Links between microscopic and macroscopic fluid mechanics

The microscopic and macroscopic versions of fluid mechanics differ qualitatively. Microscopic particles obey time-reversible ordinary differential equations. The resulting particle trajectories {q(t)} may be time-averaged or ensemble-averaged so as to generate field quantities corresponding to macroscopic variables. On the other hand, the macroscopic continuum fields described by fluid mechanics follow irreversible partial differential equations. Smooth particle methods bridge the gap separating these two views of fluids by solving the macroscopic field equations with particle dynamics that resemble molecular dynamics. Recently, nonlinear dynamics have provided some useful tools for understanding the relationship between the microscopic and macroscopic points of view. Chaos and fractals play key roles in this new understanding. Non-equilibrium phase-space averages look very different from their equilibrium counterparts. Away from equilibrium the smooth phase-space distributions are replaced by fractional-dimensional singular distributions that exhibit time irreversibility.     

Gaussian Property of the Rings R(X) and R〈X〉

The content of a polynomial f over a commutative ring R is the ideal c(f) of R generated by the coefficients of f. A commutative ring R is said to be Gaussian if c(fg) = c(f)c(g) for every polynomials f and g in R[X]. A number of authors have formulated necessary and sufficient conditions for R(X) (respectively, R?X?) to be semihereditary, have weak global dimension at most one, be arithmetical, or be Prüfer. An open question raised by Glaz is to formulate necessary and sufficient conditions that R(X) (respectively, R?X?) have the Gaussian property. We give a necessary and sufficient condition for the rings R(X) and R?X? in terms of the ring R in case the square of the nilradical of R is zero.     

Solubilization chromatography: Ethers,carboxylic acids,and hydrocarbons

Synthetic mixtures of aliphatic and aromatic ethers, satmated fatty acids, and substituted benzenes and naphthalenes were separated by elution through columns of ion-exchange resins with aqueous solutions of acetic acid as eluent An attempt was made to use a resin of low capacity for the separation of such mixtures, and the results of this attempt are used to help elucidate the theory of solubilization chromatography     

Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?

There is currently far more sequence information than structural information available, and the ability to use homology models for virtual screening applications is desirable in many cases where structures have not yet been solved. This review focuses on the application of protein kinase homology models for virtual screening use. In addition to reviewing previous cases in which kinase homology models have been used in inhibitor design, we present new data - useful for template selection in homology modeling applications - indicating that the template structure with the highest sequence or structural similarity with the target structure may not always be the best choice. This new work explored the simple hypothesis that better results might be obtained for docking a ligand to a target receptor using a homology model of the target created from a different kinase template co-crystallized with the ligand, than from a crystal structure of the actual kinase target that is unliganded or bound to an unrelated ligand. This hypothesis was tested in docking studies of staurosporine with eight different kinases: AutoDock was used to dock staurosporine to homology models of each kinase created from staurosporine-bound template structures, and the results were compared with docking staurosporine to crystal structures of the target kinase that were obtained in complex with a non-staurosporine ligand or no ligand. It was found that the homology models performed as well as or better than the crystal structures, suggesting that using a homology model created from a template crystallized with a representative ligand may in some cases be a preferred approach, especially in virtual screening experiments that focus on enriching for members of a particular inhibitor class.     

Adsorbate-substrate bonding and the growth of naphthalene thin films on Ag(1 1 1)

The adsorption kinetics, energetics and growth of naphthalene thin films, from submonolayer to about 10 layers, on a Ag(1 1 1) surface at low temperature in a ultrahigh vacuum chamber are examined by using temperature programmed desorption spectroscopy. The first layer adsorption occurs with a desorption energy of 85 ± 5 kJ/mole and results in an interface dipole of 5 ± 1 D, from charge transfer of approximately 0.2 e from naphthalene to Ag. The surface dipole induced inter-adsorbate repulsion causes the lowering of the adsorption energy within the first layer near the saturation coverage so that the second layer deposition begins before the completion of the first layer. The second layer is a metastable phase with desorption energy, 74 ± 3 kJ/mole, smaller than the multilayer desorption energy of 79 ± 5 kJ/mole. Fractional order desorption kinetics were found for both the metastable and the multilayer phases, suggesting desorption from 2-D islanding and 3-D islanding, respectively.     

Rapid catalytic oxidation of CO to CO(2) - On the development of a new approach to on-line oxygen isotope analysis of organic matter

A new approach to on-line oxygen isotope analysis has been developed which utilises existing elemental analyser and mass spectrometry technology to produce a sample of carbon dioxide gas for oxygen isotople analysis. The method relies on on-line high temperature pyrolysis of the sample over a carbon source followed by a rapid, non-contributive partial catalytic oxidation over nickel powder at between 550 and 600 degrees C. Initial results demonstrate both good precision (better than 0.2 per thousand) and accuracy for both cellulose and silver nitrate samples. Copyright 1999 John Wiley & Sons, Ltd.     

Adsorption energies, inter-adsorbate interactions, and the two binding sites within monolayer benzene on Ag(111)

The adsorption of monolayer and multilayer benzene on the Ag(111) surface was characterized using temperature programmed desorption (TPD). TPD spectra revealed two broad peaks at approximately 205 and approximately 150 K at submonolayer coverage and a sharper, multilayer peak at 140 K. Analysis of the coverage-dependent shape and shift of the two submonolayer peaks has resulted in their assignment to desorption from two different binding geometries on threefold-hollow sites with symmetries C(3v)(sigma d) and C(3v)(sigma v). The TPD peak analysis incorporated inter-adsorbate repulsive interaction that resulted from the local dipole moment at the adsorption site induced by the adsorbate-surface charge transfer bonding. The analysis has yielded desorption energies of 54.9 +/- 0.8 and 50.4 +/- 0.4 kJ/mol for the C(3v)(sigma d) and C(3v)(sigma v) configurations, respectively. The interface dipole and polarizability of the benzene-silver complex have been determined to be 5.4 +/- 1.8 D and 14 +/- 10 A3, respectively. Repulsive interactions in the monolayer were found to lower the desorption energy from the zero-coverage value by 14.8 kJ/mol. Leading edge analysis of the multilayer peak yielded a desorption energy of 40.9 +/- 0.7 kJ/mol.