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Multi-Material ALE with AMR for Modeling Hot Plasmas and Cold Fragmenting Materials

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Plasma Science and Technology 2015年第2期17卷 117-128页

作者： Alice KONIGES Nathan MASTERS Aaron FISHER David EDER wangyi liu Robert ANDERSON David BENSON Andrea BERTOZZI Lawrence Berkeley National Laboratory Lawrence Livermore National Laboratory Jacobs School of Engineering 9500 Gilman Dr.UCSDLa JollaCA 92093USA Department of Mathematics 520 Portola PlazaUCLALos AngelesCA 90095USA

We have developed a new 3D multi-physics multi-material code, ALE-AMR, which combines Arbitrary Lagrangian Eulerian （ALE） hydrodynamics with Adaptive Mesh Refinement （AMR） to connect the continuum to the microstructural regimes. The code is unique in its ability to model hot radiating plasmas and cold fragmenting solids. New numerical techniques were developed for many of the physics packages to work efficiently on a dynamically moving and adapting mesh. We use interface reconstruction based on volume fractions of the material components within mixed zones and reconstruct interfaces as needed. This interface reconstruction model is also used for void coalescence and fragmentation. A flexible strength/failure framework allows for pluggable material models, which may require material history arrays to determine the level of accumulated damage or the evolving yield stress in J2 plasticity models. For some applications laser rays are propagating through a virtual composite mesh consisting of the finest resolution representation of the modeled space. A new 2nd order accurate diffusion solver has been implemented for the thermal conduction and radiation transport packages. One application area is the modeling of laser/target effects including debris/shrapnel generation. Other application areas include warm dense matter, EUV lithography, and material wall interactions for fusion devices.

关键词： multi-physics simulations arbitrary lagrangian eulerian hydrodynamics,adaptive mesh refinement fragmentation laser ray tracing NIF

The Earliest Discovery of the Role of Magnesium Ions on Stabilizing the Tertiary Structure of the Transfer RNA and Its Biological Significance —A Short Memoir

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Advances in Biological Chemistry 2016年第5期6卷 147-151页

作者： wangyi liu Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences The Chinese Academy of Sciences Shanghai China

In early of 1960s, I was a graduate student studying on tRNA biochemistry. In the course of the research, the magnesium ions stabilized the tertiary structure of tRNA, resulting in its resistance to enzymatic degradation was discovered independently. The experiment of deaminated (denatured) tRNA obtained from native tRNA was designed and conducted and further proved the validity of this finding. It was found that magnesium ions could stabilize the tertiary structure of the natrive tRNA but could not stabilize structure of the deaminated tRNA. In term of the methodology, this stabilization technique has been widely applied in sequencing analysis of RNA and has greatly promoted the progress in the study of primary structure of RNA. More importantly, the stabilization of the tertiary structure of RNA by magnesium ions plays a key role both in the processing of messenger RNAs and the ribozyme activity. After our first article in Chinese was published in 1963, a paper of Nishimura & Novelli came into our note. The received date of their paper was March 22 of 1963, only 4 days earlier than that of our first paper. Thus, we and Nishimura & Novelli made almost at the same time the earliest discovery of the role of magnesium ions on stabilizing the tertiary structure of the transfer RNA and thus resulted in resistance of tRNA degradation by enzymes. However, this discovery was not initially appreciated for a period of time but was finally “visualized” and proved by X-ray crystal structure of yeast phenylalanine tRNA, which has provided more accurate information on the geometry of the magnesium-binding sites in tRNA.

关键词： Deaminated tRNA Earliest Discovery Enzymatic Degradation Magnesium Ion Tertiary Structure Transfer RNA

Lipidomics reveals association of circulating lipids with body mass index and outcomes in IgA nephropathy patients

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Journal of Molecular Cell Biology 2021年第8期13卷 565-575页

作者： Yueyi Deng Qingqing Wu Wanjia Chen Li Zhu wangyi liu Fangying Xia Liang Sun Xu Lin Rong Zeng Department of Nephrology Longhua HospitalShanghai University of Traditional Chinese MedicineShanghai 200032China Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China Shanghai Institute of Nutrition and Health Chinese Academy of SciencesShanghai 200031China

IgA nephropathy(IgAN)is a leading cause of chronic kidney disease(CKD),which are commonly accompanied by *** is also associated with dyslipidemia and risk of CKD,but the relation of the dyslipidemia patterns with obesity and disease progression in IgAN patients remains *** Chinese medicine(TCM)and the combined treatment with corticosteroids and TCM have been shown to be of benefit for IgAN patients,but predictive markers for guiding these treatments are ***,we quantified 545 lipid species in the plasma from 196 participants,including 140 IgAN patients and 56 healthy volunteers,and revealed an altered plasma lipidome in IgAN patients as compared to healthy *** analysis showed that a subgroup of glycerides,particularly triacylglycerols(TGs)containing docosahexaenoic acid,were positively associated with high body mass index(BMI)in under-or normal-weight IgAN patients,while several free fatty acids and sphingomyelins were positively associated with high BMI in overweight or obese IgAN ***,our study suggested that elevated levels of eight lipids,mainly TG species containing linolenic acid,were independent risk factors for IgAN progression and also reported the prospective association of circulating lipids with treatment outcomes in *** together,our findings may not only help to achieve precision medicine but also provide a knowledge base for dietary intervention in the treatment of IgAN.

关键词： IgA nephropathy circulating lipids body mass index lipidomics dyslipidemia traditional Chinese medicine

肾活检时高尿酸血症与IgA肾病临床及牛津病理相关性研究

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安徽医科大学学报 2020年第3期55卷 456-460页

作者：鲁珍珍邓跃毅刘旺意上海中医药大学附属龙华医院肾内科上海200032

目的探讨肾活检高尿酸血症(HUA)与IgA肾病临床特征及牛津病理分型的相关性。方法回顾性分析经肾活检确诊为原发性IgA肾病患者289例,根据肾活检时尿酸水平分为高尿酸组120例,尿酸正常组169例,收集肾活检时临床及牛津病理资料,分析HUA与... 详细信息

目的探讨肾活检高尿酸血症(HUA)与IgA肾病临床特征及牛津病理分型的相关性。方法回顾性分析经肾活检确诊为原发性IgA肾病患者289例,根据肾活检时尿酸水平分为高尿酸组120例,尿酸正常组169例,收集肾活检时临床及牛津病理资料,分析HUA与临床及牛津病理相关性。结果289例IgA肾病患者肾活检时HUA的发病率为41.5%,相较于尿酸正常组,高尿酸组的高血压发生率更高,肌酐、尿素氮、24 h尿蛋白水平更高,三酰甘油、总胆固醇、高密度脂蛋白、低密度脂蛋白等脂代谢更为异常。Spearman相关分析显示血尿酸与牛津病理分型中系膜增生(r=0.254,P<0.0001)、小球节段硬化(r=0.145,P=0.013)以及肾小管萎缩或间质纤维化(r=0.315,P<0.0001)相关。多因素Logistic回归对其他临床指标进行调整后显示HUA是系膜增生和小球节段硬化的独立危险因素。结合不同临床指标分别建立3个模型,采用ROC曲线联合诊断显示,尿酸可提高对系膜增生和小球节段硬化的诊断能力,且联合指标越多,诊断效能越大。结论肾活检时HUA与IgA肾病肾功能异常及脂代谢紊乱相关。同时,HUA与肾脏病理损伤有关,肾活检时HUA作为系膜增生和小球硬化的独立危险因素,可以提高对IgA肾病系膜增生和小球硬化的诊断价值。

关键词： IgA肾病高尿酸血症牛津病理系膜增生小球节段硬化

核糖体RNA拓扑学与RNAN－糖苷酶研究进展（下）

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生物化学与生物物理进展 1994年第2期21卷 113-117页

作者：张劲松刘望夷中国科学院上海生物化学研究所中国科学院上海细胞生物学研究所

２８ＳｒＲＮＡ的α－ｓａｒｃｉｎ结构域直接参与核糖体催化的蛋白质合成反应，已经证明天花粉蛋白是一种ＲＮＡＮ－糖苷酶，一种测定ＲＮＡＮ－糖苷酶活力的新方法也已初步建立。天花粉蛋白能使超螺旋ＤＮＡ解旋并断裂为缺口环状和线... 详细信息

２８ＳｒＲＮＡ的α－ｓａｒｃｉｎ结构域直接参与核糖体催化的蛋白质合成反应，已经证明天花粉蛋白是一种ＲＮＡＮ－糖苷酶，一种测定ＲＮＡＮ－糖苷酶活力的新方法也已初步建立。天花粉蛋白能使超螺旋ＤＮＡ解旋并断裂为缺口环状和线状ＤＮＡ．并已发现其它ＲＮＡＮ－糖苷酶也具有这一核酸内切活性。天花粉蛋白对２８ＳｒＲＮＡ，超螺旋ＤＮＡ和艾滋病毒（ＨＩＶ－１）ＲＮＡ三种底物可能有相同的分子作用机制．

关键词：核糖体拓扑学 RNA N-糖苷酸

核糖体RNA拓扑学与RNAN－糖苷酶研究进展（上）

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生物化学与生物物理进展 1994年第1期21卷 23-27页

作者：张劲松刘望夷中国科学院上海生物化学研究所中国科学院上海细胞生物学研究所

核糖体ＲＮＡ拓扑学的研究对阐明核糖体ＲＮＡ（ｒＲＮＡ）在蛋白质生物合成中的作用具有重要的意义。ＲＮＡＮ－糖苷０酶是一类核糖体失活蛋白．它只水解ｒＲＮＡ特定位置上一个腺苷酸的糖苷键，释放一个腺嘌呤碱基，使核糖体失活。Ｒ... 详细信息

核糖体ＲＮＡ拓扑学的研究对阐明核糖体ＲＮＡ（ｒＲＮＡ）在蛋白质生物合成中的作用具有重要的意义。ＲＮＡＮ－糖苷０酶是一类核糖体失活蛋白．它只水解ｒＲＮＡ特定位置上一个腺苷酸的糖苷键，释放一个腺嘌呤碱基，使核糖体失活。ＲｉｃｉｎＡ链是研究得最早和最详细的ＲＮＡＮ－糖苷酶，迄今已发现有二十五种核糖体失活蛋白具有ＲＮＡＮ－糖苷酶活性。ＲＮＡＮ－糖苷酶作用于２８ＳｒＲＮＡ的α－ｓａｒｃｉｎ结构域，改变核糖体的构象而使其失活。

关键词：拓扑核苷酶核糖核蛋白体 RNA

A NEW FLUORESCENT HYDRAZIDE FOR SEQUENCING RIBONUCLEIC ACIDS

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Science in China,Ser.A 1980年第10期 1296-1308页

作者：刘望夷辜祥荣蔡菊娥 Shanghai Institute of Biochemistry Academia Sinica

This paper deals with the synthesis and properties of a fluorescent hydrazide and its hydrazones of nucleoside dialdehydes and of 5’-methylene nucleoside *** of 1-dimethylaminonaphthalene-5-sulphonyl-glycyl ethyl ester （DNS-GlyOC2H5） gives the fluorescent carbonyl reagent, 1-dimethylaminonaphthalene-5-sulphonyl-glycyl hydrazide （DNS-Gly-NHNH2）. The reaction of DNS-Gly-NHNH2 with the nucleoside dialdehydes or the 5’-methylene nucleoside dialdehydes produced by the oxidation of the corresponding nucleosides or 5’-nucleotides with sodium periodate forms the respective fluorescent *** coupling ratio of nucleoside dialdehydo to DNS-Gly-NHNH2 is 1:1. The nucleoside hydrazones can be clearly resolved by polyamide plate chromatography with a sensitivity of 1 × 10-10 mole. The ultraviolet absorption spectra, the molar extinction coefficients, the fluorescent spectra as well as the quantum yields of the hydrazide and its nucleoside hydrazones in water, ethanol and dioxane

关键词： DNS NHN A NEW FLUORESCENT HYDRAZIDE FOR SEQUENCING RIBONUCLEIC ACIDS Gly

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苏铁树叶细胞质55rRNA的一级结构分析

复旦学报（自然科学版） 1989年第3期28卷 325-330页

作者：周雪琼王鸣岐刘望夷复旦大学上海生物化学研究所

用热酚法抽提苏铁(Cycas revoluta)树叶细胞质的总RNA,经10%聚丙烯酰胺凝胶电泳分离得到5S rRNA。用核糖核酸酶和化学降解凝胶直读法测定出5S rRNA 的一级结构由121个核苷酸组成,且3′一端有连续三个尿苷酸。并具有真核生物5S rRNA的一... 详细信息

用热酚法抽提苏铁(Cycas revoluta)树叶细胞质的总RNA,经10%聚丙烯酰胺凝胶电泳分离得到5S rRNA。用核糖核酸酶和化学降解凝胶直读法测定出5S rRNA 的一级结构由121个核苷酸组成,且3′一端有连续三个尿苷酸。并具有真核生物5S rRNA的一般结构特征。按真核生物5S rRNA的二级结构模型,构建了苏铁树叶细胞质5S rRNA的二级结构。

关键词：苏铁细胞质结构分析树叶核糖体

酰胺质子转移成像和扩散加权成像鉴别诊断乳腺良恶性病变

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中国医学影像技术 2020年第12期36卷 1820-1824页

作者：王雪佳王竞刘文玲张梦刘旺毅韩东明新乡医学院第一附属医院核磁共振科河南新乡453100

目的观察MR酰胺质子转移成像(APTWI)和扩散加权成像(DWI)鉴别诊断乳腺良恶性病变的价值,并分析不同参数间的相关性。方法对65例乳腺病变患者行APTWI及DWI,测量并比较乳腺良恶性病变间平均ADC(ADCmean)、最小ADC(ADCmin)及非对称磁化转移... 详细信息

目的观察MR酰胺质子转移成像(APTWI)和扩散加权成像(DWI)鉴别诊断乳腺良恶性病变的价值,并分析不同参数间的相关性。方法对65例乳腺病变患者行APTWI及DWI,测量并比较乳腺良恶性病变间平均ADC(ADCmean)、最小ADC(ADCmin)及非对称磁化转移率[MTRasym(3.5 ppm)]值的差异;采用ROC曲线评估各参数鉴别乳腺良恶性病变的诊断效能,并分析良恶性病变中各参数间的相关性。结果共70个病灶纳入研究,包括32个良性(良性组)和38个恶性病灶(恶性组)。良性组ADCmean、ADCmin及MTRasym(3.5 ppm)值均高于恶性组(t=-5.63、-5.94、-0.24,P均0.05)。恶性组MTRasym(3.5 ppm)值与ADC_(mean)(r=-0.325,P=0.046)和ADCmin值(r=-0.384,P=0.017)均呈负相关;良性组MTRasym(3.5 ppm)值与ADCmin值呈负相关(r=-0.357,P=0.045)。结论 APTWI及DWI均可用于鉴别诊断乳腺良恶性病变;相比DWI,APTWI的诊断效能有待进一步提高。

关键词：乳腺疾病诊断鉴别磁共振成像