Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Monomer adsorption on equilateral triangular lattices with attractive first-neighbor interactions

We have recently studied a model of monomer adsorption on infinitely long equilateral triangular lattices with terraces of finite width M and nonperiodic boundaries. This study was restricted to the case of repulsive adsorbate-adsorbate first-neighbor interactions but included attractive, repulsive, and negligible second-neighbor interactions. The present work extends this study to the case of attractive first-neighbors, and the phases are determined, as before, with a confidence exceeding 10 significant figures. Phase diagrams are included for terrace widths M < or =11. Most of the occupational characteristics of the phases fit exact analytic expressions in M. The infinite-M limit of these expressions, combined with other analyses, provide the complete phase diagram for the infinite two-dimensional lattice. In addition to the empty and full coverage phases, there are three phases exhibiting stripe and cluster features that were not observed in the case of repulsive first-neighbors.     

Computable error bounds for pointwise derivatives of a Neumann problem

In this paper we discuss the recovery of derivatives and thecomputation of rigorous and useful upper bounds for the pointwiseerror in the recovered derivatives, for finite element approximationsof the Laplace equation with Neumann boundary conditions, especiallyat points close to or on a smooth, curved boundary. We analyzethe dipole image technique for the case of curved boundaries,and show how to compute reliable recovered derivatives and errorbounds even in the limiting case of points lying on the curvedboundary. Numerical experiments show reasonably tight errorbounds for points both close to and away from a curved boundary.     

Dimer adsorption on square surfaces with first- and second-neighbor interactions

Dimer adsorption on surfaces simulates the adsorption of particles that bind onto two nearest-neighbor sites. In 1993, we constructed a transfer matrix (T-matrix) for the study of dimers on stepped surfaces, consisting of M-sites wide square terraces, considering only first-neighbor interaction energies. Here, we consider a more realistic model by including both first- and second-neighbor interaction energies, V and W. The non-trivial construction of the T-matrix to include second-neighbor interactions is used to obtain the low-temperature energy phase diagrams of the dimer system for any M, when first-neighbors are attractive, and for values of M<7 when first-neighbors are repulsive. New crystallization patterns and phases are observed and extrapolated to infinite M. Monte Carlo simulation techniques confirm our T-matrix results, but the T-matrix method is found to be computationally more efficient and more precise. However, Monte Carlo parallel tempering simulations combined with finite-size scaling, while limited in precision, are more efficient to obtain the critical temperature of the various order-disorder transitions as a function of W/|V|, from the study of the heat capacity and the order parameter as functions of temperature. We also discuss the relevance of these results to experiments.     

Adsorption on an equilateral triangular terrace three atomic sites in width: Application to chemisorption of CO on Pt(112)

A model of monomer adsorption on equilateral triangular terraces three atomic sites in width is presented where step sites are considered first neighbors. Adsorbate-substrate interactions at the terrace step are treated differently than at bulk sites. Adsorbate-adsorbate first neighbor interactions are considered to be repulsive while second neighbors are allowed to be either repulsive or attractive. All low temperature phases have been identified under these conditions. The effect of increasing the temperature has also been investigated. Application of the model to chemisorption of CO on Pt(112) suggests experiments that would allow the various interaction energies to be obtained from a knowledge of the relatively low temperature phases and the conditions prevailing at the transitions between phases. Currently available experimental data is very extensive on the manner in which step sites are filled. However, there is insufficient data on the sequence of low temperature phases which appear when the pressure is gradually increased that would show the manner in which bulk sites are filled until full coverage of the terrace is reached.     

Adsorption on nanotubes having equilateral triangular geometry with first- and second-neighbor interactions: attractive first neighbors

The recently published general method of studying adsorption on terraces and nanotubes is applied to adsorption on nanotubes in hollows or on-tops, which form a zigzag equilateral triangular adsorbate lattice. We consider adsorbate-adsorbate first- and second-neighbor interactions, with attractive first neighbors. In addition to empty and full coverage, there are three phases of occupational characteristics which are independent of the diameter of the nanotube. The low temperature energy phase diagram is the same for nanotubes of increasing diameters and, thus, is also valid in the infinite-diameter limit. As expected, this diagram is the same as that of the infinite-width limit of an equilateral triangular terrace, on which we have recently reported. The current study also includes temperature effects on the phases and the transition between phases.     

Monomer adsorption on terraces and nanotubes

We construct a nonsparse transfer matrix (T-matrix) for a lattice gas model of monomers adsorbed on planar and nanotube surfaces of arbitrary geometry. The model can accommodate any number of higher-order pairwise adsorbate-adsorbate interactions. The technique is sufficiently general for application to nonequivalent adsorption sites and coadsorption of two or more monomer species. The T-matrices for monomer adsorption on a finite width terrace and for monomer adsorption on a nanotube, both of the same lattice geometry, share a basic G-matrix. First, the G-matrix is diagrammatically and recursively constructed. Then, its elements are modified to provide the T-matrix elements for either the terrace or the nanotube. The T-matrices for several particular lattice geometries previously studied as special cases are easily recovered with the generalized technique presented here. This generalization also provides a vectorized algorithm for efficient use on multi-parallel processors and supercomputers.     

Monomer adsorption on equilateral triangular lattices with repulsive first-neighbor interactions

A model of monomer adsorption on infinitely long, finite-width M equilateral triangular lattices with nonperiodic boundaries is presented. The study includes adsorbate-adsorbate first- and second-neighbor interactions with results obtained for repulsive first neighbors. The matrix method and numerical algorithms presented here allow determination of the occupational characteristics of the adsorption crystallization phases, which fit exact analytic expressions in the width M of the lattice. The limit as M approaches infinity provides the complete energy phase diagram for the infinite two-dimensional surface and recovers the results obtained by different methods that were often applied only in restricted energy regions of the phase diagram. The ordered phases are (2x1), (2x2), (3x1), (square root of 3xsquare root of 3) R30 degrees, and the complementary phases of (2x2) and (square root of 3xsquare root of 3) R30 degrees. Comparison is made with other theoretical studies and with experimental observations on adsorption systems consistent with the limitations of the model. In some cases, comparison with experimental data yields bounds on the interaction energies between adsorbates. On the basis of the model, suggestions are made on the manner in which to conduct relatively low temperature experiments to allow determination of most, if not all, of the interaction energies from the knowledge of the sequences of phases and the conditions prevailing at the transitions between phases.