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Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

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Science china(life Sciences) 2007年第3期50卷 392-402页

作者： li jing1 & wang wei1,2 1 national laboratory of solid state microstructure and department of physics, nanjing univer.ity, nanjing 210093, china 2 Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, china 1. national laboratory of solid state microstructure and department of physics Nanjing University Nanjing 210093 China 2. Interdisciplinary Center of Theoretical Studies Chinese Academy of Sciences Beijing 100080 China

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned se- quences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitu- tion matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9.

关键词： Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

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Quantitative lithium substitution of carboxyl hydrogens in polyacrylic acid binder enables robust SiO electrodes with durable lithium storage stability

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Journal of Energy Chemistry 2024年第10期97卷 352-360,I0007页

作者： weihua wang Wenyi li Siyi jing Huiping Yang Huiqun wang ling Huang Yuxiang Mao Xikun Pang Yudai Huang li Zhang state Key laboratory of Physical Chemistry of solid Surfaces Department of Chemical and Biochemical EngineeringCollege of Chemistry and Chemical EngineeringCollaborative Innovation Centre of Chemistry for Energy Materials(iChEM)Xiamen UniversityXiamen 361005FujianChina state Key laboratory of Chemistry and Utilization of Carbon-Based Energy Resources College of ChemistryXinjiang UniversityUrumqi 830017XinjiangChina

The design of advanced binders plays a critical role in stabilizing the cycling performance of large-volume-effect silicon monoxide(SiO)*** the classic polyacrylic acid(PAA)binder,the self-association of-COOH groups in PAA leads to the formation of intramolecular and intermolecular hydrogen bonds,greatly weakening the bonding force of the binder to SiO ***,strengthening the binder-material interaction from the perspective of binder molecular regulation poses a significant ***,a modified PAA-li_(x)(0.25≤x≤1)binder with prominent mechanical properties and adhesion strength is specifically synthesized for SiO anodes by quantitatively substituting the carboxylic hydrogen with *** appropriate lithium substitution(x=0.25)not only effectively increases the number of hydrogen bonds between the PAA binder and SiO surface owing to charge repulsion effect between ions,but also guarantees moderate entanglement between PAA-li_x molecular chains through the ion-dipole *** such,the PAA-li_(0.25)/SiO electrode exhibits exceptional mechanical properties and the lowest volume change,as well as the optimum cycling(1237.3 mA h g^(-1)after 100cycles at 0.1 C)and rate performance(1000.6 mA h g^(-1)at 1 C),significantly outperforming the electrode using pristine PAA *** work paves the way for quantitative regulation of binders at the molecular level.

关键词： Polyacrylic acid binder SiO anode Quantitative lithium substitution Charge repulsion effect Adhesion strength

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Composition analysis of Compound Shenhua Tablet,a seven-herb Chinese medicine for IgA nephropathy:evaluation of analyte-capacity of the assays

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Chinese Journal of Natural Medicines 2024年第2期22卷 178-192页

作者： ZHANG Haiyan wang Qiuyue wang Jianan ZHANG Sichao JIA weiwei HE Ning XIA Xiaoyan wang Ting LAI liyu li Jiaying DU jing OLALEYE Olajide E CHEN Xiangmei YANG Junling li Chuan Graduate School Tianjin University of Traditional Chinese MedicineTianjin 301617China state Key laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China School of Pharmacy University of Chinese Academy of SciencesChinese Academy of SciencesBeijing 100049China department of Nephrology First Medical Center of Chinese PLA General HospitalNephrology Institute of the Chinese People’s Liberation ArmyNational Key Laboratory of Kidney DiseasesNational Clinical Research Center for Kidney DiseasesBeijing Key Laboratory of Kidney Disease ResearchBeijing 100853China Zhongshan Institute for Drug Discovery Zhongshan 528400China Haihe laboratory of Modern Chinese Medicine Tianjin 301617China

Compound Shenhua Tablet,a medicine comprising seven herbs,is employed in treating IgA *** study aimed to meticulously analyze its chemical *** on a list of candidate compounds,identified through extensive literature review pertinent to the tablet’s herbal components,the composition analysis entailed the systematic identification,characterization,and quantification of the *** analyte-capacity of LC/ESI-MS-based and GC/EI-MS-based assays was *** identified and characterized constituents were quantified to determine their content levels and were ranked based on the constituents’daily doses.A total of 283 constituents,classified into 12 distinct categories,were identified and characterized in the Compound Shenhua *** constituents exhibited content levels of 1−10982μg·g^(−1),with daily doses of 0.01−395μmol·d^(−1).The predominant constituents,with daily doses of≥10μmol·d^(−1),include nine organic acids(citric acid,quinic acid,chlorogenic acid,cryptochlorogenic acid,gallic acid,neochlorogenic acid,isochlorogenic acid C,isochlorogenic acid B,and linoleic acid),five iridoids(specnuezhenide,nuezhenoside G13,nuezhenidic acid,secoxyloganin,and secologanoside),two monoterpene glycosides(paeoniflorin and albiflorin),a sesquiterpenoid(curzerenone),a triterpenoid(oleanolic acid),and a phenylethanoid(salidroside).Additionally,there were 83,126,and 55 constituents detected in the medicine with daily doses of 1–10,0.1–1,and 0.01–0.1μmol·d^(−1),*** combination of the LC/ESI-MS-based and GC/EI-MS-based assays demonstrated a complementary relationship in their analyte-capacity for detecting the constituents present in the *** comprehensive composition analysis establishes a solid foundation for further pharmacological research on Compound Shenhua Tablet and facilitates the quality evaluation of this complex herbal medicine.

关键词： Compound Shenhua Tablet Composition analysis Analyte-capacity

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A Polyvinyl Alcohol/Acrylamide Hydrogel with Enhanced Mechanical Properties Promotes Full-Thickness Skin Defect Healing by Regulating Immunomodulation and Angiogenesis Through Paracrine Secretion

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Engineering 2024年第6期37卷 138-151页

作者： Peng wang liping Qian Huixin liang Jianhao Huang jing Jin Chunmei Xie Bin Xue Jiancheng Lai Yibo Zhang lifeng Jiang Lan li Qing Jiang state Key laboratory of Pharmaceutical Biotechnology Division of Sports Medicine and Adult Reconstructive SurgeryDepartment of Orthopedic SurgeryNanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjing UniversityNanjing 210008China Jiangsu Engineering Research Center for 3D Bioprinting Nanjing 210008China Institute of Medical 3D Printing Nanjing UniversityNanjing 210093China Centre for Experimental Animals Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjing UniversityNanjing 210008China College of Aeroplane Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China national laboratory of solid state microstructures Department of PhysicsNanjing UniversityNanjing 210093China department of Chemical Engineering Stanford UniversityStanfordCA 94305USA department of Orthopedic Surgery The Second Affiliated Hospital Zhejiang University School of MedicineOrthopedic Research Institute of Zhejiang UniversityKey Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang ProvinceHangzhou 310009China

Hydrogel-based tissue-engineered skin has attracted increased attention due to its potential to restore the structural integrity and functionality of ***,the mechanical properties of hydrogel scaffolds and natural skin are substantially ***,we developed a polyvinyl alcohol(PVA)/acrylamide based interpenetrating network(IPN)hydrogel that was surface modified with polydopamine(PDA)and termed *** Dopa-gel exhibited mechanical properties similar to native skin tissue and a superior ability to modulate paracrine ***,a tough scaffold with tensile resistance was fabricated using this hydrogel by three-dimensional *** results showed that the interpenetration of PVA,alginate,and polyacrylamide networks notably enhanced the mechanical properties of the *** modification with PDA endowed the hydrogels with increased secretion of immunomodulatory and proangiogenic *** an in vivo model,Dopa-gel treatment accelerated wound closure,increased vascularization,and promoted a shift in macrophages from a proinflammatory M1 phenotype to a prohealing and anti-inflammatory M2 phenotype within the wound ***,the focal adhesion kinase(FAK)/extracellular signal-related kinase(ERK)signaling pathway may mediate the promotion of skin defect healing by increasing paracrine secretion via the ***,proangiogenic factors can be induced through Rho-associated kinase-2(ROCK-2)/vascular endothelial growth factor(VEGF)-mediated paracrine secretion under tensile stress *** together,these findings suggest that the multifunctional Dopa-gel,which has good mechanical properties similar to those of native skin tissue and enhanced immunomodulatory and angiogenic properties,is a promising scaffold for skin tissue regeneration.

关键词： Polyvinyl alcohol/acrylamide hydrogel Mechanical property enhancement Paracrine effect Skin regeneration Signaling pathways

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Negative enthalpy alloys and local chemical ordering:a concept and route leading to synergy of strength and ductility

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national Science Review 2024年第4期11卷 172-184页

作者： Zibing An Tao Yang Caijuan Shi Shengcheng Mao lihua wang Ang li wei li Xianmeng Xue Ming Sun Yifan Bai Yapeng He Fuzeng Ren Zhouguang Lu Ming Yan Yang Ren Chain-Tsuan liu Ze Zhang Xiaodong Han Beijing Key Lab of microstructure and Property of Advanced Materials College of Materials Science &Engineering Beijing University of Technology department of Materials Science and Engineering City University of Hong Kong Key laboratory of Partial Acceleration physics& Technology Institute of High Energy PhysicsChinese Academy of Sciences department of Materials Science &Engineering Southern University of Science and Technology department of physics City University of Hong Kong state Key laboratory of Silicon Materials Department of Materials Science and Engineering Zhejiang University

solid solutions are ubiquitous in metals and alloys. Local chemical ordering(LCO) is a fundamental sub-nano/nanoscale process that occurs in many solid solutions and can be used as a microstructure to optimize strength and ductility. However, the formation of LCO has not been fully elucidated, let alone how to provide efficient routes for designing LCO to achieve synergistic effects on both superb strength and ductility. Herein, we propose the formation and control of LCO in negative enthalpy alloys. With engineering negative enthalpy in solid solutions, genetic LCO components are formed in negative enthalpy refractory high-entropy alloys(RHEAs). In contrast to conventional ‘trial-and-error' approaches, the control of LCO by using engineering negative enthalpy in RHEAs is instructive and results in superior strength(1160 MPa) and uniform ductility(24.5%) under tension at ambient temperature, which are among the best reported so far. LCO can promote dislocation cross-slip, enhancing the interaction between dislocations and their accumulation at large tensile strains; sustainable strain hardening can thereby be attained to ensure high ductility of the alloy. This work paves the way for new research fields on negative enthalpy solid solutions and alloys for the synergy of strength and ductility as well as new functions.

关键词： negative enthalpy alloys local chemical ordering strength ductility dislocation

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Mechanical property and thermal shock behavior of tungsten-yttria-stabilized zirconia cermet fabricated by spark plasma sintering

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Tungsten 2024年第1期6卷 134-140页

作者： lin-Chao Zhang Ke jing Rui liu Zhuo-Ming Xie Jun-Feng Yang Gang li Xian-Ping wang Xue-Bang Wu Qian-Feng Fang Chang-Song liu Key laboratory of Materials physics Institute of Solid State PhysicsHFIPSChinese Academy of SciencesHefei 230031China univer.ity of Science and Technology of china Hefei 230026China Science and Technology on Reactor Fuel and Materials laboratory Nuclear Power Institute of ChinaChengdu 610041China

The cermet fuels have been considered as a potential key component for the nuclear thermal propulsion,and the homogeneity of the fuel particles in the metal matrix plays a crucial role in stabilizing the structure at extremely high *** this work,liquid paraffin was used as additive to improve the distribution of yttria-stabilized zirconia(YSZ,an appropriate surrogate for UO_(2) fuel)microspheres in the tungsten(W)matrix,and the W-YSZ cermet wafers(volume ratio 1:1)with a relative density of 97.6%were fabricated by spark plasma sintering with a specifically designed *** effects of the paraffin dosage(0-5 wt.%)on the homogeneity,microstructure,mechanical properties,and the thermal conductivity of W-YSZ cermet were *** W-YSZ sample with 2 wt.%paraffin shows the highest homogeneity and exhibits the best comprehensive properties,including the ultimate tensile strength of 132.2 MPa at 600℃,the bending strength of455 MPa and thermal conductivity of 50 W·m^(-1)·K^(-1)at room ***,the cermet could keep structurally sound after thermal shocked at a heat load of 20 MW·m^(-2).These results would be helpful for the design and optimization of the cermet fuels in the nuclear thermal propulsion.

关键词： Nuclear thermal propulsion Tungsten Cermet liquid paraffin Thermal shock

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Two-dimensional materials for future information technology: status and prospects

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Science china(Information Sciences) 2024年第6期67卷 1-147页

作者： Hao QIU Zhihao YU Tiange ZHAO Qi ZHANG Mingsheng XU Peifeng li Taotao li Wenzhong BAO Yang CHAI Shula CHEN Yiqi CHEN Hui-Ming CHENG Daoxin DAI Zengfeng DI Zhuo DONG Xidong DUAN Yuhan FENG Yu FU jingshu GUO Pengwen GUO Yue HAO Jun HE Xiao HE jingyi HU weida HU Zehua HU Xinyue HUANG Ziyang HUANG Ali IMRAN Ziqiang KONG Jia li Qian li weisheng li Lei liAO Bilu liU Can liU Chunsen liU Guanyu liU Kaihui liU liwei liU Sheng liU Yuan liU Donglin LU likuan MA Feng MIAO Zhenhua NI jing NING Anlian PAN Tian-ling REN Haowen SHU litao SUN Yue SUN Quanyang TAO Zi-Ao TIAN Dong wang Hao wang Haomin wang Jialong wang Junyong wang Wenhui wang Xingjun wang Yeliang wang Yuwei wang Zhenyu wang Yao WE... School of Electronic Science and Engineering Nanjing University School of Integrated Circuits Interdisciplinary Research Center for Future Intelligent Chips (Chip-X)Nanjing University School of Integrated Circuit Science and Engineering Nanjing University of Posts and Telecommunications state Key laboratory of Infrared physics Shanghai Institute of Technical Physics Chinese Academy of Sciences School of physics and Key Lab of Quantum Materials and Devices of the Ministry of Education School of Electronic Science & EngineeringSoutheast University College of Integrated Circuits State Key Laboratory of Silicon and Advanced Semiconductor MaterialsZhejiang University Suzhou laboratory state Key laboratory of Integrated Chips and Systems School of MicroelectronicsFudan University Shaoxin laboratory department of Applied physics The Hong Kong Polytechnic University Key laboratory for Micro-Nano physics and Technology of Hunan Province College of Materials Science and EngineeringHunan University College of Integrated Circuits Zhejiang University Shenzhen Geim Graphene Center Shenzhen Key Laboratory of Layered Materials for Value-Added ApplicationsTsinghua-Berkeley Shenzhen Institute & Institute of Materials ResearchTsinghua Shenzhen International Graduate SchoolTsinghua University state Key laboratory of Extreme Photonics and Instrumentation College of Optical Science and EngineeringInternational Research Center for Advanced PhotonicsZijingang CampusZhejiang University national Key laboratory of Materials for Integrated Circuits Shanghai Institute of Microsystem and Information TechnologyChinese Academy of Sciences CAS Key laboratory of Nanophotonic Materials and Devices & Key laboratory of Nanodevices and Applications i-LabSuzhou Institute of Nano-Tech and Nano-Bionics (SINANO)Chinese Academy of Sciences College of Chemistry and Chemical Engineering Hunan University Key laboratory of Quantum state Construction and Manipulation (Ministry of Education) Department of PhysicsRenmin University of China School

Over the past 70 years, the semiconductor industry has undergone transformative changes,largely driven by the miniaturization of devices and the integration of innovative structures and materials. Two-dimensional(2D) materials like transition metal dichalcogenides(TMDs) and graphene are pivotal in overcoming the limitations of silicon-based technologies, offering innovative approaches in transistor design and functionality, enabling atomic-thin channel transistors and monolithic 3D integration. We review the important progress in the application of 2D materials in future information technology, focusing in particular on microelectronics and optoelectronics. We comprehensively summarize the key advancements across material production, characterization metrology, electronic devices, optoelectronic devices, and heterogeneous integration on silicon. A strategic roadmap and key challenges for the transition of 2D materials from basic research to industrial development are outlined. To facilitate such a transition, key technologies and tools dedicated to 2D materials must be developed to meet industrial standards, and the employment of AI in material growth, characterizations, and circuit design will be essential. It is time for academia to actively engage with industry to drive the next 10 years of 2D material research.

关键词： two-dimensional (2D) materials information technology production technology standardization of characterization microelectronic devices optoelectronic devices multi-functional integration

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Detailed assessment of homology detection using different substitution matrices

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Chinese Science Bulletin 2006年第13期51卷 1538-1545页

作者： li jing wang wei national Lab of solid state microstructure Department of Physics and Institute of Biophysics Nanjing University Nanjing 210093 China

Homology detection plays a key role in bioinformatics, whereas substitution matrix is one of the most important components in homology detec- tion. Thus, besides the improvement of alignment algorithms, another effective way to enhance the accuracy of homology detection is to use proper substitution matrices or even construct new matrices. A study on the features of various matrices and on the comparison of the performances between differ- ent matrices in homology detection enable us to choose the most proper or optimal matrix for some specific applications. In this paper, by taking BLOSUM matrices as an example, some detailed features of matrices in homology detection are stud- ied by calculating the distributions of numbers of recognized proteins over different sequence identities and sequence lengths. Our results clearly showed that different matrices have different preferences and abilities to the recognition of remote homologous proteins. Furthermore, detailed features of the vari- ous matrices can be used to improve the accuracy of homology detection.

关键词：替代矩阵序列一致性序列长度同种探测

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Cracking Behavior in Additively Manufactured Pure Tungsten

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Acta Metallurgica Sinica(English Letters) 2019年第1期32卷 127-135页

作者： Dian-Zheng wang Kai-Lun li Chen-Fan Yu jing Ma wei liu Zhi-Jian Shen state Key laboratory of New Ceramic and Fine Processing School of Materials Science and Engineering Tsinghua University department of Materials and Environmental Chemistry Arrhenius Laboratory Stockholm University

In this study, near fully dense(96.5%) pure tungsten bulks were additively manufactured and the cracking behavior was investigated. A crack network with a spacing of ～100 lm was observed in the fabricated bulks. It was observed that the laser scanning strategy, which could tailor the microstructure, affected the crack distribution pattern in fabricated *** calculated surface temperature difference(7300 K) was much higher than the cracking criterion(800 K) of tungsten,indicating that cracking is almost inevitable in laser additive manufacturing of tungsten. It could be concluded that crack network formed because the cracks emerged in every laser molten track and then interconnected in the layer-by-layer building process.

关键词： Tungsten Selective laser melting Cracking microstructure

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Non-monotonic influence of a magnetic field on the electrochemical behavior of Fe_(78)Si_9B_(13) glassy alloy in NaOH and NaCl solutions

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International Journal of Minerals,Metallurgy and Materials 2014年第10期21卷 1009-1018页

作者： Hong-di Zhang Xiao-yu li jing Pang li-juan Yin Hai-jian Ma Ying-jie li Yan liu wei-min wang Key laboratory for liquid-solid Structural Evolution and Processing of Materials (Ministry of Education) Shandong University Qingdao Yunlu Energy Technology Co. Ltd. School of Mechanical and Electrical Engineering Weifang University

The corrosion behavior and microstructure of Fe78Si9B13 glassy alloy in NaOH and NaCl solutions under a 0.02-T magnetic field were investigated through electrochemical testing and scanning electron microscopy （SEM）. The current-density prepeak （PP） in the anodic polarization curves in low-concentration NaOH solutions （classified as type I） tends to disappear when the NaOH concentration is increased to 0.4 mol/L and the magnetic field is applied. Under the magnetic field, the height of the second current-density peak is increased in low-concentration NaOH solutions （type I） but decreased in high-concentration NaOH solutions （type Ⅱ）. The non-monotonic effect of the magnetic field was similarly observed in the case of polarization curves of samples measured in NaCl solutions, Ring-like corroded patterns and round pits are easily formed under the magnetic field in NaOH and NaC1 solutions. These experimental results were discussed in terms of the magnetohydrodynamic （MHD） effect.

关键词： amorphous alloys electrochemical behavior magnetic field anodic polarization micrographs

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