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  • 1
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    Synthesis of Ag9(SiO4)2NO3 through a reactive flux method and its visible-light photocatalytic performances (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-08-13
    Description: Ag 9 (SiO 4 ) 2 NO 3 was prepared by a reactive flux method. The structures, morphologies, and light absorption properties were investigated. Owing to the polar crystal structure, an internal electric field can be formed inside the material, which can facilitate the photogenerated charge separation during the photocatalytic process. Based on both the wide light absorption spectra and high charge separation efficiency originated from the polarized internal electric field, Ag 9 (SiO 4 ) 2 NO 3 exhibit higher efficiency over Ag 3 PO 4 during the degradation of organic dyes under visible light irradiation, which is expected to be a potential material for solar energy harvest and conversion.
    Electronic ISSN: 2166-532X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by American Institute of Physics (AIP)
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  • 2
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    Dependence of dislocation creation on tensile orientation in face-centered-cubic ductile metals under high strain rate loading (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-09-23
    Description: We investigate through molecular dynamic simulations the dependence of dislocation creation on tensile orientation in face-centered-cubic ductile metals under high strain rate loading. It is found that while dislocations generally originate from the double-layer defect clusters consisting of flatted octahedral structures (FOSs), the formation mechanism and the types of FOSs, as well as the types of nucleated dislocations, depend on the applied loading directions. For the loading along the [ 1 ¯ 10 ] ,   [ 1 ¯ 1 ¯ 2 ] , and [111] crystal directions, it is shown that a pair of the nearest-neighboring atoms move away to form the elongated FOS. However, for the loading along the [100] crystal direction, a pair of the next-nearest-neighboring atoms move close to form the compressed FOS. According to the uniform deformation amount of the spacing vector for a pair of neighboring atoms and the stress component along the Burgers vector on the stacking fault plane, we analytically predict the activated types of FOSs and dislocations for different loading directions, which turn to be remarkably consistent with our numerical simulations.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Generalized flexibility-rigidity index (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-06-21
    Description: Flexibility-rigidity index (FRI) has been developed as a robust, accurate, and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility index. In this work, we introduce alternative rigidity and flexibility formulations. The structure of the classic Gaussian surface is utilized to construct a new type of rigidity index, which leads to a new class of rigidity densities with the classic Gaussian surface as a special case. Additionally, we introduce a new type of flexibility index based on the domain indicator property of normalized rigidity density. These generalized FRI (gFRI) methods have been extensively validated by the B-factor predictions of 364 proteins. Significantly outperforming the classic Gaussian network model, gFRI is a new generation of methodologies for accurate, robust, and efficient analysis of protein flexibility and fluctuation. Finally, gFRI based molecular surface generation and flexibility visualization are demonstrated.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Strategies to improve phase-stability of ultrafast swept source optical coherence tomography for single shot imaging of transient mechanical waves at 16 kHz frame rate (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-05-11
    Description: We present single-shot phase-sensitive imaging of propagating mechanical waves within tissue, enabled by an ultrafast optical coherence tomography (OCT) system powered by a 1.628 MHz Fourier domain mode-locked (FDML) swept laser source. We propose a practical strategy for phase-sensitive measurement by comparing the phases between adjacent OCT B-scans, where the B-scan contains a number of A-scans equaling an integer number of FDML buffers. With this approach, we show that micro-strain fields can be mapped with ∼3.0 nm sensitivity at ∼16 000 fps. The system's capabilities are demonstrated on porcine cornea by imaging mechanical wave propagation launched by a pulsed UV laser beam, promising non-contact, real-time, and high-resolution optical coherence elastography.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Photodissociation dynamics of OCS near 214 nm using ion imaging (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-07-14
    Description: The OCS photodissociation dynamics of the dominant S( 1 D 2 ) channel near 214 nm have been studied using velocity map ion imaging. We report a CO vibrational branching ratio of 0.79:0.21 for v = 0:v = 1, indicating substantially higher vibrational excitation than that observed at slightly longer wavelengths. The CO rotational distribution is bimodal for both v = 0 and v = 1, although the bimodality is less pronounced than at longer wavelengths. Vector correlations, including rotational alignment, indicate that absorption to both the 2 1 A′ (A) and 1 1 A″ (B) states is important in the lower- j part of the rotational distribution, while only 2 1 A′ state absorption contributes to the upper part; this conclusion is consistent with work at longer wavelengths. Classical trajectory calculations including surface hopping reproduce the measured CO rotational distributions and their dependence on wavelength well, though they underestimate the v = 1 population. The calculations indicate that the higher- j peak in the rotational distribution arises from molecules that begin on the 2 1 A′ state but make nonadiabatic transitions to the 1 1 A′ (X) state during the dissociation, while the lower- j peak arises from direct photodissociation on either the 2 1 A′ or the 1 1 A″ states, as found in previous work.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-08-19
    Description: Herein we have used combined static electronic structure calculations and “on-the-fly” global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the 1 ππ ∗ , 1 nπ ∗ , and S 0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated 1 ππ ∗ system. The first is the diabatic ESIPT process along the 1 ππ ∗ potential energy profile. The generated 1 ππ ∗ keto species then decays to the S 0 state via the keto 1 ππ ∗ /gs conical intersection. The second is internal conversion to the dark 1 nπ ∗ state near the 1 ππ ∗ / 1 nπ ∗ crossing point in the course of the diabatic 1 ππ ∗ ESIPT process. Our following dynamics simulations have shown that the ESIPT and 1 ππ ∗ → S 0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the 1 ππ ∗ → S 0 internal conversion in the keto region, the 1 ππ ∗ → 1 nπ ∗ internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Using in-process measurements of open-gate structures to evaluate threshold voltage of normally-off GaN-based high electron mobility transistors (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-10-20
    Description: The parameters of open-gate structures treated with different etching time were monitored during the gate recess process, and their impacts on the threshold voltage ( V th ) of final fabricated AlGaN/GaN high electron mobility transistors (HEMTs) based on open-gate structures were discussed in this paper. It is found that V th can exceed 0 V when channel resistance in the recessed region ( R on-open ) increases over ∼275 Ω mm, maximum current ( I Dmax ) decreases below ∼29 mA/mm, or recessed barrier thickness ( t RB ) is below ∼7.5 nm. In addition, t RB obtained by atomic force microscopy measurements and C-V measurements are also compared. Finally, theoretical common criteria based on the experimental results of this work for t RB and R on-open were established to evaluate the V th of a regular normally-off AlGaN/GaN HEMTs. The results indicate that these parameters of open-gate structure can be utilized to achieve normally-off HEMTs with controllable V th .
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 8
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    Communication: Capturing protein multiscale thermal fluctuations (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-06-03
    Description: Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different length scales to capture protein interactions at corresponding scales. It is about 20% more accurate than the Gaussian network model (GNM) in the B-factor prediction of a set of 364 proteins. Additionally, the present method is able to deliver accurate predictions for some large macromolecules on which GNM fails to produce accurate predictions. Finally, for a protein of N residues, mFRI is of linear scaling ( O ( N ) ) in computational complexity, in contrast to the order of O ( N 3 ) for GNM.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 9
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    Communication: Capturing protein multiscale thermal fluctuations (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-06-03
    Description: Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different length scales to capture protein interactions at corresponding scales. It is about 20% more accurate than the Gaussian network model (GNM) in the B-factor prediction of a set of 364 proteins. Additionally, the present method is able to deliver accurate predictions for some large macromolecules on which GNM fails to produce accurate predictions. Finally, for a protein of N residues, mFRI is of linear scaling ( O ( N ) ) in computational complexity, in contrast to the order of O ( N 3 ) for GNM.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Multiresolution persistent homology for excessively large biomolecular datasets (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-10-02
    Description: Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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