Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms

Several parallel algorithms for Fock matrix construction are described. The algorithms calculate only the unique integrals, distribute the Fock and density matrices over the processors of a massively parallel computer, use blocking techniques to construct the distributed data structures, and use clustering techniques on each processor to maximize data reuse. Algorithms based on both square and row-blocked distributions of the Fock and density matrices are described and evaluated. Variants of the algorithms are discussed that use either triple-sort or canonical ordering of integrals, and dynamic or static task clustering schemes. The algorithms are shown to adapt to screening, with communication volume scaling down with computation costs. Modeling techniques are used to characterize algorithm performance. Given the characteristics of existing massively parallel computers, all the algorithms are shown to be highly efficient for problems of moderate size. The algorithms using the row-blocked data distribution are the most efficient. © 1996 by John Wiley & Sons, Inc.     

H,C, N and S stable isotopes and mineral profiles to objectively guarantee the authenticity of grated hard cheeses

In compliance with the European law (EC No. 510/2006), geographical indications and designations of origin for agricultural products and foodstuffs must be protected against mislabelling. This is particularly important for PDO hard cheeses, as Parmigiano Reggiano, that can cost up to the double of the no-PDO competitors.     

Advances in electrochemical detection for study of neurodegenerative disorders

Several severe neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and prion-associated transmissible spongiform encephalopathies, have been linked to dysregulation of specific proteins capable of self-assembly into deleterious fibrillar aggregates termed amyloids. A wide range of analytical techniques has been used to clarify the mechanisms of these protein-misfolding processes, in the hope of developing effective therapeutic treatment. Most of these studies have relied heavily on conventional methods of protein characterization, notably circular dichroism spectroscopy, thioflavin T fluorescence, transmission electron microscopy, and atomic force microscopy, which are particularly suitable for monitoring later-stage aggregate formation. Although electrochemical methods of protein detection have existed for some time, they have only recently gained prominence as a powerful tool for studying the early stages of protein aggregation during which the more toxic soluble amyloid species form. Electrochemical detection methods include direct detection of intrinsic redox-active amino acid residues, protein-catalyzed hydrogen evolution, use of extrinsic β-sheet binding mediators, and impedance spectroscopy. In this review, we evaluate the use of electrochemistry for study of protein aggregation related to neurodegenerative disorders.

High resolution feshbach spectroscopy of cesium

We measure high-resolution Feshbach resonance spectra for ultracold cesium atoms colliding in different hyperfine and magnetic sublevels. More than 25 resonances are observed for magnetic fields up to 230 G and their positions are measured with an accuracy down to 0.03 G. From these spectra several ground-state molecular interaction parameters can be extracted with sufficient accuracy to permit for the first time an unambiguous and accurate determination of cesium's ultracold collision properties [P. J. Leo, C. J. Williams, and P. S. Julienne, following Letter, Phys. Rev. Lett. 85, 2721 (2000)].     

Solution equilibria of aromatic dinitroso compounds: a combined NMR and DFT study

Solution-state nitroso monomer-azodioxide equilibria and conformational freedom of several aromatic dinitroso derivatives, differing in the spacer group between the aromatic rings, were studied by one- and two-dimensional variable temperature ¹H NMR spectroscopy and by quantum chemical calculations. The proton signals of nitroso monomer-azodioxide mixtures revealed by low-temperature NMR were assigned and validated using B3LYP-D3/6-311+G(2d,p)/SMD level of theory. In almost all cases, a preference towards the formation of only one azodioxy isomer of aromatic dinitroso compounds was found, which was assigned to Z-dimer according to computational data. Nevertheless, the computed small energy difference between the Z- and E-isomer could not account for the extreme preference for Z-dimer formation, indicating an influence of entropic or solvent effects. The formation of shorter oligomers in solution was excluded based on integrated ¹H NMR signal intensities. The experimental results indicated an average dimerization Gibbs energy of about ??5 kJ/mol at 223 K and were found to be in very good correlation with dimerization energies obtained by solution-phase optimization.

     

Independent systems of representatives in weighted graphs

The following conjecture may have never been explicitly stated, but seems to have been floating around: if the vertex set of a graph with maximal degree Δ is partitioned into sets V _i of size 2Δ, then there exists a coloring of the graph by 2Δ colors, where each color class meets each V _i at precisely one vertex. We shall name it the strong 2Δ-colorability conjecture. We prove a fractional version of this conjecture. For this purpose, we prove a weighted generalization of a theorem of Haxell, on independent systems of representatives (ISR’s). En route, we give a survey of some recent developments in the theory of ISR’s. The research of the first author was supported by grant no 780/04 from the Israel Science Foundation, and grants from the M. & M. L. Bank Mathematics Research Fund and the fund for the promotion of research at the Technion. The research of the third author was supported by the Sacta-Rashi Foundation.     

The Max-Flow Min-Cut theorem for countable networks

We prove a strong version of the Max-Flow Min-Cut theorem for countable networks, namely that in every such network there exist a flow and a cut that are “orthogonal” to each other, in the sense that the flow saturates the cut and is zero on the reverse cut. If the network does not contain infinite trails then this flow can be chosen to be mundane, i.e. to be a sum of flows along finite paths. We show that in the presence of infinite trails there may be no orthogonal pair of a cut and a mundane flow. We finally show that for locally finite networks there is an orthogonal pair of a cut and a flow that satisfies Kirchhoff's first law also for ends.     

Studies of Hindered Rotation and Magnetic Anisotropy by 1H, 13C and 19F NMR. The Diels-Alder Adduct of N- Pentafluorophenylmaleimide and Phencyclone: A Model for Drugs.

The potent Diels-Alder diene, phencyclone, 1, reacts with N-pentafluorophenylmaleimide, 2, to form an adduct, 3, characterized by ¹H, ¹³C, and ¹⁹F NMR at 300, 75 and 282 MHz, respectively. The one-dimensional (1D) and two-dimensional (2D) ¹H and ¹³C NMR spectra of 3 at ambient temperatures imply a slow exchange limit (SEL) regime with respect to rotation of the unsubstituted bridgehead phenyl groups about severely hindered C(sp²)-C(sp³) bonds. Major non-bonded interactions are expected between the ortho protons of the C₆H₅ groups and H-1, 8 of the phenanthrenoid moiety of 3. ¹⁹F 1D and 2D (COSY) NMR spectra show that the SEL regime also obtains for rotation about the N-C₆F₅ bond of 3, with five separate fluorine signals seen, consistent with a preferred conformation in which the C₆F₅ may lie roughly perpendicular to the plane of the pyrrolidinedione moiety, and may be in the mirror symmetry plane of 3. The results are considered relevant to hindered aryl rotations in numerous Pharmaceuticals. Selected spectral data for 2 and precursors are also presented.