Showing papers by "ETH Zurich published in 1991"

Protein hydration in aqueous solution.

Abstract: High-resolution proton nuclear magnetic resonance studies of protein hydration in aqueous solution show that there are two qualitatively different types of hydration sites. A well-defined, small number of water molecules in the interior of the protein are in identical locations in the crystal structure and in solution, and their residence times are in the range from about 10(-2) to 10(-8) second. Hydration of the protein surface in solution is by water molecules with residence times in the subnanosecond range, even when they are located in hydration sites that contain well-ordered water in the x-ray structures of protein single crystals.

A synthetic gallophosphate molecular sieve with a 20-tetrahedral-atom pore opening

Abstract: THE most widely used catalyst in petroleum cracking and reforming processes is the synthetic zeolite Y. Its unique properties arise from the fact that the enormous inner surface area created by the three-dimensional channel system is accessible to sorbed molecules through 12-ring pore openings. These windows, with free diameters of 7-8A, allow both aliphatic and small aromatic molecules to enter the zeolite. Attempts to synthesize zeolitic structures with even wider pores, to accommodate larger molecules, have produced two aluminophosphates with one-dimensional channels: VPI-5 (ref. 1), which has 18-ring channels with free diameters of 12-13A, and AlPO48 (refs 2, 3), with oval 14-ring channels. We now report the structure of a new cubic gallophosphate with a pore opening comprising 20 tetrahedrally coordinated atoms in the shape of a four-leafed clover (Fig. 1) and a three-dimensional channel system. The unusual shape of the window is due to the presence of terminal hydroxyl groups in the framework, and provides new possibilities for shape-selective sorption. The supercage formed aHhe intersection of the channels has a body diagonal of 29-30 A, and could thus accommodate larger intermediates in zeolite catalytic processes.

Markov ciphers and differential cryptanalysis

Abstract: This paper considers the security of iterated block ciphers against the differential cryptanalysis introduced by Biham and Shamir. Differential cryptanalysis is a chosen-plaintext attack on secret-key block ciphers that are based on iterating a cryptographically weak function r times (e.g., the 16-round Data Encryption Standard (DES)). It is shown that the success of such attacks on an r-round cipher depends on the existence of (r-1)-round differentials that have high probabilities, where an i-round differential is defined as a couple (α, β) such that a pair of distinct plaintexts with difference α can result in a pair of i-th round outputs that have difference β, for an appropriate notion of "difference". The probabilities of such differentials can be used to determine a lower bound on the complexity of a differential cryptanalysis attack and to show when an r-round cipher is not vulnerable to such attacks. The concept of "Markov ciphers" is introduced for iterated ciphers because of its significance in differential cryptanalysis. If an iterated cipher is Markov and its round subkeys are independent, then the sequence of differences at each round output forms a Markov chain. It follows from a result of Biham and Shamir that DES is a Markov cipher. It is shown that, for the appropriate notion of "difference", the Proposed Encryption Standard (PES) of Lai and Massey, which is an 8-round iterated cipher, is a Markov cipher, as are also the mini-version of PES with block length 8, 16 and 32 bits. It is shown that PES(8) and PES(16) are immune to differential cryptanalysis after sufficiently many rounds. A detailed cryptanalysis of the full-size PES is given and shows that the very plausibly most probable 7-round differential has a probability about 2-58. A differential cryptanalysis attack of PES(64) based on this differential is shown to require all 264 possible encryptions. This cryptanalysis of PES suggested a new design principle for Markov ciphers, viz., that their transition probability matrices should not be symmetric. A minor modification of PES, consistent with all the original design principles, is proposed that satisfies this new design criterion. This modified cipher, called Improved PES (IPES), is described and shown to be highly resistant to differential cryptanalysis.

Partial melting of two amphibolites: contrasting experimental results under fluid-absent conditions

Abstract: A large portion of the lower continental crust may be amphibolitic in composition and without a free fluid phase. As a consequence, H2O-undersaturated or fluid-absent melting of amphibolites may be responsible for the formation of some granites and migmatites produced during major orogenic events. In an attempt to determine the systematics of melting under fluid-absent conditions, a series of piston-cylinder experiments was conducted on two natural amphibolites; one, a meta-alkali basalt (ABA) with a total water content of ∼ wt% contained in hornblende, and the other, a meta-island-arc tholeiite (IAT) which has ∼1–1.3 wt% water contained in hornblende, cummingtonite and biotite. The experimentally determined melting ranges of the two amphibolites showed that the solidus temperatures, and sta temperature interval over which amphibole was stable, were controlled by the amphibolites' different bulk compositions and their resulting metamorphic assemblages. The volume % of melt produced by melting of the two amphibolites were compared with estimated amounts, based on Burnham's (1979) water-melt solubility model and the fluid-absent melting model presented by Clemens and Vielzeuf (1987). The observed melt volumes were greater than estimated. As the water content of melt largely detemines the volume % of melt produced, independent measurements of the water-content of the glass formed during partial melting in the ABA were made by thermogravimetric analyses. The water content of the ABA glass is ∼2 wt%, which is less than the assumed “melt-water” content (water content of the melt) used in previous modeling of fluidabsent anatexis in mafic lithologies. As a consequence, more melt can be expected during fluid-absent partial melting of mafic lower crust, as is observed in the experiments. A modification of the Clemens and Vielzeuf (1987) fluid-absent melting model for mafic compositions has been made using the experimental data available on melting in basaltic systems and is presented here for pressures of 5, 8 and 10 kbar. Tectonic scenarios in which the crust is thickened (i.e. by collision) then undergoes extension or where a previously thinned crust is later rethickened, provide enough heat so that amphibolite melting under fluid-absent conditions can become importan and hence responsible for some melts produced during post-collisional magmatism. The results may also have applications to melting in hydrated oceanic crust in subduction zones and in island arc terains.

Discrete versions of some classical integrable systems and factorization of matrix polynomials

Abstract: Discrete versions of several classical integrable systems are investigated, such as a discrete analogue of the higher dimensional force-free spinning top (Euler-Arnold equations), the Heisenberg chain with classical spins and a new discrete system on the Stiefel manifold. The integrability is shown with the help of a Lax-pair representation which is found via a factorization of certain matrix polynomials. The complete description of the dynamics is given in terms of Abelian functions; the flow becomes linear on a Prym variety corresponding to a spectral curve. The approach is also applied to the billiard problem in the interior of anN-dimensional ellipsoid.

Principles and realization strategies of multilevel transaction management

Abstract: One of the demands of database system transaction management is to achieve a high degree of concurrency by taking into consideration the semantics of high-level operations. On the other hand, the implementation of such operations must pay attention to conflicts on the storage representation levels below. To meet these requirements in a layered architecture, we propose a multilevel transaction management utilizing layer-specific semantics. Based on the theoretical notion of multilevel serializability, a family of concurrency control strategies is developed. Suitable recovery protocols are investigated for aborting single transactions and for restarting the system after a crash. The choice of levels involved in a multilevel transaction strategy reveals an inherent trade-off between increased concurrency and growing recovery costs. A series of measurements has been performed in order to compare several strategies. Preliminary results indicate considerable performance gains of the multilevel transaction approach.

Bonding Patterns in Intermetallic Compounds

Abstract: Intermetallic phases have long been among the black sheep in the family of chemical compounds. Their chemical bonding has eluded description by the valence rules, which otherwise are extremely effective. As a result, understanding of the structure–bonding relationships in these phases to date has remained nebulous, even though they form the largest group of inorganic compounds. Their broad industrial applicability and richly varied structural chemistry call for new approaches for explaining their structures, electronic structures, and physical properties. A combination of new experimental and theoretical investigations has revealed interesting local aspects of chemical bonding in metals and thereby pointed to a route from the valence compounds, through the cluster and electron-deficient compounds, to the intermetallic phases.

Updatable Views in Object-Oriented Databases

Abstract: Object-oriented database systems (ooDBMSs) are supposed to offer at least the functionality available in commercial relational DBMSs of today. One important consequence of this is that they have to provide a separation of the global (conceptual) database schema from the external schema (“subschema”) of a particular task. Views are a mechanism to realize this data independence. In addition, they also support multiple levels of detail, security and authorization, and interoperability in a heterogeneous environment. In a relational DBMS, views are defined by queries. However, they can not be freely updated. We describe concepts of an object model and query language that are necessary for object view definitions. We show that updating object views is much more feasible than in the case of relational views. The key property of a query language leading to this result is object preserving operator semantics. That is, in contrast to many previous object algebras, query results are sets of existing objects instead of data tuples or new objects. Consequently, we have to solve the classification problem: where to include the view in the type and class lattices.

The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution.

Abstract: Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform {sup 15}N- or {sup 13}C-labeling of cyclosporin A and heteronuclear spectral editing techniques. With an input of 108 intramolecular NOEs and four vicinal {sup 3}J{sub HN{alpha}} coupling constants, the three-dimensional structure of cyclosporin A bound to cyclophilin was calculated with the distance geometry program DISMAN, and the structures resulting from 181 converged calculations were energy refined with the program FANTOM. A group of 120 conformers was selected on the basis of the residual constraint violations and energy criteria to represent the solution structure. The average of the pairwise root-mean-square distances calculated for the backbone atoms of the 120 structures was 0.58 {angstrom}. The structure represents a novel conformation of cyclosporin A, for which the backbone conformation is significantly different from the previously reported structures in single crystals and in chloroform solution. The structure has all peptide bonds in the trans form, contains no elements of regular secondary structure and no intramolecular hydrogen bonds, and exposes nearly all polar groups to its environment. The root-mean-square distance between the backbone atoms of the crystal structure of cyclosporin Amore » and the mean of the 120 conformers representing the NMR structure of cyclosporin A bound to cyclophilin is 2.5 {angstrom}.« less

Efficient analysis of protein 2D NMR spectra using the software package EASY.

Abstract: The programEASY supports the spectral analysis of biomacromolecular two-dimensional (2D) nuclear magnetic resonance (NMR) data. It provides a user-friendly, window-based environment in which to view spectra for interactive interpretation. In addition, it includes a number of automated routines for peakpicking, spin-system identification, sequential resonance assignment in polypeptide chains, and cross peak integration. In this uniform environment, all resulting parameter lists can be recorded on disk, so that the paper plots and handwritten notes which normally accompany manual assignment of spectra can be largely eliminated. For example, in a protein structure determination by 2D1H NMR,EASY accepts the frequency domain datasets as input, and after combined use of the automated and interactive routines it can yield a listing of conformational constraints in the format required as input for the calculation of the 3D structure. The program was extensively tested with current protein structure determinations in our laboratory. In this paper, its main features are illustrated with data on the protein basic pancreatic trypsin inhibitor.

On repeated-root cyclic codes

Abstract: A parity-check matrix for a q-ary repeated-root cyclic code is derived using the Hasse derivative. Then the minimum distance of a q-ary repeated-root cyclic code is expressed in terms of the minimum distance of a certain simple-root cyclic code. With the help of this result, several binary repeated-root cyclic codes of lengths up to n=62 are shown to contain the largest known number of codewords for their given length and minimum distance. The relative minimum distance d/sub min//n of q-ary repeated-root cyclic codes of rate r>or=R is proven to tend to zero as the largest multiplicity of a root of the generator g(x) increases to infinity. It is further shown that repeated-root cycle codes cannot be asymptotically better than simple-root cyclic codes. >

A wide area network information filter

Abstract: A discussion is given on an intelligent wide area network-based clipping service used as a test-bed for the development and effectiveness measurement of high-performance retrieval algorithms. The system taps news wire and other information sources aperiodically, several times daily. It maintains a local 100 Mbyte news database that changes at a rate of 10 Mbytes per day. The system stores and manages user interest profiles, each of which includes several query texts. News items are selected for presentation by a completely automatic four-stage information filtering process; expert system rules and database knowledge criteria are used in the first three stages; vector-space ranking is used in the final stage. News items are actively and selectively disseminated to users via electronic mail. >

Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli.

Abstract: Summary Anaerobic growth of Pseudomonas aeruginosa on nitrate or arginine requires the anr gene, which codes for a positive control element (ANR) capable of functionally complementing an fnr mutation in Escherichia coli. The anr gene was sequenced; it showed 51% identity with the fnr gene at the amino acid sequence level. Four cysteine residues known to be essential in the FNR protein are conserved in ANR. The anr gene product (deduced Mr 27129) was visualized by the maxicell method and migrated like a 32kDa protein in gel electrophoresis under denaturing conditions. An anr mutant of P. aeruginosa constructed by gene replacement was defective in nitrate respiration, arginine deiminase activity, and hydrogen cyanide biosynthesis, underscoring the diverse metabolic functions of ANR during oxygen limitation. Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas syringae, and Pseudomonas mendocina all had a functional analogue of ANR, indicating that similar anaerobic control mechanisms exist in these bacteria.

Effect of molecular elasticity on out-of-plane orientations in shearing flows of liquid-crystalline polymers

Abstract: The Doi equation for the time-dependent orientational Distribution function of rodlike molecules in a nematic monodomain is solved for Startup of a simple shearing flow with director orientation initially oriented at various angles with respect to the shearing plane, where the shearing plane is defined to be parallel to both the velocity and its gradient. Two numerical solution techniques are used; one is an expansion in spherical harmonic functions, which is a generalization of a technique derived earlier for a director confined to the shearing plane, and the second is a stochastic method that integrates the equations of motion for a large ensemble of molecules. We find that at low and modest shear rates, the director can be attracted either to a time-periodic tumbling orbit that lies in the shearing plane or to an orbit that lies out of the shearing plane. This latter orbit is either a steady "log-rolling" state with average orientation perpendicular to the shearing plane or a time-periodic "kayaking" state with an orbit oblique to the shearing plane. The final state of the system depends on the shear rate and the strength of the nematic potential. In some cases both the in-plane tumbling and log-rolling (or kayaking) states are attractors; the final state then depends on the initial director.

Spatial variability of energy fluxes in suburban terrain

Abstract: Energy fluxes over an area of “homogeneous” suburban residential land-use in Vancouver, B.C., Canada are shown to vary by up to 25–40% within horizontal scales on the order of 102–103 m. Previously, variability of this magnitude has been expected to occur only at larger scales, between land-use zones or as urban-rural differences. In view of these findings, it is recognized that microadvective interaction between surface types at small scales may be important and can affect the energy balance even at larger scales. The present study discusses the small-scale spatial variability of energy fluxes and shows that it varies greatly for each term in the surface energy balance. Net radiation shows a relatively conservative behaviour (via albedo-surface temperature feedback) with little spatial variability. The turbulent fluxes (measured by eddy correlation at 28 m height), on the other hand, show a link between their temporal and spatial variability as the result of a temporally shifting source area which contains varying combinations of surface cover (using the dynamical source area concept of Schmid and Oke, 1990). As a result, part of the measured temporal variation is attributable to spatial differences in surface cover. Anthropogenic heat flux and storage heat flux (both modelled using a high resolution surface data-base) exhibit temporally varying spatial distributions. Their spatial pattern, however, is governed by nested scales of urban morphology (blocks, streets, properties, etc.). These differences in the source of variability between each component flux suggest a difficulty in the interpretation of the energy balance over urban areas, unless each term is spatially-averaged over the principal morphological units occurring in the area.

Positive FNR-like control of anaerobic arginine degradation and nitrate respiration in Pseudomonas aeruginosa.

Abstract: A mutant of Pseudomonas aeruginosa was characterized which could not grow anaerobically with nitrate as the terminal electron acceptor or with arginine as the sole energy source. In this anr mutant, nitrate reductase and arginine deiminase were not induced by oxygen limitation. The anr mutation was mapped in the 60-min region of the P. aeruginosa chromosome. A 1.3-kb chromosomal fragment from P. aeruginosa complemented the anr mutation and also restored anaerobic growth of an Escherichia coli fnr deletion mutant on nitrate medium, indicating that the 1.3-kb fragment specifies an FNR-like regulatory protein. The arcDABC operon, which encodes the arginine deiminase pathway enzymes of P. aeruginosa, was rendered virtually noninducible by a deletion or an insertion in the -40 region of the arc promoter. This -40 sequence (TTGAC....ATCAG) strongly resembled the consensus FNR-binding site (TTGAT....ATCAA) of E. coli. The cloned arc operon was expressed at low levels in E. coli; nevertheless, some FNR-dependent anaerobic induction could be observed. An FNR-dependent E. coli promoter containing the consensus FNR-binding site was expressed well in P. aeruginosa and was regulated by oxygen limitation. These findings suggest that P. aeruginosa and E. coli have similar mechanisms of anaerobic control.

Pulsed Electron Spin Resonance Spectroscopy: Basic Principles, Techniques, and Examples of Applications [New Analytical Methods (43)]

Abstract: Electron spin resonance (ESR) Spectroscopy has recently undergone a major innovative advance, which is described by the magical phrase pulsed ESR. To the spectroscopist who rubs this Aladdin's lamp there now opens up the mysterious world of spin acrobatics with its many novel and surprising phenomena. The use of pulse techniques makes it possible to reduce measurement times, increase sensitivity, improve resolution and simplify spectra. This article describes the most important pulse techniques used in ESR spectroscopy. Mathematical descriptions are kept to a minimum, space being devoted instead to examples of applications in various areas of chemical research.

Membrane technology and dynamic response of ion-selective liquid-membrane electrodes

Abstract: In order to study the parameters affecting the dynamic response behavior of neutral-carrier-based liquid-membrane electrodes, the potential response vs time curves of Na + -, Ca 2+ , and Mg 2+ -selective electrodes with different membrane compositions were recorded. The effects of the lipophilicity of ionophores and plasticizers, of the presence of incorporated mobile anionic sites and of modifications of the memrbane matrix were investigated. The experimental potential-time curves were compared to fitted functions on the basis of theoretical models

Recent advances in the molecular characterization of plasma membrane Ca2+ pumps.

Abstract: Since its discovery some 25 years ago (Schatzmann, 1966) the plasma membrane Ca 2+ pump (PMCA) has constantly gained in importance as a model membrane protein to study the structural, functional, regulatory and genetic basis of ATP-driven cation transport. The success in the characterization of this enzyme parallels that made in the molecular analysis of other complex low-abundance proteins spanning the lipid bilayer and reflects to a large extent the impressive technical progress made during the past two decades in all areas of modern biological research. It is not surprising, therefore, that several reviews have already been devoted mostly, if not exclusively, to the various aspects of the plasma membrane Ca 2+ pump. Rather than trying to resummarize the contents of previous reviews, the present contribution will focus on those developments concerning the characterization of the Ca 2 § pump which have only recently (i.e., during the past three to five years) been added to our existing views on this important enzyme. Accordingly, no attempt will be made to present a comprehensive picture of the subject; for more detailed information on different aspects of the plasma membrane Ca 2+ pump the reader is referred to previously published reviews and references found therein. A recent summary of the general properties, and particularly of ion transportrelated characteristics, of the pump can be found in Garrahan and Rega (1990), and a synopsis of the problems related to the mechanism of calcium pumping has been given by Jencks (1989). A limited selection of further reviews published during the past decade includes contributions by Sarkadi [1980 (emphasis on early results on the enzymatic properties

Quantum E(2) group and its Pontryagin dual

Abstract: The quantum deformation of the group of motions of the plane and its Pontryagin dual are described in detail. It is shown that the Pontryagin dual is a quantum deformation of the group of transformations of the plane generated by translations and dilations. An explicit expression for the unitary bicharacter describing the Pontryagin duality is found. The Heisenberg commutation relations are written down.

Bradyrhizobium japonicum has two differentially regulated, functional homologs of the sigma 54 gene (rpoN).

Abstract: Recognition of -24/-12-type promoters by RNA polymerase requires a special sigma factor, sigma 54 (RpoN NtrA GlnF). In the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum, two functional, highly conserved rpoN genes (rpoN1 and rpoN2) were identified and sequenced. The two predicted B. japonicum RpoN protein sequences were 87% identical, and both showed different levels of homology to the RpoN proteins of other bacteria. Downstream of rpoN2 (but not of rpoN1), two additional open reading frames were identified that corresponded to open reading frames located at similar positions in Klebsiella pneumoniae and Pseudomonas putida. Both B. japonicum rpoN genes complemented the succinate- and nitrate-negative phenotypes of a Rhizobium meliloti rpoN mutant. B. japonicum strains carrying single or double rpoN mutations were still able to utilize C4-dicarboxylates as a carbon source and histidine, proline, or arginine as a nitrogen source, whereas the ability to assimilate nitrate required expression of at least one of the two rpN genes. In symbiosis both rpoN genes could replace each other functionally. The rpoN1/2 double mutant induced about twice as many nodules on soybeans as did the wild type, and these nodules lacked nitrogen fixation activity completely. Transcription of a nifH'-'lacZ fusion was not activated in the rpoN1/2 mutant background, whereas expression of a fixR'-'lacZ fusion in this mutant was affected only marginally. By using rpoN'-'lacZ fusions, rpoN1 expression was shown to be activated at least sevenfold in microaerobiosis as compared with that in aerobiosis, and this type of regulation involved fixLJ. Expression of rpoN2 was observed under all conditions tested and was increased fivefold in an rpoN2 mutant. The data suggested that the rpoN1 gene was regulated in response to oxygen, whereas the rpoN2 gene was negatively autoregulated.