Strong Hotspots Research Articles

Plasmonic Nanowire‐Enhanced Upconversion Luminescence for Anticounterfeit Devices

A novel, efficient, cost‐effective, and high‐level security performance anticounterfeit device achieved by plasmonic‐enhanced upconversion luminescence (UCL) is demonstrated. The plasmonic architecture consists of the randomly dispersed Ag nanowires (AgNWs) network, upconversion nanoparticles (UCNPs) monolayer, and metal film, in which the UCL is enhanced by a few tens, compared to reference sample, becuase the plasmonic modes lead to the concentration of the incident near infrared (NIR) light in the UCNPs monolayer. In the configuration, both the localized surface plasmons (LSPs) around the metallic nanostructures and gap plasmon polaritons (GPPs) confined in the UCNPs monolayer, significantly contribute to the UCL enhancement. The UCL enhancement mechanism resulting from enhanced NIR absorption, boosted internal quantum process, and formation of strong plasmonic hot spots in the plasmonic architecture is analyzed theoretically and numerically. More interestingly, a proof‐of‐concept anticounterfeit device using the plasmonic‐enhanced UCL is proposed, through which a nonreusable and high‐level cost‐effective security device protecting the genuine products is realized.

Improving SERS uniformity by isolating hot spots in gold rod-in-shell nanoparticles

Surface-enhanced Raman scattering (SERS) tags show ultrasensitivity and multiplexing abilities due to strong and characteristic Raman signals and therefore can be utilized as optical labeling agents similar to fluorescent dyes and quantum dots for biosensing and bioimaging. However, SERS tags have the difficulty to realize quantitative analysis due to the uniformity and reproducibility issue. In this work, we have reported on a new type of SERS tag called Au rod-in-shell (RIS) gap-enhanced Raman tag (GERT). With the high-resolution transmission electron microscopy (TEM) and optical absorbance measurements, we have demonstrated the subnanometer sized gap junctions inside the RIS GERTs. SERS measurements and FDTD calculations show that the core–shell subnanometer gap geometry in the RIS GERTs not only generates strong SERS hot spots but also isolates SERS hot spots by Au shells to avoid the influence when the particle aggregates form, therefore showing better SERS uniformity and stronger SERS intensity than normal Au nanorods. Those RIS NPs exhibit great potential as the labeling agents for SERS-based bioimaging and biosensing applications.

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.

Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.

Non-Rankine–Hugoniot Shock Zone of Mach Reflection in Hypersonic Rarefied Flows

This study investigates the non-Rankine–Hugoniot shock zone of Mach reflections in hypersonic flows with different flight altitudes using the direct simulation Monte Carlo method and Navier–Stokes approach. In the non-Rankine–Hugoniot shock zone, the flow viscosity induces the numerical deviation from the inviscid theoretical value with a smooth and continuous variation. It is determined and illuminated by comparing it with shock polars. A suitable and novel definition of the height of the non-Rankine–Hugoniot shock zone is then derived to facilitate the study of its size. The computations demonstrate that the height of the non-Rankine–Hugoniot shock zone grows as flight height increases, whereas a reduced Mach stem is observed. The growth of the non-Rankine–Hugoniot shock zone can be explained by the increase in the curvature of shock waves in the three-shock intersection. Computational results show the existence of a strong pressure hot spot and a weak temperature hot spot near the triple point and reveal that the slipstream starting from the triple point divides off these two hot spots. The peak values in the hot spot only fluctuate within a small range with increasing flight altitude. The direct simulation Monte Carlo results of additional cases indicate that rarefaction caused by the reduction of computational size does not affect the peak value in the hot spot.

A radial velocity study of the intermediate polar EX Hydrae

A study on the intermediate polar EX Hya is presented, based on simultaneous photometry and high dispersion spectroscopic observations, during four consecutive nights. The strong photometric modulation related to with the 67-min spin period of the primary star is clearly present, as well as the narrow eclipses associated to the orbital modulation. Since our eclipse timings have been obtained almost 91,000 cycles since the last reported observations, we present new linear ephemeris, although we cannot rule out a sinusoidal variation suggested by previous authors. The system mainly shows double-peaked H$\alpha$, H$\beta$ and HeI $\lambda$5876 \AA emission lines. From the profile of the H$\alpha$ line, we find two components; one with a steep rise and velocities not larger than $\sim$1000 km s$^{-1}$ and another broader component extending up to $\sim$2000 km s$^{-1}$, which we interpret as coming mainly from the inner disc. A strong and variable hotspot is found and a stream-like structure is seen at times. We show that the best solution correspond to $K_1 = 58 \pm 5$ km s$^{-1}$ from H$\alpha$, from the two emission components, which are both in phase with the orbital modulation. We remark on a peculiar effect in the radial velocity curve around phase zero, which could be interpreted as a Rositter-MacLaughlin-like effect, which has been taken into account before deriving $K_1$. This value is compatible with the values found in high-resolution both in the ultraviolet and X-ray. We find: $M_{1} = 0.78 \pm 0.03$ M$_{\odot}$, $ M_{2} = 0.10 \pm 0.02$ M$_{\odot}$ and $a = 0.67 \pm 0.01$ R$_{\odot}$. Doppler Tomography has been applied, to construct six Doppler tomograms for single orbital cycles spanning the four days of observations to support our conclusions. Our results indicate that EX Hya has a well formed disc and that the magnetosphere should extend only to about $3.75\,R_{\rm{WD}}$.

Fabrication of Au-Decorated 3D ZnO Nanostructures as Recyclable SERS Substrates

Highly roughened Au-decorated 3D ZnO nano-structures were prepared using a combination of prism holographic lithography and atomic layer deposition techniques. Prism holographic lithography is a simple and rapid method for fabricating ordered 3D nanostructures using the optical interference effects of multiple beams derived from a specially designed prism. Highly ordered reproducible surface-enhanced Raman scattering (SERS) substrates are needed for the reliable calibration of target analyte concentrations. A high density of Au nanoparticles separated by nanoscale gaps was generated on the Au-coated ZnO inverse structures. The nanogaps may function as strong hot spots for highly sensitive SERS-based chemical/biological sensors. The optimized SERS intensity from the prepared Au-coated 3D ZnO inverse structures was 20 times the intensity obtained from an Au-coated flat glass control substrate. The surfaces could be reused after the photocatalytic degradation and removal of adsorbates in the presence of ZnO. The Au-coated 3D ZnO structures described here offer an alternative to traditional single-use SERS substrates.

Assemble of high-density gold nanodots on TiO2 substrate for surface-e nhanced Raman spectroscopy

The cost-effective assemble of Au nanodots on TiO2 substrate over a large domain for high-sensitivity and reproducible surface enhanced Raman spectroscopy (SERS) is demonstrated. Au nanoparticles of defined size are immobilized on TiO2 to form high-density Au nanodots with removal of surface ligand meanwhile. The Au nanodots exhibit pronounced surface Plasmon resonance (SPR) due to strong interparticle coupling and hot spots formed in these gaps which enable large amplification of SERS signals. Using the Au nanodots (3.8nm) assemble a 5 times stronger SERS enhancement than larger Au nanoparticles (NPs) of same Au amount is experimentally demonstrated. The facile fabrication of SERS-active substrate over a large area and cost-effective character enable this high-density Au nanodots on TiO2 substrate practical application for SERS detection of trace amount of molecule of interest.

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm.

Design of protein-protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides, especially short ones (5-15 amino acid long), are natural candidates for inhibition of protein-protein complexes due to several attractive features such as high structural compatibility with the protein binding site (mimicking the surface of one of the proteins), small size and the ability to form strong hotspot binding connections with the protein surface. Efficient rational peptide design is still a major challenge in computer aided drug design, due to the huge space of possible sequences, which is exponential in the length of the peptide, and the high flexibility of peptide conformations. In this article we present PinaColada, a novel computational method for the design of peptide inhibitors for protein-protein interactions. We employ a version of the ant colony optimization heuristic, which is used to explore the exponential space ([Formula: see text]) of length n peptide sequences, in combination with our fast robotics motivated PepCrawler algorithm, which explores the conformational space for each candidate sequence. PinaColada is being run in parallel, on a DELL PowerEdge 2.8 GHZ computer with 20 cores and 256 GB memory, and takes up to 24 h to design a peptide of 5-15 amino acids length. An online server available at: http://bioinfo3d.cs.tau.ac.il/PinaColada/. danielza@post.tau.ac.il; wolfson@tau.ac.il.

A molecular plasmonic Fano-router: Using hotspots in a single-stone ring-like structure

In the past decade there has been outstanding, continuing interest in developing novel structures to engineer and control light-matter interactions in subwavelength dimensions with desired optical characteristics. Herein, we propose a unique plasmonic configuration consisting of a split-ring and a nanosphere in the split section (resembles a single-stone ring). We show that this simple and antisymmetric structure is able to support pronounced antisymmetric Fano resonance at the near-infrared region, while strong hotspots form at the gap space between the split-ring terminals and the nanosphere. The antisymmetric feature of the structure facilitates strong-dependency on the polarization of the incident beam. Having strong sensitivity to the incident polarization angle, we tailored a fast plasmonic Fano-router based on the behavior of Fano resonant mode. This study could help realizing Fano resonance based photonic devices using simple and antisymmetric nanostructures.

Land surface–atmosphere interaction in future South American climate using a multi‐model ensemble

AbstractThe land–atmosphere interaction for reference and future climate is estimated with a regional climate model ensemble. In reference climate, more than 50% of the models show interaction in southeastern South America during austral spring, summer and autumn. In future climate, the region remains a strong hotspot although somewhat weakened due to the wet response that enhance energy limitation on the evapotranspiration. The region of the Brazilian Highlands and Matto Grosso appears as a new extensive hotspot during austral spring. This is related to a dry response which is probably accentuated by land surface feedbacks.

Unusual Weak Interparticle Distance Dependence in Raman Enhancement from Nanoparticle Dimers

Here, we report surprisingly weak distance dependence in Raman enhancement from a raspberry-like gold nanoparticle termed raspberry-MM. A raspberry-MM is composed of closely packed gold nanobeads assembled on a polymer core. Due to the abundant “built-in” hot spots between adjacent gold nanobeads, bright and uniform Raman signals were observed from isolated single raspberry-MMs. Interestingly, dimers of raspberry-MMs also showed highly reproducible Raman signals, indicating that the dimer SERS signal is not strongly dependent on the nanoparticle separation. Finite-difference time-domain (FDTD) modeling shows that a strong hot spot is created at the dimer-gap, as expected. However, since there are many more built-in hot spots in each raspberry-MM, the contribution of the dimer-gap hot spot to the total Raman enhancement remains low even for 2 nm separation, which explains the observed weak distance dependence. This result is in stark contrast with many previous SERS studies on nanoparticle dimers and clusters, and provides an important guideline on how to design bright and highly reproducible Raman substrates.

Toroidal dipolar response by a dielectric microtube metamaterial in the terahertz regime.

Due to metal losses in plasmonic metamaterials, high-refractive-index dielectrics are promising to improve optical performances of their metallic counterparts. In this paper, a LiTaO(3) microtube metamaterial is numerically investigated to explore the toroidal dipolar resonance based on the multipole expansion theory. The local field strength probed on the central axis of the microtube is greatly enhanced for the toroidal dipolar mode, forming a strong hot spot concentrated in the deep-subwavelength scale. Furthermore, we also show the influences of geometrical parameter on the quality (Q) factor of the toroidal mode. The high Q factor and strongly concentrated field strength in the toroidal microtube metamaterial offer application potentials such as sensing, energy havesting, particle trapping, and nonlinear optical effects.

Silver-coated elevated bowtie nanoantenna arrays: Improving the near-field enhancement of gap cavities for highly active surface-enhanced Raman scattering

Improving hot-spot intensity is a key issue in surface-enhanced Raman scattering (SERS). The bowtie nanoantenna (BNA) is an effective device used to concentrate light energy into a nanoscale volume and produce strong hot spots. Nanosphere lithography (NSL) is a large-area and low-cost technique to produce BNA arrays; however, the SERS activity of NSL-fabricated BNAs is limited. In this paper, we present a simple method to improve the SERS activity of conventional NSL-fabricated BNAs by modifying their geometry. The new configuration is termed “silver-coated elevated bowtie nanoantenna” (SCEBNA). SCEBNAs perform intensive near-field enhancement in the gap cavities owing to the integrated contribution of the “lightning rod” effect, resonance coupling, and the formation of the plasmonic Fabry–Perot cavity. Experimental measurements and finite-difference time-domain simulations revealed that the hot-spot intensity and the substrate enhancement factor can be optimized by adjusting the silver thickness. The optimal sample has the capability of trace-amount detection with fine reproducibility.

High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae.

Meiotic recombination initiates with DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, many DSBs occur in "hotspots" coinciding with nucleosome-depleted gene promoters. Transcription factors (TFs) stimulate DSB formation in some hotspots, but TF roles are complex and variable between locations. Until now, available data for TF effects on global DSB patterns were of low spatial resolution and confined to a single TF. Here, we examine at high resolution the contributions of two TFs to genome-wide DSB distributions: Bas1, which was known to regulate DSB activity at some loci, and Ino4, for which some binding sites were known to be within strong DSB hotspots. We examined fine-scale DSB distributions in TF mutant strains by deep sequencing oligonucleotides that remain covalently bound to Spo11 as a byproduct of DSB formation, mapped Bas1 and Ino4 binding sites in meiotic cells, evaluated chromatin structure around DSB hotspots, and measured changes in global messenger RNA levels. Our findings show that binding of these TFs has essentially no predictive power for DSB hotspot activity and definitively support the hypothesis that TF control of DSB numbers is context dependent and frequently indirect. TFs often affected the fine-scale distributions of DSBs within hotspots, and when seen, these effects paralleled effects on local chromatin structure. In contrast, changes in DSB frequencies in hotspots did not correlate with quantitative measures of chromatin accessibility, histone H3 lysine 4 trimethylation, or transcript levels. We also ruled out hotspot competition as a major source of indirect TF effects on DSB distributions. Thus, counter to prevailing models, roles of these TFs on DSB hotspot strength cannot be simply explained via chromatin "openness," histone modification, or compensatory interactions between adjacent hotspots.

Gallium plasmonics: deep subwavelength spectroscopic imaging of single and interacting gallium nanoparticles.

Gallium has recently been demonstrated as a phase-change plasmonic material offering UV tunability, facile synthesis, and a remarkable stability due to its thin, self-terminating native oxide. However, the dense irregular nanoparticle (NP) ensembles fabricated by molecular-beam epitaxy make optical measurements of individual particles challenging. Here we employ hyperspectral cathodoluminescence (CL) microscopy to characterize the response of single Ga NPs of various sizes within an irregular ensemble by spatially and spectrally resolving both in-plane and out-of-plane plasmonic modes. These modes, which include hybridized dipolar and higher-order terms due to phase retardation and substrate interactions, are correlated with finite difference time domain (FDTD) electrodynamics calculations that consider the Ga NP contact angle, substrate, and native Ga/Si surface oxidation. This study experimentally confirms previous theoretical predictions of plasmonic size-tunability in single Ga NPs and demonstrates that the plasmonic modes of interacting Ga nanoparticles can hybridize to produce strong hot spots in the ultraviolet. The controlled, robust UV plasmonic resonances of gallium nanoparticles are applicable to energy- and phase-specific applications such as optical memory, environmental remediation, and simultaneous fluorescence and surface-enhanced Raman spectroscopies.

Topoisomerase I plays a critical role in suppressing genome instability at a highly transcribed G-quadruplex-forming sequence.

G-quadruplex or G4 DNA is a non-B secondary DNA structure that comprises a stacked array of guanine-quartets. Cellular processes such as transcription and replication can be hindered by unresolved DNA secondary structures potentially endangering genome maintenance. As G4-forming sequences are highly frequent throughout eukaryotic genomes, it is important to define what factors contribute to a G4 motif becoming a hotspot of genome instability. Using a genetic assay in Saccharomyces cerevisiae, we previously demonstrated that a potential G4-forming sequence derived from a guanine-run containing immunoglobulin switch Mu (Sμ) region becomes highly unstable when actively transcribed. Here we describe assays designed to survey spontaneous genome rearrangements initiated at the Sμ sequence in the context of large genomic areas. We demonstrate that, in the absence of Top1, a G4 DNA-forming sequence becomes a strong hotspot of gross chromosomal rearrangements and loss of heterozygosity associated with mitotic recombination within the ∼20 kb or ∼100 kb regions of yeast chromosome V or III, respectively. Transcription confers a critical strand bias since genome rearrangements at the G4-forming Sμ are elevated only when the guanine-runs are located on the non-transcribed strand. The direction of replication and transcription, when in a head-on orientation, further contribute to the elevated genome instability at a potential G4 DNA-forming sequence. The implications of our identification of Top1 as a critical factor in suppression of instability associated with potential G4 DNA-forming sequences are discussed.

Mutagenesis in the lacI gene target of E. coli: Improved analysis for lacId and lacO mutants

The lacI gene of Escherichia coli has been a highly useful target for studies of mutagenesis, particularly for analysis of the specificity (spectrum) of mutations generated under a variety of conditions and in various genetic backgrounds. The gene encodes the repressor of the lac operon, and lacI-defective mutants displaying constitutive expression of the operon are readily selected. DNA sequencing of the lacI mutants has often been confined to the N-terminal region of the protein, as it presents a conveniently short target with a high density of detectably mutable sites. Mutants in this region are easily selected due to their dominance in a genetic complementation test (lacId mutants). A potential complication in these studies is that constitutive expression of lac may also arise due to mutations in the lac operator (lacO mutants). Under some conditions, for example when analyzing spontaneous mutations, lacO mutants can comprise a very high fraction of the constitutive mutants due to a strong base-substitution hotspot in the lac operator. Such mutational hot spots diminish the return of the sequencing effort and do not yield significant new information. For this reason, a procedure to eliminate the lacO mutants prior to DNA sequencing is desirable. Here, we report a simple method that allows screening out of lacO mutants. This method is based on the lack of resistance of lacO mutants to kanamycin under conditions when the kan gene is expressed from a plasmid under control of the lac promoter-operator (lacPO). We show data validating the new approach with sets of known lacId and lacO mutants, and further apply it to the generation of a new collection of spontaneous mutations, where lacO mutants have historically been a significant contributor.

Modeling of black carbon in Asia using a global-to-regional seamless aerosol-transport model

In Asia, the evaluation of black carbon (BC) using global aerosol-transport models has been incomplete due to a lack of available measurements. Recently, new measurements and datasets at various Asian sites have become available for use in model validation. In this study, we compared the BC mass concentrations obtained by an aerosol-coupled global nonhydrostatic model adopting a uniform-grid system with in-situ measurements and other models over Asia. The results revealed that our model, as well as other global models, was unable to reproduce the observed BC values at most sites in China and India, most likely due to strong local hotspots. To overcome the inconsistency between the models and measurements, we developed a new aerosol-transport model using a stretched-grid system for high-resolution simulations with up to approximately 10 km grids. Our model can be used as a global-to-regional seamless aerosol-transport model for low to high horizontal resolution simulations.

Differences in meiotic recombination rates in childhood acute lymphoblastic leukemia at an MHC class II hotspot close to disease associated haplotypes.

Childhood Acute Lymphoblastic Leukemia (ALL) is a malignant lymphoid disease of which B-cell precursor- (BCP) and T-cell- (T) ALL are subtypes. The role of alleles encoded by major histocompatibility loci (MHC) have been examined in a number of previous studies and results indicating weak, multi-allele associations between the HLA-DPB1 locus and BCP-ALL suggested a role for immunosusceptibility and possibly infection. Two independent SNP association studies of ALL identified loci approximately 37 kb from one another and flanking a strong meiotic recombination hotspot (DNA3), adjacent to HLA-DOA and centromeric of HLA-DPB1. To determine the relationship between this observation and HLA-DPB1 associations, we constructed high density SNP haplotypes of the 316 kb region from HLA-DMB to COL11A2 in childhood ALL and controls using a UK GWAS data subset and the software PHASE. Of four haplotype blocks identified, predicted haplotypes in Block 1 (centromeric of DNA3) differed significantly between BCP-ALL and controls (P = 0.002) and in Block 4 (including HLA-DPB1) between T-ALL and controls (P = 0.049). Of specific common (>5%) haplotypes in Block 1, two were less frequent in BCP-ALL, and in Block 4 a single haplotype was more frequent in T-ALL, compared to controls. Unexpectedly, we also observed apparent differences in ancestral meiotic recombination rates at DNA3, with BCP-ALL showing increased and T-ALL decreased levels compared to controls. In silico analysis using LDsplit sotware indicated that recombination rates at DNA3 are influenced by flanking loci, including SNPs identified in childhood ALL association studies. The observed differences in rates of meiotic recombination at this hotspot, and potentially others, may be a characteristic of childhood leukemia and contribute to disease susceptibility, alternatively they may reflect interactions between ALL-associated haplotypes in this region.

Nano-optical conveyor belt, part I: Theory.

We propose a method for peristaltic transport of nanoparticles using the optical force field over a nanostructured surface. Nanostructures may be designed to produce strong near-field hot spots when illuminated. The hot spots function as optical traps, separately addressable by their resonant wavelengths and polarizations. By activating closely packed traps sequentially, nanoparticles may be handed off between adjacent traps in a peristaltic fashion. A linear repeating structure of three separately addressable traps forms a "nano-optical conveyor belt"; a unit cell with four separately addressable traps permits controlled peristaltic transport in the plane. Using specifically designed activation sequences allows particle sorting.