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Engineering 2024年第1期32卷 18-28页

作者： Wei Chen Chi Song Liang Leng Sanyin Zhang Shilin Chen State Key Laboratory of Southwestem chinese Medicine Resources Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revo-lutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identi-fication and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were sum-marized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable for-mats were introduced.Subsequently,the key applications of Al methods in the different stages of GPCR drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an Al-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of Al in GPCR research were deliberated.In conclusion,continued advance-ments in Al techniques coupled with interdisciplinary collaborations will offer great potential for improv-ing the efficiency of GPCR ligand discovery.

关键词： G protein-coupled receptor Ligand Artificial intelligence Multi-omics Drug discovery

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First-principles study of substitutional solute and carbon interactions in tungsten

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Tungsten 2022年第3期4卷 231-238页

作者： Xiang-Shan Kong Chi Song Liang Chen Zhuo-Ming Xie Chang-song Liu Jie Hou Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials Ministry of EducationShandong UniversityJinan250061China Key Laboratory of Materials Physics Institute of Solid State PhysicsChinese Academy of SciencesHefei230031China College of Science Jinling Institute of TechnologyNanjing211169China Department of Mining and Materials Engineering McGill UniversityMontrealQCH3A 0C5Canada

Interstitial carbon and substitutional transition metal(TM)solutes are common impurities in tungsten and tungsten alloys.Yet,despite its important role in affecting mechanical and irradiation performances of tungsten,the interplay between these impurities remains largely unknown.In this work,we performed systematic first-principles simulations to study the interaction between carbon and TM solutes.By calculating related binding energies,we found that interplay between carbon and TM solutes is dominated by elastic interactions,with carbon generally showing attractions to TM solutes.Further,including vacancies in our calculation,we found that all solute-vacancy-carbon complexes are energetically stable with respect to associated point defects.Additional analysis shows that vacancy-carbon binding is generally weakened by TM solutes,while carbon also in turn reduces the binding energy between vacancy and TM solutes.Based on these binding energy results,we,respectively,evaluated the effect of solute and carbon on each other’s diffusion behaviors.We found that Cr and V slightly decrease the carbon diffusivity while other commonly seen TM solutes show little impacts on carbon diffusion,and we also expect carbon to slow down vacancy-mediated TM solute diffusion in tungsten.

关键词： Tungsten Carbon Transition metal solute Interactions First-principles calculations

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ChatGPT能取代科学家吗?

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科学通报:英文版 2023年第19期68卷 2128-2131,M0003页

作者： Paul song 王赤 Space Science Laboratory Department of Physics and Applied PhysicsUniversity of MassachusettsLowell MA 01852USA National Space Science Center Chinese Academy of SciencesBeijing 100190China

We examine chat generative pre-trained transformer(ChatGPT)from philosophy of science point of view[1]to address the question of whether ChatGPT can replace scientists in the foreseeable future.We show that ChatGPT mostly reflects social consensus than emulates human intelligence.GPT or other artificial intelligence(AI)systems will have to make some fundamental changes in its architectures.An inductive reasoning-based search system alone,no matter how sophisticated,will not be able to challenge human intelligence at a level above that of a good college student.To compete with human intelligence,AI has to include more major capabilities:deductive reasoning,dialectical reasoning,and discontinuous reasoning.

关键词： reasoning artificial GPT

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Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis

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Horticulture Research 2023年第9期10卷 1-12页

作者： Fanbo Meng Tianzhe Chu Pengmian Feng Nan Li Chi Song Chunjin Li Liang Leng Xiaoming song Wei Chen State Key Laboratory of Southwestern chinese Medicine Resources School of Basic MedicineChengdu University of Traditional Chinese MedicineChengdu 611137China State Key Laboratory of Southwestern chinese Medicine Resources Innovative Institute of Chengdu University of Traditional Chinese MedicineChengdu University of Traditional Chinese MedicineChengdu 611137China School of Life Sciences North China University of Science and TechnologyTangshan 063210China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional chinese medicine for treating mental diseases.However,the lack of genomic resources limits the insight into its evolutionary and biological characterization.In the present work,we reported the P.tenuifolia genome,the first genome assembly of the Polygalaceae family.We sequenced and assembled this genome by a combination of Illumnina,PacBio HiFi,and Hi-C mapping.The assembly includes 19 pseudochromosomes covering∼92.68%of the assembled genome(∼769.62 Mb).There are 36463 protein-coding genes annotated in this genome.Detailed comparative genome anal-ysis revealed that P.tenuifolia experienced two rounds of whole genome duplication that occurred∼39–44 and∼18–20 million years ago,respectively.Accordingly,we systematically reconstructed ancestral chromosomes of P.tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species.Based on the transcriptomics data,enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P.tenuifolia were identified.Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families,which contributed to the synthesis of triterpenoid saponins.The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae,but also shed light on the synthesis of triterpenoid saponin.

关键词： insight synthesis evolution

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Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

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Acupuncture and Herbal Medicine 2023年第4期3卷 323-332页

作者： Longlong Gao Lijun Hao Wenjie Xu Tianyi Xin Chi Song Yulin Lin Lingping Zhu Jingyuan song Key Lab of chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People’s Republic of ChinaEngineering Research Center of Chinese Medicine Resource of Ministry of EducationInstitute of Medicinal Plant DevelopmentPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina Institute of Herbgenomics State Key Laboratory of Southwest Chinese Medicine ResourcesPharmacy CollegeChengdu University of Traditional Chinese MedicineChengduChina

Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of R.palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification.Methods:Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R.palmatum.A variety of bioinformatics tools were employed to characterize the R.palmatum mitogenome,compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis.Results:The mitogenome of R.palmatum was assembled into a single master circle of 302,993 bp,encoding 35 known protein-coding genes,18 transfer RNA genes,and three ribosome RNA genes.A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome.The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb.Among them,23 mitogenomes were circular molecules,one was linear,and one consisted of relaxed circles,linear molecules,and supercoiled DNA.Out of the total mitogenomes,11 were single-chromosome structure,whereas the remaining 14 were multi-chromosomal organizations.The phylogenetic analysis is consistent with both the Engler system(1964)and the Angiosperm Phylogeny Group III system.Conclusions:We obtained the first mitogenome of R.palmatum,which consists of a master circle.Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species.Circular molecules are still the dominant pattern in Caryophyllales.Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales,in contrast to previous studies.It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.

关键词： Caryophyllales Mitochondrial genome Molecular identification Phylogenetic analysis Rheum palmatum

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Improving Smoothing Efficiency of Rigid Conformal Polishing Tool Using Time-Dependent Smoothing Evaluation Model

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Photonic Sensors 2017年第2期7卷 171-181页

作者： Chi Song Xuejun ZHANG Xin ZHANG Haifei HU Xuefeng ZENG Changchun Institute of Optics Fine Mechanics and Physics Chinese Academy of Sciences Changchun 130033 China Key Laboratory of Optical System Advanced Manufacturing Technology Chinese Academy of Sciences Changchun 130033 China University of chinese Academy of Sciences Beijing 100049 China

A rigid conformal （RC） lap can smooth mid-spatial-frequency （MSF） errors, which are naturally smaller than the tool size, while still removing large-scale errors in a short time. However, the RC-lap smoothing efficiency performance is poorer than expected, and existing smoothing models cannot explicitly specify the methods to improve this efficiency. We presented an explicit time-dependent smoothing evaluation model that contained specific smoothing parameters directly derived from the parametric smoothing model and the Preston equation. Based on the time-dependent model, we proposed a strategy to improve the RC-lap smoothing efficiency, which incorporated the theoretical model, tool optimization, and efficiency limit determination. Two sets of smoothing experiments were performed to demonstrate the smoothing efficiency achieved using the time-dependent smoothing model. A high, theory-like tool influence function and a limiting toolspeed of 300 RPM were obtained.

关键词： Optics design and fabrication optics fabrication polishing

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Apparent activation energy of mineral in open pit mine based upon the evolution of active functional groups

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International Journal of Coal Science & Technology 2023年第4期10卷 77-91页

作者： Shipng Lu Jingyu Zhao Jiajia song Jiaming Chang chi‑Min Shu School of Safety Science and Engineering Xi’an University of Science and TechnologyXi’an 710054China Shaanxi Industrial Process Safety and Emergency Rescue Engineering Technology Research Center Xi’an 710054ShaanxiChina Department of Safety Healthand Environmental EngineeringNational Yunlin University of Science and TechnologyDouliou 64002YunlinTaiwan

This study aimed to investigate the mechanism of mineral spontaneous combustion in an open pit. On the study of coal and mineral mixture in open pit mines, as well as through the specifc surface area and Search Engine Marketing (SEM) experiments, the specifc surface area and aperture characteristics of distribution of open pit coal sample and pit mineral mixture samples were analyzed. Thermal analysis experiments were used to divide the oxidation process was divided into three stages, and the thermal behavior characteristics of experimental samples were characterized. On the basis of the stage division, we explored the transfer law of the key active functional groups of the experimental samples. The apparent activation energy calculation of the key active groups, performed by combining the Achar diferential method with the Coats–Redfern integral method, microstructural and oxidation kinetic properties were revealed. The resulted showed that the mixed sample had high ash, the fxed carbon content was reduced, the specifc surface area was far lower than the raw coal, the large aperture distribution was slightly higher than the medium hole, the micropore was exceptionally low, the gas adsorption capacity was weaker than the raw coal, the pit coal sample had the exceedingly more active functional groups, easy to react with oxygen, more likely to occur naturally, and its harm was relatively large. The mixed sample contained the highest C–O–C functional group absorbance. The functional groups were mainly infuenced by the self-OH content, alkyl side chain, and fatty hydrocarbon in the sample. The main functional groups of the four-like mixture had the highest apparent activation energy, and the two reactions were higher in the low-temperature oxidation phase.

关键词： Specifc surface area Aperture distribution characteristics Thermal behavior characteristics Oxidation kinetic properties Gas adsorption capacity

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Herbgenomics: Decipher molecular genetics of medicinal plants

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The Innovation 2022年第6期3卷 17-18页

作者： Wei Sun Zhichao Xu Chi Song Shilin Chen Institute of chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100070China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China College of Life Science Northeast Forestry UniversityHarbin 150040China

Medicinal plants synthesize a huge repertoire of specialized compounds as protective metabolites when they are confronted with complex abiotic and biotic conditions.Humans have used medicinal plants to treat ailments and maintain health throughout civilization.Paleontological studies have shown that the application of medicinal plants,such as Ephedra altissima and Centaurea solstitialis,could be dated back to 60,000 years ago,since their fossils were found in the tomb of prehistoric Neanderthals.

关键词： Ephedra protective medicinal

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Analysis of wave shoaling and shore-breakers on a low tide terrace beach based on in-situ measurements at Xisha Bay on South china coast

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Acta Oceanologica Sinica 2023年第7期42卷 175-184页

作者： Yuan Li chi Zhang Hongshuai Qi Jiacheng song Weiqi Dai Shanhang chi Jian Shi Dake Chen The National Key Laboratory of Water Disaster Prevention Hohai UniversityNanjing 210024China College of Harbour Coastal and Offshore EngineeringHohai UniversityNanjing 210024China State Key Laboratory of Estuarine and Coastal Research East China Normal UniversityShanghai 200241China Third Institute of Oceanography Ministry of Natural ResourcesXiamen 361005China Shanghai Waterway Engineering Design and Consulting Co. LtdShanghai 200120China Yellow River Institute of Hydraulic Research Yellow River Conservancy CommissionZhengzhou 450000China Nanjing Hydraulic Research Institute Nanjing 210029China

Low tide terrace beach is a main beach type along South china coasts with strong tidal actions.How strong tides affect wave transformations on low tide terrace beach still remains unclear.In this study,in-situ measurements are conducted on the low terrace beach at Xisha Bay to provide quantitative descriptions of wave shoaling and shore-breaker phenomena under the tidal effects.It is found that wave breaking is unsaturated on the low tide terrace beach at Xisha Bay.Magnitudes of wave skewness and asymmetry increase as wave shoals and achieve the maximum value at the shore-breaker,and then decrease rapidly.Mean energy dissipation rates of shore-breakers are tide-modulated since the bottom slope changes at the shoreward boundary of wave propagation in a tidal cycle.The remaining wave energy flux at the initialization of the shore-breaker is 1%–12%of offshore wave energy flux,and the energy flux ratio decreases with increasing offshore wave heights.Wave attenuation at shore-breakers can be estimated directly from offshore wave conditions based on findings in this study,favoring designs of seawalls or beach nourishment projects.Field datasets on wave transformations can also be used for verifications of wave numerical models.

关键词： sandy beach low tide terrace waves shore-breakers South china coasts

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Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

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Journal of Genetics and Genomics 2012年第7期39卷 361-368页

作者： Chi Song Juan Guo Wei Sun Ying Wang Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhanHubei 430074China Graduate University of chinese Academy of Sciences Beijing 100049China South china Botanical Garden Chinese Academy of SciencesGuangzhouGuangdong 510650China

Whole genome duplication （WGD） events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods： synonymous substitution rates （Ks） and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes con- structed. It was evident that chromosome 2 had experienced an intra-chromosomat duplication event. Major inter-chromosomal dupli- cation occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36-82 million years ago （MYA） and 148--205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosidasterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis （monocot-dicot）.

关键词： Whole genome duplication Collinearity block Phylogenetic tree

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