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Active Template Synthesis of Protein[n]Catenanes Using Engineered Peptide–Peptide Ligation Tools

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CCS Chemistry 2024年第2期6卷 377-389页

作者： Fan Zhang Yajie Liu Yu Shao Wen-Bin Zhang Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of EducationCenter for Soft Matter Science and EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871 Beijing Academy of Artificial Intelligence Beijing 100084

The expansion of protein topological diversity requires new and efficient synthetic tools.Herein,we report the second and third generations of the SpyStapler-mediated SpyTag/BDTag ligation system for the efficient synthesis of 4-arm star proteins and the repurposing of the third generation as an active template to enable the synthesis of higher-order protein[n]catenanes(n=3,4,and 5).SpyStapler003 has a higher affinity to its cognate SpyTag and BDTag reactive pairs relative to the original SpyStapler.Hence,it can overcome much more profound steric hindrance in protein ligation and improve the efficiency of the resulting active template tool to facilitate the construction of radial protein[n]catenanes.Various proteins of interest,such as dihydrofolate reductase and the nanobody KN035,can be modularly incorporated into the[n]catenanes with intact activity.Combination of passive and active template strategies gives rise to linear protein[4]catenanes,which further expands the current topological diversity.Moreover,higher-order protein catenation not only leads to enhanced thermal stability and proteolytic resistance but also higher affinity of the nanobody via multivalent effects.Our study provides tools useful for bioconjugation and new topological protein scaffolds for the multivalent display of enzymes and antibodies.

关键词： SpyTag SpyCatcher catenane topology active template ligation

Quantum Fibrations: Quantum computation on an arbitrary topological space

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Acta Mathematica Sinica,English Series 2024年

作者： Kazuki IKEDA Co-design center for Quantum Advantage (C2QA) & center For Nuclear Theory Department of Physics and Astronomy Stony Brook University Department of Mathematics and Statistics & Centre for Quantum Topology and its applications(quanTA) University of Saskatchewan

Using operator algebras, we extend the theory of quantum computation on a graph to a theory of computation on an arbitrary topological space. Quantum computation is usually implemented on finite discrete sets, and the purpose of this study is to extend this to theories on arbitrary sets. The conventional theory of quantum computers can be viewed as a simplified algebraic geometry theory in which the action of SU (2) is defined on each point of a discrete set. In this study, we extend this in general as a theory of quantum fibrations in which the action of the von Neumann algebra is defined on an arbitrary topological space. The quantum channel is then naturally extended as a net of von Neumann algebras. This allows for a more mathematically rigorous discussion of general theories,including physics and chemistry, which are defined on sets that are not necessarily discrete, from the perspective of quantum computer science.

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Graphene/Molybdenum Dichalcogenide-Based van der Waals Heterostructure Photodetectors: a Review

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新型炭材料(中英文) 2024年

作者： ZHANG Xin-hua LIU Wei-Di GONG You-pin LIU Qing-feng CHEN Zhi-Gang center of Quantum Materials and Devices at Institute of Advanced Interdisciplinary Studies Soft Matter and Interdisciplinary Research Center College of Physics Chongqing University School of Chemistry and Physic ARC Research Hub in Zero-emission Power Generation for Carbon Neutrality and Center for Materials Science Queensland University of Technology State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University

Graphene is widely used in photodetection due to its high carrier mobility and wide spectral absorption range.However, the high dark current due to its low light absorption severely limits the performance of photodetection. Molybdenum dihalide(MoX2, X= S, Se and Te) has a high absorption coefficient, which can compensate high dark current in graphene-based photodetectors and result in outstanding photoelectronic properties in graphene/MoX2 van der Waals heterostructure(vdWH) photodetectors.In this review, we firstly review working principles, performance indicators, and structures of photodetectors. After that, the significance of graphene/MoX2 vdWH photodetectors are highlighted from the material fundamental perspective. Preparation methodologies and performance enhancement strategies of graphene/MoX2 vdWH photodetectors are correspondingly summarized. In the end, we highlight the current challenges and future directions of the graphene/MoX2 vdWH photodetectors. This review will guide the design of high-performance vdWH photodetectors.

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Literature classification and its applications in condensed matter physics and materials science by natural language processing

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Chinese physics B 2024年第5期33卷 117-123页

作者：吴思远朱天念涂思佳肖睿娟袁洁吴泉生李泓翁红明 Institute of physics Chinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100190China College of Materials Science and Optoelectronic Technology University of Chinese Academy of SciencesBeijing 100049China Condensed matter physics Data center of Chinese Academy of Sciences Beijing 100190China

The exponential growth of literature is constraining researchers’access to comprehensive information in related fields.While natural language processing(NLP)may offer an effective solution to literature classification,it remains hindered by the lack of labelled dataset.In this article,we introduce a novel method for generating literature classification models through semi-supervised learning,which can generate labelled dataset iteratively with limited human input.We apply this method to train NLP models for classifying literatures related to several research directions,i.e.,battery,superconductor,topological material,and artificial intelligence(AI)in materials science.The trained NLP‘battery’model applied on a larger dataset different from the training and testing dataset can achieve F1 score of 0.738,which indicates the accuracy and reliability of this scheme.Furthermore,our approach demonstrates that even with insufficient data,the not-well-trained model in the first few cycles can identify the relationships among different research fields and facilitate the discovery and understanding of interdisciplinary directions.

关键词： natural language processing text mining materials science

Towards growth of pure AB-stacked bilayer graphene single crystals

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Nano Research 2024年第5期17卷 4616-4621页

作者： Xiaowen Zhang Tao Zhou Yunlong Ren Zuo Feng Ruixi Qiao Qinghe Wang Bin Wang Jinxia Bai Muhong Wu Zhilie Tang Xu Zhou Kaihui Liu Xiaozhi Xu Guangdong Basic Research center of Excellence for Structure and Fundamental Interactions of matter Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum MaterialsSchool of PhysicsSouth China Normal UniversityGuangzhou 510006China Guangdong-Hong Kong Joint Laboratory of Quantum matter School of PhysicsSouth China Normal UniversityGuangzhou 510006China Physical Science and Engineering Division King Abdullah University of Science and TechnologyThuwal 23955–6900Saudi Arabia State Key Laboratory for Mesoscopic physics Frontiers Science Center for Nano-optoelectronicsSchool of PhysicsPeking UniversityBeijing 100871China Institute for Frontier Science Nanjing University of Aeronautics and AstronauticsNanjing 210094China International Centre for Quantum Materials Collaborative Innovation Centre of Quantum MatterPeking UniversityBeijing 100871China Songshan Lake Materials Laboratory Institute of PhysicsChinese Academy of SciencesDongguan 523808China

Given its intriguing band structure and unique tunable bandgap,AB-stacked bilayer graphene has great potentials in the applications of high-end electronics,optoelectronics and semiconductors.The epitaxial growth of AB-stacked single-crystal bilayer graphene films requires a strict AB-stacked lattice,identical orientations and seamless stitching of bilayer graphene islands.However,the particles inevitably present on the metal surface that produced during high temperature growth would induce random orientations,twisted stacking islands,and uncontrollable multilayers,which is a great challenge to overcome.Here,we propose a heat-resisting-box assisted strategy to produce nearly pure AB-stacked bilayer graphene single-crystal films on Cu/Ni(111)foils.With our technique,the particles on the Cu/Ni(111)surface are effectively eliminated,which greatly minimizes the occurrence of randomly twisted islands and uncontrollable multilayers.The as-grown AB-stacked bilayer graphene films show>99%alignment and>99%AB stacking order.Our work provides a promising method towards the growth of pure AB-stacked bilayer graphene single crystals and would accelerate its device applications.

关键词： bilayer graphene AB stacking uniform growth heat-resisting box

Matrix-Mediated Color-Tunable Ultralong Organic Room Temperature Phosphorescence of 7H-Benzo[c]carbazole Derivatives

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CCS Chemistry 2024年第3期6卷 798-811页

作者： Chen Qian Xue Zhang Zhimin Ma Xiaohua Fu Zewei Li Huiwen Jin Mingxing Chen Hong Jiang Zhiyong Ma Beijing Advanced Innovation center for soft matter Science and Engineering State Key Laboratory of Organic–Inorganic CompositesCollege of Chemical EngineeringBeijing University of Chemical TechnologyBeijing 100029 Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871

Building on the recent systematic research on 1Hbenzo[f]indole(Bd),an important advancement in constructing ultralong organic room temperature(UORTP)materials with a universal strategy via a readily obtained unit(7H-Benzo[c]carbazole,BCz)is proposed in this work.Pure powders of BCz and its derivatives merely exhibit blue fluorescence at ambient condition.However,when BCz and its derivatives are dispersed into polymer or powder matrixes,strong photo-activated green UORTP can be observed from their doped systems at room temperature.Moreover,the UORTP color can be tuned between green and yellow depending on the matrix.The ultralong phosphorescence originates from the generation of charge-separated states via radicals.The matrixes play a key role in both stabilizing charge-separated states and controlling UORTP color.More interestingly,when using polymethyl methacrylate as matrix,the doped films achieve stronger photo-activated ultralong phosphorescence underwater than in air at room temperature.Comparedwith Bd,BCz achieves better performance not only in ultralong phosphorescence properties but also in practical applications.This work gains a deeper insight into the mechanism of UORTP and paves a new approach to applying organic phosphorescent materials to underwater coating and imaging.

关键词： 7H-Benzo[c]carbazole ultralong organic room temperature phosphorescence ion radical matrix-mediated color tunning underwater application

Advances of machine learning in materials science: Ideas and techniques

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Frontiers of physics 2024年第1期19卷 155-194页

作者： Sue Sin Chong Yi Sheng Ng Hui-Qiong Wang Jin-Cheng Zheng Department of New Energy Science and Engineering Xiamen University MalaysiaSepang 43900Malaysia Engineering Research center of Micro-nano Optoelectronic Materials and Devices Ministry of EducationFujian Key Laboratory of Semiconductor Materials and ApplicationsCI Center for OSEDand Department of PhysicsXiamen UniversityXiamen 361005China

In this big data era, the use of large dataset in conjunction with machine learning (ML) has been increasingly popular in both industry and academia. In recent times, the field of materials science is also undergoing a big data revolution, with large database and repositories appearing everywhere. Traditionally, materials science is a trial-and-error field, in both the computational and experimental departments. With the advent of machine learning-based techniques, there has been a paradigm shift: materials can now be screened quickly using ML models and even generated based on materials with similar properties;ML has also quietly infiltrated many sub-disciplinary under materials science. However, ML remains relatively new to the field and is expanding its wing quickly. There are a plethora of readily-available big data architectures and abundance of ML models and software;The call to integrate all these elements in a comprehensive research procedure is becoming an important direction of material science research. In this review, we attempt to provide an introduction and reference of ML to materials scientists, covering as much as possible the commonly used methods and applications, and discussing the future possibilities.

关键词： machine learning materials science

Pressure-Tuned Intrinsic Anomalous Hall Conductivity in Kagome Magnets RV_(6)Sn_(6)(R=Gd,Tb)

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Chinese physics Letters 2024年第4期41卷 139-151页

作者：孔祥明陶咨成张蕊夏威陈旭裴翠颖应天平齐彦鹏郭艳峰杨小帆李世燕 State Key Laboratory of Surface physics Department of PhysicsFudan UniversityShanghai 200438China Shanghai Research center for Quantum Sciences Shanghai 201315China School of Physical Science and Technology ShanghaiTech UniversityShanghai 201210China ShanghaiTech Laboratory for Topological physics Shanghai 201210China Northwest Institute for Non-Ferrous Metal Research Xi'an 710016China Beijing National Laboratory for Condensed matter physics and Institute of PhysicsChinese Academy of SciencesBeijing 100190China Shanghai Key Laboratory of High-resolution Electron Microscopy Shanghai 201210China Collaborative Innovation center of Advanced Microstructures Nanjing 210093China

Exploration of exotic phenomena in magnetic topological systems is at the frontier of condensed matter physics,holding a significant promise for applications in topological spintronics.However,complex magnetic structures carrying nontrivial topological properties hinder its progresses.Here,we investigate the pressure effect on the novel topological kagome magnets GdV_(6)Sn_(6) and TbV_(6)Sn_(6) to dig out the interplay between magnetic Gd/Tb layers and nonmagnetic V-based kagome sublattice.The pressure-tuned magnetic transition temperature Tm in both the compounds exhibit a turning point at the critical pressure P_(c),accompanied with a sign reversal in anomalous Hall effect(AHE).The separation of intrinsic and extrinsic contributions using the Tian-Ye-Jin scaling model suggests that the intrinsic mechanism originating from the electronic Berry curvature holds the priority in the competition with extrinsic mechanism in AHE.The above-mentioned findings can be attributed to the combined effect of pressure-tuned band topology and magnetic interaction in segregated layers.Our results provide a practical route to design and manipulate the intrinsic AHE in magnetic topological materials.

关键词： holds frontier hinder

探索Bi_(2)SeO_(5)的高介电性能:从块体到双层和单层

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Science China Materials 2024年第3期67卷 906-913页

作者：董欣月何育彧管乐祝元昊吴金雄付会霞颜丙海 Tianjin Key Lab for Rare Earth Materials and applications Center for Rare Earth and Inorganic Functional MaterialsSmart Sensor Interdisciplinary Science CenterSchool of Materials Science and EngineeringNankai UniversityTianjin 300350China center of Quantum Materials and Devices College of PhysicsChongqing UniversityChongqing 401331China Chongqing Key Laboratory for Strongly Coupled physics Chongqing UniversityChongqing 401331China Department of Condensed matter physics Weizmann Institute of ScienceRehovot 7610001Israel

Bi_(2)SeO_(5)是一种具有优异电绝缘性能的范德华(vdW)层状介电材料,引起了极大关注.然而,目前关于Bi_(2)SeO_(5)的研究主要停留在实验层面,仍然缺乏对其原子级薄膜的介电性能的相关理论认识.本文通过第一性原理计算确定了Bi_(2)SeO_(5... 详细信息

Bi_(2)SeO_(5)是一种具有优异电绝缘性能的范德华(vdW)层状介电材料,引起了极大关注.然而,目前关于Bi_(2)SeO_(5)的研究主要停留在实验层面,仍然缺乏对其原子级薄膜的介电性能的相关理论认识.本文通过第一性原理计算确定了Bi_(2)SeO_(5)的介电性能,发现其块体、双层和单层均具有超高平均介电常数(εr>20).研究表明,单层Bi_(2)SeO_(5)与双层Bi_(2)O_(2)Se之间的导带和价带能量偏移量均大于1 eV,表明单层Bi_(2)SeO_(5)依然可作为原子薄Bi_(2)O_(2)Se的良好介电层.此外,不同于h-BN或其他2D vdW绝缘体,Bi_(2)SeO_(5)的εr由其离子部分主导,且随着厚度的减小几乎保持不变.计算发现,单层Bi_(2)SeO_(5)的等效氧化层厚度可薄至0.3 n m,且单层Bi_(2)SeO_(5)在拉伸或压缩应变达到6%时均能保持高介电常数,这极大地促进了它与各种二维半导体的集成.本工作证明单层Bi_(2)SeO_(5)可以作为高性能二维电子器件良好的封装和介电层.

关键词： Bi_(2)SeO_(5) high-κ equivalent oxide thickness dielectric constant van der Waals first-principles calculations