Matching subsequences in trees

Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new algorithms improving the previously best known time and space bounds.     

Comparison of chromatographic ion-exchange resins. III. Strong cation-exchange resins

A comparative study was performed on strong cation-exchangers to investigate the pH dependence, efficiency, binding strength, particle size distribution, static and dynamic capacity, and SEM pictures of chromatographic resins. The resins tested included: SP Sepharose XL, Poros 50 HS, Toyopearl SP 550c, SP Sepharose BB, Source 30S, TSKGel SP-5PW-HR20, and Toyopearl SP 650c. Testing was performed with four different proteins: anti-FVII Mab (IgG), aprotinin, lysozyme, and myoglobin. Dependence of pH on retention was generally very low for proteins with high pI. An unexpected binding at pH 7.5 of anti-FVII Mab with pI < 7.5 was observed on several resins. Efficiency results show the expected trend of higher dependence of the plate height with increasing flow rate of soft resins compared to resins for medium and high-pressure operation. Determination of particle size distribution by two independent methods, Coulter counting and SEM, was in very good agreement. The mono-dispersed nature of Source 30S was confirmed. Binding to cation-exchange resins as a function of ionic strength varies depending on the specific protein. Generally, binding and elution at high salt concentration may be performed with Toyopearl SP 550c and Poros 50 HS, while binding and elution at low salt concentration may be performed with Toyopearl SP 650c. A very high binding capacity was obtained with SP Sepharose XL. Comparison of static capacity and dynamic capacity at 10% break-through shows in general approximately 50-80% utilisation of the total available capacity during chromatographic operation. A general good agreement was obtained between this study and data obtained by others. The results of this study may be used for selection of resins for testing in process development. The validity of experiments and results with model proteins were tested using human insulin precursor in pure state and in real feed-stock on Toyopearl SP 550c, SP Sepharose BB, and Toyopearl SP 650c. Results showed good agreement with experiments with model proteins.     

Efficient generation,storage, and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching

Pharmacophore triplets and quartets have been used by many groups in recent years, primarily as a tool for molecular diversity analysis. In most cases, slow processing speeds and the very large size of the bitsets generated have forced researchers to compromise in terms of how such multiplets were stored, manipulated, and compared, e.g., by using simple unions to represent multiplets for sets of molecules. Here we report using bitmaps in place of bitsets to reduce storage demands and to improve processing speed. Here, a bitset is taken to mean a fully enumerated string of zeros and ones, from which a compressed bitmap is obtained by replacing uniform blocks ("runs") of digits in the bitset with a pair of values identifying the content and length of the block (run-length encoding compression). High-resolution multiplets involving four features are enabled by using 64 bit executables to create and manipulate bitmaps, which "connect" to the 32 bit executables used for database access and feature identification via an extensible mark-up language (XML) data stream. The encoding system used supports simple pairs, triplets, and quartets; multiplets in which a privileged substructure is used as an anchor point; and augmented multiplets in which an additional vertex is added to represent a contingent feature such as a hydrogen bond extension point linked to a complementary feature (e.g., a donor or an acceptor atom) in a base pair or triplet. It can readily be extended to larger, more complex multiplets as well. Database searching is one particular potential application for this technology. Consensus bitmaps built up from active ligands identified in preliminary screening can be used to generate hypothesis bitmaps, a process which includes allowance for differential weighting to allow greater emphasis to be placed on bits arising from multiplets expected to be particularly discriminating. Such hypothesis bitmaps are shown to be useful queries for database searching, successfully retrieving active compounds across a range of structural classes from a corporate database. The current implementation allows multiconformer bitmaps to be obtained from pregenerated conformations or by random perturbation on-the-fly. The latter application involves random sampling of the full range of conformations not precluded by steric clashes, which limits the usefulness of classical fingerprint similarity measures. A new measure of similarity, The Stochastic Cosine, is introduced here to address this need. This new similarity measure uses the average number of bits common to independently drawn conformer sets to normalize the cosine coefficient. Its use frees the user from having to ensure strict comparability of starting conformations and having to use fixed torsional increments, thereby allowing fully flexible characterization of pharmacophoric patterns.     

Surface analysis of a cold leg section of an SS316-lithium loop

Compatibility studies of austenitic stainless steel AISI 316 with liquid lithium for fusion application have shown that a porous ferritic layer is formed on the surface of the steel in the hot leg of a loop experiment due to depletion of alloying elements. The concentration profiles of the removed elements across the cross section of the tube reveal a pronounced step between the austenite matrix and the porous ferrite which is not expected in a normal diffusion process. The removed elements are partly deposited on the surface of the cold leg.In this study we looked at the boundary between the nickel rich deposit and the original matrix of a section of the cold (435 °C) leg. On the surface of the austenite, the expected grain boundary attack of lithium was observed. Additionally, to a depth of about one grain size, chromium and molybdenum were depleted and lithium seemed to also have attacked the bulk material, resulting in a splitting up into smaller grains with decomposed concentrations of the alloying elements, i.e. iron with large amounts of nickel and iron with chromium and small nickel amounts.In this paper a suggestion is put forward describing a reaction mechanism leading to the porous layer in the hot leg as a result of the instability of AISI 316 and its decomposition into two phases under the influence of liquid lithium.Dedicated to Professor Günther Tölg on the occasion of his 60th birthday     

A multiblock/multilevel mesh refinement procedure for CFD computations

A multiblock/multilevel algorithm with local refinement for general two‐ and three‐dimensional fluid flow is presented. The patched‐based local refinement procedure is presented in detail and algorithmic implementations are also presented. The multiblock implementation is essentially block‐unstructured, i.e. each block having its own local curvilinear co‐ordinate system. Refined grid patches can be put anywhere in the computational domain and can extend across block boundaries. To simplify the implementation, while still maintaining sufficient generality, the refinement is restricted to a refinement of the grid successively halving the grid size within a selected patch. The multiblock approach is implemented within the framework of the well‐known SIMPLE solution strategy. Computational experiments showing the effect of using the multilevel solution procedure are presented for a sample elliptic problem and a few benchmark problems of computational fluid dynamics (CFD). Copyright © 2001 John Wiley & Sons, Ltd.     

Two-dimensional, pyrazine-based nonlinear optical chromophores with ruthenium(II) ammine electron donors

Six new nonlinear optical (NLO) chromophores with pyrazinyl-pyridinium electron acceptors have been synthesized by complexing a known pro-ligand with electron donating {Ru(II)(NH(3))(5)}(2+) or trans-{Ru(II)(NH(3))(4)(py)}(2+) (py = pyridine) centers. These cationic complexes have been characterized as their PF(6)(-) salts by using various techniques including electronic absorption spectroscopy and cyclic voltammetry. The visible d → π* metal-to-ligand charge-transfer (MLCT) absorptions gain intensity on increasing the number of Ru(II) centers from one to two, but remain at constant energy. One or two Ru(III/II) redox processes are observed which are reversible, quasi-reversible, or irreversible, while all of the ligand-based reductions are irreversible. Molecular first hyperpolarizabilities β have been determined by using hyper-Rayleigh scattering (HRS) at 1064 nm, and depolarization studies show that the NLO responses of the symmetric species are strongly two-dimensional (2D) in character, with dominant "off-diagonal" β(zyy) components. Stark (electroabsorption) spectroscopic measurements on the MLCT bands also allow the indirect determination of estimated static first hyperpolarizabilities β(0). Both the HRS and the Stark-derived β(0) values increase on moving from mono- to bimetallic complexes, and substantial enhancements in NLO response are achieved when compared with one-dimensional (1D) and 2D monometallic Ru(II) ammine complexes reported previously.