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.     

Evolution of Protein Binding Modes in Homooligomers

The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of protein binding modes from nine families of homooligomers and mapped 60 different binding modes and oligomerization states onto the phylogenetic trees of these families. We observed a significant tendency for the same binding modes to be clustered together and conserved within clades on phylogenetic trees; this trend is especially pronounced for close homologs with 70% sequence identity or higher. Some binding modes are conserved among very distant homologs, pointing to their ancient evolutionary origin, while others are very specific for a certain phylogenetic group. Moreover, we found that the most ancient binding modes have a tendency to involve symmetrical (isologous) homodimer binding arrangements with larger interfaces, while recently evolved binding modes more often exhibit asymmetrical arrangements and smaller interfaces.     

Plasmonic Modes of Ag Nanoshell Excited by Bi-Dipole

We studied plasmonic dipole, quadrupole, and sextupole modes of Ag nanoshell (NS) excited by a pair of aligned radial electric dipoles (bi-dipole) in symmetric and antisymmetric configurations by using dyadic Green’s functions. The mutual excitation rate and the radiative and nonradiative powers of bi-dipole in the presence of Ag NS were analyzed. Our results show that these modes are in accordance with the surface plasmon resonances of Ag NS irradiated by a polarized plane wave. In addition, the mutual excitation rate retains local maxima at these modes. Moreover, the quadrupole and octupole modes are only excited in the cases of the symmetric radial bi-dipole, while the dipole and sextupole modes are only excited in the cases of the antisymmetric ones. The dipole mode is broadband, while the other higher-order modes are narrowband. Moreover, all of these plasmonic modes are red-shifted as the ratio of the core radius to the shell thickness increases.     

Guided Plasmon Modes of a Graphene-Coated Kerr Slab

We study analytically propagating surface plasmon modes of a Kerr slab sandwiched between two graphene layers. We show that some of the modes that propagate forward at low field intensities start propagating with negative slope of dispersion and positive flux of energy (fast-light surface plasmons) when the field intensity becomes high. We also discover that our structure supports an additional branch of low-intensity fast-light guided modes. The possibility of dynamically switching between the forward and the fast-light plasmon modes by changing the intensity of the excitation light or the chemical potential of the graphene layers opens up wide opportunities for controlling light with light and electrical signals on the nanoscale.     

Instantaneous Normal Modes and the Protein Glass Transition

In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at ∼220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.     

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Vibrational excitations of low frequency collective modes are essential for functionally important conformational transitions in proteins. Here we report the first direct measurement on the lifetime of vibrational excitations of the collective modes at 87 pm (115 cm^-1) in bacteriorhodopsin, a transmembrane protein. The data show that these modes have extremely long lifetime of vibrational excitations, over 500 picoseconds, accommodating 1500vibrations. We suggest that there is a connection between this relativelyslow anharmonic relaxation rate of approximately 10 g sec^-1 and thesimilar observed rate of conformational transitions in proteins, which require require multi-level vibrational excitations and energy exchanges with othervibrational modes and collisional motions of solvent molecules.     

In-Plane Plasmonic Modes in a Quasicrystalline Array of Metal Nanoparticles

We investigated the plasmonic modes in a two-dimensional quasicrystalline array of metal nanoparticles. The polarization of the modes is in the array plane. A simplified eigen-decomposition method is presented with the help of rotational symmetry. Two kinds of anti-phase ring modes with radial and tangential polarizations are of highest spatial localizations among all of plasmonic modes. For the leaky characteristic of the anti-phase ring modes, the highest fidelity mode in the quasicrystalline array is found to be tangential polarized mode, whereas normal-to-plane polarized mode in the circular ring. The leaky characteristics and spatial localizations of other plasmonic modes are also studied, for example, collective vortex mode that may be a candidate to form negative responses in plasmonic device and collective radial mode that may be used to generate light sources with radial polarizations.     

Plasmonic Quantum Dot Nanocavity Laser: Hybrid Modes

Plasmonics - The hybrid modes in the plasmonic quantum dot (QD) laser are modeled using the Marctili method. The model is then used to study the mode characteristics. The modes are going to cutoff...     

Modes Manipulation Within Subwavelength Metallic Gratings

Plasmonics - Surface plasmon polariton (SPP) and cavity modes supported by the plasmonic gratings are often of hybrid nature in ruling light-nanostructure interactions. The coupling of incident...     

不同栽培模式下小麦灌浆期蛋白质周转研究

通过田间试验研究5种栽培模式对小麦灌浆期蛋白质周转的影响。5种栽培模式分别为常规栽培、秸秆覆盖、地膜覆盖、垄沟种植和补灌栽培,施氮量为120kg／hm^2。结果表明：不同栽培模式下小麦灌浆期蛋白质周转变化基本一致,覆膜栽培模式旗叶可溶性蛋白含量和蛋白水解酶活性较高,旗叶蛋白水解酶和籽粒蛋白积累能力大于其它栽培模式;垄沟栽培模式的旗叶各指标含量较高,但其蛋白质周转效率低,导致贪青晚熟不利于蛋白质周转,从而影响产量的形成。     

Higher Order Plasmonic Modes Excited in Ag Triangular Nanoplates by an Electron Beam

Ag triangular nanoplates are known to generate strong plasmonic resonances when excited by both light and electron beams. Experimental electron energy-loss spectra (EELS) and maps were acquired using an aberration-corrected JEOL-ARM microscope. The corner, edge and centre modes that are often observed in such structures were also observed in these measurements. In addition, novel higher order internal modes were observed and were found to be well reproduced by theoretical calculations using boundary element method (BEM). These modes are “dark modes” so are not observed in the optical extinction spectra. They are confined surface propagating modes and are analogous to laser cavity modes.     

Coupled Surface Plasmon-Polariton Modes of Metallic Single-Walled Carbon Nanotubes

The propagation of the coupled surface plasmon-polariton modes in the metallic single-walled carbon nanotubes are investigated, taking into account the retardation effects. A simple model based on the classical electrodynamics and the two-fluid hydrodynamic theory is proposed. The dispersion relation of the surface polariton modes is obtained in order to survey the effects of the two-fluid model and the insulating dielectric media.     

Interpretation of DNA Vibration Modes: III - The Behaviour of the Sugar Pucker Vibration Modes as a Function of its Pseudorotation Parameters

Abstract

A systematic study of the sugar pucker characteristic vibration modes as a function of its geometrical conformations, has been performed. The present investigation is based on the Wilson GF method and a non-redundant valence force field. The calculated results allow to assign the modes arising mainly from the sugar motions and present in quasi whole vibrational spectra related to the right or left-handed double-helices (i.e., 1050 cm^?1,960 cm^?1 and 890 cm^?1). Moreover, the conformation dependent modes as those at 860 cm^?1 and around 810 cm^?1 (A form) as well as the one located around 830 cm^?1 (B form) are interpreted by the present investigation. The possibility of the interaction of the latter modes with the phosphate group motions along the DNA double-helical chains are also discussed.     

Coupling of Graphene Plasmonics Modes Induced by Near-Field Perturbation at Terahertz Frequencies

Plasmonics - The coupling between graphene surface plasmonic (GSP) modes and evanescent wave modes induced by near-field perturbation is investigated systematically in the grating-spacer-graphene...     

Refinement of F-Actin Model against Fiber Diffraction Data by Long-Range Normal Modes

The atomic model of F-actin was refined against fiber diffraction data using long-range normal modes as adjustable parameters to account for the collective long-range filamentous deformations. To determine the effect of long-range deformations on the refinement, each of the four domains of G-actin was treated as a rigid body. It was found that among all modes, the bending modes make the most significant contributions to the improvement of the refinement. Inclusion of only 7–9 bending modes as adjustable parameters yielded a lowest R-factor of 6.3%. These results demonstrate that employing normal modes as refinement parameters has the advantage of using a small number of adjustable parameters to achieve a good fitting efficiency. Such a refinement procedure may therefore prevent the refinement from overfitting the structural model. More importantly, the results of this study demonstrate that, for any fiber diffraction data, a substantial amount of refinement error is due to long-range deformations, especially the bending, of the filaments. The effects of these intrinsic deformations cannot be easily compensated for by adjusting local structural parameters, and must be properly accounted for in the refinement to achieve improved fit of refined models with experimental diffraction data.     

Calculation of the Raman frequencies as a function of pressure in the solid phases II and III (III’) of benzene

We calculate here the Raman frequencies of the lattice modes A(A _g ), B(B _2g ) and C(B _1g B _3g ) as a function of pressure at room temperature for the solid phases (II, III and III’) of benzene. This calculation is performed using volume data through the mode Grüneisen parameter. It is found that our calculated frequencies of those lattice modes increase with increasing pressure, as expected. Calculated frequencies are in good agreement with the measurements of the three lattice modes for the solid phases studied in benzene.     

Behavioral Modes Arise From a Random Process in the Nudibranch Melibe

Stochastic analysis was applied to observations of spontaneous behavior in the carnivorous mollusc Melibe leonina. Six behaviors were denned that could be easily recognized on inspection and it was found that transitions between each of these behaviors could be fully described by a first-order random process without memory of past behavioral choices. The behaviors are organized by frequency of transition into two modes, a feeding mode and a resting mode. Transitions within modes are more likely than transitions between modes, and the feeding and resting modes are linked by a preferred pair of behavioral transitions. The amount of time spent in the feeding mode is positively correlated with body size, but the average length of a feeding episode is independent of size. This suggests that body size regulates the probability of entry into feeding behavior but does not influence the basic pattern of feeding. In the presence of food the animals express nearly continuous feeding behavior, suggesting that food reduces the probability of exiting the feeding mode. This model of spontaneous behavior in Melibe is used to form hypotheses amenable to further exploration through neurophysiological experiments.     

Efficient Extraction of Fluorescence Emission Utilizing Multiple Surface Plasmon Modes from Gold Wire Gratings

We demonstrate directional enhanced fluorescence emission from fluorophores located above gold wire gratings. In contrast to previous studies on corrugated films, efficient coupling was recorded for multiple plasmon modes associated with both the active and substrate side of the wires. This difference is likely due to the subtle differences in how light interacts with corrugated films versus metal films with periodic subwavelength slots. For corrugated films, coupling between modes on opposite sides of the grating are out of phase, and therefore plasmon modes on the opposite side of the grating are only weakly excited. For wire gratings, transmission and reflection features have been modeled well with a dynamical diffraction model that includes surface plasmons, which allows for efficient coupling to surface plasmon modes on both sides of the grating. We also compared the two mechanisms for fluorescent enhancement, namely the intense electromagnetic field associated with surface plasmons and excited fluorophores radiating via surface plasmon modes. We found the latter mechanism clearly dominant.     

Modes of neuronal migration in the developing cerebral cortex

The conventional scheme of cortical formation shows that postmitotic neurons migrate away from the germinal ventricular zone to their positions in the developing cortex, guided by the processes of radial glial cells. However, recent studies indicate that different neuronal types adopt distinct modes of migration in the developing cortex. Here, we review evidence for two modes of radial movement: somal translocation, which is adopted by the early-generated neurons; and glia-guided locomotion, which is used predominantly by pyramidal cells. Cortical interneurons, which originate in the ventral telencephalon, use a third mode of migration. They migrate tangentially into the cortex, then seek the ventricular zone before moving radially to take up their positions in the cortical anlage.     

Spectral Tunability and Selectivity Based on Multiple Resonance Modes in End-Coupled Sectorial-Ring Cavity Waveguide

A plasmonic nanodevice in end-coupled sectorial-ring cavity waveguide is reported, and the spectral characteristic of the novel system is studied. It is built with sectorial-ring cavity resonator end-coupled to plasmonic waveguide, and  this resonator is an oversize central angle (θ), alterable symmetry plane angle (ϕ), and fixed radius and gap, which has the advantages of forming split-ring-like, realizing asymmetrical cavity, and achieving spectral tunability and selectivity. The two-dimensional simulation indicates that the extra noninteger and traditional integer resonance modes are excited in the novel system, and the noninteger resonance modes are not achievable for the circular-ring cavity waveguide. It displays that these resonance modes of the novel system are drastically affected by changing the position of ϕ, which has different changes on maximum transmittances but is almost unchanged on resonance wavelengths. Importantly, the multiple resonance modes are highly sensitive to ϕ, and the proper modes are significantly enhanced, weakened, excited, or disappeared. It also displays that these resonance modes of the novel system are efficiently affected by changing the size of θ, which has similar and different influences on resonance wavelengths and maximum transmittances. This work shows that the method helps in designing accurately the transmission spectrum with prospective modes in nanophotonics, and the structure facilitates for realization of tunable and selective multichannel nanofilter or nanosensor in integration.