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Christos Boutopoulos, Adrien Dagallier, Maria Sansone, Andre-Pierre Blanchard-Dionne, Évelyne Lecavalier-Hurtubise, Étienne Boulais, Michel Meunier
Precise spatial and temporal control of pressure stimulation at the nanometer scale is essential for the fabrication and manipulation of nano-objects, and for exploring single-molecule behaviour of matter under extreme conditions. However, state-of-the-art nano-mechanical transducers require sophisticated driving hardware and are currently limited to moderate pressure regimes. Here we report a gold plasmonic bowtie (AuBT) nano-antennas array that can generate extreme pressure stimulus of ∼100 GPa in the ps (10(-12) s) time scale with sub-wavelength resolution upon irradiation with ultra-short laser pulses...
October 6, 2016: Nanoscale
Dete van Eeden, Freek du Plessis
INTRODUCTION: A mathematical 3D model of an existing computed tomography (CT) scanner was created and used in the EGSnrc-based BEAMnrc and egs_cbct Monte Carlo codes. Simulated transmission dose profiles of a RMI-465 phantom were analysed to verify Hounsfield numbers against measured data obtained from the CT scanner. METHODS AND MATERIALS: The modelled CT unit is based on the design of a Toshiba Aquilion 16 LB CT scanner. As a first step, BEAMnrc simulated the X-ray tube, filters, and secondary collimation to obtain phase space data of the X-ray beam...
September 24, 2016: Physica Medica: PM
Yu Lu, Guangqing Du, Feng Chen, Qing Yang, Hao Bian, Jiale Yong, Xun Hou
In this paper, the tunable optical trapping dependence on wavelength of incident beam is theoretically investigated based on numerical simulations. The Monte Carlo method is taken into account for exploring the trapping characteristics such as average deviation and number distribution histogram of nanoparticles. It is revealed that both the width and the depth of potential well for trapping particles can be flexibly adjusted by tuning the wavelength of the incident beam. In addition, incident wavelengths for the deepest potential well and for the strongest stiffness at bottom are separated...
September 26, 2016: Scientific Reports
Irene Rodriguez-Lujan, Jeff Hasty, Ramón Huerta
MOTIVATION: Despite RNA-seq reads provide quality scores that represent the probability of calling a correct base, these values are not probabilistically integrated in most alignment algorithms. Based on the quality scores of the reads, we propose to calculate a lower bound of the probability of alignment of any fast alignment algorithm that generates SAM files. This bound is called Fast Bayesian Bound (FBB) and serves as a canonical reference to compare alignment results across different algorithms...
September 23, 2016: Bioinformatics
Yuan-Fong Chou Chau, Chung-Ting Chou Chao, Jhin-Yu Rao, Hai-Pang Chiang, Chee Ming Lim, Ren Chong Lim, Nyuk Yoong Voo
We propose a design method to tune the near-field intensities and absorption spectra of a periodic array of plasmonic bowtie nanoantennas (PBNAs) by introducing the hollow cavities inside the metal nanostructures. The numerical method is performed by finite element method that demonstrates the engineered hollow PBNAs can tune the optical spectrum in the range of 400-3000 nm. Simulation results show the hollow number is a key factor for enhancing the cavity plasmon resonance with respect to the hotspot region in PBNAs...
December 2016: Nanoscale Research Letters
Bashir Fotouhi, Vahid Ahmadi, Vahid Faramarzi
We propose novel nano-plasmonic-based structures for rapid sequencing of DNA molecules. The optical properties of DNA nucleotides have notable differences in the ultraviolet (UV) region of light. Using nanopore, bowtie, and bowtie-nanopore compound structures, probable application of the surface plasmon resonance (SPR) in DNA sequencing is investigated by employing the discrete dipole approximation method. The effects of different materials like chromium (Cr), aluminum (Al), rhodium (Rh), and graphene (Gr) are studied...
September 15, 2016: Optics Letters
Jui-Hung Hung, Zhiping Weng
This protocol describes mapping short sequence reads to a reference genome using several programs. The example in this protocol starts with a ChIP-seq data set in FASTQ format, aligns the reads to the human genome using Bowtie, and uses some useful utilities of SAMtools and BEDTools. SAMtools and BEDTools are two collections of executables for manipulating the results of short-read aligners. By combining these tools, one can summarize and visualize alignments produced by Bowtie and perform basic analysis, such as determining the number of reads that are mapped to a certain gene...
August 29, 2016: Cold Spring Harbor Protocols
Meijun Huo, Haijun Han, Zilong Sun, Zhaojing Lu, Xinglei Yao, Shaolin Wang, Jundong Wang
We sequenced RNA transcripts from the testicles of healthy male mice, divided into a control group with distilled water and two experimental groups with 50 and 100 mg/l NaF in drinking water for 56 days. Bowtie/Tophat were used to align 50-bp paired-end reads into transcripts, Cufflinks to measure the relative abundance of each transcript and IPA to analyze RNA-Sequencing data. In the 100 mg/l NaF-treated group, four pathways related to IL-17, TGF-β and other cellular growth factor pathways were overexpressed...
2016: Scientific Reports
Chia-Hua Lee, Shih-Chieh Liao, Tzy-Rong Lin, Shing-Hoa Wang, Dong-Yan Lai, Po-Kai Chiu, Jyh-Wei Lee, Wen-Fa Wu
Photoresist and electron beam lithography techniques were used to fabricate embedded Ag bowtie and diabolo nanostructures with various apex angles on the surface of a TiO<sub>2</sub> film. The reinforced localized surface plasmon resonance (LSPR) and electric field generated at both the Ag/TiO<sub>2</sub> and air/TiO<sub>2</sub> interfaces enabled high light absorbance in the TiO<sub>2</sub> nanostructure. Results for both the bowtie and diabolo nanostructures showed that a reduction in the apex angle enhances both LSPR and Raman intensity...
August 8, 2016: Optics Express
V Bogdan Neculaes, Antonio Caiafa, Yang Cao, Bruno De Man, Peter M Edic, Kristopher Frutschy, Satish Gunturi, Lou Inzinna, Joseph Reynolds, Mark Vermilyea, David Wagner, Xi Zhang, Yun Zou, Norbert J Pelc, Brian Lounsberry
PURPOSE: This paper summarizes the development of a high-power distributed x-ray source, or "multisource," designed for inverse-geometry computed tomography (CT) applications [see B. De Man et al., "Multisource inverse-geometry CT. Part I. System concept and development," Med. Phys. 43, 4607-4616 (2016)]. The paper presents the evolution of the source architecture, component design (anode, emitter, beam optics, control electronics, high voltage insulator), and experimental validation...
August 2016: Medical Physics
Daniel Gomez-Cardona, Juan Pablo Cruz-Bastida, Ke Li, Adam Budde, Jiang Hsieh, Guang-Hong Chen
PURPOSE: Noise characteristics of clinical multidetector CT (MDCT) systems can be quantified by the noise power spectrum (NPS). Although the NPS of CT has been extensively studied in the past few decades, the joint impact of the bowtie filter and object position on the NPS has not been systematically investigated. This work studies the interplay of these two factors on the two dimensional (2D) local NPS of a clinical CT system that uses the filtered backprojection algorithm for image reconstruction...
August 2016: Medical Physics
Jennifer Xu, Alejandro Sisniega, Wojciech Zbijewski, Hao Dang, J Webster Stayman, Xiaohui Wang, David H Foos, Nafi Aygun, Vassillis E Koliatsos, Jeffrey H Siewerdsen
The effects of detector readout gain mode and bowtie filters on cone-beam CT (CBCT) image quality and dose were characterized for a new CBCT system developed for point-of-care imaging of the head, with potential application to diagnosis of traumatic brain injury, intracranial hemorrhage (ICH), and stroke. A detector performance model was extended to include the effects of detector readout gain on electronic digitization noise. The noise performance for high-gain (HG), low-gain (LG), and dual-gain (DG) detector readout was evaluated, and the benefit associated with HG mode in regions free from detector saturation was quantified...
August 21, 2016: Physics in Medicine and Biology
Michelle Drewry, Inas Helwa, R Rand Allingham, Michael A Hauser, Yutao Liu
PURPOSE: Because microRNAs (miRNAs) have been associated with eye diseases, our study aims to profile ocular miRNA expression in normal human ciliary body (CB), cornea, and trabecular meshwork (TM) using miRNA-Seq to provide a foundation for better understanding of miRNA function and disease involvement in these tissues. METHODS: Total RNAs were extracted from seven normal human CB, seven cornea, and seven TM samples using mirVana total RNA isolation kit. miRNA-Seq was done with Illumina MiSeq...
July 1, 2016: Investigative Ophthalmology & Visual Science
M Vala, J Homola
A novel method enabling rapid fabrication of 2D periodic arrays of plasmonic nanoparticles across large areas is presented. This method is based on the interference of multiple coherent beams originating from diffraction of large-diameter collimated beam on a transmission phase mask. Mutual orientation of the interfering beams is determined by parameters of the used phase mask. Herein, parameters of the phase mask (periods and modulation depth) are selected to yield an interference pattern with high contrast and narrow well-separated maxima...
July 11, 2016: Optics Express
Jie Zhang, Flavius D Raslau, Nathan Hill, Edward J Escott
No abstract text is available yet for this article.
July 2016: Radiologic Technology
Mats Persson, Robert Bujila, Patrik Nowik, Henrik Andersson, Love Kull, Jonas Andersson, Hans Bornefalk, Mats Danielsson
PURPOSE: The highest photon fluence rate that a computed tomography (CT) detector must be able to measure is an important parameter. The authors calculate the maximum transmitted fluence rate in a commercial CT scanner as a function of patient size for standard head, chest, and abdomen protocols. METHODS: The authors scanned an anthropomorphic phantom (Kyoto Kagaku PBU-60) with the reference CT protocols provided by AAPM on a GE LightSpeed VCT scanner and noted the tube current applied with the tube current modulation (TCM) system...
July 2016: Medical Physics
Kotni Santhosh, Ora Bitton, Lev Chuntonov, Gilad Haran
The strong interaction of individual quantum emitters with resonant cavities is of fundamental interest for understanding light-matter interactions. Plasmonic cavities hold the promise of attaining the strong coupling regime even under ambient conditions and within subdiffraction volumes. Recent experiments revealed strong coupling between individual plasmonic structures and multiple organic molecules; however, strong coupling at the limit of a single quantum emitter has not been reported so far. Here we demonstrate vacuum Rabi splitting, a manifestation of strong coupling, using silver bowtie plasmonic cavities loaded with semiconductor quantum dots (QDs)...
2016: Nature Communications
Li Ding, Jin Qin, Songpo Guo, Tao Liu, Edward Kinzel, Liang Wang
Nanoscale bowtie aperture antennas can be used to focus light well below the diffraction limit with extremely high transmission efficiencies. This paper studies the spectral dependence of the transmission through nanoscale bowtie apertures defined in a silver film. A realistic bowtie aperture is numerically modeled using the Finite Difference Time Domain (FDTD) method. Results show that the transmission spectrum is dominated by Fabry-Pérot (F-P) waveguide modes and plasmonic modes. The F-P resonance is sensitive to the thickness of the film and the plasmonic resonant mode is closely related to the gap distance of the bowtie aperture...
2016: Scientific Reports
Vasilii I Artyukhov, Zhili Hu, Zhuhua Zhang, Boris I Yakobson
A large number of experimental studies over the past few years observed the formation of unusual highly symmetric polycrystalline twinned nanoislands of transition metal dichalcogenides, resembling bowties or stars. Here, we analyze their morphology in terms of equilibrium and growth shapes. We propose a mechanism for these complex shapes' formation via collision of concurrently growing islands and validate the theory with phase-field simulations that demonstrate how highly symmetric structures can actually emerge from arbitrary starting conditions...
June 8, 2016: Nano Letters
Tomokazu Shohji, Yo Kato, Nobutaka Yanano, Kazuki Kuriyama, Rika Goto, Megumi Iijima
OBJECTIVE: The purpose of this study was to analyze in detail the quality of abdominal CT images obtained using three protocols reported by Image Gently in 2014 (hereafter referred to as Image Gently 2014), with the use of a handmade body phantom adapted to typical body sizes of the Japanese population. Moreover, we converted the findings of Image Gently 2014 to match Japanese body sizes and referred to our converted findings as Image Gently Japan. MATERIALS AND METHODS: We scanned each phantom in a mechanical isocenter in accordance with the Image Gently 2014 abdominal imaging protocol...
July 2016: AJR. American Journal of Roentgenology
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