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arXiv 2020年

作者： Bell, Kevan Abbasi, Saad Dinakaran, Deepak Taher, Muba Bigras, Gilbert van Landeghem, Frank K.H. Mackey, John R. Reza, Parsin Haji PhotoMedicine Labs Department of Systems Design Engineering University of Waterloo WaterlooONN2L 3G1 Canada illumiSonics Inc. Department of Systems Design Engineering University of Waterloo WaterlooONN2L 3G1 Canada Department of Oncology University of Alberta EdmontonABT6G 1Z2 Canada Division of Dermatology Department of Medicine University of Alberta EdmontonABT6G 2V1 Canada Department of Laboratory Medicine and Pathology University of Alberta EdmontonABT6G 2V1 Canada E7-6416 200 University Avenue West WaterlooONN2L 3G1 Canada

Histological visualizations are critical to clinical disease management and are fundamental to biological understanding. However, current approaches that rely on bright-field microscopy require extensive tissue preparation prior to imaging. These processes are labor intensive and contribute to delays in clinical feedback that can extend to two to three weeks for standard paraffin-embedded tissue preparation and interpretation. Here, we present a label-free reflection-mode imaging modality that reveals cellular-scale morphology by detecting intrinsic endogenous contrast. We accomplish this with the novel photoacoustic remote sensing (PARS) detection system that permits non-contact optical absorption contrast to be extracted from thick and opaque biological targets with optical resolution. PARS was examined both as a rapid assessment tool that is capable of managing large samples (>1 cm2) in under 10 minutes, and as a high contrast imaging modality capable of extracting specific biological contrast to simulate conventional histological stains such as hematoxylin and eosin (H&E). The capabilities of the proposed method are demonstrated in a variety of human tissue preparations including formalin-fixed paraffin-embedded tissue blocks and unstained slides sectioned from these blocks, including normal and neoplastic human brain, and breast epithelium involved with breast cancer. Similarly, PARS images of human skin prepared by frozen section clearly demonstrated basal cell carcinoma and normal human skin tissue. Finally, we imaged unprocessed murine kidney and achieved histologically relevant subcellular morphology in fresh tissue. This represents a vital step towards an effective real-time clinical microscope that overcomes the limitations of standard histopathologic tissue preparations and enables real-time pathology assessment. Copyright © 2020, The Authors. All rights reserved.

关键词： Remote sensing

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Anisotropic and asymmetric deformation mechanisms of nanolaminated graphene/Cu composites

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Nano Materials Science 2019年第2期1卷 121-130页

作者： Shayuan Weng Huiming Ning Tao Fu Ning Hu Shu Wang Kaiyan Huang Xianghe Peng H. Jerry Qi Cheng Yan College of Aerospace Engineering Chongqing University Chongqing 400044 PR China Key Laboratory of Optoelectronic Technology and Systems of the Education Ministry of China Chongqing University Chongqing 400044 PR China State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body Changsha 410082 PR China The George W. Woodruff School of Mechanical Engineering Renewable Bioproduct Institute Georgia Institute of Technology Atlanta GA 30332 United States School of Chemistry Physics and Mechanical Engineering Science and Engineering Faculty Queensland University of Technology (QUT) 2 George Street G.P.O. Box 2434 Brisbane Australia

We conducted molecular dynamics (MD) simulations of tension and compression along the direction and MD simulations of compression along the and directions on nanolaminated graphene/Cu (NGCu) composites to investiga... 详细信息

We conducted molecular dynamics (MD) simulations of tension and compression along the <112> direction and MD simulations of compression along the <110> and <111> directions on nanolaminated graphene/Cu (NGCu) composites to investigate the effects of the incorporated graphene and the deformation mechanisms related to the loading direction. The deformation behavior and the defect structures were found to be strongly dependent on the loading conditions. An asymmetric tension-compression deformation behavior was thus found in graphene/Cu nanolaminates under the <112> loading, which was dominated by stacking faults and deformation twins formed by dislocation slide under tension and compression, respectively. High density and ordered nanotwins were formed at the graphene/Cu interfaces. Two different formation mechanisms of the twins were found under the <112> compression, and the nucleated twins were easy to be thickened with the assistance of the graphene wrinkles. Multiple twins were formed under the <110> compression by the dislocation cross-slip. This study provides a way to introduce graphene reinforcement and twin boundary to Cu matrix composites and design nanotwinned graphene/Cu composites with excellent mechanical performance.

关键词： Deformation Mechanisms Molecular Dynamics Graphene/Cu Composites interface Twin

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Accurate RNA 3D structure prediction using a language model-based deep learning approach

arXiv

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arXiv 2022年

作者： Shen, Tao Hu, Zhihang Sun, Siqi Liu, Di Wong, Felix Wang, Jiuming Chen, Jiayang Wang, Yixuan Hong, Liang Xiao, Jin Zheng, Liangzhen Krishnamoorthi, Tejas King, Irwin Wang, Sheng Yin, Peng Collins, James J. Li, Yu Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong Zelixir Biotech Shanghai China Research Institute of Intelligent Complex Systems Fudan University Shanghai China Wyss Institute for Biologically Inspired Engineering Harvard University BostonMA United States Department of Systems Biology Harvard Medical School BostonMA United States Institute for Medical Engineering and Science Massachusetts Institute of Technology CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Synthetic Biology Center Massachusetts Institute of Technology CambridgeMA United States Integrated Biosciences Redwood CityCA United States OneAIM Ltd. Hong Kong Shanghai AI Laboratory Shanghai China The CUHK Shenzhen Research Institute Hi-Tech Park Shenzhen Nanshan China Shenzhen Institute of Advanced Technology Guangdong Shenzhen China School of Molecular Sciences Center for Molecular Design and Biomimetics the Biodesign Institute Arizona State University TempeAZ United States School of Computing and Augmented Intelligence Arizona State University TempeAZ United States

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates computational prediction efforts. Here, we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pre-trained on ∼23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate RhoFold+’s superiority over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and inter-helical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies. Copyright © 2022, The Authors. All rights reserved.

关键词： Deep learning

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Chiral Metal-Free Anti-Perovskite with Strong Chiroptical Nonlinearity

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Angewandte Chemie 2024年第6期137卷

作者： Zhaoyu Wang Xin Qiu Hebin Wang Wenkai Zhao Sehrish Gull Haolin Lu Zechen Hao Bing Sun Xin Zeng Prof. Xinfeng Liu Hao-Li Zhang Prof. Yongsheng Chen Prof. Tingchao He Prof. Guankui Long School of Materials Science and Engineering Tianjin Key Lab for Rare Earth Materials and Applications Smart Sensing Interdisciplinary Science Center Renewable Energy Conversion and Storage Center (RECAST) National Institute for Advanced Materials Nankai University Tianjin 300350 China Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Physics and Optoelectronic Engineering Shenzhen University Shenzhen 518060 China State Key Laboratory of Applied Organic Chemistry (SKLAOC) Key Laboratory of Special Function Materials and Structure Design (MOE) College of Chemistry and Chemical Engineering Lanzhou University Lanzhou 730000 China CAS Key Laboratory of Standardization and Measurement for Nanotechnology National Center for Nanoscience and Technology Beijing 100190 China The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials Institute of Polymer Chemistry Renewable Energy Conversion and Storage Center (RECAST) College of Chemistry Nankai University Tianjin 300071 China

The nonlinear chiroptical properties of chiral metal halide perovskite has attracted substantial attention in recent years. In order to overcome the inherent limitations of metal halide, such as high costs, potential toxicity, challenges with recycling, especially the limited laser-induced damage threshold (LDT), we have successfully constructed the first chiral metal-free anti-perovskite, with the aim of utilizing it in second harmonic generation-circular dichroism (SHG-CD). Moreover, the anti-perovskite composed entirely of small organic ions typically display a more extensive transparent window, which could contribute a high LDT. Herein two chiral metal-free anti-perovskites, R / S -MCN [( R / S -MBA) 6 Cl(NH 4 Cl 6 )] were constructed, and exhibit strong second-harmonic generation response from 800 to 980 nm. The second-order nonlinear optical coefficient of the chiral metal-free anti-perovskite reaches 0.89 pm/V, which is higher than that of commercial Y-cut quartz. Most importantly, both R - and S -MCN exhibit a large nonlinear optical activity with a high SHG dissymmetry factor ( g SHG-CD ) of 0.60 and a high laser-induced damage threshold of 71 mJ/cm 2 , which is higher than that of most reported chiral perovskites. Our findings indicate that chiral metal-free anti-perovskite have the potential to be a valuable addition to the development of next-generation nonlinear chiroptical devices.

关键词： Chiral Anti-Perovskite Metal-Free Material Second-Harmonic Generation Laser-Induced Damage Threshold Nonlinear Chiroptics

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Exploring the hysteresis properties of nanocrystalline permanent magnets using deep learning

arXiv

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arXiv 2022年

作者： Kovacs, Alexander Exl, Lukas Kornell, Alexander Fischbacher, Johann Hovorka, Markus Gusenbauer, Markus Breth, Leoni Oezelt, Harald Yano, Masao Sakuma, Noritsugu Kinoshita, Akihito Shoji, Tetsuya Kato, Akira Schrefl, Thomas Christian Doppler Laboratory for Magnet design through physics informed machine learning Viktor Kaplan-Straße 2E Wiener Neustadt2700 Austria Department for Integrated Sensor Systems Danube University Krems Viktor Kaplan-Straße 2E Wiener Neustadt2700 Austria Department of Mathematics University of Vienna Oskar-Morgenstern-Platz 1 Vienna1090 Austria Wolfgang Pauli Institute Oskar-Morgenstern-Platz 1 Vienna1090 Austria Research Platform MMM Mathematics-Magnetism-Materials Oskar-Morgenstern-Platz 1 Vienna1090 Austria Advanced Materials Engineering Div. Toyota Motor Corporation 1200 Mishuku Susono Shizuoka410-1193 Japan

We demonstrate the use of model order reduction and neural networks for estimating the hysteresis properties of nanocrystalline permanent magnets from microstructure. With a data-driven approach, we learn the demagnetization curve from data-sets created by grain growth and micromagnetic simulations. We show that the granular structure of a magnet can be encoded within a low-dimensional latent space. Latent codes are constructed using a variational autoencoder. The mapping of structure code to hysteresis properties is a multi-target regression problem. We apply deep neural network and use parameter sharing, in order to predict anchor points along the demagnetization curves from the magnet’s structure code. The method is applied to study the magnetic properties of nanocrystalline permanent magnets. We show how new grain structures can be generated by interpolation between two points in the latent space and how the magnetic properties of the resulting magnets can be *** Codes 68T07 Copyright © 2022, The Authors. All rights reserved.

关键词： Permanent magnets

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The β-Ketoacyl-ACP Synthase FabF Catalyzes Carbon-Carbon Bond Formation in a Bimodal Pattern for Fatty Acid Biosynthesis

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Angewandte Chemie 2024年第47期136卷

作者： Yuzhou Huang Yiran Wang Chang Cai Lin Zhang Fei Ye Liang Zhang Department of Pharmacology and Chemical Biology State Key Laboratory of Systems Medicine for Cancer School of Medicine Shanghai Jiao Tong University 200025 Shanghai China School of Pharmaceutical Science and Technology Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 310024 Hangzhou China Drug Discovery and Design Center The Center for Chemical Biology State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences 201203 Shanghai China College of Life Sciences and Medicine Zhejiang Sci-Tech University 310018 Hangzhou China Department of Chemical Biology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 200240 Shanghai China

Fatty acids produced by the type-II fatty acid biosynthetic pathway (FAS-II) are essential biomaterials for bacterial membrane construction and numerous metabolic routes. The β-ketoacyl-ACP synthase FabF catalyzes the key C−C bond formation step for fatty acid elongation in FAS-II. Here, we revealed the substrate recognition and catalytic mechanisms of FabF by determining FabF-ACP complexes. FabF displays a distinctive bimodal catalytic pattern specifically on C6 and C10 acyl-ACP substrates. It utilizes positively charged residues located on the η3-helix and loop1 regions near the catalytic tunnel entrance to bind ACP, and two hydrophobic cavities as well as “front”, “middle”, and “back” door residues to specifically stabilize C6 and C10 acyl substrates for preferential catalysis. Further quantum chemistry calculations suggest that the FabF catalytic residues Lys336 and His304 facilitate proton transfer during condensation catalysis and C−C bond formation. Our results provide key mechanistic insights into the biosynthesis of molecular carbon skeletons based on ketosynthases that are highly conserved through the FAS and polyketide synthase (PKS) analogous biosynthetic routes, broaden the understanding of the tricarboxylic acid cycle that utilizes lipoic acid derived from C8-ACP accumulated due to the FabF distinctive catalytic pattern for oxidative decarboxylations, and may facilitate the development of narrow-spectrum antibacterial drugs.

关键词： Fatty acid biosynthesis β-ketoacyl-ACP synthase Carbon-carbon bond formation Bimodal enzymatic catalysis

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Berberrubine-mediated pH indicator response enhances the efficacy of hydroxycamptothecin by reversing lysosomal drug resistance

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Chinese Chemical Letters 2024年

作者： Daili Liu Changxiang Yu Liyuan Lin Zhidong Liu Guiqian Fang Qingqiang Yao Qixin Chen Xintian Shao School of Chinese Materia Medica Tianjin University of Traditional Chinese Medicine Tianjin 301617 China School of Life Sciences Medical Science and Technology Innovation Center Shandong First Medical University & Shandong Academy of Medical Sciences Ji'nan 250117 China School of Pharmaceutical Sciences & Institute of Materia Medica Medical Science and Technology Innovation Center State Key Laboratory of Advanced Drug Delivery and Release Systems Shandong First Medical University & Shandong Academy of Medical Sciences Ji'nan 250117 China State Key Laboratory of Chinese Medicine Modernization Tianjin University of Traditional Chinese Medicine Tianjin 301617 China Departments of Diagnostic Radiology Surgery Chemical and Biomolecular Engineering and Biomedical Engineering Yong Loo Lin School of Medicine and College of Design and Engineering National University of Singapore Singapore 119074 Singapore

Drug resistance poses a significant challenge to effective long-term treatment across various medical fields. This study proposed a feasible strategy to enhance lysosomal alkalinization by transporting mitochondria-targeting quaternary ammonium salts into lysosomes, creating a deprotonated environment. This environment allows drugs to bypass protonation issues in lysosomes, thereby reversing drug resistance and improving therapeutic efficacy. As a proof of concept, a quaternary ammonium salt-based pH indicator was developed, berberrubine (BRB), enhancing the action of the anticancer drug hydroxycamptothecin (HCPT) in resistant cells. BRB-induced alkalinization increased lysosomal pH and deactivated lysosomal activity, enabling HCPT to bypass protonation constraints. This enhancement markedly improved the anticancer efficacy of HCPT in resistant cells, providing an innovative approach to address drug resistance and advancing therapeutic technologies.

关键词： Drug resistance Lysosomes Berberrubine Hydroxycamptothecin Quaternary ammonium salts Alkalinization

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A meta-inspired termite queen algorithm for global optimization and engineering design problems

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engineering Applications of Artificial Intelligence 2022年 111卷

作者： Peng Chen Shihua Zhou Qiang Zhang Nikola Kasabov Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian 116622 China School of Computer Science and Technology Dalian University of Technology Dalian 116024 China Knowledge Engineering and Discovery Research Institute Auckland University of Technology Auckland 1010 New Zealand Intelligent Systems Research Center Ulster University Londonderry BT52 1SA UK

This paper proposes a novel bio-inspired termite queen algorithm (TQA) to solve optimization problems by simulating the division of labor in termite populations under a queen’s rule. TQA is benchmarked on a set of 23 functions to test its performance at solving global optimization problems, and applied to six real-world engineering design problems to verify its reliability and effectiveness. Comparative simulation studies with other algorithms are conducted, from whose results it is observed that TQA satisfactorily solves global optimization problems and engineering design problems.

关键词： Termite queen algorithm Benchmarked functions Loss minimization Metaheuristic technique engineering design problems

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Training effectiveness evaluation of helicopter emergency relief based on virtual simulation

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Chinese Journal of Aeronautics 2018年第10期31卷 2000-2012页

作者： Xue SUN Hu LIU Guanghui WU Yaoming ZHOU School of Aeronautic Science and Engineering Beihang UniversityBeijing 100083China Key Laboratory of Aircraft Advanced Design Technology Ministry of Industry and Information TechnologyBeijing 100083China State Key Laboratory of Virtual Reality Technology and Systems Beijing 100083China Commercial Aircraft Corporation of China Ltd.Shanghai 200126China

Helicopters are playing an increasingly important part in emergency relief, such as earthquake rescue, firefighting and medical transport. With the development of virtual simulation technology, virtual simulation-based training is widely used in the training of the helicopter crew especially for the dangerous and costly missions mentioned above. A complete training effectiveness evaluation method is proposed to evaluate the trainees＇ training effect based on virtual simulation in this paper. A key to this method is regarding the complicated process as a discrete event-activity flow system and establishing the evaluation indicator system. Then expert group and Analytical Network Process（ANP） are applied to determine the weight of indicators. When the training data are processed, there is a novel attempt to apply Fuzzy Comprehensive Evaluation（FCE） model to calculate the two categories of indicators. Eventually, an experiment and the analysis were carried out to validate the evaluation method.

关键词： Analytical network process Emergency relief Fuzzy comprehensive evaluation Helicopter Training effectiveness evaluation Virtual simulation

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Resolving the Origins of Superior Cycling Performance of Antimony Anode in Sodium-ion Batteries: A Comparison with Lithium-ion Batteries

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Angewandte Chemie 2024年第11期136卷

作者： Ruiwen Shao Zhefei Sun Lei Wang Jianhai Pan Luocai Yi Yinggan Zhang Jiajia Han Zhenpeng Yao Jie Li Zhenhai Wen Shuangqiang Chen Shu-Lei Chou Dong-Liang Peng Qiaobao Zhang Beijing Advanced Innovation Center for Intelligent Robots and Systems School of Medical Technology Beijing Institute of Technology Beijing China State Key Laboratory of Physical Chemistry of Solid Surfaces College of Materials Xiamen University Xiamen Fujian 361005 China Institute for Carbon Neutralization College of Chemistry and Materials Engineering Wenzhou University Wenzhou 325035 China Department of Chemical Engineering School of Environmental and Chemical Engineering Shanghai University Shangda Road 99 Shanghai 200444 China CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen Energy Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China Center of Hydrogen Science Shanghai Jiao Tong University Shanghai China State Key Laboratory of Metal Matrix Composites School of Materials Science and Engineering Shanghai Jiao Tong University Shanghai China Department of Energy Politecnico di Milano Via Lambruschini 4 20156 Milano Italy

Alloying-type antimony (Sb) with high theoretical capacity is a promising anode candidate for both lithium-ion batteries (LIBs) and sodium-ion batteries (SIBs). Given the larger radius of Na + (1.02 Å) than Li + (0.76 Å), it was generally believed that the Sb anode would experience even worse capacity degradation in SIBs due to more substantial volumetric variations during cycling when compared to LIBs. However, the Sb anode in SIBs unexpectedly exhibited both better electrochemical and structural stability than in LIBs, and the mechanistic reasons that underlie this performance discrepancy remain undiscovered. Here, using substantial in situ transmission electron microscopy, X-ray diffraction, and Raman techniques complemented by theoretical simulations, we explicitly reveal that compared to the lithiation/delithiation process, sodiation/desodiation process of Sb anode displays a previously unexplored two-stage alloying/dealloying mechanism with polycrystalline and amorphous phases as the intermediates featuring improved resilience to mechanical damage, contributing to superior cycling stability in SIBs. Additionally, the better mechanical properties and weaker atomic interaction of Na−Sb alloys than Li−Sb alloys favor enabling mitigated mechanical stress, accounting for enhanced structural stability as unveiled by theoretical simulations. Our finding delineates the mechanistic origins of enhanced cycling stability of Sb anode in SIBs with potential implications for other large-volume-change electrode materials.

关键词： Antimony anode Lithium-ion batteries Sodium-ion batteries In situ transmission electron microscopy Electrochemical performance

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