Tailoring Plasmon Lifetime in Suspended Nanoantenna Arrays for High-Performance Plasmon Sensing

We demonstrate significantly longer plasmon lifetime and stronger electric field enhancement by lifting the nanoantenna arrays above the substrate by dielectric nanopillars. The role of the pillar is to offer a more homogeneous dielectric background allowing stronger diffraction coupling among plasmonic nanoantennas leading to a Fanolike asymmetric lineshape. It is found that the electric fields around the nanoantennas can be greatly enhanced when the Fanolike resonance is excited, and a 4.2 times enhancement is achieved compared with the pure resonance in individual nanoantennas. Furthermore, only a collective surface mode with its electric fields of the same direction as the induced electric moment in the nanoantennas could mediate the excitation of such a Fanolike resonance. More importantly, the sensitivity and the figure of merit (FOM) of this plasmonic structure can reach as high as 900 nm/RIU and 53, respectively. Our study offers a new, simple, and efficient way to design the plasmonic systems with desired electric field enhancement and spectral lineshape for different applications.     

Morphology dependent optical response tuning in planar square-shaped array of sodium nanoparticles

Among the plasmonic nanostructures, ordered arrangement of metal nanoparticles with inter-particle gap distances in the nanometer scale is becoming increasingly important due to their ability to confine huge electromagnetic fields and tunable optical properties. Using time dependent density functional theory calculations, we study the optical response evolution in a planar square-shaped array of Sodium nanoparticles via morphology deformation. To this aim, we vary the inter-particle gap distance in the range of 2 to 30 Å separately along one and two directions. We compare and cross-examine the optical response evolution for both deformation process, and we find that the interaction between sodium nanoparticles in an ordered arrangement can be controlled to a large extent by simple deformation process. We believe that our theoretical results will be useful for designing ultra-small and tunable plasmonic devices that utilize quantum effects.     

Substrate-Independent Lattice Plasmon Modes for High-Performance On-Chip Plasmonic Sensors

We systematically study the lattice plasmon resonance structures, which are known as core/shell SiO₂/Au nanocylinder arrays (NCAs), for high-performance, on-chip plasmonic sensors using the substrate-independent lattice plasmon modes (LPMs). Our finite-difference time-domain simulations reveal that new modes of localized surface plasmon resonances (LSPRs) show up when the height-diameter aspect ratio of the NCAs is increased. The height-induced LSPRs couple with the superstrate diffraction orders to generate the substrate-independent LPMs. Moreover, we show that the high wavelength sensitivity and the narrow linewidth of the substrate-independent LPMs lead to the plasmonic sensors with high figure of merit (FOM) and high signal-to-noise ratio (SNR). In addition, the plasmonic sensors are robust in asymmetric environments for a wide range of working wavelengths. Our further study of both far- and near-field electromagnetic distribution in the NCAs confirms the height-enabled tunability of the plasmonic “hot spots” at the sub-nanoparticle resolution and the large field enhancement in the substrate-independent LPMs, which are responsible for the high FOM and SNR of the plasmonic sensors.     

A feature-based approach to modeling protein–protein interaction hot spots

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions.     

Enhancement of Molecular Fluorescence in the UV Spectral Range Using Aluminum Nanoantennas

We investigate the fluorescence rate of a dipolar emitter coupled to Al nanoparticles of varying shapes and sizes and to dimer nanoantennas in the deep-ultraviolet (UV) spectral range, using the surface integral equation method. In particular, we show that the shape of the Al nanostructures plays a fundamental role in controlling the complex interplay between the excitation rate and the quantum yield in radiative plasmonic systems. In addition, we also investigate the role of the near-field interaction of two coupled Al nanoparticles in enhancing the fluorescence rate of the dipole. This study is important for the engineering of more efficient light-emitting nanostructures in the UV spectral range, such as Al-based material systems or light-emitting fluorophores for biodetection.     

High Optical Transmission in a Hybrid Plasmonic-Optical Structure with a Continuous Metal Film

Metals are naturally opaque for electromagnetic (EM) waves below violet frequency due to the Coulomb screening effect. In this letter, we demonstrate high optical transparency of a seamless continuous metal film by sandwiching it in a hybrid plasmonic-optical structure. The proposed structure consists of a plasmonic array and an optical cavity, which exhibits magnetic plasmon (MP) resonance and optical Fabry-Perot (FP) resonance, respectively. An optical transparency of 84% in the near-IR regime is achieved making use of interaction between the plasmonic and optical modes. Furthermore, spectral tunability of the high transparency is demonstrated and robustness under oblique incidence is examined. This work may give insights into plasmonic-optical interactions and may be a potential candidate for transparent electrodes.     

Efficient localization of hot spots in proteins using a novel S-transform based filtering approach

Protein-protein interactions govern almost all biological processes and the underlying functions of proteins. The interaction sites of protein depend on the 3D structure which in turn depends on the amino acid sequence. Hence, prediction of protein function from its primary sequence is an important and challenging task in bioinformatics. Identification of the amino acids (hot spots) that leads to the characteristic frequency signifying a particular biological function is really a tedious job in proteomic signal processing. In this paper, we have proposed a new promising technique for identification of hot spots in proteins using an efficient time-frequency filtering approach known as the S-transform filtering. The S-transform is a powerful linear time-frequency representation and is especially useful for the filtering in the time-frequency domain. The potential of the new technique is analyzed in identifying hot spots in proteins and the result obtained is compared with the existing methods. The results demonstrate that the proposed method is superior to its counterparts and is consistent with results based on biological methods for identification of the hot spots. The proposed method also reveals some new hot spots which need further investigation and validation by the biological community.     

Design Optimisation of Plasmonic Metasurfaces for Mid-Infrared High-Sensitivity Chemical Sensing

In this paper, we report on a general method to optimise the optical characteristics of 2D-arrays of plasmonic gold nanoantennas performing as band-pass filter functionalised metasurfaces to be used as high-sensitivity mid-infrared spectroscopic sensors. We demonstrate that it is possible to increase their sensitivity in the detection of chemical and biological substances when the sensors are used in the surface-enhanced infrared absorption (SEIRA) technique. This technique allows revealing the presence of a substance adsorbed on the nanoantennas by measuring its optical absorption under the conditions for which the maximum value of the functionalised metasurface reflectivity occurs at the same wavelength of the substance maximum absorption peak. In particular, numerical simulations based on finite element method of the metasurface detection response demonstrate the possibility to increase the sensor sensitivity of more than four orders of magnitude with respect to that one achievable if the same amount of the substance is deposited on an unstructured planar metal surface. These results can be obtained by acting on the 2D-array periodicity, nanoantenna shape (i.e. rod and cross), size and thickness independently from the wavelength at which the substance absorption occurs. Moreover, in the case of cross-shaped nanoantennas, we report a complete numerical characterisation of the dependence of the metasurface maximum reflectivity and peak wavelength on the variation of the geometrical parameters of both the nanoantennas and the 2D-array.     

Predicting Hot Spots of Herpetofauna Road Mortality Along Highway Networks

ABSTRACT Road mortality is often spatially aggregated, and there is a need for models that accurately and efficiently predict hot spots within a road network for mitigation. We surveyed 145 points throughout a 353-km highway network in New York State, USA, for roadkill of reptiles and amphibians. We used land cover, wetland configuration, and traffic volume data to identify features that best predicted hot spots of herpetofauna road mortality. We resampled 40 points an additional 4 times over 4 years to evaluate temporal repeatability. Both amphibian and reptile road mortality were spatially clustered, and road-kill hot spots of the 2 taxa overlapped. One survey provided a valid snapshot of spatial patterns of road mortality, and spatial patterns remained stable across time. Road-kill hot spots were located where wetlands approached within 100 m of the road, and the best predictor was a causeway configuration of wetlands (wetlands on both sides of the road). We validated causeways as predictors of road mortality by surveying 180 causeways and 180 random points across 5 regions (17,823 km²) of northeastern New York. Causeways were 3 times more likely than random locations to have amphibian and 12 times more likely to have reptile mortality present, and causeways had a 4 times higher total number of amphibian roadkill and 9 times higher reptile roadkill than did random points. We conclude it is possible to identify valid predictors of hot spots of amphibian and reptile road mortality for use when planning roads or when conducting surveys on existing roads to locate priority areas for mitigation.     

Plasmon-Enhanced Second Harmonic Generation: from Individual Antennas to Extended Arrays

We analyze the emission yield of the second harmonic generation (SHG) from dense ordered arrays of L-shaped Au nanoantennas within a well-defined collection angle and compare it to that of the isolated nanostructures designed with the same geometrical parameters. Thanks to the high antenna surface density, arrays display one order of magnitude higher SHG yield per unit surface with respect to isolated nanoantennas. The difference in the collected nonlinear signals becomes even more pronounced by reducing the collection angle, because of the efficient angular filtering that can be attained in dense arrays around the zero order. Albeit this key-enabling feature allows envisioning application of these platforms to nonlinear sensing, a normalization of the SHG yield to the number of excited antennas in the array reveals a reduced nonlinear emission from each individual antenna element. We explain this potential drawback in terms of resonance broadening, commonly observed in densely packed arrays, and angular filtering of the single antenna emission pattern provided by the array 0th order.

     

Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking

Hot spot residues contribute dominantly to protein-protein interactions. Statistically, conserved residues correlate with hot spots, and their occurrence can distinguish between binding sites and the remainder of the protein surface. The hot spot and conservation analyses have been carried out on one side of the interface. Here, we show that both experimental hot spots and conserved residues tend to couple across two-chain interfaces. Intriguingly, the local packing density around both hot spots and conserved residues is higher than expected. We further observe a correlation between local packing density and experimental deltadeltaG. Favorable conserved pairs include Gly coupled with aromatics, charged and polar residues, as well as aromatic residue coupling. Remarkably, charged residue couples are underrepresented. Overall, protein-protein interactions appear to consist of regions of high and low packing density, with the hot spots organized in the former. The high local packing density in binding interfaces is reminiscent of protein cores.     

Spatial Distribution of Optical Near-Fields in Plasmonic Gold Sphere Segment Voids

We present a comprehensive experimental and computational study on the electromagnetic field distribution in sphere segment void arrays. Surface plasmon polaritons can be excited in these void arrays, resulting in greatly enhanced electromagnetic fields. With the scanning near-field optical microscope (SNOM) we are able to measure the electromagnetic field distribution at the sample surface. For this purpose, an array of relatively large voids with a sphere diameter of 900 nm was fabricated, allowing for an easy access of the scanning glass-fibre tip and yielding very detailed scans. Complementary, finite-difference time-domain (FDTD) calculations on a complete void array have been performed and compared with the SNOM intensity maps and experimental reflectivity data. We show in a direct way both the existence of extended and localised modes in the Au void array for three different void depths. We also show and discuss the changes that the modes undergo for the different void depths and excitation wavelengths. Moreover, since the simulations were performed for two different void geometries, one containing perfectly spherical void surfaces and another more realistic one, which considers the presence of interstitial wall holes and other imperfections, as observed in scanning electron micrographs, we were able to determine by comparison with the experiment under which conditions an array of idealised sphere segment voids is a meaningful model. This demonstrates that both SNOM and FDTD simulations are powerful tools for understanding the plasmonic response of metallic nanostructures, thus enabling, for instance, a design for applications in ultra-sensitive optical detection.     

A phenomenological model of the current filamentation instability driven by cathode processes in the Livermore spheromak

The current density on the open field lines of the Livermore spheromak (SSPX) typically exceeds the saturation current density of the bulk plasma. We assume that the mechanism that provides conditions for that is associated with the formation of a thin layer near the cathode surface, where both the plasma and the neutral density are higher than in the bulk plasma and where intense ionization occurs. The ions formed in this layer fall back onto the cathode, whereas electrons contribute to the high current density in the bulk plasma. The particle balance in the ionizing layer is determined by the recycling coefficient, which, in turn, depends on the cathode temperature and the sheath voltage. As it turns out, these dependences give rise to an instability that leads to the current filamentation and the formation of hot spots on the cathode surface. The instability can be characterized in a phenomenological manner without going into the details of the structure of the ionizing layer, whose effect on the instability shows up in the form of a couple of numerical coefficients of the order of one. We predict the characteristic size and the shape of the filaments (and the hot spots), which are in a general agreement with discoloration patterns on the surface of the cathode in the SSPX. If the magnetic field is tilted to the surface, the footpoints of the filaments move with a significant velocity, whose direction depends on the ratio of the ion gyroradius and the thickness of the ionizing layer. This instability, although primarily considered in conjunction with the SSPX experiment, may play a role in spherical tokamaks and other systems with coaxial helicity injection.     

Efficient Plasmonic Au/CdSe Nanodumbbell for Photoelectrochemical Hydrogen Generation beyond Visible Region

In this communication, light harvesting and photoelectrochemical (PEC) hydrogen generation beyond the visible region are realized by an anisotropic plasmonic metal/semiconductor hybrid photocatalyst with precise control of their topology and heterointerface. Controlling the intended configuration of the photocatalytic semiconductor to anisotropic Au nanorods' plasmonic hot spots, through a water phase cation exchange strategy, the site‐selective overgrowth of a CdSe shell evolving from a core/shell to a nanodumbbell is realized successfully. Using this strategy, tip‐preferred efficient photoinduced electron/hole separation and plasmon enhancement can be realized. Thus, the PEC hydrogen generation activity of the Au/CdSe nanodumbbell is 45.29 µmol cm^?2 h^?1 (nearly 4 times than the core/shell structure) beyond vis (λ > 700 nm) illumination and exhibits a high faradic efficiency of 96% and excellent stability with a constant photocurrent for 5 days. Using surface photovoltage microscopy, it is further demonstrated that the efficient plasmonic hot charge spatial separation, which hot electrons can inject into CdSe semiconductors, leads to excellent performance in the Au/CdSe nanodumbbell.     

Systematic peptide array-based delineation of the differential beta-catenin interaction with Tcf4, E-cadherin, and adenomatous polyposis coli

Nuclear accumulation of the complex between beta-catenin and proteins of the T-cell factor (Tcf) family is a hallmark of many cancers. Targeting this interaction for drug development is complicated by the fact that E-cadherin and adenomatous polyposis coli (APC) bind to overlapping sites on beta-catenin. Inhibiting their interactions might actually promote tumor growth. To identify selective beta-catenin binding hot spots of Tcf4, E-cadherin, and APC, array technology with peptides of up to 53 amino acids length was used. Interactions were monitored by a quantitative fluorescent readout, which was shown to represent a monitor of true equilibrium binding constants. We identified minimal binding motifs in the beta-catenin ligands and showed that most of the 15-mer and 20-mer repeats of APC did not interact, at least when non-phosphorylated, and defined a consensus binding motif also present in APC. We confirmed previously found hot spots and identified new ones. The method allowed us to locate a hydrophobic pocket that was relevant for the Tcf, but not the E-cadherin interaction, and would thus constitute an ideal drug target site.     

Multilayer Hybrid Plasmonic Nano Patch Antenna

This is the first report of a hybrid plasmonic nano patch antenna having metal insulator metal (HMIM) multilayer configuration. It is designed in a footprint area of 1.7 × 1.175 μm² to resonate at 1.55 μm wavelength. The proposed antenna is inset fed by an HMIM plasmonic waveguide for achieving proper impedance matching. It is observed, through electromagnetic numerical simulation, that the proposed plasmonic nano patch antenna emits a directional beam with a bandwidth, gain, and efficiency of 0.194 μm, 8.3 dB, and 96% respectively, which are significantly higher than previously reported designs. Since inset-fed antennas are suitable for developing high-gain antenna array, hence further, we examined antenna performance by designing antenna array. The proposed antenna is practically realizable and can be fabricated using standard semiconductor fabrication process. Moreover, it could be used for numerous chip scale applications such as wireless interconnects energy harvesting, photoemission, photo detection, scattering, heat transfer, spectroscopy, and optical sensing.

     

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications

Methods for rapid surface immobilization of bioactive small molecules with control over orientation and immobilization density are highly desirable for biosensor and microarray applications. In this Study, we use a highly efficient covalent bioorthogonal [4+2] cycloaddition reaction between trans-cyclooctene (TCO) and 1,2,4,5-tetrazine (Tz) to enable the microfluidic immobilization of TCO/Tz-derivatized molecules. We monitor the process in real-time under continuous flow conditions using surface plasmon resonance (SPR). To enable reversible immobilization and extend the experimental range of the sensor surface, we combine a non-covalent antigen-antibody capture component with the cycloaddition reaction. By alternately presenting TCO or Tz moieties to the sensor surface, multiple capture-cycloaddition processes are now possible on one sensor surface for on-chip assembly and interaction studies of a variety of multi-component structures. We illustrate this method with two different immobilization experiments on a biosensor chip; a small molecule, AP1497 that binds FK506-binding protein 12 (FKBP12); and the same small molecule as part of an immobilized and in situ-functionalized nanoparticle.     

Broadband Optical Response in Ternary Tree Fractal Plasmonic Nanoantenna

The ability to precisely tailor lineshapes, operational bandwidth, and localized electromagnetic field enhancements (“hot spots”) in nanostructures is currently of interest in advancing the performance of plasmonics-based chemical and biological sensing techniques. Fractal geometries are an intriguing alternative in the design of plasmonic nanostructures as they offer tunable multiband response spanning the visible and infrared spectral regions. A numerical study of the optical behavior of ternary tree fractal plasmonic nanoantenna is presented. Self-similar features are seen to emerge in the extinction spectra with the increase in fractal order N of the tree structure. Plasmon oscillations occurring at different length scales are shown to correspond to the multiple peaks and are compared with the spatial maps of electric field enhancement at the surface of the nanoantenna. The multiple peaks are shown to be independently tunable by structural variation. The robustness of the spectral response and polarization dependence arising due to various asymmetries is discussed.     

Electron Energy Loss and One- and Two-Photon Excited SERS Probing of “Hot” Plasmonic Silver Nanoaggregates

We report electron energy loss spectroscopy (EELS) and one- and two-photon excited surface-enhanced Raman scattering (SERS) and hyper Raman studies on plasmonic silver nanoaggregates. By comparison with computations, EELS imaging reveals an inverse relationship between local field intensity in an optical experiment and electron energy loss intensity at energies corresponding to excitation wavelengths used for optical probing. This inverse relation exists independent on specific nanoaggregate geometries and is mainly controlled by the gap size between the particles forming the aggregate. The ratio between two- and one-photon excited SERS measured at different excitation wavelengths provides information about local fields in the hottest spots and their dependence on the photon energy. Our data verify experimentally the predicted increase of local optical fields in the hot spots with increasing wave lengths. The reported findings show new experimental ways to characterize local fields of plasmonic nanostructures. This is of particular importance for complex structures which are not easily approachable by computations.