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Descriptor-augmented machine learning for enzyme-chemical interaction predictions

Synthetic and Systems Biotechnology 2024年第2期9卷 259-268页

作者： yilei han Haoye Zhang Zheni Zeng Zhiyuan Liu Diannan Lu Zheng Liu Department of Chemical Engineering Tsinghua UniversityBeijing100084China Department of Computer Science and Technology Tsinghua UniversityBeijing100084China

Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals,as they could characterize enzymes and chemicals from the physicochemical and evolutionary *** study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships *** curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold *** influence of protein and chemical descriptors was assessed in three scenarios,which were predicting the activity of unknown relations between known enzymes and known chemicals(new relationship evaluation),predicting the activity of novel enzymes on known chemicals(new enzyme evaluation),and predicting the activity of new chemicals on known enzymes(new chemical evaluation).The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes,whereas chemical descriptors appear no effect.A variety of sequence-based and structure-based protein descriptors were constructed,among which the esm-2 descriptor achieved the best *** enzyme families as labels showed that descriptors could cluster proteins well,which could explain the contributions of descriptors to the machine learning *** a counterpart,in the new chemical evaluation,chemical descriptors made significant improvement in four out of the seven datasets,while protein descriptors appear no *** attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the *** results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein

关键词： Enzyme-substrate interaction Enzyme design Machine learning Descriptor

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Recent progress in enzymatic functionalization of carbon-hydrogen bonds for the green synthesis of chemicals

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Chinese Journal of Chemical Engineering 2020年第10期28卷 2499-2506页

作者： Zheyu Wang Yupei Jian yilei han Zhongwang Fu Diannan Lu Jianzhong Wu Zheng Liu Key Lab of Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Department of Chemical and Environmental Engineering University of CaliforniaRiversideCA 92521USA

Enzymatic reactions take place with high chemo-, regio-, and stereo-selectivity, appealing for the direct functionalization of abundant and inexpensive compounds with C-H bonds to make fine chemicals such as high-value intermediates and pharmaceuticals. This review summarizes recent progress in the enzymatic functionalization of C-H bonds with an emphasis on heme enzymes such as cytochrome P450 s, chloroperoxidase and unspecific peroxygenases. Specific examples are discussed to elucidate the applications of the molecular and process engineering approaches to overcome the challenges hindering enzymatic C-H functionalization. Also discussed is the recent development of the chemo-enzymatic cascade as an effective way to integrate the power of metal catalysis and enzymatic catalysis for C-H functionalization.

关键词： Biocatalysis Biochemical engineering Enzyme C-H functionalization Chloroperoxidase

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基于理论可行性的生物合成路径评估方法

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清华大学学报（自然科学版） 2023年第5期63卷 697-703页

作者：魏奕新韩一蕾卢滇楠邱彤清华大学化学工程系北京100084 工业大数据系统与应用北京市重点实验室北京100084

合成生物学是实现化工绿色化、可持续发展的有效方法之一。代谢途径重构是合成生物学中工业菌种开发与化学品生物催化合成的关键步骤,目的在于确定宿主内合成目标化合物的反应路径与底物,是酶定向进化、实现目标物质生物合成的基础。考... 详细信息

合成生物学是实现化工绿色化、可持续发展的有效方法之一。代谢途径重构是合成生物学中工业菌种开发与化学品生物催化合成的关键步骤,目的在于确定宿主内合成目标化合物的反应路径与底物,是酶定向进化、实现目标物质生物合成的基础。考虑到生物代谢网络的复杂性,代谢途径重构一般会得到较为庞大的路径结果。为了提高效率、减少无效的实验尝试,合理、有效的路径评估与筛选是重要与必须的。针对已有路径评估方法存在的问题,该文构建了一种生物合成路径评估与排序方法,设计了6个反映路径理论可行性的评估指标,结合层次分析法实现了合理、可解释的路径推荐。通过实例测试,证明了所提出的路径评估方法的有效性。该路径评估方法可降低实验的试错成本,为增加生物逆合成工具的实用性提供了基础。

关键词：合成生物学生物逆合成路径评估层次分析法生物催化合成

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Physicochemical principles of hydrogen metallurgy in blast furnace

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Journal of Iron and Steel Research International 2024年第1期31卷 46-63页

作者： han-jie Guo School of Metallurgical and Ecological Engineering University of Science and Technology BeijingBeijing100083China Beijing Key Laboratory of Special Melting and Preparation of High-End Metal Materials Beijing100083China

Based on the stoichiometric method and the free energy minimization method,an ideal model for the reduction of iron oxides by carbon and hydrogen under blast furnace conditions was established,and the reduction efficiency and theoretical energy consumption of the all-carbon blast furnace and the hydrogen-rich blast furnace were *** results show that after the reduction reaction is completed at the bottom of the blast furnace,the gas produced by reduction at 1600℃still has a certain excessive reduction capacity,which is due to the hydrogen brought in by the hydrogen-rich blast as well as the excess carbon monoxide generated by the reaction of the coke and the oxygen brought in by the *** the process of the gas with excessive reduction capacity rising from the bottom of the blast furnace and gas reduction process,the excessive reduction capacity of the gas gradually decreases with the increase in the dydrogen content in the *** the all-carbon blast furnace,the excess gas reduction capacity is the strongest,and the total energy consumption per ton of iron reduction is the *** shows that,for the current operation mode of the blast furnace,adding hydrogen in the blast furnace cannot reduce the consumption of carbon required for reduction per ton of iron,but rather increases the consumption of carbon.

关键词： Hydrogen metallurgy Excess gas reduction capacity Theoretical energy consumption Hydrogen-rich blast furnace Thermodynamic model Gibbs minimum free energy method

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Engineered plant extracellular vesicles for autoimmune diseases therapy

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Nano Research 2024年第4期17卷 2857-2873页

作者： Ruina han Yan Wu Yafei han Xiangfei Liu han Liu Jiacan Su Institute of Translational Medicine Shanghai UniversityShanghai 200444China Organoid Research Center Shanghai UniversityShanghai 200444China National Center for Translational Medicine(Shanghai)SHU Branch Shanghai UniversityShanghai 200444China Department of Orthopedics Shanghai Zhongye HospitalShanghai 200941China Department of Orthopedics Xinhua HospitalShanghai Jiao Tong University School of MedicineShanghai 200092China

Autoimmune diseases(AID)encompass a diverse array of conditions characterized by immune system dysregulation,resulting in aberrant responses of B cells and T cells against the body’s own healthy *** extracellular vesicles(PEVs)are nanoscale particles enclosed by phospholipid bilayers,secreted by plant cells,which facilitate intercellular communication by transporting various bioactive *** to their nanoscale structure,safety,abundant sources,low immunogenicity,high yield,biocompatibility,and effective targeting of the colon and liver,PEVs are regarded as a promising platform for the treatment of *** review provides a comprehensive summary of PEV biogenesis,physicochemical and biological properties,internalization mechanisms,isolation methods,and their applications in various diseases,with a specific focus on their potential roles in ***,we propose engineering approaches and administration methods for ***,we present an overview of the advantages and challenges associated with utilizing PEVs for the treatment of *** gaining a comprehensive understanding of PEVs,we anticipate the development of innovative therapeutic strategies for *** and engineered PEVs hold substantial promise as a valuable resource for innovative technologies in AID treatment.

关键词： autoimmune diseases plant extracellular vesicles extracellular vesicles engineering modification

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FAST unveils a new era in the discovery of long-period pulsars in globular clusters

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Science China(Physics,Mechanics & Astronomy) 2024年第6期67卷 185-186页

作者： Zhanwen han International Centre of Supernovae Yunnan Key LaboratoryYunnan ObservatoriesChinese Academy of SciencesKunming 650011China

Globular clusters(GC)are among the oldest celestial bodies in the Milky *** possessing millions of stars and have been going through abundant stellar interactions,GCs are futile ground for hunting for compact objects,particularly,neutron stars.A significant number of fast-spinning millisecond pulsars(MSPs)have been discovered,comprising the majority of known GC pulsars.

关键词： stars pulsars abundant

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On equivalence of state-based potential games

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Science China(Information Sciences) 2024年第6期67卷 313-327页

作者： han WU Jinhuan WANG Institute of Mathematics School of ScienceHebei University of Technology

In this paper, we explore state-based potential games using the semi-tensor product of ***, applying the potential equation, we derive both a necessary and sufficient condition as well as a sufficient condition to verify whether a state-based game qualifies as a potential game. Next, we present two static equivalence conditions of state-based potential games. We then delve into dynamic equivalence. We propose a criterion that allows us to identify state-based games that are dynamically equivalent to state-based potential games and share similar dynamic properties. Ultimately, we introduce the concept of state-based networked evolutionary games. We provide a necessary and sufficient condition to ensure that a state-based networked evolutionary game can be classified as a state-based potential game.

关键词： semi-tensor product of matrices state-based potential game verification equivalence state-based networked evolutionary game

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Track-before-detect for bistatic radar based on pseudo-spectrum

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Chinese Journal of Aeronautics 2024年第1期37卷 236-246页

作者： Tao han Gongjian ZHOU School of Electronics and Information Engineering Harbin Institute of TechnologyHarbin 150001China Key Laboratory of Marine Environmental Monitoring and Information Processing Ministry of Industry and Information TechnologyHarbin 150001China

Track-Before-Detect(TBD) is an efficient method to detect dim targets for radars. Conventional TBD usually follows an approximate motion model of the target, which may cause an inaccurate integration of the target energy. A TBD technique on basis of pseudo-spectrum in mixed coordinates adopting an accurate motion model for bistatic radar system is developed in this *** predicted position in bistatic polar plane is derived according to a nonlinear function that exactly describes the constant Cartesian velocity motion. Then around the predicted position, a pseudo-spectrum is formulated and its samples are accumulated to the integration frame for energy integration. The evolution of the state and the procedure of accumulation of the target energy are derived elaborately. The superior performance of the proposed method is demonstrated by some simulations.

关键词： Weak target detection Bistatic radar Track-before-detect Pseudo-spectrum Multiframe integration

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Thermodynamic and experimental study of high-temperature roasting of blast furnace gas ash for recovery of metallic zinc and iron

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Journal of Iron and Steel Research International 2024年第1期31卷 108-120页

作者： Zi-han Wang Jing Guo han-jie Guo Bin Li School of Metallurgical Engineering University of Science and Technology BeijingBeijing100083China School of Metallurgical Engineering Xi’an University of Architecture and TechnologyXi’an710055ShaanxiChina

A high-temperature reduction roasting method was used to achieve metallic iron and zinc recovery from blast furnace gas ash(BFA).The reduction processes for Zn-containing and Fe-containing oxides were analyzed in detail by using ther-modynamic equilibrium calculation and the principle of minimum free *** results showed that the main reaction in the system is the reduction of ZnFe_(2)_(4)and iron *** the full temperature range,iron oxides were more easily reduced than zinc *** of the amount of CO contained in the system,the reduction of ZnO to Zn was difficult to proceed below the boiling point(906℃)of *** the reduction temperature is below 906℃,the reduction process of zinc ferrate was ZnFe_(2)_(4)→ZnO;when the reduction temperature is above 906℃,its reduction process becomed ZnFe_(2)_(4)→ZnO→Zn(g).The metallization and dezincification rates of the BFA gradually increased with increasing reaction *** the C/O ratio increased,the metallization and dezincification rates first increased and then *** effect of reduction time on BFA reduction was similar to that of reaction temperature.

关键词： Blast furnace gas ash Thermodynamics Zinc removal Iron reduction High-temperature reduction roasting Integrated utilization

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In situ probing of electron transfer at the dynamic MoS_(2)/graphene–water interface for modulating boundary slip

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Nano Research 2024年第8期17卷 7513-7521页

作者： Yishu han Dameng Liu State Key Laboratory of Tribology in Advanced Equipment Tsinghua UniversityBeijing 100084China

The boundary slip condition is pivotal for nanoscale fluid *** research has primarily focused on simulating the interaction mechanism between the electronic structure of two-dimensional materials and slip of water at the nanoscale,raising the possibility for ultralow friction flow of water at the ***,experimentally elucidating electronic interactions at the dynamic solid–liquid interface to control boundary slip poses a significant *** this study,the crucial role of electron structures at the dynamic solid–liquid interface in regulating slip length was ***,the slip length of water on the molybdenum disulfide/graphene(MoS_(2)/G)heterostructure(100.9±3.6 nm)significantly exceeded that of either graphene(27.7±2.2 nm)or MoS_(2)(5.7±3.1 nm)*** was also analyzed how electron transfer significantly affected interface *** electrons played a crucial role in determining the type and proportion of excitons at both MoS_(2)–water and MoS_(2)/G–water ***,by applying voltage,distinct photoluminescence(PL)responses at static and dynamic interfaces were discovered,achieving a 5-fold modulation in PL intensity and a 2-fold modulation in the trion to exciton intensity *** electrons transfer from the top graphene to the bottom MoS_(2)at the MoS_(2)/G–water interface,reducing surface charge ***,the reduction of electrostatic interactions between the solid and water leads to an increased slip length of water on the MoS_(2)/G *** process aids in comprehending the origin of frictional resistance at the subatomic *** work establishes a foundation for actively controlling and designing of fluid transport at the nanoscale.

关键词： two-dimensional materials solid-liquid interface photoluminescence excitons electron transfer slip length

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