Controllable Steering and Tuning of Surface Plasmons on the Metallic Nano-film with Nanoslits Array

Plasmonics - A scheme of steering and tuning surface plasmon wakes (SWs) on the metallic nano-film (MNF) excited by a free-electron-beam is demonstrated. With a well-designed array of nanoslits...     

Structure Effect on Sensitivity of Gold Nanoslits Studied by Spectral Integration Method

Gold nanoslit arrays have multiple resonances due to localized plasmons, Bloch wave surface plasmon polaritons, and Wood’s anomaly. Different structures result in different resonances and affect the detection sensitivity of the nanoslits. We systematically compared different structure parameters such as period, slit widths, and gold film thickness by using a spectral integration method. The experimental results show the detection sensitivity had an optimal value for a 500-nm period and 130-nm-thick nanoslits. Moreover, the sensitivity increases with the decrease of the slit widths. It was improved about three times when the size was reduced from 230 to 56 nm. The optimized structure can achieve a detection limit of 5 × 10⁻⁶ refractive index unit when the stability is 0.2%. Combining multispectral images and the spectral integration method, we demonstrate real-time and multiple detections of antigen–antibody interactions.     

Manipulating DNA probe presentation via enzymatic cleavage of diluent strands

We previously reported a system for the controlled redispersion of DNA-linked aggregates using secondary, competitive hybridization events and found that complete redispersion is contingent upon dilution of the active 20 base-long probe strands with 20 base-long nonhybridizing strands. Here, to reduce the steric interference of nonhybridizing or diluent strands on probe activity, we investigate the effect of shorter diluent strands on the hybridization activity of immobilized probes using the following two approaches: (1) simultaneously coupling shorter diluent strands and longer probe strands to microspheres and (2) simultaneously coupling diluent and probe strands of the same base length to microspheres and then clipping diluent strands with the restriction endonuclease AluI. Results indicate that one can reduce the duplex density down by 50-70% of its initial value, depending on the location of the recognition motif along the hybridization segment. In addition, tighter control over the number of probe-target duplexes is achieved with the enzyme-based approach.     

Manipulating the salt and thermal stability of DNA multilayer films via oligonucleotide length

DNA films are promising materials for diverse applications, including sensing, diagnostics, and drug/gene delivery. However, the ability to tune the stability of DNA films remains a crucial aspect for such applications. Herein, we examine the role of oligonucleotide length on the formation, and salt and thermal stability, of DNA multilayer films using oligonucleotides of homopolymeric diblocks (polyAG and polyTC), with each block (A, G, T, or C) ranging from 5 to 30 bases (10-, 20-, 30-, 40-, and 60-mer). Using a combination of quartz crystal microgravimetry, dual polarization interferometry, and flow cytometry, we demonstrate that at least 10 bases per hybridizing block in the DNA diblocks (that is, 20-mer) are required for successful hybridization and, hence, DNA multilayer film formation. Films assembled using longer oligonucleotide blocks were more stable in low salt conditions, with the DNA multilayer films assembled from the 60-mer oligonucleotides remaining intact in solutions of about 25 mM NaCl. A systematic increase in film melting temperature ( T m) was observed for the DNA multilayer films (assembled on colloids) with increasing oligonucleotide length, ranging from 38.5 degrees C for the 20-mer films to 53 degrees C for the 60-mer films. Further, an alternating trend in T m of the DNA multilayer films was observed with layer number (AG or TC); DNA multilayer films terminated with an AG layer exhibited a higher T m (44-49 degrees C) than films with an outermost TC layer (ca. 38 degrees C), suggesting a rearrangement of the film structure upon hybridization of the outermost layer. This work shows that the stability of DNA multilayer films can be tuned by varying the length of the oligonucleotide building blocks, thus providing a versatile means to tailor the salt and thermal stability of DNA films, which is necessary for the application of such films.     

Perpendicular axes of differentiation generated by mitochondrial introgression

Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north–south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north–south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial‐nuclear combinations. This likely generated an axis of coastal‐inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north–south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).     

Localized Bumps of Activity Sustained by Inhibition in a Two-Layer Thalamic Network

Based on head direction experiments in rats, the existence of localized bumps of thalamic activity has been proposed. We computationally demonstrate the existence of a novel class of localized bump solutions in a two-layer conductance-based thalamic network and analyze the mechanisms behind these stable patterns. In contrast to previous models of bump activity, here inhibition plays a crucial role in initially spreading neuronal firing and in subsequently sustaining it. In our model, we incorporate local strong, fast GABA(A) inhibition and diffuse weak, slow GABA(B) inhibition, based on previous biophysical experiments. These forms of inhibition contribute in different, yet complementary, ways to the observed pattern formation.     

Model of a Plasma Layer Formed by an Electron Beam

Plasma Physics Reports - Results are presented of the particle-in-cell numerical simulations by the KARAT code of the formation of a plasma–beam discharge in the absence of both the...     

Electronic Beam Switching of Circularly Polarized Plasma Magneto-Electric Dipole Array with Multiple Beams

In this paper, different array arrangements based on magneto-electric (ME) dipole antenna with wideband circular polarization (CP) characteristics are designed and investigated. Planar, triangular prism, square prism, and hexagonal prism array arrangements are considered. Each prism face has a sub-array comprises 2 × 2 ME-dipole elements. Each sub-array has wide impedance matching of 73.7%, a maximum gain of 16.6 dBi, and CP bandwidth of 78.2%. It employs the plasma frequency of the ME-dipole antenna to control its radiation characteristics. Frequency-independent lumped element equivalent circuit is constructed for a single antenna element. It is used to represent the antenna input impedance at different plasma electron densities with fixed physical structure. The proposed equivalent circuit comprises a single series section used for matching enhancement with feeder circuit, and three parallel tuned circuits corresponding to the three resonance frequencies in the input impedance. The best values of the equivalent circuit elements are computed using the particle swarm optimization (PSO) technique. Different array arrangements, planar, triangular, square, and hexagonal prism are designed to create single or multiple beams in different directions. An electronic beam switching is achieved by tuning in the plasma inside the ME-dipole in the desired direction. The radiation characteristics are analyzed and investigated using the finite integration technique (FIT).

     

Manipulating waterbody hydroperiod affects movement behaviour and occupancy dynamics in an amphibian

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Seedless Growth of Bismuth Nanowire Array via Vacuum Thermal Evaporation

Here a seedless and template-free technique is demonstrated to scalably grow bismuth nanowires, through thermal evaporation in high vacuum at RT. Conventionally reserved for the fabrication of metal thin films, thermal evaporation deposits bismuth into an array of vertical single crystalline nanowires over a flat thin film of vanadium held at RT, which is freshly deposited by magnetron sputtering or thermal evaporation. By controlling the temperature of the growth substrate the length and width of the nanowires can be tuned over a wide range. Responsible for this novel technique is a previously unknown nanowire growth mechanism that roots in the mild porosity of the vanadium thin film. Infiltrated into the vanadium pores, the bismuth domains (~ 1 nm) carry excessive surface energy that suppresses their melting point and continuously expels them out of the vanadium matrix to form nanowires. This discovery demonstrates the feasibility of scalable vapor phase synthesis of high purity nanomaterials without using any catalysts.     

Density Profile of a Plasma Layer Formed by an Electron Beam

Plasma Physics Reports - Results of particle-in-cell simulation of the formation of a near-wall plasma layer produced by an ionization source remote from the chamber walls are verified...     

Manipulating lek size and composition using decoys: an experimental investigation of lek evolution models

Four theoretical models have been proposed to account for the origin and maintenance of leks: hotspot, female preference, hotshot, and black hole models. Each has been validated in particular cases, and most are not mutually exclusive; therefore, it has been difficult to contrast and separate them, empirically and experimentally. By using decoys to mimic natural leks in the little bustard, artificial leks attracted wild birds. Then, by manipulating artificial lek size and structure (sex ratio, male phenotype), the study of responses of wild males and females allowed us to test specific predictions derived from the four classical models of lek evolution. The hotspot model was not supported because female decoys did not attract wild males. Conversely, hotshot males do exist in this species (attracting both wild females and males), as does a female preference for a particular lek size (four males). Finally, males aggressive toward decoys attracted fewer females, consistent with one of the mechanisms by which the black hole model may work. Therefore, three models of lek evolution were partly or fully supported by our experimental results: hotshot, female preference, and black hole models. We suggest that these models actually fit within each other, ensuring the evolution, functioning, and long-term maintenance of leks.     

Manipulating the QT interval of the ECG by cognitive effort

Abnormal prolongation of the QT interval of the ECG has been reported to indicate a hazard of sudden arrhythmic death. Therefore, with the aid of biofeedback from a newly devised instrument capable of measuring and recording the QT interval of the ECG in real time, ten healthy subjects, aided by biofeedback, attempted to shorten and also to lengthen QT. Although the changes achieved were relatively small, the ten subjects as a group were successful in both shortening and lengthening QT at the 0.01 level of significance. The degree of success varied, however, from person to person and from time to time in the same individual. If the findings reported here can be applied more generally to patients at risk for sudden death, and if biofeedback effects can be made to persist without reinforcement, it or other cognitive techniques may prove clinically useful for shortening QT.     

Practical Applications of Manipulating Plant Architecture by Regulating Gibberellin Metabolism

The international trade in floriculture is estimated to be worth about US$150 billion, with the global demand for ornamentals steadily increasing. Consumer choice is influenced by factors such as plant architecture and flower colour. Conventional breeding has been responsible for the introduction of novel traits into ornamental plants and has played an important role in the development of new cultivars. However, a restricted gene pool and failure of distant crosses have led to the exploitation of somatic cell techniques, particularly genetic transformation, to generate plants with desirable traits. Gibberellins (GAs) are endogenous plant hormones that control key aspects of growth and development. Chemical growth regulators that modify GA biosynthesis are used extensively in horticulture to control plant stature, increasing production costs, manpower, and environmental risks. An alternative strategy involves genetic manipulation of GA metabolism to induce phenotypic changes, particularly alteration of stature. Because ornamentals are not used for human consumption, genetic manipulation approaches with these plants may be more acceptable in the immediate future to the general public, in certain parts of the world, than genetically manipulated food crops.     

Modified habitats influence kelp epibiota via direct and indirect effects

Addition of man-made structures alters abiotic and biotic characteristics of natural habitats, which can influence abundances of biota directly and/or indirectly, by altering the ecology of competitors or predators. Marine epibiota in modified habitats were used to test hypotheses to distinguish between direct and indirect processes. In Sydney Harbour, kelps on pier-pilings supported greater covers of bryozoans, particularly of the non-indigenous species Membranipora membranacea, than found on natural reefs. Pilings influenced these patterns and processes directly due to the provision of shade and indirectly by altering abundances of sea-urchins which, in turn, affected covers of bryozoans. Indirect effects were more important than direct effects. This indicates that artificial structures affect organisms living on secondary substrata in complex ways, altering the biodiversity and indirectly affecting abundances of epibiota. Understanding how these components of habitats affect ecological processes is necessary to allow sensible prediction of the effects of modifying habitats on the ecology of organisms.     

Theoretical and Experimental Investigation of Enhanced Transmission Through Periodic Metal Nanoslits for Sensing in Water Environment

Experimental and theoretical study of sensors based on enhanced transmission through periodic metal nanoslits is presented. Our approach consists of the design of one-dimensional nanoslits array and its application in sensing for water quality control. Rigorous coupled waves analysis was used for the design and fit to the experimental data. Two types of surface plasmon resonance excitations are shown to be possible, one at the upper grating–analyte interface and one at the lower grating–substrate interface. This latter resonance is shown to be affected by the multiple interference or cavity-type effects. Those structures were fabricated by deposition of the metal layer and electron beam lithography of the nanostructure. We found that Ag-based periodic array exhibits the highest sensitivity to refractive index variations. Sensitivity enhancement was measured by ethanol concentrations in water. Stability of the Ag-based sensor was improved by covering the grating with less than 15 nm polymethyl methacrylate capping layer without deterioration of the sensitivity.     

Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.     

Manipulating monomer-dimer equilibrium of bovine Beta -lactoglobulin by amino acid substitution

Bovine beta-lactoglobulin, a major protein in cow's milk composed of nine beta-strands (betaA-betaI) and one alpha-helix, exists as a dimer at neutral pH while it dissociates to a native monomer below pH 3.0. It is assumed that the intermolecular beta-sheet formed between I-strands and salt bridges at AB-loops play important roles in dimer formation. Several site-directed mutants in which intermolecular interactions stabilizing the dimer would be removed were expressed in the methylotrophic yeast Pichia pastoris, and their monomer-dimer equilibria were studied by analytical ultracentrifugation. Various I-strand mutants showed decreases in K(a), suggesting that the intermolecular beta-sheet is essential for dimer formation. By substituting either Asp(33) or Arg(40) on the AB-loop to oppositely charged residues (i.e. R40D, R40E, and D33R), a large decrease in K(a) was observed probably because of the charge repulsion, which is consistent with the role of electrostatic attraction between Arg(40) on one monomer and Asp(33) on the other monomer in the wild-type dimer. However, when two of these mutants, R40D and D33R, were mixed, a heterodimer was formed by the electrostatic attraction between Arg(33) and Asp(40) of different molecules. These results suggested that protein-protein interactions of bovine beta-lactoglobulin can be manipulated by redesigning the residues on the interface without affecting global folding.