Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

聚1-氨基蒽醌在二次锂电池正极材料中的应用

采用化学方法合成聚1-氨基蒽醌并用于二次锂电池正极材料,通过红外光谱、扫描电镜、粒度测试、循环伏安以及充放电测试等方法对材料的官能团结构、微观形貌、颗粒大小以及电化学性能等进行了研究与分析.实验表明,与金属锂组成二次锂电池后,聚1-氨基蒽醌达到了218.3 mAh•g－1的首次放电容量,经过25次循环后仍可保持较高的充放电效率.由于材料具有较高的能量密度且不含对环境有污染的元素S,因此是二次锂电池非常有希望的正极材料.     

Surface transient effects in ultralow‐energy Cs+ sputtering of Si

This study examines the dependence of the sputter rate and the transient width (z_tr) as a function of Cs⁺ primary ion energy (impact energy (E_p) = 320 eV, 500 eV and 1 keV) and incident angles between 0 and 70° . The instrument used was the ATOMIKA 4500 SIMS depth profiler and the sample was Si with ten delta layers of Si_0.7 Ge_0.3. We observed the narrowest transient widths of between 1.4 and 2.0 nm apparent depth. This was achieved at incident angles (θ) of 30–50° . An extended transient effect was observed when profiled at θ > 50° . Below this incident angle, the transient width is less than twice the penetration depth (z_tr < 2R_norm). At minimum z_tr, z_tr ≈ R_norm. The detection sensitivity is best achieved at θ ≈ 30° for all energies investigated. The sputter rate is lowest at normal incidence, rising gradually to a maximum at θ ≈ 50–60° . This is similar to that observed with ultralow‐energy O₂⁺ primary ion beams. 1 At ultralow energies, reducing E_p does not have a significant effect in reducing z_tr. We conclude that for E_p < 1 keV, the optimum condition to achieve minimum z_tr while maintaining good sensitivity and high sputter rate is at θ ≈ 30° . Copyright © 2007 John Wiley & Sons, Ltd.     

水滴在撞击不同厚度水膜条件下产生的二次液滴特性

采用高速相机对水滴撞击水膜的飞溅过程进行了详细测量,分析了水滴撞击水膜的飞溅临界值、二次液滴的直径分布和二次液滴的速率等飞溅特性。结果表明,在实验参数范围内,当韦伯数增大时发生飞溅现象。此外,可以使用量纲为一参数K 来描述飞溅临界值,K=We·Oh^-0.4。当K值大于2 100时发生飞溅现象,二次液滴的量纲为一直径和二次液滴的量纲为一速率随着K值的增大而增大。水膜量纲为一厚度对二次液滴直径分布的影响不明显,但由冠状水花产生的二次液滴的平均量纲为一速率随水膜量纲为一厚度的增加而减小。     

考虑偏差值的中立型区间交叉效率研究

在不确定性环境下,当决策单元(DMU)的投入产出数据为区间数形式时,为解决决策单元之间既不是合作也不是竞争关系时的交叉评价问题,本文提出一种中立型区间交叉效率模型。从所有被评价者的角度出发解决评价权重的选取问题,以决策单元投入得分的平均偏差与产出得分的平均偏差之和最小化为目标,建立决策单元在最佳和最差两种生产状态下的中立型区间交叉效率模型。在本文提出的中立型模型视角下,DMU的投入得分平均偏差和产出得分平均偏差之和达到最小。算例结果表明该中立型区间交叉效率模型的有效性,解决了不确定性环境下的交叉评价问题,保证评价的客观公正,更加符合现实。     

Growth functions for semi-regular tilings of the hyperbolic plane

This paper studies the growth function, with respect to the generating set of edge identifications, of a surface group with fundamental domainD in the hyperbolic plane ann-gon whose angles alternate between /p and /q. The possibilities ofn,p andq for which a torsion-free surface group can have such a fundamental polygon are classified, and the growth functions are computed. Conditions are given for which the denominator of the growth function is a product of cyclotomic polynomials and a Salem polynomial.This work was supported in part by NSF Research Grants.     

Coniveau of classes of flat bundles trivialized on a finite smooth covering of a complex manifold

On a smooth algebraic complex varietyX, we show that the classes of a flat bundle, which is trivialized on a finite cover ofX, with values in the odd-dimensional cohomology of the underlying complex manifold with / (i), are living in the bottom part of Grothendieck's coniveau filtration. This answers positively when the basis is smooth complex a question of Bruno Kahn [K-Theory (1992), conjecture 2].     

On nonnegative solvability of linear operator equations

LetE be a Banach lattice having order continuous norm. Suppose, moreover,T is a nonnegative reducible operator having a compact iterate and which mapsE into itself. The purpose of this work is to extend the previous results of the authors, concerning nonnegative solvability of (kernel) operator equations on generalL ^p-spaces. In particular, we provide necessary and sufficient conditions for the operator equation x=T x+y to possess a nonnegative solutionxE wherey is a given nonnegative and nontrivial element ofE and is any given positive parameter.     

计入次近邻作用的─维点阵的定＂长＂比热

计算了计入次近邻相互作用后一维点阵在低温下的定＂长＂比热,结果表明次近邻的影响使比热减小．比热;次近邻作用