Plasmon-Matter Interactions in Optoelectronic Metamaterials with Negative Refractive Index

Optoelectronic metamaterials composed of nanoscale metallic structures and semiconductor quantum structures constitute a powerful platform to explore light-matter interaction and new devices. In this work, we numerically study an optoelectronically coupled metamaterial consisting of metallic double fishnet (DF) layers and semiconductor quantum well (QW) spacing layer. When the electronic intersubband transition (ISBT) in the QW coincides with the plasmonic resonances of the DF structure, the plasmon-matter interaction (PMI) can modify the optical properties considerably. In case of the ISBT-matching localized surface plasmons (LSP), i.e., f _QW?=?f _LSP, the polarization-selection-rule forbidden ISBT absorption can be enabled due to the nonnegligible E _z ?field distributions while the retrieved optical constants remain almost unchanged. However, when the gap surface plasmons (GSP) are matched, i.e., f _QW?=?f _GSP, PMI exhibits a clear anti-crossing behavior implying strong coupling effects between ISBT and GSP resonance and formation of intersubband polaritons. The effective optical constants are therefore modulated appreciably. The large difference between GSP and LSP can be attributed to their distinctive resonance qualities (Q-factors) and polarization conversion ratios (99.28 % for GSP and 1.54 % for LSP) from the transverse electric (TE) to transverse magnetic (TM) mode. Our results provide insight into the physical mechanism of PMI in nanoscale semiconductor-plasmon hybrid systems and suggest an alternative means in tunable negative refractive index (NRI) applications.     

Magnetic Coupling Effect on Nonlinear Properties in Negative Index Metamaterials with a Kerr Nonlinearity

We investigate magnetic coupling effect on nonlinear electromagnetic properties in a three-dimensional negative index metamaterial constituted by arrays of conducting wires and split-ring resonators embedded into a Kerr nonlinear dielectric. Numerical results show that the switches of nonlinear electromagnetic properties between right-handed and left-handed properties depend closely on magnetic coupling strength, which can be divided into several different coupling regions according to the angular frequency of incident light and the nonlinear types (focused or defocused) of the dielectric. These properties may be instructive for designing optimizely composite metamaterials with negative refraction and provide various routes to manipulating light.     

Aminoacylation of RNA Minihelices: Implications for tRNA Synthetase Structural Design and Evolution

Abstract

The genetic code is based on the aminoacylation of tRNA with amino acids catalyzed by the aminoacyl-tRNA synthetases. The synthetases are constructed from discrete domains and all synthetases possess a core catalytic domain that catalyzes amino acid activation, binds the acceptor stem of tRNA, and transfers the amino acid to tRNA. Fused to the core domain are additional domains that mediate RNA interactions distal to the acceptor stem. Several synthetases catalyze the aminoacylation of RNA oligonucleotide substrates that recreate only the tRNA acceptor stems. In one case, a relatively small catalytic domain catalyzes the aminoacylation of these substrates independent of the rest of the protein. Thus, the active site domain may represent a primordial synthetase in which polypeptide insertions that mediate RNA acceptor stem interactions are tightly integrated with determinants for aminoacyl adenylate synthesis. The relationship between nucleotide sequences in small RNA oligonucleotides and the specific amino acids that are attached to these oligonucleotides could constitute a second genetic code.     

Structural Evidence for the Evolution of Pyrogenic Toxin Superantigens

Cells from metazoan organisms are eliminated in a variety of physiological and pathophysiological processes by apoptosis. In this report, we describe the cloning and characterization of molecules from the marine sponges Geodia cydonium and Suberites domuncula, whose domains show a high similarity to those that are found in molecules of the vertebrate Bcl-2 superfamily and of the death receptors. The Bcl-2 proteins contain up to four Bcl-2 homology regions (BH). Two Bcl-2-related molecules have been identified from sponges that are provided with two of those regions, BH1 and BH2, and are termed Bcl-2 homology proteins (BHP). The G. cydonium molecule, BHP1_GC, has a putative size of 28,164, while the related sequence from S. domuncula, BHP1_SD, has a M _r of 24,187. Phylogenetic analyses of the entire two sponge BHPs revealed a high similarity to members of the mammalian Bcl-2 superfamilies and to the Caenorhabditis elegans Ced-9. When the two domains, BH1 and BH2, are analyzed separately, again the highest similarity was found to the members of the Bcl-2 superfamily, but a clearly lower relationship to the C. elegans BH1 and BH2 domains in Ced-9. In unrooted phylogenetic trees the sponge BH1 and BH2 are grouped among the mammalian sequences and are only distantly related to the C. elegans BH domains. The analysis of the gene structure of the G. cydonium BHP showed that the single intron present is located within the BH2 domain at the same position as in C. elegans and rat Bcl-x_L. In addition, a sponge molecule comprising two death domains has been characterized from G. cydonium. The two death domains of the potential proapoptotic molecule GC_DD2, M _r 24,970, share a high similarity with the Fas-FADD/MORT1 domains. A death domain-containing molecule has not been identified in the C. elegans genome. The phylogenetic analysis revealed that the sponge domain originated from an ankyrin building block from which the mammalian Fas-FADD/MORT1 evolved. It is suggested that the apoptotic pathways that involve members of the Bcl-2 superfamily and of the death receptors are already present in the lowest metazoan phylum, the Porifera. Received: 27 July 1999 / Accepted: 28 December 1999     

Protein Design and Evolution for Biocatalysis

Cover illustration: Protein Design and Evolution for Biocatalysis. This special issue of Biotechnology Journal contains selected contributions from scientists participating to the ESF-EMBO Symposium which took place in October 2008 in San Feliu, Spain. Guest Editor is the chair and organizer of the meeting, Jiri Damborsky from Brno (Czech Republic). He highlights a variety of topics brought up in the meeting, ranging from new methods of rational design, directed evolution, metagenomics and single-molecule techniques, to construction of useful enzymes for industrial applications. Uwe Bornscheuer (Greifswald, Germany) authored a meeting report. Image colored pencils, © PhotoDisc, Inc.; Protein logo © ESF.     

Protein Design and Evolution for Biocatalysis

Cover illustration: Soon designing proteins on demand? This is the vision expressed by the designer pencils pointing at the logo of the meeting held in September 2006 in Greifswald, Germany. This special issue was edited by Prof. Uwe Bornscheuer from Greifswald, who selected papers from keynote speakers at this meeting. With special thanks to Prof. Romas Kazlauskas, University of Minnesota, for the design of the conference logo. Pencils © FOTOLIA.     

Design and Research of Enhanced LED Performance Based on Graphical Substrate with Multilayer Hyperbolic Metamaterials

This paper mainly studies the influence of multilayer hyperbolic metamaterials (HMMs) with different structural parameters on the intensity of spontaneous radiation of quantum wells, thereby improving the coupling efficiency of incident electromagnetic waves and free electrons on metal nano-surfaces. In this paper, numerical simulations of visible light bands of 450–700 nm of Ag, Au, and Cu thin films are performed. The local field enhancements of multilayer HMMs with different shapes are compared, and it is found that circle Ag/Si multilayer HMMs have stronger field enhancement effects than other structures. At the same time, Purcell analysis was performed by changing various parameters of multilayer HMMs. It is found that the thickness of the metal/dielectric layer, the distance between the dipole and the HMMs, and the length of the multilayer HMMs change the intensity of the plasmon resonance radiation and have a great impact on the position of the resonance wavelength.

     

Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides

Viral fusogenic envelope proteins are important targets for the development of inhibitors of viral entry. We report an approach for the computational design of peptide inhibitors of the dengue 2 virus (DENV-2) envelope (E) protein using high-resolution structural data from a pre-entry dimeric form of the protein. By using predictive strategies together with computational optimization of binding “pseudoenergies”, we were able to design multiple peptide sequences that showed low micromolar viral entry inhibitory activity. The two most active peptides, DN57opt and 1OAN1, were designed to displace regions in the domain II hinge, and the first domain I/domain II beta sheet connection, respectively, and show fifty percent inhibitory concentrations of 8 and 7 µM respectively in a focus forming unit assay. The antiviral peptides were shown to interfere with virus:cell binding, interact directly with the E proteins and also cause changes to the viral surface using biolayer interferometry and cryo-electron microscopy, respectively. These peptides may be useful for characterization of intermediate states in the membrane fusion process, investigation of DENV receptor molecules, and as lead compounds for drug discovery.     

Negative Purifying Selection Drives Prion and Doppel Protein Evolution

The prion protein (PrP) when misfolded into the pathogenic conformer PrP^Sc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene (PRNP) and doppel gene (PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2.     

Permeability and Structural Characteristics of Isolated Nuclei from Chaetopterus Eggs

The germinal vesicle of the mature Chaetopterus egg is invested by an envelope which can be seen in electron micrographs to contain "pores" in its bilaminar structure. While under continuous microscopic observation, individual germinal vesicles were isolated in various test solutions by an extremely gentle method. Repeated measurements of nuclear diameter and of optical path differences with an interference microscope provided data on changes in mass after isolation. It was found that bovine serum albumin can readily penetrate the nuclear envelope of the isolated nucleus and that there are soluble elements which rapidly diffuse out. A relatively non-diffusible mass is lost at a much slower rate, the proportion of soluble to non-diffusible mass being dependent on the ionic environment. Calcium and manganese increase the proportion of the non-diffusible mass at the expense of the soluble components, while potassium decreases it. The shape and size of the isolated nucleus is at least partially dependent on the non-diffusible mass of its interior. Digestion with trypsin causes a complete structural collapse and loss of the non-diffusible elements, along with disappearance of the nucleolus. The nucleus shrinks and becomes wrinkled. A small residual mass is left which is probably associated with the nuclear envelope. Digestion with RNase or DNase causes no detectable effect on the isolated nucleus. Micromanipulation of the isolated nucleus consistently indicates that there are strands emanating from the nucleus. They may be up to several hundred microns long, are structurally strong, and are not destroyed by trypsin, RNase, or DNase. Electron micrographs of thin sections of intact cells show that the germinal vesicle is highly irregular in outline with complex evaginations extending into the cytoplasm. With the light microscope the isolated nucleus looks spherical and smooth and no emanating strands can be seen. The nature of the strands is not known.     

Seed Coat Structural and Permeability Properties of Tilia miqueliana Seeds

Journal of Plant Growth Regulation - In the present study, the structural and permeability properties of the Tilia miqueliana seed coat were primarily explored through the scanning electron...     

Design and Analysis of Ultra Broadband Nano-absorber for Solar Energy Harvesting

In this paper, we propose a metamaterial based ultra broadband nano-absorber (UBNA) for solar energy harvesting, whose elements consist of a ring column and dual hexagon pillar at the center. In this absorber, the light of shorter wavelengths is harvested at ring column, while the light of longer wavelengths is trapped by dual hexagon pillar. It is found that the average absorptivity of the UBNA is as high as 96% in 300–1300 nm waveband and the UBNA can maintain 95% in the whole visible and near-infrared waveband ranging from 300 to 2000 nm. In addition, the perfect light absorbing capability of the UBNA is independent of the incident light polarization state in the waveband of 300–1300 nm, and it can keep up an average absorptivity of 91% with an large incident angle varying between ?60^° and 60^°. We attribute the perfect absorbing property of UBNA to the synergistic effect of the slow wave effect, Fabry-Perot resonance and the localized surface plasmon resonance enhancement.     

An Ultrasensitive and Multispectral Refractive Index Sensor Design Based on Quad-Supercell Metamaterials

Plasmonics - Plasmonic metamaterials support the localized surface plasmon resonance (LSPR), which is sensitive to the change in the dielectric environment and highly desirable for ultrasensitive...     

Structural Capacitance in Protein Evolution and Human Diseases

Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism that we term “structural capacitance,” which results in the de novo generation of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opposed to gradualistic canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.     

Manipulate the Transmissions Using Index-Near-Zero or Epsilon-Near-Zero Metamaterials with Coated Defects

We investigate the wave transmissions through an index-near-zero (INZ) or epsilon-near-zero (ENZ) metamaterial containing various kinds of coated cylindrical defects. We find that thin coatings of the defects can dramatically change the transmission behaviors. For example, perfect magnetic conductor (PMC) defects embedded in an INZ or ENZ metamaterial yield total reflections for transverse magnetic polarized waves (Hao et al., Appl Phys Lett 96:101109, 2010). However, if the PMC defects are coated with dielectric shells, total transmissions could be achieved by tuning their permittivity values or geometric sizes. The permittivity differences of dielectric shells for total reflections and transmissions in the INZ or ENZ metamaterial could be very small, implying potential applications, such as ultrasensitive sensors and switches.     

A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway

Even though the Toll-like receptor (TLR) pathway is integral to inflammatory defense mechanisms, its excessive signaling may be devastating. Cells have acquired a cascade of strategies to regulate TLR signaling by targeting protein-protein interactions, or ubiquitin chains, but the details of the inhibition mechanisms are still unclear. Here, we provide the structural basis for the regulation of TLR signaling by constructing architectures of protein-protein interactions. Structural data suggest that 1) Toll/IL-1R (TIR) domain-containing regulators (BCAP, SIGIRR, and ST2) interfere with TIR domain signalosome formation; 2) major deubiquitinases such as A20, CYLD, and DUBA prevent association of TRAF6 and TRAF3 with their partners, in addition to removing K63-linked ubiquitin chains that serve as a docking platform for downstream effectors; 3) alternative downstream pathways of TLRs also restrict signaling by competing to bind common partners through shared binding sites. We also performed in silico mutagenesis analysis to characterize the effects of oncogenic mutations on the negative regulators and to observe the cellular outcome (whether there is/is not inflammation). Missense mutations that fall on interfaces and nonsense/frameshift mutations that result in truncated negative regulators disrupt the interactions with the targets, thereby enabling constitutive activation of the nuclear factor-kappa B, and contributing to chronic inflammation, autoimmune diseases, and oncogenesis.     

Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis

The redox active peptide glutathione is ubiquitous in nature, but some plants also synthesize glutathione analogs in response to environmental stresses. To understand the evolution of chemical diversity in the closely related enzymes homoglutathione synthetase (hGS) and glutathione synthetase (GS), we determined the structures of soybean (Glycine max) hGS in three states: apoenzyme, bound to γ-glutamylcysteine (γEC), and with hGSH, ADP, and a sulfate ion bound in the active site. Domain movements and rearrangement of active site loops change the structure from an open active site form (apoenzyme and γEC complex) to a closed active site form (hGSH•ADP•SO₄²⁻ complex). The structure of hGS shows that two amino acid differences in an active site loop provide extra space to accommodate the longer β-Ala moiety of hGSH in comparison to the glycinyl group of glutathione. Mutation of either Leu-487 or Pro-488 to an Ala improves catalytic efficiency using Gly, but a double mutation (L487A/P488A) is required to convert the substrate preference of hGS from β-Ala to Gly. These structures, combined with site-directed mutagenesis, reveal the molecular changes that define the substrate preference of hGS, explain the product diversity within evolutionarily related GS-like enzymes, and reinforce the critical role of active site loops in the adaptation and diversification of enzyme function.