Synthesis method of asymmetric gold particles.

Asymmetric particles can exhibit unique properties. However, reported synthesis methods for asymmetric particles hinder their application because these methods have a limited scale and lack the ability to afford particles of varied shapes. Herein, we report a novel synthetic method which has the potential to produce large quantities of asymmetric particles. Asymmetric rose-shaped gold particles were fabricated as a proof of concept experiment. First, silica nanoparticles (NPs) were bound to a hydrophobic micro-sized polymer containing 2-chlorotritylchloride linkers (2-CTC resin). Then, half-planar gold particles with rose-shaped and polyhedral structures were prepared on the silica particles on the 2-CTC resin. Particle size was controlled by the concentration of the gold source. The asymmetric particles were easily cleaved from the resin without aggregation. We confirmed that gold was grown on the silica NPs. This facile method for synthesizing asymmetric particles has great potential for materials science

A method to convert non-numeric characters into numerical values in dynamic time warping for string matching

Dynamic time warping (DTW) is one of the well-known algorithms for measuring similarity between two temporal sequences, and it can be used for character matching. It uses a distance of two character strings. However, since the characters are non-numeric, it must be assigned to numerical values to calculate a distance between two character strings. Therefore, in this paper, we propose a method to convert non-numeric characters into numerical values in dynamic time warping for string matching. The proposed method uses normalized correlation coefficient, and it makes DTW gives more accurate results. Experimental results show that the proposed method gives excellent results

Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network.

A central question in animal evolution is how multicellular animals evolved from unicellular ancestors. We hypothesize that membrane proteins must be key players in the development of multicellularity because they are well positioned to form the cell-cell contacts and to provide the intercellular communication required for the creation of complex organisms. Here we find that a major mechanism for the necessary increase in membrane protein complexity in the transition from non-metazoan to metazoan life was the new incorporation of domains from soluble proteins. The membrane proteins that have incorporated soluble domains in metazoans are enriched in many of the functions unique to multicellular organisms such as cell-cell adhesion, signaling, immune defense and developmental processes. They also show enhanced protein-protein interaction (PPI) network complexity and centrality, suggesting an important role in the cellular diversification found in complex organisms. Our results expose an evolutionary mechanism that contributed to the development of higher life forms

Nanogap Device: Fabrication and Applications

A nanogap device as a platform for nanoscale electronic devices is presented. Integrated nanostructures on the platform have been used to functionalize the nanogap for biosensor and molecular electronics. Nanogap devices have great potential as a tool for investigating physical phenomena at the nanoscale in nanotechnology. In this dissertation, a laterally self-aligned nanogap device is presented and its feasibility is demonstrated with a nano ZnO dot light emitting diode (LED) and the growth of a metallic sharp tip forming a subnanometer gap suitable for single molecule attachment. For realizing a nanoscale device, a resolution of patterning is critical, and many studies have been performed to overcome this limitation. The creation of a sub nanoscale device is still a challenge. To surmount the challenge, novel processes including double layer etch mask and crystallographic axis alignment have been developed. The processes provide an effective way for making a suspended nanogap device consisting of two self-aligned sharp tips with conventional lithography and 3-D micromachining using anisotropic wet chemical Si etching. As conventional lithography is employed, the nanogap device is fabricated in a wafer scale and the processes assure the productivity and the repeatability. The anisotropic Si etching determines a final size of the nanogap, which is independent of the critical dimension of the lithography used. A nanoscale light emitting device is investigated. A nano ZnO dot is directly integrated on a silicon nanogap device by Zn thermal oxidation followed by Ni and Zn blanket evaporation instead of complex and time consuming processes for integrating nanostructure. The electrical properties of the fabricated LED device are analyzed for its current-voltage characteristic and metal-semiconductor-metal model. Furthermore, the electroluminescence spectrum of the emitted light is measured with a monochromator implemented with a CCD camera to understand the optical properties. The atomically sharp metallic tips are grown by metal ion migration induced by high electric field across a nanogap. To investigate the growth mechanism, in-situ TEM is conducted and the growing is monitored. The grown dendrite nanostructures show less than 1nm curvature of radius. These nanostructures may be compatible for studying the electrical properties of single molecule

Carbon Nanotubes: CVD Reactor Deign and Growth of Multi-Walled Carbon Nanotubes

Carbon Nanotubes are researched to develop for new technology of transporting electrons in one dimension and have commercial potential as nanoscale transistors. Carbon Nanotubes need to be made by using chemical vapor deposition (CVD). This CVD technique is used to deposit thin film on substrates. As the gas decomposes, it frees up carbon atoms, which can recombine in the form of nanotubes. The conditions for the controlled and directed CVD growth of Nanotubes are planed being established with the use of thin film metal catalyst by using RIT’s CVD Reactor. This CVD reactor was designed and made for growing the specific, high yield, possibly phase pure, and multi-wall carbon nanotubes in RIT

Development of high-spatial and high-mass resolution mass spectrometric imaging (MSI) and its application to the study of small metabolites and endogenous molecules of plants

High-spatial and high-mass resolution laser desorption ionization (LDI) mass spectrometric (MS) imaging technology was developed for the attainment of MS images of higher quality containing more information on the relevant cellular and molecular biology in unprecedented depth. The distribution of plant metabolites is asymmetric throughout the cells and tissues, and therefore the increase in the spatial resolution was pursued to reveal the localization of plant metabolites at the cellular level by MS imaging. For achieving high-spatial resolution, the laser beam size was reduced by utilizing an optical fiber with small core diameter (25 μm) in a vacuum matrix-assisted laser desorption ionization-linear ion trap (vMALDI-LTQ) mass spectrometer. Matrix application was greatly improved using oscillating capillary nebulizer. As a result, single cell level spatial resolution of ~ 12 μm was achieved. MS imaging at this high spatial resolution was directly applied to a whole Arabidopsis flower and the substructures of an anther and single pollen grains at the stigma and anther were successfully visualized. MS imaging of high spatial resolution was also demonstrated to the secondary roots of Arabidopsis thaliana and a high degree of localization of detected metabolites was successfully unveiled. This was the first MS imaging on the root for molecular species. MS imaging with high mass resolution was also achieved by utilizing the LTQ-Orbitrap mass spectrometer for the direct identification of the surface metabolites on the Arabidopsis stem and root and differentiation of isobaric ions having the same nominal mass with no need of tandem mass spectrometry (MS/MS). MS imaging at high-spatial and high-mass resolution was also applied to cer1 mutant of the model system Arabidopsis thaliana to demonstrate its usefulness in biological studies and reveal associated metabolite changes in terms of spatial distribution and/or abundances compared to those of wild-type. The spatial distribution of targeted metabolites, mainly waxes and flavonoids, was systematically explored on various organs, including flowers, leaves, stems, and roots at high spatial resolution of ~ 12-50 μm and the changes in the abundance level of these metabolites were monitored on the cer1 mutant with respect to the wild-type. This study revealed the metabolic biology of CER1 gene on each individual organ level with very detailed high spatial resolution. The separate MS images of isobaric metabolites, i.e. C29 alkane vs. C28 aldehyde could be constructed on both genotypes from MS imaging at high mass resolution. This allows tracking of abundance changes for those compounds along with the genetic mutation, which is not achievable with low mass resolution mass spectrometry. This study supported previous hypothesis of molecular function of CER1 gene as aldehyde decarbonylase, especially by displaying hyper accumulation of aldehydes and C30 fatty acid and decrease in abundance of alkanes and ketones in several plant organs of cer1 mutant. The scope of analytes was further directed toward internal cell metabolites from the surface metabolites of the plant. MS profiling and imaging of internal cell metabolites were performed on the vibratome section of Arabidopsis leaf. Vibratome sectioning of the leaf was first conducted to remove the surface cuticle layer and it was followed by enzymatic treatment of the section to induce the digestion of primary cell walls, middle lamella, and expose the internal cells underneath to the surface for detection with the laser by LDI-MS. The subsequent MS imaging onto the enzymatically treated vibratome section allowed us to map the distribution of the metabolites in the internal cell layers, linolenic acid (C18:3 FA) and linoleic acid (C18:2 FA). The development of an assay for relative quantification of analytes at the single subcellular/organelle level by LDI-MS imaging was attempted and both plausibility and significant obstacles were seen. As a test system, native plant organelle, chloroplasts isolated from the spinach leaves were used and the localization of isolated chloroplasts dispersed on the target plate in low density was monitored by detecting the ion signal of chlorophyll a (Chl a) degradation products such as pheophytin a and pheophobide a by LDI-MS imaging in combination with fluorescence microscopy. The number of chloroplasts and their localization visualized in the MS image exactly matched those in the fluorescence image especially at low density, which first shows the plausibility of single-organelle level quantification of analytes by LDI-MS. The accumulation level of Chl a within a single chloroplast detected by LDI-MS was compared to the fluorescence signal on a pixel-to-pixel basis to further confirm the correlations of the accumulation levels measured by two methods. The proportional correlation was observed only for the chloroplasts which do not show the significant leakage of chlorophyll indicated by MS ion signal of Chl a degradation products and fluorescence signal, which was presumably caused by the prior fluorescence measurement before MS imaging. Further investigation is necessary to make this method more complete and develop LDI-MS imaging as an effective analytical tool to evaluate a relative accumulation of analytes of interest at the single subcellular/organelle level