Sampling and local models for multivariate image analysis

Local models are a very important concept for microscopic and macroscopic imaging. Different methods of sub-sampling a multivariate image are described both in general and for three examples. The need for sub-sampling and its influence on multivariate image analysis and visualization are studied. Examples from MRI (256 × 256), satellite imaging (7 × 512 × 512) and biofuel studies (6 × 512 × 512) are used to illustrate some of the principles involved.     

Linear scaling local correlation approach for solving the coupled cluster equations of large systems

A linear scaling local correlation approach is proposed for approximately solving the coupled cluster doubles (CCD) equations of large systems in a basis of orthogonal localized molecular orbitals (LMOs). By restricting double excitations from spatially close occupied LMOs into their associated virtual LMOs, the number of significant excitation amplitudes scales only linearly with molecular size in large molecules. Significant amplitudes are obtained to a very good approximation by solving the CCD equations of various subsystems, each of which is made up of a cluster associated with the orbital indices of a subset of significant amplitudes and the local environmental domain of the cluster. The combined effect of these two approximations leads to a linear scaling algorithm for large systems. By using typical thresholds, which are designed to target an energy accuracy, our numerical calculations for a wide range of molecules using the 6-31G or 6-31G* basis set demonstrate that the present local correlation approach recovers more than 98.5% of the conventional CCD correlation energy.     

Residual stress and deformation during rapid cooling process in an epoxy plate

Residual stress in the epoxy plate during a rapid cooling process was measured by the layer removal method and calculated by the linear thermoviscoelastic theory considering specific volume relaxation. The relaxations of the tensile modulus and specific volume were measured by an Instron thermomechanical analyzer. When the starting temperature of the cooling process was near the glass transition temperature of the cured epoxy, the residual stress in the epoxy plate was smaller than when the starting temperature was higher than the glass transition temperature. However, the transient stress in the cured epoxy plate was higher when the starting temperature was near the glass transition temperature than when the starting temperature was higher than the glass transition temperature. The quenched epoxy plate was compressed in the direction parallel to the surface and expanded in the thickness direction.     

Mechanical properties of SBR-networks: I. Determination of crosslink densities by stress-strain-measurements

The tube model is applied for the treatment of stress-strain measurements on SBR networks. It is shown that this theory allows the separation of crosslink and constraint contributions to the stress-strain behavior and, also, a reliable determination of crosslink densities. The consideration of dynamical contributions is discussed and a special numerical method is developed.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Rheology of polystyrene solutions around the coil overlapping concentration: A phenomenological description of stresses in simple shear flow

Linear viscoelasticity behavior is described with the sum of two terms for polystyrene solutions in tricresyl phosphate around the coil overlapping concentration (K. Osaki, T. Inoue, & T. Uematsu, J Polym Sci Part B: Polym Phys 2001, 39, 211). One is a Rouse–Zimm (RZ) term represented by the Zimm theory with arbitrarily chosen values of the hydrodynamic interaction parameter and the longest relaxation time (τ_RZ). The other (the L term) consists of a relaxation mode with a single relaxation time (τ_L > τ_RZ) and a high‐frequency limiting modulus proportional to the square of the concentration. In this study, we describe the viscosity (η) and first normal stress coefficient (Ψ₁) in steady shear with simple formulas. The stress due to the L term is assumed to be given by a Kaye, Bernstein, Kearsley, and Zapas (K‐BKZ) equation with the damping function h(γ) = (1 + 0.2γ²)^?1/2, where γ is the magnitude of shear. Contributions to η and Ψ₁ from the RZ term are derived from the RZ model, in which the relaxation time in steady flow is given by τ_st = τ + (τ_RZ ? τ)/(1 + 0.35τ_RZ γ˙) instead of τ_RZ. Here, γ˙ is the rate of shear, and τ is the τ_RZ value at the infinite dilution limit. η and Ψ₁ at various concentrations for two polystyrene samples (with molecular weights of 2890 and 8420 kg mol^?1) are well described with parameters derived from dynamic viscoelasticity. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1038–1045, 2002     

Nitrotyrosine-modified proteins and oxidative stress induced by diesel exhaust particles

Protein tyrosine nitration is a post-translational modification that occurs under conditions of oxidative stress and may play a role in the pathogenesis of diseases such as asthma. Through their ability to generate reactive oxygen species in macrophages and epithelial cells, particulate pollutants, such as diesel exhaust particles (DEPs), may lead to a worsening of the asthmatic condition. In this study, we looked for evidence of oxidative modification of proteins in RAW 264.7 cell line treated with DEP chemicals. We show that the induction of oxidative stress is accompanied by 53 newly expressed proteins which are suppressed by a thiol antioxidant, N-acetylcysteine. These include antioxidant enzymes, pro-inflammatory components, and products of intermediary metabolism. In addition, inducible nitric oxide synthase (iNOS) was identified as a biologically relevant oxidative stress protein that is induced concurrent with increased NO production and protein tyrosine-nitration in DEP-exposed RAW 264.7 cells. Utilizing two-dimensional gel electrophoresis, anti-nitrotyrosine immunoblotting, and mass spectrometry led to the identification of an additional ten nitrotyrosine modified proteins, including oxidative stress proteins involved in intermediary metabolism (e.g., GAPDH and enolase), antioxidant defense (e.g., MnSOD) and inhibition of proteosomal activity (e.g., Hsp 90alpha). These oxidative proteins may serve as markers for oxidative stress generation in vivo.     

Prepared Low Stress Cubic Boron Nitride Film by Physical Vapor Deposition

We present low stress cubic boron nitride (cBN) films with a transition layer deposited on the metal alloy substrates by tuned substrate radio-frequency magnetron sputtering. The films were characterized by Fourier transform infrared spectroscopy and transmission electron microscopy (TEM). The IR peak position of cubic boron nitride at 1006.3 cm⁻¹, which is close to the stressless state, indicates that the film has very low internal stress. The TEM image shows that pure CBN phase exists on the surface of the film. Several phases of boron nitride were found at the medium implantation dose. It is believed that the transition from the low ordered phases to cBN phase occurred during implantation.     

Momentum transfer in an agitated vessel with off-centred impellers

Momentum transfer was investigated in an unbaffled agitated vessel of inner diameter 0.3 m equipped with different off-centred impellers. The distribution of the shear rate on the tank wall as a function of the impeller type and Reynolds number was studied in the turbulent regime of the Newtonian liquid flow. The dependences of the averaged dimensionless shear rate, friction coefficient, and dissipated energy on the Reynolds number and eccentricity ratio were approximated using four-parameter equations. Presented at the 33rd International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 22–26 May 2006.     

Properties of a genetic algorithm extended by a random self-learning operator and asymmetric mutations: A convergence study for a task of powder-pattern indexing

Genetic algorithms represent a powerful global-optimisation tool applicable in solving tasks of high complexity in science, technology, medicine, communication, etc. The usual genetic-algorithm calculation scheme is extended here by introduction of a quadratic self-learning operator, which performs a partial local search for randomly selected representatives of the population. This operator is aimed as a minor deterministic contribution to the (stochastic) genetic search. The population representing the trial solutions is split into two equal subpopulations allowed to exhibit different mutation rates (so called asymmetric mutation). The convergence is studied in detail exploiting a crystallographic-test example of indexing of powder diffraction data of orthorhombic lithium copper oxide, varying such parameters as mutation rates and the learning rate. It is shown through the averaged (over the subpopulation) fitness behaviour, how the genetic diversity in the population depends on the mutation rate of the given subpopulation. Conditions and algorithm parameter values favourable for convergence in the framework of proposed approach are discussed using the results for the mentioned example. Further data are studied with a somewhat modified algorithm using periodically varying mutation rates and a problem-specific operator. The chance of finding the global optimum and the convergence speed are observed to be strongly influenced by the effective mutation level and on the self-learning level. The optimal values of these two parameters are about 6 and 5%, respectively. The periodic changes of mutation rate are found to improve the explorative abilities of the algorithm. The results of the study confirm that the applied methodology leads to improvement of the classical genetic algorithm and, therefore, it is expected to be helpful in constructing of algorithms permitting to solve similar tasks of higher complexity.