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Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea

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Nature microbiology 2025年第6期10卷 1484-1500页

作者： Gali Tzlil María Del Carmen Marín Yuma Matsuzaki Probal Nag Shota Itakura Yosuke Mizuno Shunya Murakoshi Tatsuki Tanaka Shirley Larom Masae Konno Rei Abe-Yoshizumi Ana Molina-Márquez Daniela Bárcenas-Pérez José Cheel Michal Koblížek Rosa León Kota Katayama Hideki Kandori Igor Schapiro Wataru Shihoya Osamu Nureki Keiichi Inoue Andrey Rozenberg Ariel Chazan Oded Béjà Faculty of Biology Technion-Israel Institute of Technology Haifa Israel. Physical and Analytical Chemistry Department University of Jaén Jaén Spain. Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan. Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry The Hebrew University of Jerusalem Jerusalem Israel. Department of Life Science and Applied Chemistry Nagoya Institute of Technology Nagoya Japan. The Institute for Solid State Physics The University of Tokyo Kashiwa Japan. Laboratory of Biochemistry and Molecular Biology Faculty of Experimental Sciences Marine International Campus of Excellence (CEIMAR) University of Huelva Huelva Spain. Centre Algatech Institute of Microbiology Czech Academy of Sciences Třeboň Czech Republic. Faculty of Science University of South Bohemia České Budějovice Czech Republic. OptoBioTechnology Research Center Nagoya Institute of Technology Nagoya Japan. Department of Physics Technische Universität Dortmund Germany. Research Center Chemical Sciences and Sustainability University Alliance Ruhr Bochum Germany. Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan. wtrshh9@***. Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan. nureki@bs.s.u-tokyo.ac.jp. The Institute for Solid State Physics The University of Tokyo Kashiwa Japan. inoue@issp.u-tokyo.ac.jp. Faculty of Biology Technion-Israel Institute of Technology Haifa Israel. alephreish@***. Faculty of Biology Technion-Israel Institute of Technology Haifa Israel. achazan@ethz.ch. Institute of Environmental Engineering ETH Zurich Switzerland. achazan@ethz.ch. Faculty of Biology Technion-Israel Institute of Technology Haifa Israel. beja@technion.ac.il. The Nancy and Stephen Grand Technion Energy Program (GTEP) Technion-Israel Institute of Technology Haifa Israel. beja@technion.ac.il.

Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.

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Robust anomalous Hall effect in ferromagnetic metal under high pressure

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arXiv 2023年

作者： Gao, Lingling Lai, Junwen Chen, Dong Pei, Cuiying Wang, Qi Zhao, Yi Li, Changhua Cao, Weizheng Wu, Juefei Chen, Yulin Chen, Xingqiu Sun, Yan Felser, Claudia Qi, Yanpeng School of Physical Science and Technology ShanghaiTech University Shanghai201210 China Shenyang National Laboratory for Materials Science Institute of Metal Research Chinese Academy of Sciences Shenyang110016 China Max Planck Institute for Chemical Physics of Solids Dresden01187 Germany College of Physics Qingdao University Qingdao266071 China ShanghaiTech Laboratory for Topological Physics ShanghaiTech University Shanghai201210 China Department of Physics Clarendon Laboratory University of Oxford Parks Road OxfordOX1 3PU United Kingdom School of Materials Science and Engineering University of Science and Technology of China Shenyang110016 China Shanghai Key Laboratory of High-resolution Electron Microscopy ShanghaiTech University Shanghai201210 China

Recently, the giant intrinsic anomalous Hall effect (AHE) has been observed in the materials with kagome lattice. In this study, we systematically investigate the influence of high pressure on the AHE in the ferromagnet LiMn6Sn6 with clean Mn kagome lattice. Our in-situ high-pressure Raman spectroscopy indicates that the crystal structure of LiMn6Sn6 maintains a hexagonal phase under high pressures up to 8.51 GPa. The anomalous Hall conductivity (AHC) σxyA remains around 150 Ω-1 cm-1, dominated by the intrinsic mechanism. Combined with theoretical calculations, our results indicate that the stable AHE under pressure in LiMn6Sn6 originates from the robust electronic and magnetic structure. © 2023, CC BY-NC-ND.

关键词： Crystal structure

Observation of the dual quantum spin Hall insulator by density-tuned correlations in a van der Waals monolayer

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arXiv 2024年

作者： Tang, Jian Ding, Thomas Siyuan Chen, Hongyu Gao, Anyuan Qian, Tiema Huang, Zumeng Sun, Zhe Han, Xin Strasser, Alex Li, Jiangxu Geiwitz, Michael Shehabeldin, Mohamed Belosevich, Vsevolod Wang, Zihan Wang, Yiping Watanabe, Kenji Taniguchi, Takashi Bell, David C. Wang, Ziqiang Fu, Liang Zhang, Yang Qian, Xiaofeng Burch, Kenneth S. Shi, Youguo Ni, Ni Chang, Guoqing Xu, Su-Yang Ma, Qiong Department of Physics Boston College Chestnut HillMA United States Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore Singapore Department of Chemistry and Chemical Biology Harvard University CambridgeMA United States Department of Physics and Astronomy and California NanoSystems Institute University of California Los Angeles Los AngelesCA United States Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Department of Materials Science and Engineering Texas A&M University College StationTX United States Department of Physics and Astronomy University of Tennessee KnoxvilleTN United States Min H. Kao Department of Electrical Engineering and Computer Science University of Tennessee KnoxvilleTN United States Research Center for Electronic and Optical Materials National Institute for Materials Science Tsukuba Japan Research Center for Materials Nanoarchitectonics National Institute for Materials Science Tsukuba Japan Harvard John A. Paulson School of Engineering and Applied Sciences The Center for Nanoscale system Harvard University CambridgeMA United States Department of Physics Massachusetts Institute of Technology CambridgeMA United States CIFAR Azrieli Global Scholars program CIFAR Toronto Canada

The convergence of topology and correlations represents a highly coveted realm in the pursuit of novel quantum states of matter [1, 2]. Introducing electron correlations to a quantum spin Hall (QSH) insulator can lead to the emergence of a fractional topological insulator and other exotic time-reversal-symmetric topological order [3- 10], not possible in quantum Hall and Chern insulator systems. However, the QSH insulator with quantized edge conductance remains rare, let alone that with significant correlations. In this work, we report a novel dual QSH insulator within the intrinsic monolayer crystal of TaIrTe4, arising from the interplay of its single-particle topology and density-tuned electron correlations. At charge neutrality, monolayer TaIrTe4 demonstrates the QSH insulator that aligns with single-particle band structure calculations, manifesting enhanced nonlocal transport and quantized helical edge conductance. Interestingly, upon introducing electrons from charge neutrality, TaIrTe4 only shows metallic behavior in a small range of charge densities but quickly goes into a new insulating state, entirely unexpected based on TaIrTe4's single-particle band structure. This insulating state could arise from a strong electronic instability near the van Hove singularities (VHS), likely leading to a charge density wave (CDW). Remarkably, within this correlated insulating gap, we observe a resurgence of the QSH state, marked by the revival of nonlocal transport and quantized helical edge conduction. Our observation of helical edge conduction in a CDW gap could bridge spin physics and charge orders. The discovery of a dual QSH insulator introduces a new method for creating topological flat minibands via CDW superlattices, which offer a promising platform for exploring time-reversal-symmetric fractional phases and electromagnetism [3-5, 11, 12]. Copyright © 2024, The Authors. All rights reserved.

关键词： Charge density waves

On the accurate characterization of quantum-dot light-emitting diodes for display applications

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npj Flexible Electronics 2022年第1期6卷 351-362页

作者： Wangxiao Jin Yunzhou Deng Bingbing Guo Yaxiao Lian Baodan Zhao Dawei Di Xiaowei Sun Kai Wang Shuming Chen Yixing Yang Weiran Cao Song Chen Wenyu Ji Xuyong Yang Yuan Gao Shuangpeng Wang Huaibin Shen Jialong Zhao Lei Qian Fushan Li Yizheng Jin Key Laboratory of Excited-State Materials of Zhejiang Province State Key Laboratory of Silicon MaterialsDepartment of ChemistryZhejiang University310027 HangzhouChina State Key Laboratory of Modern Optical Instrumentation College of Optical Science and EngineeringInternational Research Center for Advanced PhotonicsZhejiang University310027 HangzhouChina Department of Electronic and Electrical Engineering Southern University of Science and Technology518055 ShenzhenChina TCL Research ShenzhenGuangdongChina Shenzhen China Star Optoelectronics Semiconductor Display Technology Co. LtdShenzhenGuangdongChina College of Chemistry Chemical Engineering and Materials ScienceSoochow University199 Ren’ai Rd215123 SuzhouJiangsuChina Key Lab of Physics and Technology for Advanced Batteries(Ministry of Education) College of PhysicsJilin University130023 ChangchunChina Key Laboratory of Advanced Display and System Applications of Ministry of Education Shanghai University149 Yanchang RoadShanghai 200072China Najing Technology Corporation Ltd Hangzhou 310052China Institute of Applied Physics and Materials Engineering University of MacaoTaipaMacaoSAR 999078China Key Laboratory for Special Functional Materials of Ministry of Education National&Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technologyand Collaborative Innovation Center of Nano Functional Materials and ApplicationsHenan UniversityKaifeng 475004China School of Physical Science and Technology MOE Key Laboratory of New Processing Technology for Non-ferrous Metals and MaterialsGuangxi Key Laboratory of Processing for Non-ferrous Metals and Featured MaterialsGuangxi UniversityNanning 530004China Division of Functional Materials and Nanodevices Ningbo Institute of Materials Technology and EngineeringChinese Academy of SciencesNingbo 315201China College of Physics and Information Engineering Fuzhou UniversityFuzhou 350108China

Quantum dot light-emitting diodes(QLEDs)are a class of high-performance solution-processed electroluminescent(EL)devices highly attractive for next-generation display *** the encouraging advances in the mechanism investigation,material chemistry,and device engineering of QLEDs,the lack of standard protocols for the characterization of QLEDs may cause inaccurate measurements of device parameters and invalid comparison of different ***,we report a comprehensive study on the characterizations of QLEDs using various *** show that the emission non-uniformity across the active area,nonLambertian angular distributions of EL intensity,and discrepancies in the adopted spectral luminous efficiency functions could introduce significant errors in the device *** errors in the operational-lifetime measurements may arise from the inaccurate determination of the initial luminance and inconsistent methods for analyzing the luminance-decay ***,we suggest a set of recommended practices and a checklist for device characterizations,aiming to help the researchers in the QLED field to achieve accurate and reliable measurements.

关键词： diodes characterization luminous

Magnetism in AV3Sb5 (A = Cs, Rb, K): Complex Landscape of the Dynamical Magnetic Textures

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arXiv 2023年

作者： Karmakar, Debjani Pereiro, Manuel Hasan, Md Nur Bharati, Ritadip Hellsvik, Johan Delin, Anna Pal, Samir Kumar Bergman, Anders Sharma, Shivalika Di Marco, Igor Thunström, Patrik Oppeneer, Peter M. Eriksson, Olle Department of Physics and Astronomy Uppsala University Box 516 UppsalaSE-751 20 Sweden Technical Physics Division Bhabha Atomic Research Centre Mumbai400085 India Department of Chemical and Biological Sciences S. N. Bose National Centre for Basic Sciences Block JD Sector-III SaltLake Kolkata700 106 India School of Physical Sciences National Institute of Science Education and Research HBNI Odisha Jatni752050 India PDC Center for High Performance Computing KTH Royal Institute of Technology StockholmSE-100 44 Sweden Department of Applied Physics KTH Royal Institute of Technology StockholmSE-106 91 Sweden KTH Royal Institute of Technology StockholmSE-10044 Sweden Asia Pacific Center for Theoretical Physics Pohang37673 Korea Republic of Department of Physics Pohang University of Science and Technology Pohang37673 Korea Republic of

We have investigated the dynamical magnetic properties of the V-based kagome stibnite compounds by combining the ab-initio calculated magnetic parameters of a spin Hamiltonian like inter-site exchange parameters, magnetocrystalline anisotropy and site projected magnetic moments, with full-fledged simulations of atomistic spin-dynamics. Our calculations reveal that in addition to a ferromagnetic order along the [001] direction, the system hosts a complex landscape of magnetic configurations comprised of commensurate and incommensurate spin-spirals along the [010] direction. The presence of such chiral magnetic textures may be the key to solve the mystery about the origin of the experimentally observed inherent breaking of the C6 rotational symmetry- and the time-reversal symmetry. Copyright © 2023, The Authors. All rights reserved.

关键词： Spin dynamics

Probing the Magnetic Behaviour of Nanoscale Nickel Ferrite Magnetic System by an Ac Field-Modulated Magnetic Force Microscopy

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SSRN

SSRN 2023年

作者： Jayanthi, K. Rakshita, M. Kumar, Pawan Manorama, Sunkara V.V. Haranath, Divi Department of Physical and Chemical Sciences Sri Sathya Sai University for Human Excellence Karnataka Kalaburagi585313 India Laboratory Department of Physics National Institute of Technology Telangana Warangal506004 India Graduate School of Engineering Science Akita University Tegata Gakuen-machi 1-1 Akita010-8502 Japan Laboratoire Charles Coulomb Université de Montpellier CNRS Montpellier34095 France Nanomaterials Laboratory Polymers and Functional Materials Division CSIR-Indian Institute of Chemical Technology Hyderabad India

Nickel ferrite, is an important material due to its soft magnetic nature, intriguing and significant properties, and it has a numerous application, such as in magnetic sensors, medical diagnostic information storage system, and so on. These magnetic nanoparticles (MNPs) with particle size of about 10 to 25 nm were successfully synthesized using a simple hydrothermal chemical synthesis method at low temperature. The structural and magnetic properties of the MNPs were studied as a function of the standing time and with different concentrations of Ni2+ ions. Magnetic behaviour was investigated using temperature-dependent and field magnetization measurements as well as electronic magnetic resonance. It has been demonstrated that the Ni0.60Fe2.40O4 structures, Ni and Fe proportions favour high saturation magnetization values and a decrease in the magnetic anisotropy constant. Irreversible and reversible magnetization processes by stimulating magnetization have been measured for quantitative and qualitative measurements of the magnetic information of individual ferrite MNPs with an alternative current (AC) magnetic field based on alternating magnetic force microscopy (A-MFM) with a sensitive super paramagnetic tip. This method concurrently measures sample's Direct current (DC) and AC magnetic fields and comparison study of magnetic field image at DC magnetic field (± 250 Oe), A‐MFM imaging at 250 Oe (AC p‐p) without DC magnetic field and AC field dependency (20 to 300 Oe) of A- MFM imaging has been measured at constant DC field (60 Oe). The results are indicating that, the AC magnetic field measurement with increasing AC magnetic field intensity, the phase image signal (averaged magnetic field component) decreases, because magnetization saturates in positive magnetic field direction. © 2023, The Authors. All rights reserved.

关键词： Temperature

Magnetism in AV3Sb5 (Cs, Rb, K): Origin and Consequences for the Strongly Correlated Phases

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arXiv 2023年

作者： Hasan, Md Nur Bharati, Ritadip Hellsvik, Johan Delin, Anna Pal, Samir Kumar Bergman, Anders Sharma, Shivalika Di Marco, Igor Pereiro, Manuel Thunström, Patrik Oppeneer, Peter M. Eriksson, Olle Karmakar, Debjani Department of Chemical and Biological Sciences S. N. Bose National Centre for Basic Sciences Block JD Sector-III SaltLake Kolkata700 106 India School of Physical Sciences National Institute of Science Education and Research HBNI Odisha Jatni752050 India PDC Center for High Performance Computing KTH Royal Institute of Technology StockholmSE-100 44 Sweden Department of Applied Physics KTH Royal Institute of Technology StockholmSE-106 91 Sweden KTH Royal Institute of Technology StockholmSE-10044 Sweden Department of Physics and Astronomy Uppsala University Box 516 UppsalaSE-751 20 Sweden Asia Pacific Center for Theoretical Physics Pohang37673 Korea Republic of Department of Physics Pohang University of Science and Technology Pohang37673 Korea Republic of Technical Physics Division Bhabha Atomic Research Centre Mumbai400085 India

The V-based kagome systems AV3Sb5 (A = Cs, Rb and K) are unique by virtue of the intricate interplay of non-trivial electronic structure, topology and intriguing fermiology, rendering them to be a playground of many mutually dependent exotic phases like charge-order and superconductivity. Despite numerous recent studies, the interconnection of magnetism and other complex collective phenomena in these systems has yet not arrived at any conclusion. Using first-principles tools, we demonstrate that their electronic structures, complex fermiologies and phonon dispersions are strongly influenced by the interplay of dynamic electron correlations, non-trivial spin-polarization and spin-orbit coupling. An investigation of the first-principles-derived inter-site magnetic exchanges with the complementary analysis of q-dependence of the electronic response functions and the electron-phonon coupling indicate that the system conforms as a frustrated spin-cluster, where the occurrence of the charge-order phase is intimately related to the mechanism of electron-phonon coupling, rather than the Fermi-surface nesting. Copyright © 2023, The Authors. All rights reserved.

关键词： Electronic structure

Masked Vascular Structure Segmentation and Completion in Retinal Images

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IEEE Transactions on Medical Imaging 2025年第6期44卷 2492-2503页

作者： Yi Zhou Thiara Sana Ahmed Meng Wang Eric A. Newman Leopold Schmetterer Huazhu Fu Jun Cheng Bingyao Tan Singapore National Eye Centre Singapore Eye Research Institute 11 Third Hospital Ave Singapore Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA Department of Neuroscience University of Minnesota Minneapolis MN USA SERI-NTU Advanced Ocular Engineering (STANCE) Program Discovery Tower Singapore Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP) Duke-NUS Medical School 8 College Rd Singapore Institute of Molecular and Clinical Ophthalmology Basel Switzerland School of Chemical and Biomedical Engineering Nanyang Technological University (NTU) 50 Nanyang Ave Singapore Department of Clinical Pharmacology Medical Physics and Biomedical Engineering Medical University of Vienna Vienna Austria Rothschild Foundation Hospital Paris France Technology and Research Institute of High Performance Computing Agency for Science North Tower Singapore Institute for Infocomm Research Agency for Science Technology and Research Connexis Singapore SERI-NTU Advanced Ocular Engineering Program 50 Nanyang Ave Singapore

Early retinal vascular changes in diseases such as diabetic retinopathy often occur at a microscopic level. Accurate evaluation of retinal vascular networks at a micro-level could significantly improve our understanding of angiopathology and potentially aid ophthalmologists in disease assessment and management. Multiple angiogram-related retinal imaging modalities, including fundus, optical coherence tomography angiography, and fluorescence angiography, project continuous, inter-connected retinal microvascular networks into imaging domains. However, extracting the microvascular network, which includes arterioles, venules, and capillaries, is challenging due to the limited contrast and resolution. As a result, the vascular network often appears as fragmented segments. In this paper, we propose a backbone-agnostic Masked Vascular Structure Segmentation and Completion (MaskVSC) method to reconstruct the retinal vascular network. MaskVSC simulates missing sections of blood vessels and uses this simulation to train the model to predict the missing parts and their connections. This approach simulates highly heterogeneous forms of vessel breaks and mitigates the need for massive data labeling. Accordingly, we introduce a connectivity loss function that penalizes interruptions in the vascular network. Our findings show that masking 40% of the segments yields optimal performance in reconstructing the interconnected vascular network. We test our method on three different types of retinal images across five separate datasets. The results demonstrate that MaskVSC outperforms state-of-the-art methods in maintaining vascular network completeness and segmentation accuracy. Furthermore, MaskVSC has been introduced to different segmentation backbones and has successfully improved performance. The code and 2PFM data are available at: https://***/Zhouyi-Zura/MaskVSC .

关键词： Retina Image segmentation Biomedical imaging Imaging Angiography Training Image color analysis Fluorescence Accuracy Optical imaging

Degenerate Fluid Polyamorphism Induced by Symmetrical Molecular Interconversion

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arXiv 2025年

作者： Anisimov, Mikhail A. Buldyrev, Sergey V. Caupin, Frédéric Longo, Thomas J. Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Department of Chemical and Biomolecular Engineering University of Maryland College ParkMD20742 United States Department of Physics Yeshiva University New YorkNY10033 United States Department of Physics Boston University MA02215 United States Institut Lumière Matière Université Claude Bernard Lyon 1 CNRS Institut Universitaire de France VilleurbanneF-69622 France

Fluid polyamorphism is the existence of multiple fluid-fluid phase transitions in a single-component substance. It can occur due to interconversion between two alternative molecular or supramolecular states. In this work, we investigate a special ("degenerate") case of fluid polyamorphism, in which all three characteristic parameters of the interconversion equilibrium constant, i.e. the changes of energy, entropy, and volume, are zero. This feature of interconversion is typical for the Ising spin model of ferromagnets but is also observed in a polyamorphic chiral fluid mixture of interconverting enantiomers. To investigate the consequences of interconversion’s degeneration for fluid polyamorphism, we have performed a meanfield analysis and 3D Monte Carlo simulations of a compressible binary lattice with interconverting species (referred to as the "blinking-checkers model"), which generally demonstrates the existence of both liquid-gas and liquid-liquid transitions. By tuning the interaction parameters, we have demonstrated that, in the degenerate interconverting case, a coupling between the fraction of interconversion (a vector-like nonconserved order parameter) and the total density (a scalar conserved order parameter) may produce a symmetrical tricritical point. At this point, the line of second-order transitions between two fluids, "disordered" (with 50:50 interconversion) and "ordered" (with temperature and pressure dependent interconversion fraction), is terminated by first-order transitions between the fluid states. This point exhibits the typical features of symmetrical tricritical points as observed in a superfluid mixture of helium isotopes and in some magnetic materials. We also show that the transition between the ordered and disordered fluid could occur in either the liquid or the gaseous phase. © 2025, CC BY.

关键词： Superfluid helium