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.

     

聚合物复合材料填充剂的表面性质及其分散性的研究

本文通过反气相色谱技术研究了未处理的、硅烷偶联剂处理的和钛酸酯偶联剂处理的三种Al(OH)_3粉末的表面性质,并通过塑化仪和扫描电子显微镜研究了Al(OH)_3填充聚丙烯体系的流变行为及其在聚丙烯中的分散效果.结果表明Al(OH)_3的表面性质对其在聚丙烯介质中的分散效果有着重要的影响.     

Filtering germs: Groupoids associated to inverse semigroups

We investigate various groupoids associated to an arbitrary inverse semigroup with zero. We show that the groupoid of filters with respect to the natural partial order is isomorphic to the groupoid of germs arising from the standard action of the inverse semigroup on the space of idempotent filters. We also investigate the restriction of this isomorphism to the groupoid of tight filters and to the groupoid of ultrafilters.     

A Family of Fifth-Order Runge-Kutta Pairs

The construction of a Runge-Kutta pair of order with the minimal number of stages requires the solution of a nonlinear system of order conditions in unknowns. We define a new family of pairs which includes pairs using function evaluations per integration step as well as pairs which additionally use the first function evaluation from the next step. This is achieved by making use of Kutta's simplifying assumption on the original system of the order conditions, i.e., that all the internal nodes of a method contributing to the estimation of the endpoint solution provide, at these nodes, cost-free second-order approximations to the true solution of any differential equation. In both cases the solution of the resulting system of nonlinear equations is completely classified and described in terms of five free parameters. Optimal Runge-Kutta pairs with respect to minimized truncation error coefficients, maximal phase-lag order and various stability characteristics are presented. These pairs were selected under the assumption that they are used in Local Extrapolation Mode (the propagated solution of a problem is the one provided by the fifth-order formula of the pair). Numerical results obtained by testing the new pairs over a standard set of test problems suggest a significant improvement in efficiency when using a specific pair of the new family with minimized truncation error coefficients, instead of some other existing pairs.

     

Comparison between the adsorption behaviors of an organic cation and an organic anion on several reversed-phase liquid chromatography adsorbents

Adsorption data of an organic cation (propranololium chloride) and an organic anion (sodium 1-naphthalene sulfonate) were measured by frontal analysis on two RPLC adsorbents, Symmetry-C18 and XTerra-C18, with aqueous solutions of methanol as the mobile phases. The influence of supporting neutral salts on the adsorption behavior of these two ions are compared. The Henry constants are close (H approximately 5). The four sets of isotherm data are all well accounted for using the bi-Moreau model. However, the isotherms of the two ions behave differently at high concentrations. The initial behaviors of all the isotherms are antilangmuirian but remain so in a much wider concentration range for the cation than for the anion, due to its stronger adsorbate-adsorbate interactions on the low-energy adsorption sites. The retention times of both ions increase with increasing concentration of neutral salt in the mobile phase, suggesting the formation of ion-pair complexes, with Cl- for the cation and with Na+ for the anion. The adsorbate-adsorbate interactions vanish in the presence of salt and the bi-Moreau isotherm model tends toward a bi-Langmuir model. Differences in adsorption behavior are also observed between the cation and the anion when bivalent inorganic anions and cations, respectively, are dissolved in the mobile phase. High concentration band profiles of 1-naphthalene sulfonic acid are langmuirian, except in the presence of a trivalent cation, while those of propranolol are antilangmuirian under certain conditions even with uni- or divalent cations.     

A further breakthrough in biphasic, rhodium-catalyzed hydroformylation: the use of Per(2,6-di-O-methyl)-β-cyclodextrin as inverse phase transfer catalyst

Solvent free biphasic hydroformylalion of various water-insoluble terminal olefins can be achieved in high yields and sclcctivitics by using a water-soluble rhodium/triphenylphosphine trisulfonate catalyst and per(2,6-di-o-mclhyl)-β-cyclodcxtrin as inverse phase transfer catalyst. The catalytic activities were up to ten times higher than those observed without pcr(2,6-di-o-methyl)-β-cyclodextrin.     

Comparison between adsorption isotherm determination techniques and overloaded band profiles on four batches of monolithic columns

The adsorption isotherms of 4-tert.-butyl phenol were measured on four different monolithic columns, using three different techniques, classical frontal analysis (FA), the perturbation on a plateau method (PP) and the recently introduced numerical procedure known as the inverse numerical method (IN). This last approach requires only the recording of a few overloaded profiles and has the potential advantage of affording a dramatic decrease of the amounts of compounds, solvent, and time needed to determine accurate estimates of the coefficients of the isotherm. The reproducibility of the adsorption data measured on the four columns is discussed with reference to the specific techniques used for obtaining these data and to the most suitable equation used for modeling them. The data obtained for the different columns were highly consistent. The inverse numerical approach was confirmed to provide a powerful, accurate, and economic method for measuring single component adsorption data.     

Deactivation of silica surfaces with a silanol-terminated polysiloxane; structural sharacterization by inverse gas chromatography and solid-state NMR

Retention gape deactivated with Silicone OV-1701-OH show good chromatographic performance and remarkable stability against water induced stationary phase degradrdation. In an attempt to better understand the findamentals off the deactivation process using silanol terminated polysiloxanes, a fumed silica was deactivated with Silicon OV-1701-OH. In contrast to fused silic capillaries, fumed silica (Aerosil A-200) can be studied by ²⁹Si cross-polarization magic-angle-spinning (CPMAS) NMR, thus serving as a model substrate for fused silica. Retention data from inverse gas chromatography at infinite dilurion and ²⁹Si CP MAS NMR data of five Aerosil phases, differing in residual silanol surface concentration, are correlated with the aim of validating this approach for stationary phase characterization. A comparatively detailed model of the deactivating polymer layer that explains the observed absorption activities is deduced. Surface silanols are shown to play a key role in the polymer layer, the structure of which is of primary importance for the absorption behavior after deactivation. Contrary to common belief, the absolute silanol surface concentration after deativation is only of secondary importance for the overall absorption activity. High silanol surface concentrations enhance degradation of the polysiloxane chains into small cyclic fragments as well as subsequent absorption and immobolization to the silica substrate surface. The mobility of linear polysiloxane chains in the kHz regime (as determined bby NMR cross-polarization dynamics) appears to determine the extent which the residual silanols are accessible for analytes. It is therefore anticipated that there is an optimum silanol surface concentration of fused silica surfaces to be deactivated with silanol terminated polysiloxanes; it should be lazrge enough to adsord polymer fragments, but not large to avoid excessive residual silanol activity.     

Cyclodextrins as chiral stationary phases in capillary gas chromatography. Part VII: Cyclodextrins with an inverse substitution pattern – synthesis and enantioselectivity

Transferring the site of specific substitution of dipentylated cyclodextrins with methyl or acyl residues from the secondary 3-hydroxyl group to the primary 6-hydroxyl group was expected to provide new information on the mechanism of chiral recognition. The 3-position points towards and the 6-position points away from the cyclodextrin cavity which via inclusion complex formation is supposed to play a major role in chiral separation. The “inverse” 6-O-acyl-2,3-di-O-pentyl-cyclodextrins displayed almost no enantioselectivity but the corresponding 6-O-methyl derivatives are a versatile supplement to the chiral capillary GC phases nowadays available. Among the compounds that could be enantiomerically resolved are alcohols, amino acids, alkyl halides, bicyclic ethers, acetals, olefins, other hydrocarbons and chiral pharmaceuticals.     

Neue Kupferkomplexe mit Phosphaalkenliganden. Molekülstruktur von [Cu{P(Mes*)C(NMe2)2}2]BF4 (Mes* = 2,4,6‐tBu3C6H2)

New Copper Complexes Containing Phosphaalkene Ligands. Molecular Structure of [Cu{P(Mes*)C(NMe₂)₂}₂]BF₄ (Mes* = 2,4,6‐tBu₃C₆H₂) Reaction of equimolar amounts of the inversely polarized phosphaalkene tBuP=C(NMe₂)₂ ( 1a ) and copper(I) bromide or copper(I) iodide, respectively, affords complexes [Cu₃X₃{μ‐P(tBu)C(NMe₂)₂}₃] ( 2 ) (X =Br) and ( 3 ) (X = I) as the formal result of the cyclotrimerization of a 1:1‐adduct. Treatment of 1a with [Cu(L)Cl] (L = PiPr₃; SbiPr₃) leads to the formation of compounds [CuCl(L){P(tBu)C(NMe₂)₂}] ( 4a ) (L = PiPr₃) and ( 4b ) (L = SbiPr₃), respectively. Reaction of [(MeCN)₄Cu]BF₄ with two equivalents of PhP=C(NMe₂)₂ ( 1b ) yields complex [Cu{P(Ph)C(NMe₂)₂}₂]BF₄ ( 5b ). Similarly, compounds [Cu{P(Aryl)C(NMe₂)₂}₂]BF₄ ( 5c (Aryl = Mes and 5d (Aryl = Mes*)) are obtained from ArylP=C(NMe₂)₂ ( 1c : Aryl = Mes; 1d : Mes*) and [(MeCN)₄Cu]BF₄ in the presence of SbiPr₃. Complexes 2 , 3 , 4a , 4b , and 5b‐5d are characterized by means of elemental analyses and spectroscopy (¹H‐, ¹³C{¹H}‐, ³¹P{¹H}‐NMR). The molecular structure of 5d is determined by X‐ray diffraction analysis.