Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of this enzyme was solved by the molecular-replacement method and refined at 1.8 Å resolution to an R factor of 19.5%. Cobalt and phosphate ions were revealed in the active centers of both identical subunits (A and B) of the pyrophosphatase molecule. In subunit B, a water molecule was found between two cobalt ions. It is believed that this water molecule acts as an attacking nucleophile in the enzymatic cleavage of the pyrophosphate bond. It was demonstrated that cobalt ions and a phosphate group occupy only part of the potential binding sites (two chemically identical and crystallographically independent subunits have different binding sites). The arrangement of ligands and the structure of the nucleophile-binding site are discussed in relation to the mechanism of action of the enzyme and the nature of the metal activator.     

A power mode approach to estimating vibrational power transmitted by multiple sources

A power mode method for the estimation of the power transmitted to a flexible receiver by an array of point force excitations is described. The vibrational power transmitted by N discrete point forces is regarded as the power transmitted by N independent power modes following eigendecomposition of the mobility matrix of the receiving structure. Approximate expressions for the upper and lower bounds and the mean value of the transmitted power are then developed in terms of these power modes. The approach is extended to more general cases, including that where both force and moment excitations are applied to the structure and where there are velocity source excitations. Numerical examples are presented.     

Self-Interactions of Strands and Sheets

Physical strands or sheets that can be modelled as curves or surfaces embedded in three dimensions are ubiquitous in nature, and are of fundamental importance in mathematics, physics, biology, and engineering. Often the physical interpretation dictates that self-avoidance should be enforced in the continuum model, i.e., finite energy configurations should not self-intersect. Current continuum models with self-avoidance frequently employ pairwise repulsive potentials, which are of necessity singular. Moreover the potentials do not have an intrinsic length scale appropriate for modelling the finite thickness of the physical systems. Here we develop a framework for modelling self-avoiding strands and sheets which avoids singularities, and which provides a way to introduce a thickness length scale. In our approach pairwise interaction potentials are replaced by many-body potentials involving three or more points, and the radii of certain associated circles or spheres. Self-interaction energies based on these many-body potentials can be used to describe the statistical mechanics of self-interacting strands and sheets of finite thickness.     

A note on the necessary conditions for the algebraic Riccati equation

We derive some useful and easily computable necessary conditionsfor the existence of a positive semi-definite solution to thealgebraic Ricatti equation (ARE). A motivating example is givento highlight the usefulness of the conditions for controllerand observer designs for nonlinear systems. Further, an upperbound on the trace of the solution to the ARE is also derived.     

Karhunen–Loeve representations of turbulent channel flows using the method of snapshots

For three‐dimensional flows with one inhomogeneous spatial coordinate and two periodic directions, the Karhunen–Loeve procedure is typically formulated as a spatial eigenvalue problem. This is normally referred to as the direct method (DM). Here we derive an equivalent formulation in which the eigenvalue problem is formulated in the temporal coordinate. It is shown that this so‐called method of snapshots (MOS) has some numerical advantages when compared to the DM. In particular, the MOS can be formulated purely as a matrix composed of scalars, thus avoiding the need to construct a matrix of matrices as in the DM. In addition, the MOS avoids the need for so‐called weight functions, which emerge in the DM as a result of the non‐uniform grid typically employed in the inhomogeneous direction. The avoidance of such weight functions, which may exhibit singular behaviour, guarantees satisfaction of the boundary conditions. The MOS is applied to data sets recently obtained from the direct simulation of turbulence in a channel in which viscoelasticity is imparted to the fluid using a Giesekus model. The analysis reveals a steep drop in the dimensionality of the turbulence as viscoelasticity is increased. This is consistent with the results that have been obtained with other viscoelastic models, thus revealing an essential generic feature of polymer‐induced drag reduced turbulent flows. Published in 2006 by John Wiley & Sons, Ltd.     

Optical corrosion meter

In a previous study, a mathematical model relating surface and bulk behaviours of metals in aqueous solution has been developed. The model was established based on principles of holographic interferometry for measuring microsurface dissolution, i.e. mass loss, and on those of electrochemistry for measuring the bulk electronic current, i.e. corrosion current. In the present work, an optical corrosion meter was built based on the above model. The corrosion meter consists of an electrochemical cell in which the sample is immersed in aqueous solution. Furthermore, the corrosion meter has a holographic camera with a thermoplastic film for in situ processing of holograms in order to obtain real-time holographic interferoms of the sample in the electrochemical cell. Results of the present work indicate that optical holography is a very useful technique for measuring the corrosion current density of different alloys in aqueous solutions. As a result, the corrosion current density of aluminium, stainless steel, and low-carbon steel in 1 M KCl, 1 M NaCl, and 1 M NaOH solutions were obtained. A comparison between the corrosion data of samples showed that the corrosion current density of the stainless steel in 1 M NaCl is nearly three-folds higher than that of the aluminium in 1 M KCl and the low-carbon steel in 1 M NaOH.     

Almost-Sure Central Limit Theorem for Directed Polymers and Random Corrections

We consider a general model of directed polymers on the lattice , weakly coupled to a random environment. We prove that the central limit theorem holds almost surely for the discrete time random walk X _T associated to the polymer. Moreover we show that the random corrections to the cumulants of X _T are finite, starting from some dimension depending on the index of the cumulants, and that there are corresponding random corrections of order , , in the asymptotic expansion of the expectations of smooth functions of X _T . Full proofs are carried out for the first two cumulants. We finally prove a kind of local theorem showing that the ratio of the probabilities of the events to the corresponding probabilities with no randomness, in the region of “moderate” deviations from the average drift bT, are, for almost all choices of the environment, uniformly close, as , to a functional of the environment “as seen from (T,y)$”. Received: 14 October 1996 / Accepted: 28 March 1997     

New Classes of Toda Soliton Solutions

We provide a detailed investigation of limits of N–soliton solutions of the Toda lattice as N tends to infinity. Our principal results yield new classes of Toda solutions including, in particular, new kinds of soliton–like (i.e., reflectionless) solutions. As a byproduct we solve an inverse spectral problem for one–dimensional Jacobi operators and explicitly construct tri–diagonal matrices that yield a purely absolutely continuous spectrum in (-1,1) and give rise to an eigenvalue spectrum that includes any prescribed countable and bounded subset of . Received: 16 October 1995/Accepted: 23 July 1996