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Design of all-optical, hot-electron current-direction-switching device based on geometrical asymmetry.

ABSTRACT: We propose a nano-scale current-direction-switching device(CDSD) that operates based on the novel phenomenon of geometrical asymmetry between two hot-electron generating plasmonic nanostructures. The proposed device is easy to fabricate and economical to develop compared to most other existing designs. It also has the ability to function without external wiring in nano or molecular circuitry since it is powered and controlled optically. We consider a such CDSD made of two dissimilar nanorods separated by a thin but finite potential barrier and theoretically derive the frequency-dependent electron/current flow rate. Our analysis takes in to account the quantum dynamics of electrons inside the nanorods under a periodic optical perturbation that are confined by nanorod boundaries, modelled as finite cylindrical potential wells. The influence of design parameters, such as geometric difference between the two nanorods, their volumes and the barrier width on quality parameters such as frequency-sensitivity of the current flow direction, magnitude of the current flow, positive to negative current ratio, and the energy conversion efficiency is discussed by considering a device made of Ag/TiO2/Ag. Theoretical insight and design guidelines presented here are useful for customizing our proposed CDSD for applications such as self-powered logic gates, power supplies, and sensors.

SUBMITTER: Kumarasinghe CS

PROVIDER: S-EPMC4757840 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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Project description:BackgroundIdentifying differentially expressed genes (DEG) is a fundamental step in studies that perform genome wide expression profiling. Typically, DEG are identified by univariate approaches such as Significance Analysis of Microarrays (SAM) or Linear Models for Microarray Data (LIMMA) for processing cDNA microarrays, and differential gene expression analysis based on the negative binomial distribution (DESeq) or Empirical analysis of Digital Gene Expression data in R (edgeR) for RNA-seq profiling.ResultsHere we present a new geometrical multivariate approach to identify DEG called the Characteristic Direction. We demonstrate that the Characteristic Direction method is significantly more sensitive than existing methods for identifying DEG in the context of transcription factor (TF) and drug perturbation responses over a large number of microarray experiments. We also benchmarked the Characteristic Direction method using synthetic data, as well as RNA-Seq data. A large collection of microarray expression data from TF perturbations (73 experiments) and drug perturbations (130 experiments) extracted from the Gene Expression Omnibus (GEO), as well as an RNA-Seq study that profiled genome-wide gene expression and STAT3 DNA binding in two subtypes of diffuse large B-cell Lymphoma, were used for benchmarking the method using real data. ChIP-Seq data identifying DNA binding sites of the perturbed TFs, as well as known drug targets of the perturbing drugs, were used as prior knowledge silver-standard for validation. In all cases the Characteristic Direction DEG calling method outperformed other methods. We find that when drugs are applied to cells in various contexts, the proteins that interact with the drug-targets are differentially expressed and more of the corresponding genes are discovered by the Characteristic Direction method. In addition, we show that the Characteristic Direction conceptualization can be used to perform improved gene set enrichment analyses when compared with the gene-set enrichment analysis (GSEA) and the hypergeometric test.ConclusionsThe application of the Characteristic Direction method may shed new light on relevant biological mechanisms that would have remained undiscovered by the current state-of-the-art DEG methods. The method is freely accessible via various open source code implementations using four popular programming languages: R, Python, MATLAB and Mathematica, all available at: http://www.maayanlab.net/CD.

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Design of all-optical, hot-electron current-direction-switching device based on geometrical asymmetry.

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