H?lder条件下求解重根的Traub算法的收敛半径

2010年任宏民和Argyros~([1])对求解重根的牛顿法的收敛半径进行了分析,首次给出了重根迭代局部收敛性的分析方法.2011年毕惟红等人基于该思路计算了Halley算法的收敛半径,2018年JoséL等人给出了Osada算法的收敛半径.而对于非线性方程重根迭代算法中,Traub算法至今无人研究,本文将基于任红民和Argyros给出的基本思路计算Traub算法的收敛半径,并通过具体实例进行分析.     

构建微生物分子分类系统进化树的快速运算法与数据结构

本文介绍了构建系统进化树的NJ方法（NeighborJoiningMethod）所涉及的算法与数据结构。文中给出了基于数据复用性的算法改进,获得了快速算法──FNJ算法,从而将算法的时间复杂度由（N⁵）降低为（N³）;并给出了自动绘制进化分枝图的算法。     

参数仪器变量估计近似分布方差的一种算法

本文对更一般的结构模型给出了参数的一种常用的仪器变量估计近似分布方差的一种算法．并且给出了未知真值x服从指数分布的例子．此算法对生物科学中统计规律的探讨有一定的应用价值．     

广义Kolmogorov模型的Lyapunov函数构造新算法及其应用

本文对广义Kolmogorov模型,给出构造Lyapunov函数的新算法,在文献1中只对其中某些特殊类型给出几种特殊的构造方法,而本文给出的是这类模型的一般新算法,应用较广泛。     

原核生物基因组的CDS与ORF序列的几点分析

基因组的开放阅读框（ORF）是基因识别与基因组分析的基础,有多种软件包给出了它们的生成算法,但结果与指标并不统一.本文给出了po-MORF的定义与它的生成算法,证明了由基因组所确定的po-MORF集合的存在与唯一性,并由该生成算法可以得到全部po-MORF序列.我们还比较了若干原核生物基因组中所有CDS与po-MORF序列的相互关系,并讨论了关于基因识别中的有关问题.     

模块神经网络及其性能

提出一个不同于实现ｙ＝ｆ（ｘ）的ＢＰ网络的神经网络模型,给出了网络的结构及并行动力学方程,证明了其动力学的稳定性。通过学习算法的建立,证明网络能精确实现输入矢量对（ｘ,ｙ）映入成相联系的输出矢量ｚ,最重要的是网络能同时存诸依时变化的时序模式与静态模式。此外并给出动力学学习算法,证明此学习算法的收敛性,计算机仿真证实理论结果,最后讨论了某些可能的应用。     

演化计算的应用研究

介绍了演化计算的基本思想、特点及主要分支。在统一的枢架下给出了演化算法的设计方法和基本结构,并给出了演化计算在旅行商问题中的应用。最后讨论了演化计算的发展前景。     

对预测蛋白质结构的拟物算法的分析和改进

对预测蛋白质空间结构的拟物算法的有效性进行理论分析,证明用该拟物算法求得合法的结构存在较大的随机性;给出折叠结构发生冲突的判断条件和提高拟物算法有效性的一些修正方案。     

微生物批式流加发酵生产1,3-丙二醇过程的优化

本文考虑了微生物批式流加发酵生产1,3-丙二醇的过程优化问题.用非线性切换系统描述拙式流加发酵过程.考虑终端时刻1,3-丙二醇的浓度最大化,给出了以甘油流加速度和流加时刻为控制变量的带有连续状态变量不等式约束的最优控制问题.应用时间转换方法处理变动切换时刻,应用惩罚函数和障碍函数方法处理连续状态变量不等式约束,然后基于梯度最优化算法和粒子群优化算法给出计算方法.     

Bayes框架下DNA证据的量化研究

针对DNA（脱氧核糖核酸）证据的量化过程中常用的插入算法存在的缺陷，即量化结果与样本大小无关，小样本时过分量化了DNA证据，本文考虑了样本大小的影响，引入了Bayes模型。给出了基于Bayes模型下的似然比的计算公式，结合实际案例，对比了两种方法下的计算结果，数据结果表明基于Bayes模型下的算法比插入算法更加精确和合理。     

Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA

The nucleotide sequence of 16S rDNA from Euglena gracilis chloroplasts has been determined representing the first complete sequence of an algal chloroplast rRNA gene. The structural part of the 16S rRNA gene has 1491 nucleotides according to a comparative analysis of our sequencing results with the published 5'- and 3'-terminal "T1-oligonucleotides" from 16S rRNA from E. gracilis. Alignment with 16S rDNA from Zea mays chloroplasts and E. coli reveals 80 to 72% sequence homology, respectively. Two deletions of 9 and 23 nucleotides are found which are identical in size and position with deletions observed in 16S rDNA of maize and tobacco chloroplasts and which seem to be characteristic for all chloroplast rRNA species. We also find insertions and deletions in E. gracilis not seen in 16S rDNA of higher plant chloroplasts. The 16S rRNA sequence of E. gracilis chloroplasts can be folded by base pairing according to the general 16S rRNA secondary structure model.     

The 3''-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3''-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5s rRNA.

The sequence of the 110 nucleotide fragment located at the 3'-end of E.coli, P.vulgaris and A.punctata 23S rRNAs has been determined. The homology between the E.coli and P.vulgaris fragments is 90%, whereas that between the E.coli and A.punctate fragments is only 60%. The three rRNA fragments have sequences compatible with a secondary structure consisting of two hairpins. Using chemical and enzymatic methods recently developed for the study of the secondary structure of RNA, we demonstrated that one of these hairpins and part of the other are actually present in the three 3'-terminal fragments in solution. This supports the existence of these two hairpins in the intact molecule. Indeed, results obtained upon limited digestion of intact 23S RNA with T1 RNase were in good agreement with the existence of these two hairpins. We observed that the primary structures of the 3'-terminal regions of yeast 26S rRNA and X.laevis 28S rRNA are both compatible with a secondary structure similar to that found at the 3'-end of bacterial 23S rRNAs. Furthermore, both tobacco and wheat chloroplast 4.5S rRNAs can also be folded in a similar way as the 3'-terminal region of bacterial 23S rRNA, the 3'-end of chloroplast 4.5S rRNAs being complementary to the 5'-end of chloroplast 23S rRNA. This strongly reinforces the hypothesis that chloroplast 4.5S rRNA originates from the 3'-end of bacterial 23S rRNA and suggests that this rRNA may be base-paired with the 5'-end of chloroplast 23S rRNA. Invariant oligonucleotides are present at identical positions in the homologous secondary structures of E.coli 23S, yeast 26S, X.laevis 28S and wheat and tobacco 4.5S rRNAs. Surprisingly, the sequences of these oligonucleotides are not all conserved in the 3'-terminal regions of A.punctata or even P.vulgaris 23S rRNAs. Results obtained upon mild methylation of E.coli 50S subunits with dimethylsulfate strongly suggest that these invariant oligonucleotides are involved in RNA tertiary structure or in RNA-protein interactions.     

Analysis of RNA secondary structure by photochemical reversal of psoralen crosslinks.

Aminomethyltrioxsalen (AMT), a psoralen, is known to cause interstrand crosslinks in double stranded nucleic acids. We have demonstrated the photochemical reversal of this reaction, and have used this result to develop a method for identification of specific sequences which are adjacent because of RNA secondary structure formation. E. coli 5S rRNA is used as a model system. We isolated and characterized a product that is derived from the stem region of 5S RNA.     

Erythromycin and 5S rRNA binding properties of the spinach chloroplast ribosomal protein CL22.

The spinach chloroplast ribosomal protein (r-protein) CL22 contains a central region homologous to the Escherichia coli r-protein L22 plus long N- and C-terminal extensions. We show in this study that the CL22 combines two properties which in E. coli ribosome are split between two separate proteins. The CL22 which binds to the 5S rRNA can also be linked to an erythromycin derivative added to the 50S ribosomal subunit. This latter property is similar to that of the E. coli L22 and suggests a similar localization in the 50S subunit. We have overproduced the r-protein CL22 and deleted forms of this protein in E. coli. We show that the overproduced CL22 binds to the chloroplast 5S rRNA and that the deleted protein containing the N- and C-terminal extensions only has lost the 5S rRNA binding property. We suggest that the central homologous regions of the CL22 contains the RNA binding domain.     

Improved procedure for the isolation of a double-strand-specific ribonuclease and its application to structural analysis of various 5S rRNAs and tRNAs

An improved method for the isolation of a double-strand-specific RNase from snake venom is presented. This RNase, called CSV, was used to cleave yeast tRNAPhe and tRNA2Glu and tRNAfMet from Escherichia coli. In addition these RNAs and E. coli tRNAPhe were examined with the single-strand-specific nuclease S1. The results are discussed in terms of the specificity of CSV RNase and the structure of tRNAs. S1 nuclease digestions at increasing temperatures allowed the melting of tertiary and secondary structure to be monitored. 5S rRNA from E. coli, Thermoplasma acidophilum and the chloroplasts of Spinacia oleracea were digested with CSV and S1. The information these results give on the secondary-structural differences between different classes of 5S rRNA are discussed. Supporting evidence is found for tertiary interactions between hairpin loop c and internal loop d of eubacterial 5S rRNA.     

Electron microscopic mapping of secondary structures in bacterial 16S and 23S ribosomal ribonucleic acid and 30S precursor ribosomal ribonucleic acid

Electron microscopy revealed reproducible secondary structure patterns within partially denatured 16S and 23S ribosomal ribonucleic acid (rRNA) from Escherichia coli. When prepared with 50% formamide-100 mM ammonium acetate, 16S rRNA included two small hairpins that appeared in over 50% of all molecules. Three open loops were observed with frequencies of less than 25%. In contrast, 23S rRNA included a terminal open loop and two additional large structures in over 75% of all molecules. These secondary structure patterns were conserved in the 16S and 23S rRNA from Pseudomonas aeruginosa. The secondary structure of the 30S precursor rRNA from the ribonclease III-deficient E. coli mutant AB105 was mapped after partial denaturation in 70% formamide-100 mM ammonium acetate. Two large open loops were superimposed on the 16S and 23S rRNA secondary structure patterns. These loops were the most frequent structures found on the precursor, and their stems coincided with ribonuclease III cleavage sites. A tentative 5'-3 orientation was determined for the secondary structure patterns of 16S and 23S rRNA from their relative locations within 30S precursor rRNA. The relation of secondary structure to ribosomal protein binding and ribonuclease III cleavage is discussed.     

RNA大分子的二极结构预测

本文提出能预测单链核酸分子的具有最小自由能的二级结构的计算方法。方法的基础是拓扑平面图的最大C—匹配原理和现有的单链核酸分子折叠构象的热力学数据资料。为了说明算法的能力,对免疫球蛋白r1重链的mRNA片段序列(459个核苷酸残基)大肠杆菌16s rRNA片段序列(567一883)以及脊髓灰白质炎病毒RNA片段序列(1—74O)的二级结构进行了计算机预测并同现有的结构模型进行了比较和讨论。由计算机预测的大肠杆菌16s rRNA中心域的二级结构与Noller和Woese提出的结构模型基本一致。