Nanoscale characterization of graphene and polymer blends using tip-enhanced Raman spectroscopy and 3D surface-enhanced Raman spectroscopy

関西学院大

New consensus-based algorithms for quality assessment in protein structure prediction

Title from PDF of title page (University of Missouri--Columbia, viewed on April 6, 2011).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Thesis advisor: Dr. Yi Shang.M.S. University of Missouri--Columbia 2010.Two of the essential tasks in protein tertiary structure prediction are predicting quality and selecting the best quality model from given model structures. Finding solutions to these problems are fundamental to understanding the nature of proteins and advancing in protein research area. In this thesis, we present efficient algorithms that tackle both problems effectively. The algorithms are developed on the well-known consensus-based idea that has been continuously successful since CASP6. For assessing the quality of structures, we develop several new methods based on the idea of removing redundant structures and outliers. The algorithms aims at finding suitable reference sets in computing the consensus-score in order to improve the existing algorithms. The methods can use any suitable pair-wise similarity measurement between a pair of models such as GDT-TS and Q score. We also develop a very efficient method for computing Q score for large size problem. In our experimental results, the algorithms are applied to CASP8 dataset and have achieved the superior performance over existing state-of-the-art methods including the top1 method in the QA category of CASP8. For the selecting the best model structure, our new methods are effective and perform better than other best-performing scoring functions by up to 7.6% based on the actual GDT-TS of top1 selected model to the native structure. The selection result is obtained by our method using Q score are slightly worse than those obtained using GDT-TS, but using pair-wise Q score method is in general about 15 times faster than using pair-wise GDT-TS method.Includes bibliographical reference

Two-step fabrication of nanoporous copper films with tunable morphology for SERS application

peer-reviewedIt is important to design and fabricate nanoporous metals (NPMs) with optimized microstructures for specific applications. In this contribution, nanoporous coppers (NPCs) with controllable thicknesses and pore sizes were fabricated via the combination of a co-sputtering of Cu/Ti with a subsequent dealloying process. The effect of dealloying time on porous morphology and the corresponding surface enhanced Raman scattering (SERS) behaviors were systematically investigated. Transmission electron microscopy (TEM) identified the presences of the gaps formed between ligaments and also the nanobumps on the nanoparticle-aggregated ligament surface, which were likely to contribute as the “hot spots” for electromagnetic enhancement. The optimal NPC film exhibited excellent SERS performance towards Rhodamine 6G (R6G) with a low limiting detection (10−9 M), along with good uniformity and reproducibility. The calculated enhancement factor of ca. 4.71 × 107 was over Au substrates and comparable to Ag systems, promising the proposed NPC as a cheap candidate for high-performance SERS substrate

Launching and Control of Graphene Plasmons by Nanoridge Structures

The unique properties of graphene plasmons show great potential for plasmonic nanodevice applications such as sensors and modulators. Graphene plasmon launching, propagation control, and ultimately launching with directional control are therefore crucial for the development of such devices. However, previous studies have used foreign objects or external influencing factors to attain directional plasmon launching on graphene, which introduce defects and add complexity to the system. This study introduces a theoretical framework for a graphene-only approach to direction-controlled plasmon launching. We use graphene nanoridges, a defect-free natural structure of graphene, as a plasmon launcher. Through proper arrangement of the nanoridges, unidirectional, bidirectional, and wavelength-sorted plasmon launching with normal illumination can be achieved

Launching and Control of Graphene Plasmons by Nanoridge Structures

The unique properties of graphene plasmons show great potential for plasmonic nanodevice applications such as sensors and modulators. Graphene plasmon launching, propagation control, and ultimately launching with directional control are therefore crucial for the development of such devices. However, previous studies have used foreign objects or external influencing factors to attain directional plasmon launching on graphene, which introduce defects and add complexity to the system. This study introduces a theoretical framework for a graphene-only approach to direction-controlled plasmon launching. We use graphene nanoridges, a defect-free natural structure of graphene, as a plasmon launcher. Through proper arrangement of the nanoridges, unidirectional, bidirectional, and wavelength-sorted plasmon launching with normal illumination can be achieved