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Combining stochastic density functional theory with deep potential molecular dynamics to study warm dense matter

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Matter and Radiation at Extremes 2024年第1期9卷 44-57页

作者： Tao Chen Qianrui Liu Yu Liu liang sun Mohan Chen HEDPS CAPTCollege of Engineering and School of PhysicsPeking UniversityBeijing 100871People’s Republic of China

In traditional finite-temperature Kohn–Sham density functional theory(KSDFT),the partial occupation of a large number of high-energy KS eigenstates restricts the use of first-principles molecular dynamics methods at extremely high ***,stochastic density functional theory(SDFT)can overcome this ***,SDFT and the related mixed stochastic–deterministic density functional theory,based on a plane-wave basis set,have been implemented in the first-principles electronic structure software ABACUS[*** and ***,***.B 106,125132(2022)].In this study,we combine SDFT with the Born–Oppenheimer molecular dynamics method to investigate systems with temperatures ranging from a few tens of eV to 1000 ***,we train machine-learning-based interatomic models using the SDFT data and employ these deep potential models to simulate large-scale systems with long ***,we compute and analyze the structural properties,dynamic properties,and transport coefficients of warm dense matter.

关键词： stochastic theory functional

Accelerating Factor Xa inhibitor discovery with a de novo drug design pipeline

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CHINESE JOURNAL OF CHEMICAL ENGINEERING 2024年第8期72卷 85-94页

作者： Zhao, Yujing Liu, Qilei Du, Jian Meng, Qingwei sun, liang Zhang, Lei Dalian Univ Technol Inst Chem Proc Syst Engn Frontiers Sci Ctr Smart Mat Oriented Chem Engn Sch Chem EngnState Key Lab Fine Chem Dalian 116024 Peoples R China Dalian Univ Technol Ningbo Inst Ningbo 375076 Peoples R China Shenzhen Shuli Tech Co Ltd Shenzhen 578726 Peoples R China City Univ Hong Kong Dept Phys Kowloon Tat Chee Ave Hong Kong Peoples R China

Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, DrugCAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking, binding pose metadynamics (BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859 shows potential Factor Xa inhibition, with an IC50 value of 34.57 mmol$L-1. Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa. (c) 2024 The Chemical Industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights reserved.

关键词： Chemical product design Mathematical programming method Deep learning Binding affinity Factor Xa inhibitor PROTEIN PREDICTION OPTIMIZATION FRAMEWORK MODELS

Practical assessment of the energy density of potassium-ion batteries

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Science China Chemistry 2024年第1期67卷 4-12页

作者： liang sun Guanjie Li Shilin Zhang Sailin Liu Jodie Yuwono Jianfeng Mao Zaiping Guo School of Chemical Engineering and Advanced Materials The University of AdelaideAdelaide 5000Australia

1 Introduction The evolution of modern human society closely depends on affordable,efficient,and safe energy storage ***,lithium-ion batteries(LIBs)are the dominant energy storage systems to power portable electronics... 详细信息

关键词： energy lithium smart

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A Fluorine-Functionalized 3D Covalent Organic Framework with Entangled 2D Layers

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Chinese Journal of Polymer Science 2024年第8期42卷 1210-1216页

作者： Li-Bang Xiao Zi-Han Wu Jun-Jie Xin Yuan-Peng Cheng Bo Gui Jun-liang sun Cheng Wang College of Chemistry and Molecular Sciences Wuhan UniversityWuhan 430072China College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular SciencesPeking UniversityBeijing 100871China

Constructing three dimensional(3D)covalent organic frameworks(COFs)through the entanglement of two dimensional(2D)nets is a promising but underdeveloped ***,we report the design and synthesis of a fluorine functionalized 3DCOF(3D-An-COF-F)formed by entangled 2D sql *** structure of 3D-An-COF-F was determined by the combination of continuous rotation electron diffraction technique and modelling based on the chemical information from real ***,compared to the isostructural 3D-An-COF without F atom s,3DAn-COF-F showed an improved CO_(2)sorption ability and higher CO_(2)/N_(2)*** study not only demonstrated the generality of constructing 3D COFs with entangled 2D nets by introducing bulky groups vertically in planar building blocks,but also will expand the diversity of 3D COFs for various applications.

关键词： 3D covalent organic frameworks Fluorine Entangled 2D layers Electron diffraction CO_(2)adsorption

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ZNF554 Inhibits Endometrial Cancer Progression via Regulating RBM5 and Inactivating WNT/β-Catenin Signaling Pathway

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Current Medical Science 2024年第2期44卷 406-418页

作者： Cheng-cheng ZHU Heng-liang sun Teng-fei LONG Yuan-yuan LYU Jiang-li LIU Guan-tai NI Anhui Medical University Hefei 230032China Department of Obstetrics and Gynecology The First Affiliated Hospital of Wannan Medical CollegeWuhu 241001China

Objective:Uterine corpus endometrial carcinoma(UCEC),a kind of gynecologic malignancy,poses a significant risk to women’s *** precise mechanism underlying the development of UCEC remains *** finger protein 554(ZNF554),a member of the Krüppel-associated box domain zinc finger protein superfamily,was reported to be dysregulated in various illnesses,including malignant *** study aimed to examine the involvement of ZNF554 in the development of ***:The expression of ZNF554 in UCEC tissues and cell lines were examined by qRT-PCR and Western blot *** with stably overexpressed or knocked-down ZNF554 were established through lentivirus ***-8,wound healing,and Transwell invasion assays were employed to assess cell proliferation,migration,and *** iodide(PI)staining combined with fluorescence-activated cell sorting(FACS)flow cytometer was utilized to detect cell cycle ***-PCR and Western blotting were conducted to examine relative mRNA and protein *** immunoprecipitation assay and luciferase reporter assay were used to explore the regulatory role of ZNF554 in RNA binding motif 5(RBM5).Results:The expression of ZNF554 was found to be reduced in both UCEC samples and cell *** expression of ZNF554 was associated with higher tumor stage,decreased overall survival,and reduced disease-free survival in ***554 overexpression suppressed cell proliferation,migration,and invasion,while also inducing cell cycle *** contrast,a decrease in ZNF554 expression resulted in the opposite ***,ZNF554 transcriptionally regulated RBM5,leading to the deactivation of the Wingless(WNT)/β-catenin signaling ***,the findings from rescue studies demonstrated that the inhibition of RBM5 negated the impact of ZNF554 overexpression onβ-catenin and p-glycogen synthase kinase-3β(p-GSK-3β).Similarly,the deliberate activation of RBM5 reduced the increase inβ-catenin and

关键词： zinc finger protein 554 endometrial carcinoma RNA binding motif 5 Wingless/β-catenin signaling pathway

Limited Sea Surface Temperature Cooling Due to the Barrier Layer Promoting Super Typhoon Mangkhut (2018)

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ADVANCES IN ATMOSPHERIC SCIENCES 2024年第11期41卷 2156-2172页

作者： Wang, Huipeng Li, Jiagen Song, Junqiang sun, liang Liu, Fu Zhang, Han Ren, Kaijun Wang, Huizan Wang, Chunming Zhang, Jinrong Leng, Hongze Natl Univ Def Technol Coll Meteorol & Oceanog Changsha 410073 Peoples R China Univ Sci & Technol China Sch Earth & Space Sci Hefei 230000 Peoples R China Minist Nat Resources Inst Oceanog 2 State Key Lab Satellite Ocean Environm Dynam Hangzhou 310012 Peoples R China Southern Marine Sci & Engn Guangdong Lab Zhuhai Zhuhai 519082 Peoples R China

This study investigates the impact of the salinity barrier layer (BL) on the upper ocean response to Super Typhoon Mangkhut (2018) in the western North Pacific. After the passage of Mangkhut, a noticeable increase (similar to 0.6 psu) in sea surface salinity and a weak decrease (< 1 degrees C) in sea surface temperature (SST) were observed on the right side of the typhoon track. Mangkhut-induced SST change can be divided into the three stages, corresponding to the variations in BL thickness and SST before, during, and after the passage of Mangkhut. During the pre-typhoon stage, SST slightly warmed due to the entrainment of BL warm water, which suppressed the cooling induced by surface heat fluxes and horizontal advection. During the forced stage, SST cooling was controlled by entrainment, and the preexisting BL reduced the total cooling by 0.89 degrees C d(-1), thus significantly weakening the overall SST cooling induced by Mangkhut. During the relaxation stage, the SST cooling was primarily caused by the entrainment. Our results indicate that a preexisting BL can limit typhoon-induced SST cooling by suppressing the entrainment of cold thermocline water, which contributed to Mangkhut becoming the strongest typhoon in 2018.

关键词： sea surface cooling mixed-layer depth barrier layer typhoon UPPER-OCEAN RESPONSE TROPICAL CYCLONES INTENSITY ATMOSPHERE IMPACT AMAZON EDDY

The Impact of Cardiac Pacing Site on Patient's Cardiac Function and Psychological State

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Expert Review of Chinese Medical

Expert Review of Chinese Medical 2024年第2期2卷 18-22页

作者： Haiyang Xiao liang sun Cardiology Department of Hefei Eighth People's Hospital Medical College of Jinzhou Medical University

With the widespread application of artificial permanent pacemakers in clinical practice,there have been new changes in the indications for pacemaker *** current clinical indications include high atrioventricular block,sick sinus syndrome,cardiac resynchronization therapy for heart failure,and implantation of cardioverter defibrillators for ventricular *** implantation of a pacemaker can improve the quality of life and prognosis of patients with *** the past,permanent pacemaker implantation was performed in clinical practice,and the right ventricular pacing electrode was often fixed at the apex of the right ventricle,which belongs to non physiological *** long-term clinical follow-up,it was found that apex pacing can easily cause abnormal depolarization of the left ventricle,asynchronous contraction of the myocardium,and ultimately lead to myocardial fibrosis,which has adverse effects on the patient's cardiac function and psychological *** recent years,Scholars have found that pacing in the right ventricular outflow tract septum is closer to the atrioventricular node and closer to the His bundle Purkinje *** pacing impulse almost simultaneously expands towards both ventricles,closer to the physiological pacing state,thereby reducing the occurrence of cardiovascular events in *** article explores the impact of pacing in different parts of the heart on the cardiac function and psychological state of patients based on clinical data from the past three years.

关键词： pacing site cardiac function psychological state

Accelerating Factor Xa inhibitor discovery with a de novo drug design pipeline

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Chinese Journal of Chemical Engineering 2024年第08期 85-94页

作者： Yujing Zhao Qilei Liu Jian Du Qingwei Meng liang sun Lei Zhang State Key Laboratory of Fine Chemicals Frontiers Science Center for Smart Materials Oriented Chemical Engineering Institute of Chemical Process Systems Engineering School of Chemical Engineering Dalian University of Technology Ningbo Institute of Dalian University of Technology Shenzhen Shuli Tech Co. Ltd Department of Physics City University of Hong Kong

Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics（BPMD）, binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC50value of 34.57 μmol·L-1. Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa.

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Association of insomnia with diet quality and eating behavior

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中华医学杂志(英文版) 2024年第16期137卷 2002-2004页

作者： Jigeer Guliyeerke Huang Zhe Zou Jiaojiao Zhu Siwei Li Yaqi Chen Shuohua Yang Qishan sun liang Wu Shouling Gao Xiang Department of Nutrition and Food Hygiene School of Public Health Institute of Nutrition Fudan University Shanghai China Department of Cardiology Kailuan General Hospital Tangshan Hebei China Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA Key Laboratory of Public Health Safety of the Ministry of Education Fudan University Shanghai China