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Optimizing weighting functions for cryo-electron microscopy

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Biophysics Reports 2021年第2期7卷 152-158页

作者： Jing Cheng xinzheng zhang National Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Center for Biological Imaging CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences University of Chinese Academy of Sciences

The frequency-dependent signal to noise ratio of cryo-electron microscopy data varies dramatically with the frequency and with the type of the data. During different steps of data processing, data with distinct SNR are used for calculations. Thus, specific weighting function based on the particular SNR should be designed to optimize the corresponding calculation. Here, we deduced these weighting functions by maximizing the signal to noise ratio of cross correlated coefficients. Some of our weighting functions for refinement resemble that used in the existing software packages. However, weighting functions we deduced for motion correction, particle picking and the refinement with overlapping densities differ from those employed by existing programs. Our new weighting functions may improve the calculation in these steps.

关键词： Cryo-electron microscopy (Cryo-EM) Cross correlation coefficient (CCC) Weighting function

Surface Exciton-Plasmon Polariton Enhanced Light Emission via Integration of Single Semiconductor Nanowires with Metal Nanostructures

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Nano Research 2009年第1期2卷 47-53页

作者： Xuejin zhang Pengwei Wang xinzheng zhang Jun Xu Yongyuan Zhu Dapeng Yu State Key Laboratory for Mesoscopic Physics and Electron Microscopy LaboratoryDepartment of PhysicsPeking UniversityBeijing 100871China National Laboratory of Solid State Microstructures Nanjing UniversityNanjing 210093China

The light emission enhancement behavior from single ZnO nanowires integrated with metallic contacts is investigated by micro-photoluminescence *** from surface plasmon polaritons at the air/metal interface,the emission of a single ZnO nanowire can be coupled into guided modes of surface exciton-plasmon polaritons(SEPPs).The out-coupling avenues of SEPP guided modes are modeled in the presence of nanostructures,such as corrugation and gratings,on the metal *** guided modes of SEPPs in metal-contacted ZnO nanowires are calculated using the effective index *** enhanced light emission from single semiconductor nanowires shows promise for use in highly efficient nano-emitters and nano-lasers,as well as macroscopic solid state light sources with very high efficiency.

关键词： Semiconductor nanowires surface plasmon polaritons nanowire waveguides emission enhancement gratings

Single-crystal star-like zinc oxide: synthesis, characterization and growth mechanism

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Rare Metals 2006年第z2期25卷 193-199页

作者： WANG Qingxiao YOU Liping zhang xinzheng WANG Rongming LV Yuzhen GUO Lin School of Physics Beijing University Beijing 100871 China School of Physics Beijing University Beijing 100871 China School of Physics Beijing University Beijing 100871 China School of Science Beijing University of Aeronautics and Astronautics Beijing 100083 China 　 School of Materials Science and Technology Beijing University of Aeronautics and Astronautics Beijing 100083 China

A novel star-like single-crystal ZnO structure was synthesized by a simple solvothermal method. The as-prepared products were characterized by XRD, SEM and TEM. The star-like ZnO, which shows sixfold symmetry, was constructed by six uniform arms distributing symmetrically around the [0001] zone axis. It is also found that the arms are not perpendicular to the [0001] zone axis and each arm is grown at a certain angle with the [0001] direction. CBED pattern and corresponding simulation demonstrate that the convex part of the star-like ZnO is O-terminated (000-1) plane and the concave part is Zn-terminated (0001) plane. H2S plays a crucial role in the synthesis process. The anisotropic growth habit along [0001] and [000-1] results in the formation of star-like structure.

关键词： star-like single-crystal solvothermal method CBED

High-spatial-resolution composition analysis of micro/nanostructures with a nanoscale compositional variation

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Nano Research 2023年第1期16卷 1090-1095页

作者： Meng Wang Xiaofeng Wang Zhican Zhou Feng Xia Haoran zhang Artem Shelaev xinzheng zhang Chuanfei Guo Jingjun Xu Qian Liu Chinese Academy of Sciences(CAS)Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology&University of Chinese Academy of SciencesBeijing 100190China The MOE Key Laboratory of Weak-Light Nonlinear Photonics TEDA Applied Physics SchoolNankai UniversityTianjin 300457China Sino-German College of Intelligent Manufacturing Shenzhen Technology UniversityShenzhen 518118China Department of Materials Science and Engineering Southern University of Science and TechnologyShenzhen 518055China College of Physics Qingdao UniversityQingdao 26607China NT-MDT Co.Building 100 ZelenogradMoscow 124482Russia Institute of Physics Kazan Federal UniversityKazan 420008Russia Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices Southern University of Science and TechnologyShenzhen 518055China College of Material Science and Technology Nanjing University of Aeronautics and AstronauticsNanjing 210016China

The composition of materials in a micro-/nano-devices plays a key role in determining their mechanical,physical,and chemical ***,for devices with a compositional change on nanoscale which can often be achieved by point-by-point direct writing technology using a focused ion beam(FIB),electron beam(EB),or laser beam(LB),but so far,nanoscale composition analysis of a large-area micro/nano structures with a variation composition remains a big challenge in cost,simpleness,and *** we present a feasible route to realize large-area composition analysis with nanoscale spatial resolution by using Raman *** experimentally verified the capability of this method by analyzing a complex Sn-SnOx system of a microscale grayscale mask with nanoscale spatial resolution of *** analyses using Auger electron spectroscopy,transmission electron microscopy,and atomic force microscopy indicated the effectiveness and practicality of our *** work opens up a way to analyze the composition of a large-area complex system at a nanoscale spatial resolution,and the method can be extended to many other material systems.

关键词： Raman spectroscopy nanoscale resolution composition analysis large-area

Coherence preservation during light-surface plasmon polaritons-light transformation

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Science China(Physics,Mechanics & Astronomy) 2013年第9期56卷 1679-1683页

作者： TAN XinHui WANG JunQiao CAI Wei MENG Tao XIANG YinXiao LI Wei zhang xinzheng The MOE Key Laboratory of Weak-Light Nonlinear Photonics TEDA Applied Physics School and School of PhysicsNankai University School of Physical Science and Engineering and MOE Key Laboratory of Materials Physics Zhengzhou University

We constructed a four-layer system composed of a prism,a silver film,an air layer and a lithium niobate *** we used two coherent light beams to excite surface *** surface plasmons were then decoupled into light in the photorefractive crystal where a holographic grating was *** two beams remained coherent through light to surface plasmons to light *** the characteristics of the holographic grating we found out that the thickness of the grating was to the order of hundreds of *** thick holographic grating suggests that the holographic recording in the photorefractive materials was induced by the leaky waves rather than by surface plasmon polaritons directly.

关键词： coherence preservation light-SPPs-light transformation surface plasmons holographic grating

Wavelength dependence of light propagation in a water suspension of anisotropic scatterers

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Science China(Physics,Mechanics & Astronomy) 2011年第11期54卷 1948-1952页

作者： SHI Fan zhang xinzheng LI Jun WANG PiDong XU Yan YU XuanYi XU JingJun The MOE Key Laboratory of Weak-Light Nonlinear Photonics TEDA Applied Physics School and School of Physics Nankai University Tianjin 300457 China

We experimentally study the wavelength dependence of light propagation in a water suspension of lithium niobate microcrystalline ***,the ballistic transmission in the visible range of the suspension is *** nonlinear relationship is observed between the transport mean free path and the wavelength of the incident ***,we measure the coherent backscattering (CBS) of the sample at different *** full width at half maximum of the CBS cone at 532 nm is about 1.24 times as large as that at 671 *** results indicate that the light with a long wavelength propagates further than the short wavelength light and the localization state of the short one is ***,we investigate the light-controllable CBS experiments in the disordered materials of anisotropic scatterers,which show that the configuration of pump light with the longer wavelength and the probe light with the shorter wavelength performs better.

关键词： wavelength dependence light propagation in random media anisotropic scatterers light-control

Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem Ⅰfrom Arabidopsis thaliana

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Molecular Plant 2022年第3期15卷 454-467页

作者： Xiaodong Su Duanfang Cao Xiaowei Pan Lifang Shi Zhenfeng Liu Luca Dall’Osto Roberto Bassi xinzheng zhang Mei Li National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101P.R.China University of Chinese Academy of Sciences Beijing 100049P.R.China College of Life Science Capital Normal UniversityBeijing 100101P.R.China Dipartimento di Biotecnologie Universitàdi Verona37134 VeronaItaly Center for Biological Imaging CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101P.R.China

Cyclic electron transport/flow(CET/CEF)in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency.A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like(NDH)complex that contains at least 29 protein subunits and associates with photosystem I(PSI)to form the NDH-PSI ***,we report the 3.9Åresolution structure of the Arabidopsis thaliana NDH-PSI(AtNDH-PSI)*** constructed structural models for 26 AtNDH subunits,among which 11 are unique to chloroplasts and stabilize the core part of the NDH *** the supercomplex,one NDH can bind up to two PSI-light-harvesting complex I(PSI-LHCI)complexes at both sides of its membrane *** minor LHCIs,Lhca5 and Lhca6,each present in one PSI-LHCI,interact with NDH and contribute to supercomplex formation and ***,our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.

关键词： cyclic electron transport/flow NADH dehydrogenase-like(NDH)complex photosystem I structure Arabidopsis thaliana

Architecture of severe fever with thrombocytopenia syndromevirus

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Protein & Cell 2023年第12期14卷 914-918页

作者： Zixian Sun Jing Cheng Yuan Bai Lin Cao Daoxin Xie Fei Deng xinzheng zhang Zihe Rao Zhiyong Lou Department of Basic Research Guangzhou LaboratoryGuangzhou 510005China MOE Key Laboratory of Protein Science School of MedicineTsinghua UniversityBeijing 100084China University of Chinese Academy of Sciences Beijing100049China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China National Virus Resource Center Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China State Key Laboratory of Medicinal Chemical Biology and College of Life Science and Pharmacy Nankai UniversityTianjin 300350China

Dear Editor,Severe fever with thrombocytopenia syndrome(SFTS)is an acute infectious disease caused by severe fever with thrombocytopenia syndrome virus(SFTSV)and is characterized by rapid onset,high mortality and widespread *** fatality rate can be as high as 10%-30%,which is significantly higher than that of the hemorrhagic fever caused by Hantavirus in the same area(Song et al.,2018).However,no effective treatments or vaccines are available yet,and the underlying pathogenic mechanisms of the virus are poorly understood.

关键词： fever mortality

Bending-Induced Conductance Increase in Individual Semiconductor Nanowires and Nanobelts

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Nano Research 2009年第7期2卷 553-557页

作者： Xiaobing Han Guangyin Jing xinzheng zhang Renmin Ma Xuefeng Song Jun Xu Zhimin Liao NingWang Dapeng Yu State Key Laboratory for Mesoscopic Physics and Electron Microscopy LaboratoryDepartment of PhysicsPeking UniversityBeijing 100871China Physics Department Hong Kong University of Science and TechnologyHong KongChina

Reliable ohmic contacts were established in order to study the strain sensitivity of nanowires and *** conductance increases of up to 113%were observed on bending individual ZnO nanowires or CdS *** bending strain-induced conductance enhancement was confirmed by a variety of bending measurements,such as using different manipulating tips(silicon,glass or tungsten)to bend the nanowires or nanobelts,and is explained by bending-induced effective tensile strain based on the principle of the piezoresistance effect.

关键词： ZnO nanowires bending strain piezoresistance conductance enhancement