| 1. |
- Yang, Xi-Xi, et al.
(författare)
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Theoretical study of the mechanism of the manganese catalase KatB
- 2019
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 24:1, s. 103-115
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism of the H2O2 disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger models of increasing sizes were employed with the help of the high-resolution X-ray structure. In the reaction pathway suggested for KatB using the Large chemical model, the O-O homolysis of the first substrate H2O2 occurs through a -(1):(1) coordination mode and requires a barrier of 10.9kcal/mol. In the intermediate state of the bond cleavage, two hydroxides form as terminal ligands of the dimanganese cluster at the Mn-2(III,III) oxidation state. One of the two Mn(III)-OH- moieties and a second-sphere tyrosine stabilize the second substrate H2O2 in the second-sphere of the active site via hydrogen bonding interactions. The H2O2, unbound to the metals, is first oxidized into HO2 through a proton-coupled electron transfer (PCET) step with a barrier of 9.5kcal/mol. After the system switches to the triplet surface, the uncoordinated HO2 replaces the product water terminally bound to the Mn(II) and is then oxidized into O-2 spontaneously. Transition states with structural similarities to those obtained for TTC, where -(2)-OH-/O2- groups play important roles, were found to be higher in energy.
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
- Ablikim, M., et al.
(författare)
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Measurements of cross section of e(+)e(-) -> p(p)over-bar pi(0) at center-of-mass energies between 4.008 and 4.600 GeV
- 2017
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Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 771, s. 45-51
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Tidskriftsartikel (refereegranskat)abstract
- Based on e(+)e(-) annihilation data samples collected with the BESIII detector at the BEPCII collider at 13 center-of-mass energies from 4.008 to 4.600 GeV, measurements of the Born cross section of e(+)e(-) -> p (p) over bar pi(0) are performed. No significant resonant structure is observed in the measured energy dependence of the cross section. The upper limit on the Born cross section of e(+)e(-) -> Y (4260) -> p (p) over bar pi(0) at the 90% C. L. is determined to be 0.01 pb. The upper limit on the ratio of the branching fractions B(Y(4260) -> p (p) over bar pi(0))/B(Y(4260) -> pi(+)pi(-) j/Psi) at the 90% C. L. is determined to be 0.02%.
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| 5. |
- Chen, Xi, et al.
(författare)
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Nanosecond Photothermal Effects in Plasmonic Nanostructures
- 2012
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 6:3, s. 2550-2557
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Tidskriftsartikel (refereegranskat)abstract
- Photothermal effects in plasmonic nanostructures have great potentials in applications for photothermal cancer therapy, optical storage, thermo-photovoltaics, etc. However, the transient temperature behavior of a nanoscale material system during an ultrafast photothermal process has rarely been accurately investigated. Here a heat transfer model is constructed to investigate the temporal and spatial variation of temperature in plasmonic gold nanostructures. First, as a benchmark scenario, we study the light-induced heating of a gold nanosphere in water and calculate the relaxation time of the nanosphere excited by a modulated light. Second, we investigate heating and reshaping of gold nanoparticles in a more complex metamaterial absorber structure induced by a nanosecond pulsed light. The model shows that the temperature of the gold nanoparticles can be raised from room temperature to >795 K in just a few nanoseconds with a low light luminance, owing to enhanced light absorption through strong plasmonic resonance. Such quantitative predication of temperature change, which Is otherwise formidable to measure experimentally, can serve as an excellent guideline for designing devices for ultrafast photothermal applications.
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| 6. |
- Chen, Xi, et al.
(författare)
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Ordered Au nanocrystals on a substrate formed by light-induced rapid annealing
- 2014
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1756-1762
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Tidskriftsartikel (refereegranskat)abstract
- Light-induced rapid annealing (LIRA) is a widely used method to modify the morphology and crystallinity of noble metal nanoparticles, and the nanoparticles generally evolve into nanospheres. It is rather challenging to form faceted Au nanocrystals on a substrate using LIRA. Here the formation of spatially ordered Au nanocrystals using a continuous wave infrared laser is reported, assisted by a metamaterial perfect absorber. Faceted Au nanocrystals in truncated-octahedral or multi-twinned geometries can be obtained. The evolution of morphology and crystallinity of the Au nanoparticles during laser annealing is also revealed, where the crystal grain growth and the surface melting are shown to play key roles in nanocrystal formation. The evolution of morphology also gives the freedom of tuning the absorption spectrum of the metamaterial absorber. These findings provide a novel way for tailoring the morphology and crystallinity of metallic nanoparticles and may pave the way to fabricate refined nano-devices in many potential applications for optics, electronics, catalysis, surface-chemistry and biology.
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| 7. |
- Chen, Xi, et al.
(författare)
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Photothermal direct writing of metallic microstructure for frequency selective surface at terahertz frequencies
- 2012
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Ingår i: Proceedings of the 2012 International Workshop on Metamaterials, Meta 2012. - : IEEE. - 9781467328081 ; , s. 6464923-
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Konferensbidrag (refereegranskat)abstract
- Maskless photothermal direct writing technique was investigated to fabricate planar microscale metallic structures. In this technique, we use a tightly focused nanosecond pulsed infrared light to heat the metallic thin film on substrate. With sufficient volumic power density, the metal inside a "hot spot" could be removed from substrate. This technique benefits from not only the enhanced optical absorption, thanks to the surface plasmon resonance of metallic thin film, but also the reduced thermal conductivity, due to the frequent boundary scattering of phonons inside the thin film. To verify the performance of our direct writing technique, a cross-slot periodic array is scribed in gold thin film on silica substrate. Such a pattern can serve as a frequency selective surface at terahertz, which has many applications in terahertz radio system, e. g. rejecting thermal noise before terahertz receiver or serving as reflectors in Fabry-Perot etalon for astronomy spectroscopy.
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| 8. |
- Chen, Xi, 1983-
(författare)
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Photothermal Effect in Plasmonic Nanostructures and its Applications
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plasmonic resonances are characterized by enhanced optical near field and subwavelength power confinement. Light is not only scattered but also simultaneously absorbed in the metal nanostructures. With proper structural design, plasmonic-enhanced light absorption can generate nanoscopically confined heat power in metallic nanostructures, which can even be temporally modulated by varying the pump light. These intrinsic characters of plasmonic nanostructures are investigated in depth in this thesis for a range of materials and nanophotonic applications. The theoretical basis for the photothermal phenomenon, including light absorption, heat generation, and heat conduction, is coherently summarized and implemented numerically based on finite-element method. Our analysis favours disk-pair and particle/dielectric-spacer/metal-film nanostructures for their high optical absorbance, originated from their antiparallel dipole resonances. Experiments were done towards two specific application directions. First, the manipulation of the morphology and crystallinity of Au nanoparticles (NPs) in plasmonic absorbers by photothermal effect is demonstrated. In particular, with a nanosecond-pulsed light, brick-shaped Au NPs are reshaped to spherical NPs with a smooth surface; while with a 10-second continuous wave laser, similar brick-shaped NPs can be annealed to faceted nanocrystals. A comparison of the two cases reveals that pumping intensity and exposure time both play key roles in determining the morphology and crystallinity of the annealed NPs. Second, the attempt is made to utilize the high absorbance and localized heat generation of the metal-insulator-metal (MIM) absorber in Si thermo-optic switches for achieving all-optical switching/routing with a small switching power and a fast transient response. For this purpose, a numerical study of a Mach-Zehnder interferometer integrated with MIM nanostrips is performed. Experimentally, a Si disk resonator and a ring-resonator-based add-drop filter, both integrated with MIM film absorbers, are fabricated and characterized. They show that good thermal conductance between the absorber and the Si light-guiding region is vital for a better switching performance. Theoretical and experimental methodologies presented in the thesis show the physics principle and functionality of the photothermal effect in Au nanostructures, as well as its application in improving the morphology and crystallinity of Au NPs and miniaturized all-optical Si photonic switching devices.
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| 9. |
- Chen, Xi, et al.
(författare)
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Photothermal phenomena in plasmonics and metamaterials
- 2011
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Ingår i: ADVANCES IN OPTICAL THIN FILMS IV. - : SPIE. - 9780819487940 ; , s. 81681K-
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Konferensbidrag (refereegranskat)abstract
- Our recent theoretical and experimental investigation of the photothermal effect in a planar metamaterial absorber is reviewed in the present paper. The observed ultrasensitive photothermal heating in such an absorber nanostructure irradiated by a pulsed white-light source is elaborated with a simple yet compelling heat transfer model, which is subsequently solved with a finite-element method. The simulation results not only agree with the experimental finding, but also provide more detailed understanding of the temperature transition in the complex system.
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| 10. |
- Chen, Xi, et al.
(författare)
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Photothermal Switching of SOI Waveguide-Based Mach-Zehnder Interferometer with Integrated Plasmonic Nanoheater
- 2014
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Ingår i: Plasmonics. - : Springer. - 1557-1955 .- 1557-1963. ; 9:5, s. 1197-1205
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Tidskriftsartikel (refereegranskat)abstract
- We theoretically and numerically investigated the photothermal switching of a Mach-Zehnder interferometer (MZI) based on two Si waveguides integrated with plasmonic nanoheaters. The nanoheater is a composite nanowire with Au/Al2O3/Au three-layer structure, which is designed to have a highly efficient optical absorption peak at wavelength of 1,064 nm. Based on this finding, we further analyze a MZI built with two 40-μm-long symmetric waveguide branches, each integrated with a 20-μm-long nanoheater. The optical switching power of the MZI device is 190 mW (280 mW) for the capped (buried) channel waveguide, when pumped by a circular Gaussian beam with a waist of 10 μm. Alternatively, the switching power can be reduced to 38 mW (56 mW) by using an astigmatic Gaussian beam, with a semi-major axis of 10 μm and an aspect ratio of 5. The switching response time of the MZI is 0.7 μs (1.0 μs) for capped (buried) channel waveguide design. Our design opens a new route for optically driven non-contact optical on-off switching with sub-microsecond time response.
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