity among quantum dots at different emission wavelengths. We anticipate that our technique will provide tunable light-matter interaction and energy transfer that could yield hybrid QDs-graphene based optoelectronic devices with novel functionalities, and additionally, may be useful as a spectroscopic ruler, for example, in bioimaging and biomolecular sensing. We propose that graphene can be used as an electrically tunable and wavelength selective fluorescence quencher. � 2016 The Author(s)

Tuning surface plasmon-exciton coupling via thickness dependent plasmon damping

In this paper, we report experimental and theoretical investigations on tuning of the surface plasmon-exciton coupling by controlling the plasmonic mode damping, which is defined by the plasmonic layer thickness. The results reveal the formation of plasmon-exciton hybrid state characterized by a tunable Rabi splitting with energies ranging from 0 to 150 meV. Polarization-dependent spectroscopic reflection measurements were employed to probe the dispersion of the coupled system. The transfer matrix method and analytical calculations were used to model the self-assembled J-aggregate/metal multilayer structures in excellent agreement with experimental observations. © 2012 American Physical Society

BACE1 inhibition more effectively suppresses initiationthan progression of β-amyloid pathology

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Weighing graphene with QCM to monitor interfacial mass changes

In this Letter, we experimentally determined the mass density of graphene using quartz crystal microbalance (QCM) as a mechanical resonator. We developed a transfer printing technique to integrate large area single-layer graphene on QCM. By monitoring the resonant frequency of an oscillating quartz crystal loaded with graphene, we were able to measure the mass density of graphene as ∼118 ng/cm2, which is significantly larger than the ideal graphene (∼76 ng/cm2) mainly due to the presence of wrinkles and organic/inorganic residues on graphene sheets. High sensitivity of the quartz crystal resonator allowed us to determine the number of graphene layers in a particular sample. Additionally, we extended our technique to probe interfacial mass variation during adsorption of biomolecules on graphene surface and plasma-assisted oxidation of graphene. © 2016 Author(s)