Parallel computation in biological sequence analysis

A massive volume of biological sequence data is available in over 36 different databases worldwide, including the sequence data generated by the Human Genome project. These databases, which also contain biological and bibliographical information, are growing at an exponential rate. Consequently, the computational demands needed to explore and analyze the data contained in these databases is quickly becoming a great concern. To meet these demands, we must use high performance computing systems, such as parallel computers and distributed networks of workstations. We present two parallel computational methods for analyzing these biological sequences. The first method is used to retrieve sequences that are homologous to a query sequence. The biological information associated with the homologous sequences found in the database may provide important clues to the structure and function of the query sequence. The second method, which helps in the prediction of the function, structure, and evolutionary history of biological sequences, is used to align a number of homologous sequences with each other. These two parallel computational methods were implemented and evaluated on an Intel IPSC/860 parallel computer. The resulting performance demonstrates that parallel computational methods can significantly reduce the computational time needed to analyze the sequences contained in large databases     

Design of seismic retrofit measures for concrete and masonry structures

The concept of seismic retrofit of older concrete and masonry structures possessing substandard seismic resistance using jackets or skins of composite fibres bonded with a polymer matrix to the surface is discussed. Results from extensive experimental research are presented to support simple design models enabling retrofit measures to be designed for enhanced shear strength, flexural ductility or lap-slice performance.     

Protocol verification using database technology

A novel application of databases in communications networks, namely, protocol verification on a parallel database machine, is described. An approach to protocol verification that uses database algorithms executing on a commercially available, parallel architecture called a hypercube multicomputer is introduced. The goal is to achieve the high degree of computational parallelism necessary to explore rapidly the global state space of even very complex protocols, significantly reducing the time required to verify a protocol and allowing formal verification to be included as part of the process of protocol design. An overview is provided of the relational model of protocol verification used, and extensions to the model are described. The hypercube multicomputer and the algorithms for relational database operations designed to execute in that environment are then described. Estimates of the performance improvements achievable by parallel executing of verification algorithms in the proposed system are given     

Synthesis, Properties, and Functionalization of Poly(ferrocenylsilane)s with Chloroalkyl Side Chains

A series of poly(ferrocenylsilane)s containing chloroalkyl side chains of increasing length is reported. By reacting fcLi₂· tmeda with Cl₂SiMeR, the corresponding [1]ferrocenophanes were prepared (2a, R=CH₂Cl; 2b, R=CH₂CH₂Cl; and 2c, R=CH₂CH₂CH₂Cl). Transition metal-catalyzed or thermal ring-opening polymerization (ROP) of these monomers yielded the polyferrocenes 3a, 3b, and 3c. The chlorine substituents of polymers 3a and 3b were unreactive toward nucleophilic substitution. In contast, polymer 3c could be reacted with 4-dimethylaminopyridine in DMF to afford the water-soluble poly(ferrocenylsilane) 4. This represents a new method for the preparation of water-soluble polyferrocenes.     

Vorstellung und Test eines apparativ einfachen Messsystems für pneumatische Slug-Tests zur integralen Bestimmung der hydraulischen Leitfähigkeit

Grundwasser - Die in der Geotechnik zur Bestimmung der hydraulischen Leitfähigkeit gebräuchlichen Standardverfahren Sieblinienanalyse und Pumpversuch sind hinsichtlich ihrer Eigenschaften...     

Per-O-methylated α- and β-CD: Cyclodextrins with Inverse Hydrophobicity

The investigation focuses on the computer-aided generation of the molecular geometries, contact surfaces, and lipophilicity patterns of per-O-methylated α-CD ( 1 ) and its β-CD homolog 2 , and compares them with their parent non-substituted cyclodextrins. The molecular geometries, compared via statistical analysis of crystal structure data available, reveal 1 and 2 to be considerably more flexible than α-and β-CD, allowing wide variations in the tilting of the glucose units relative to the macrocyclic ring axes. The comparative evaluation of their contact surfaces not only discloses a substantial increase of the torus heights upon per-O-methylation (from ∼8.0Å in α- and β-CD, to → 11.1Å in 1 and 2 ), but also an enlargement of their cavity areas by 40% (+35Ų for α-CD → 1 ) and 70% (+75Ų for β-CD → 2 ), respectively. The hydrophobic characteristics of 1 and 2 , emerging from the molecular lipophilicity patterns (MLPs) generated and projected onto the contact surfaces in color-coded from, are inverse to those for α- and β-CD: the most hydrophobic surface regions of 1 and 2 are located at the torus rims made up by the 2-OMe and 3-OMe groups at one side, and the 6-CH₂OMe moieties at the other, with a hydrophobic „band”︁ wrapping around the outside of the macrocycles; these „exo-lipophilic”︁ topographies are opposed by pronouncedly hydrophilic central cavities. A variety of experimental findings can be rationalized on the basis of the opposite lipophilicity profiles of the CDs and their permethylated analogs, such as for example the opposite orientation of benzaldehyde, p-nitrophenol, and 3-iodopropionic acid in the cavities of α-CD and of 1 . Thus, the notion is substantiated that the operation of dispersive interactions between guest and CD-host cavities play a more dominant role in inclusion complex formation than hitherto appreciated.     

The Hydrophobic Topographies of Amylose and its Blue Iodine Complex

Two polymorphs of amylose, the native double‐helical A‐form and the single‐stranded V_H counterpart, as well as the amylose polyiodide complex were subjected to a molecular modeling study. Based on their X‐ray diffraction‐derived structures, the "solvent‐accessible" contact surfaces were generated, onto which the computed molecular lipophilicity profiles (MLPs) were projected in color‐coded form, easily allowing to locate hydrophobic and hydrophilic surface regions. Their detailed analysis revealed the double‐stranded A‐form to be a rather compact structure with an irregular distribution of hydrophilic and hydrophobic regions over the entire outer surface, with the interior of the double helix being inaccessible even for small molecules. By contrast, V_H‐amylose, in accord with its water solubility, has a pronouncedly hydrophilic outside surface with an as distinctly hydrophobic channel. — In the darkblue amylose‐polyiodide complex, the hydrophobic channel of the single‐helical V_H‐form serves as a well‐ordered matrix for incorporation and alignment of the iodine‐iodide species to elaborate a linear polyiodide chain in a nearly perfect steric fit and in full complementarity of hydrophobic regions of guest and host. Thus, the MLPs provide substantive credence to the view, that not only the amylose‐iodine complex formation is mediated to an essential degree by hydrophobic attractions at the guest‐host interface, but that the same factors determine the stability of this unique supramolecular assembly.     

Towards Understanding Formation and Stability of Cyclodextrin Inclusion Complexes: Computation and Visualization of their Molecular Lipophilicity Patterns[1]

Five cyclodextrin inclusion complexes - typical examples for their solid state as well as exemplary „frozen molecular images”︁ of their status in solution - were subjected to a molecular modelling study comprising the computer-assisted generation of the molecular lipophilicity patterns (MLP's), i. e. the p-iodoaniline inclusion into α-CD, the complexes of β-CD with 1,4-butanediol, adamantane-1-carboxylic acid, and adamantane-1-methanol, and the unique 12-crown-4 ether inclusion compound of γ-CD. Based on their solid state structures, the „solvent-accessible”︁ contact surfaces were generated by the MOLCAD program. Calculation and color-coded projection of the MLP's onto these surfaces easily allows to locate the hydrophobic and hydrophilic surface regions of CD-host and guest alike. Their detailed analysis revealed a far-reaching, mostly complete conformity between the hydrophobic surface areas of the guest and the hydrophobic domains in the CD cavity. This striking tendency to optimize the reciprocal concurrence of lipophilic as well as hydrophilic domains at the guest-host-interface may accordingly be concluded to be an important, if not the decisive element in orienting the guest into the cavity and in determining the stability of the complex, particularly in cases where the guest is devoid of polar groups; if these are present, dipole-dipole alignments and the need for their solvation may diminish the importance of hydrophobic attractions for orienting and stabilizing the guest in the CD cavity.