Characterization of the organization in shear layers via the Proper Orthogonal Decomposition

Experiments are performed in an incompressible plane turbulent mixing layer, using various hot wire rake configurations. From these experiments, the Proper Orthogonal Decomposition is applied for kernels where the space-time correlation tensor is evaluated over different spatial meshes and velocity components configurations. The resulting decompositions are then discussed in terms of characterization of the organization of the flow for various scalar or vectorial approaches of the POD. An incrtial range law is evidenced. The instantaneous contribution of the first modes of the POD to the organization of the flow is analyzed. A dynamical behavior for the organization of the flow is observed from the correlation between the first two modes contribution.     

The Newton modified barrier method for QP problems

The Modified Barrier Functions (MBF) have elements of both Classical Lagrangians (CL) and Classical Barrier Functions (CBF). The MBF methods find an unconstrained minimizer of some smooth barrier function in primal space and then update the Lagrange multipliers, while the barrier parameter either remains fixed or can be updated at each step. The numerical realization of the MBF method leads to the Newton MBF method, where the primal minimizer is found by using Newton's method. This minimizer is then used to update the Lagrange multipliers. In this paper, we examine the Newton MBF method for the Quadratic Programming (QP) problem. It will be shown that under standard second-order optimality conditions, there is a ball around the primal solution and a cut cone in the dual space such that for a set of Lagrange multipliers in this cut cone, the method converges quadratically to the primal minimizer from any point in the aforementioned ball, and continues, to do so after each Lagrange multiplier update. The Lagrange multipliers remain within the cut cone and converge linearly to their optimal values. Any point in this ball will be called a hot start. Starting at such a hot start, at mostO(In In ^-1) Newton steps are sufficient to perform the primal minimization which is necessary for the Lagrange multiplier update. Here, >0 is the desired accuracy. Because of the linear convergence of the Lagrange multipliers, this means that onlyO(In ^-1)O(In In ^-1) Newton steps are required to reach an -approximation to the solution from any hot start. In order to reach the hot start, one has to perform Newton steps, wherem characterizes the size of the problem andC>0 is the condition number of the QP problem. This condition number will be characterized explicitly in terms of key parameters of the QP problem, which in turn depend on the input data and the size of the problem.Partially supported by NASA Grant NAG3-1397 and National Science Foundation Grant DMS-9403218.     

Metal-containing ditopic receptors for molecular recognition of diammonium cations

Two new ditopic receptors for α,ω-alkanediyldiammonium cations based on a tetraazamacrocyclic (cyclidene) nickel(II) complex bearing two crown-ether residues were synthesized. The studies of the host-guest interaction between the receptors and a series of α,ω-diammonium salts by NMR titration in acetonitrile-d₃ showed that 1:1 complexes are formed with K_assoc∼10³-10⁵ M⁻¹. Receptor 1 with benzo-15-crown-5 arms showed substantial selectivity in binding of trimethylene- and tetramethylenediammonium dications, and 1-2 orders of magnitude weaker binding of shorter (C₂) or longer (C₅ and C₆) diammonium cations. Receptor 2 with benzo-18-crown-6 arms showed higher affinity to all studied diammonium cations, but the recognition of the length of α,ω-diammonium cations was less pronounced.     

Evolution of the structural stability of large Cu,Ni, Pd,and Ag clusters with size: An analysis within the embedded atom method

A study of the structural stability of clusters made up of a single component has been carried out within the Embedded Atom Method. Perfect icosahedral and cuboctahedral Cu, Ni, Pd, and Ag clusters with up to 5083 atoms have been compared. The icosahedron is found to be the stable structure for small clusters, and a change of structure from icosahedral to cuboctahedral is found as the cluster size increases. A contraction of the interatomic distances results when the cluster size decreases.     

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K.     

The study of terbium generated bacterirhodopsin

The localization of Terbium (Tb³⁺) cations binding to deionized bacteriorhodopsin (bR) has been studied by using spectroscopic methods. It was found that adding Tb³⁺ cations to deionized bR affects the fluorescence lifetimes of tryptophan (Trp) in bR, the wavelength of fluorescence peak shifts “blue” and the peak value of fluorescence decreases. It was also found that adding one Tb³⁺ cation to deionized bR can restore the purple state from its blue state obviously. The measurements of absorbance, fluorescence and lifetime of fluorescence also show that when more than three Tb³⁺ cations are added, no further changes can be found. It is suggested that one Tb³⁺ specific binding site for the color-controlling is located on the exterior of the bR trimer structure to negatively charged lipids near Trp-10 and Trp-12. Three Tb³⁺ cations binding per bR is needed for the regenerated bR.     

Uncertainty of the Thermal Conductivity Measurement Using the Transient Hot Wire Method

This work deals with uncertainty analysis of the thermal conductivity measurement using the transient hot wire method. The characterization is made from a sample of low-density, polyethylene BRALEN SA 200-22. The utilized experimental data are obtained from the test measurements performed on the air at room temperature. The sources of measurement errors are analyzed and the uncertainty of the measured value of the thermal conductivity is evaluated. The analysis shows that in the present case the uncertainty of the thermal conductivity measurement is about ±3.3% for 68% confidence level.This revised version was published online in November 2005 with corrections to the Cover Date.     

Studies on the Interaction of Beryllon Ш with Proteins by Voltammetric Technique and its Application

A new quantitative determination method of proteins using beryllon Ш by voltammetric technique was developed in this paper. In pH 3.5 Britton-Robinson (B-R) buffer solution, beryllon Ш can bind with human serum albumin (HSA) to form an electro-inactive supermolecular complex. Beryllon Ш has a well-defined voltammetric reduction peak at -0.38 V (vs. SCE) and the addition of protein in this solution can cause the decrease of the reductive peak current. Based on the decrease of the reduction peak current, a new electrochemical method for the determination of HSA was established with linear range of 1.0~40.0 mg/L and the detection limit of 1.0 mg/L. This method is further applied to the determination of real sample of healthy human serum.     

Tröger's base scaffold in racemic and chiral fashion as a spacer for bisdistamycin formation. Synthesis and DNA binding study

‘Head-to-head’ oligo-N-methylpyrrole peptide dimers linked by a methano[1,5]diazocin scaffold are presented in racemic as well as chiral fashion. Their DNA binding activities were assayed on calf thymus DNA, poly(dA-dT)₂, and poly(dC-dG)₂ by NMR and ECD spectroscopies, and fluorescence probe displacement assay. The presented dimers prefer AT sequences, but show higher affinity to poly(dC-dG)₂ than distamycin A. The (4R,9R) configuration of methanodiazocin bridge was found to be better suited for interaction with ct-DNA and poly(dA-dT)₂ than (4S,9S) configuration.     

The Antiepileptic Lamotrigine and Its Analogues: Comparative Theoretical Electronic Properties

Electronic properties of lamotrigine (LTG) and two analogues (A1 and A2) are compared through MOPAC-AM1 calculations. Two stable conformers of LTG are calculated to exist in agreement with X-ray crystallography. In the three compounds and the two conformers for each of them, the more favorable protonation sites are N₂ and N₄; these should then be the sites appropriate for interaction with a receptor, and group valence reinforces the supposition. The molecular electrostatic potentials show that a region between the two chlorine atoms in LTG could be the site for an electrostatic interaction with a corresponding site in the receptor. The fluorine atom in A1 would play an equivalent role. A simple model for LTG-receptor interaction is proposed.