Extraordinary Optical Transmission Property of X-Shaped Plasmonic Nanohole Arrays

Optical transmission properties of periodic X-shaped plasmonic nanohole arrays in a silver film are investigated by performing the finite element method. Obvious peaks appear in the transmission spectra due to surface plasmon polaritons (SPPs) on the top surface of the silver film, to the Fabry–Ferot resonance effect of SPPs in the nanohole, and to the localized surface plasmon resonance of the nanohole. Besides the topologic shape parameters of the X-shaped nanohole, transmission properties strongly depend on incident polarization. The results of this study not only present a tunable plasmonic filter, but also aid in the understanding of the mechanisms of the extraordinary optical transmission phenomenon.     

Effect of Boundary Condition and Periodical Extension on Transmission Characteristics of Terahertz Filters with Periodical Hole Array Structure Fabricated on Aluminum Slab

Terahertz (THz) filters based on extraordinary optical transmission from periodical hole array structures fabricated on aluminum slab have been experimentally investigated by using THz time-domain spectroscopy. The incident THz pulses with frequency from 0.1 to 2.7 THz could be partly filtered, and the central peak was at ～0.26. The high frequency signal could be observed to decrease, especially for the frequency above ～1 THz. Moreover, the transmission peak from small-size sample with less hole arrays shifts to high frequency at ～0.53 THz due to both the effects of boundary condition and insufficient periodical extension. Furthermore, finite element method with surface plasmon polariton theory is employed to analyze this extraordinary optical transmission and filter phenomena.     

Time-of-Flight Model for the Extraordinary Transmission Through Periodic Arrays of Subwavelength Apertures at THz Frequencies

A qualitative model explaining the extraordinary optical transmission of terahertz (THz) radiation through two-dimensional periodic arrays of subwavelength apertures is presented. Systematic terahertz time-domain spectroscopy studies have been undertaken to investigate the combined effects of the lattice arrangement, aperture shape, area and aspect ratio on the transmission properties of electroformed copper arrays. The extensive results presented provide a unified example of how aperture geometry dictates SPP activity. The novel fabrication method creates exemplary peak resonances, allowing the onset of surface plasmon polariton (SPP) decoupling to be distinguished from direct transmission. Furthermore, we provide the first evidence as to how the temporal properties of SPPs are governed by the single-cycle THz pulse. The time-of-flight model presented can not only be used to explain the results observed in both the presented and previously published experiments but serves as a method to engineer specific resonances for sensor applications.     

In Situ Optical Extinction Measurement for Locally Control of Surface Plasmon Resonance During Nanosecond Laser Irradiation of Silver Ion Exchanged Silicate Glass

Online UV/visible extinction measurement have been achieved during nanosecond Nd:YAG laser irradiation at 532 nm of a silver-exchanged silicate glass after each shot. We have explained the evolution of the integrated spectral evolution with the help of a few observed spots after the laser/glass interaction and completed them by optical and surface measurements. This optical method allows to in situ follow silver ions precipitation in nanoparticles (NPs) and the consequently surface plasmon resonance evolution (SPR). In this study, we focus on the interest of this method for one silver-exchanged soda-lime glass by direct observation of the sample surface. Scanning electron microscopy measurement and optical microscopy were used to identify the various ablation mechanisms. Profilometry was used to evaluate the material distribution and the surface roughness evolution (Rms parameter). Thus, we explain the silver NPs effect on glass matrix at various micrometric scales according to the deposited fluence and silver concentration.     

Enhancement of Extraordinary Optical Transmission in a Double Heterostructure Plasmonic Bandgap Cavity

In this paper, a novel plasmonic bandgap cavity inducing the enhancement of extraordinary optical transmission is presented. Numerical simulations have been performed to model a free-standing structure made of a one-dimensional periodic arrangement of gold strips. Two different values of the lattice constant have been properly chosen to realize a double heterostructure-like cavity to accomplish extraordinary optical transmission assisted by the formation of a plasmonic bandgap in the adjacent regions. Numerical results prove the capability of this optical device to efficiently transmit input light beams with far-field transmission values close to 100% due to the excitation of surface plasmon polariton resonant modes.     

Tunnel Light Through a Continuous Optically Thick Metal Film Utilizing Higher Order Magnetic Plasmon Resonance

In this letter, we investigate the extraordinary optical transmission behavior of a flat continuous metal film sandwiched by magnetic plasmonic structures. A new mechanism by utilizing higher order magnetic plasmon resonance is proposed to enhance the transmission. Numerical simulation results show that 80 % electromagnetic energy can be transmitted through the middle 50-nm-thick continuous gold film in near-infrared regime. The excitation of the second-order magnetic plasmons and the propagating surface plasmons, as well as the interaction between them accounts for such a high transmission. The interaction of magnetic plasmons and surface plasmons leads to new hybrid modes, and the coupled oscillator model is introduced to analyze this hybridization. This work extends the application range of higher order magnetic plasmons and may have potential in transparent electrode and electromagnetic energy transfer applications.     

Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system

Cellular signaling is key for organisms to survive immediate stresses from fluctuating environments as well as relaying important information about external stimuli. Effective mechanisms have evolved to ensure appropriate responses for an optimal adaptation process. For them to be functional despite the noise that occurs in biochemical transmission, the cell needs to be able to infer reliably what was sensed in the first place. For example Saccharomyces cerevisiae are able to adjust their response to osmotic shock depending on the severity of the shock and initiate responses that lead to near perfect adaptation of the cell. We investigate the Sln1–Ypd1–Ssk1-phosphorelay as a module in the high-osmolarity glycerol pathway by incorporating a stochastic model. Within this framework, we can imitate the noisy perception of the cell and interpret the phosphorelay as an information transmitting channel in the sense of C.E. Shannon’s “Information Theory”. We refer to the channel capacity as a measure to quantify and investigate the transmission properties of this system, enabling us to draw conclusions on viable parameter sets for modeling the system.     

Extraordinary Transmission of Three-Dimensional Crescent-like Holes Arrays

We developed a method to fabricate a periodic array of three-dimensional crescent-like holes (3DCLH) via an inverted hemispherical colloidal lithography. It is found that there exists an extraordinary optical transmission in this non-planar perforated periodic array of 3DCLH when the electric field of the incident light is perpendicular to the cross-line of the crescent-like hole. This extraordinary optical peak is insensitive with the incident angles and sensitive with the angle between the electric field of the incident light to the cross-line of the 3DCLH. Numerical simulation based on finite-difference time-domain method reveals that this peak is caused by an asymmetric localized surface plasmon resonance. This structure might be useful for the optical sensing and optical-integrated circuits.     

Nanoantenna-Assisted Extraordinary Optical Transmission Under Radial Polarization Illumination

We numerically study the extraordinary optical transmission of a plasmonic structure that combines a circular nanoantenna and a vertical annular nanoslit etched into a gold film under radially polarized illumination. The nanoantenna collects the incident field and localizes it in a horizontal Fabry-Pérot cavity over the gold film. The vertical nanoslit positioned at the maximal field in the horizontal cavity couples the localized field and facilitates its transmission to the free space. Due to the symmetry matching between the structure and the illumination polarization, surface plasmons can be excited effectively and enhance the transmission. Through optimizing the structure parameters, the transmission efficiency can be greatly enhanced by 225 times for a resonant annular nanoslit and 251 times for a non-resonant annular nanoslit. This axisymmetric extraordinary optical transmission setup may be fabricated on the facet of an optical fiber for optical sensing applications.     

Tunable Extraordinary Transmission through a Graphene-Covered Hole Array: an Analytical Equivalent-Circuit Modeling Approach

Plasmonics - We study two-dimensional (2D) hole arrays drilled into a perfect conductor slab covered with a graphene sheet. Such arrays support the extraordinary transmission of electromagnetic...     

Optical Curtain Effect: Extraordinary Optical Transmission Enhanced by Antireflection

In this paper, we employ an antireflective coating which comprises inverted π-shaped metallic grooves to manipulate the behaviour of a transverse-magnetic (TM)-polarised plane wave transmitted through a periodic nanoslit array. At normal incidence, such scheme cannot only retain the optical curtain effect in the output region but also generate the extraordinary transmission of light through the nanoslits with the total transmission efficiency as high as 90 %. Besides, we show that the spatially invariant field distribution in the output region as well as the field distribution of resonant modes around the inverted π-shaped grooves can be reproduced immaculately when the system is excited by an array of point sources beneath the inverted π-shaped grooves. Furthermore, we investigate the influence of centre groove and side-corners of the inverted π-shaped grooves on suppressing the reflection of light, respectively. Based on our work, it shows promising potential in applications of enhancing the extraction efficiency as well as controlling the beaming pattern of light emitting diodes.     

DPPC Bilayers in Solutions of High Sucrose Content

The properties of lipid bilayers in sucrose solutions have been intensely scrutinized over recent decades because of the importance of sugars in the field of biopreservation. However, a consensus has not yet been formed on the mechanisms of sugar-lipid interaction. Here, we present a study on the effect of sucrose on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers that combines calorimetry, spectral fluorimetry, and optical microscopy. Intriguingly, our results show a significant decrease in the transition enthalpy but only a minor shift in the transition temperature. Our observations can be quantitatively accounted for by a thermodynamic model that assumes partial delayed melting induced by sucrose adsorption at the membrane interface.     

Scoring docking models with evolutionary information

We have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases.     

The Effects of Host Diversity on Vector-Borne Disease: The Conditions under Which Diversity Will Amplify or Dilute the Disease Risk

Multihost vector-borne infectious diseases form a significant fraction of the global infectious disease burden. In this study we explore the relationship between host diversity, vector behavior, and disease risk. To this end, we have developed a new dynamic model which includes two distinct host species and one vector species with variable preferences. With the aid of the model we were able to compute the basic reproductive rate, R ₀, a well-established measure of disease risk that serves as a threshold parameter for disease outbreak. The model analysis reveals that the system has two different qualitative behaviors: (i) the well-known dilution effect, where the maximal R₀ is obtained in a community which consists a single host (ii) a new amplification effect, denoted by us as diversity amplification, where the maximal R₀ is attained in a community which consists both hosts. The model analysis extends on previous results by underlining the mechanism of both, diversity amplification and the dilution, and specifies the exact conditions for their occurrence. We have found that diversity amplification occurs where the vector prefers the host with the highest transmission ability, and dilution is obtained when the vector does not show any preference, or it prefers to bite the host with the lower transmission ability. The mechanisms of dilution and diversity amplification are able to account for the different and contradictory patterns often observed in nature (i.e., in some cases disease risk is increased while in other is decreased when the diversity is increased). Implication of the diversity amplification mechanism also challenges current premises about the interaction between biodiversity, climate change, and disease risk and calls for retrospective thinking in planning intervention policies aimed at protecting the preferred host species.     

From receptor recognition mechanisms to bioinspired mimetic antagonists in HIV-1/cell docking

Understanding the ways in which two or more proteins interact may give insight into underlying binding and activation mechanisms in biology, methods for protein separation and structure-based antagonism. This review describes ways in which protein recognition has been explored in our laboratory for the HIV-1/cell entry process. Initial contact between an HIV-1 virion particle and a human cell occurs between gp120 (an HIV-1 envelope protein) and CD4 (a human extracellular signaling protein). This interaction leads to a sequence of events which includes a conformational change in gp120, fusion of the HIV-1 and cellular membranes and eventual infection of the cell. Using an optical biosensor and a reporter antibody, we have been able to measure the conformational change in gp120 that occurs upon CD4 binding. We also have used this biosensor system to characterize CD4 mimetics, obtained by peptide synthesis in miniprotein scaffolds. Phage display techniques have been employed to identify novel miniprotein sequences. The combination of biosensor interaction kinetics analysis and phage display provides a useful approach for understanding the recognition mechanisms involved in the HIV/cell docking process. This approach may also be useful in investigating other protein complexes of importance in health and disease.     

Spatial Mode Selection by the Phase Modulation of Subwavelength Plasmonic Grating

The extraordinary transmission of the subwavelength gold grating has been investigated by the rigorous coupled-wave analysis and verified by the metal–insulator–metal plasmonic waveguide method. The physical mechanisms of the extraordinary transmission are characterized as the excitation of the surface plasmon polariton modes. The subwavelength grating integrated with the distributed Bragg reflector is proposed to modulate the phase to realize spatial mode selection, which is prospected to be applied for transverse mode selection in the vertical cavity surface-emitting laser.     

RNAi mechanisms and applications

Within the past two decades we have become increasingly aware of the roles that RNAs play in regulation of gene expression. The RNA world was given a booster shot with the discovery of RNA interference (RNAi), a compendium of mechanisms involving small RNAs (less than 30 bases long) that regulate the expression of genes in a variety of eukaryotic organisms. Rapid progress in our understanding of RNAi-based mechanisms has led to applications of this powerful process in studies of gene function as well as in therapeutic applications for the treatment of disease. RNAi-based therapies involve two-dimensional drug designs using only identification of good Watson-Crick base pairing between the RNAi guide strand and the target, thereby resulting in rapid design and testing of RNAi triggers. To date there are several clinical trials using RNAi, and we should expect the list of new applications to grow at a phenomenal rate. This article summarizes our current knowledge about the mechanisms and applications of RNAi.     

Use of Peptide Strategy for Study of Molecular Mechanisms of Hormonal Signal Transduction into Cell

At present the peptide strategy is used extensively to study molecular mechanisms of interaction between signal proteins, components of hormonal signal systems. The strategy is based on use of synthetic peptides as probes corresponding to functionally important sites of these proteins. This review summarizes and analyzes literature data and results of our own works on use of the peptide strategy for studying functional coupling of receptors of serpentine and tyrosine kinase types with heterotrimeric G-proteins. Alongside with peptides derived from the primary structure of cytoplasmic loops and transmembrane domains as well as from different sites of G-protein α, β, and γ-subunits, natural and synthetic peptides are considered which have no homology with receptors and G-proteins, but are able to affect effectively interaction between them.     

Kinetic signatures of microRNA modes of action

MicroRNAs (miRNAs) are key regulators of all important biological processes, including development, differentiation, and cancer. Although remarkable progress has been made in deciphering the mechanisms used by miRNAs to regulate translation, many contradictory findings have been published that stimulate active debate in this field. Here we contribute to this discussion in three ways. First, based on a comprehensive analysis of the existing literature, we hypothesize a model in which all proposed mechanisms of microRNA action coexist, and where the apparent mechanism that is detected in a given experiment is determined by the relative values of the intrinsic characteristics of the target mRNAs and associated biological processes. Among several coexisting miRNA mechanisms, the one that will effectively be measurable is that which acts on or changes the sensitive parameters of the translation process. Second, we have created a mathematical model that combines nine known mechanisms of miRNA action and estimated the model parameters from the literature. Third, based on the mathematical modeling, we have developed a computational tool for discriminating among different possible individual mechanisms of miRNA action based on translation kinetics data that can be experimentally measured (kinetic signatures). To confirm the discriminatory power of these kinetic signatures and to test our hypothesis, we have performed several computational experiments with the model in which we simulated the coexistence of several miRNA action mechanisms in the context of variable parameter values of the translation.