Finite-size dimensional analysis of the superconducting vibronic interaction

Even in a finite-size system, the vibronic interaction acts as the attractive force to bind a pair of electrons. For small-size systems, the electron repulsion overwhelms the vibronic attraction. As the size of the system becomes large, the electronic repulsion diminishes to zero in proportion to the volume of the system, whereas the vibronic attraction (1) grows to infinity for a one-dimensional system, (2) converges to a finite value for a two-dimensional system, and (3) diminishes to zero for a three-dimensional system. Even for a three-dimensional system, the vibronic attraction diminishes much slower than does the electronic repulsion. This brings about a concept of the critical size for an any-dimensional system, over which size the vibronic attraction overwhelms the electronic repulsion, thereby creating purely attractive interaction for a pair of electrons, which may lead to superconductivity.     

Fast choice of separation conditions for analyses by capillary zone electrophoresis using an information system Xemic

An information system Xemic applicable in analytical chemistry is described and its use in capillary electrophoresis for searching suitable separation conditions is demonstrated. This system is capable to provide suitable separation conditions even for analytes for which no electrophoretic experiments have been published so far. The system works with a database of components of anionic character the analyses of which have been performed, published in reviewed scientific journals, and included into a database created by an expert. Moreover, the system learned to search also in abstracts or complete scientific articles to find articles dealing with the determination of a substance in a given sample matrix. When no experiments have been published so far for a defined substance in a specific matrix, Xemic shows the separation conditions for determination of the substance regardless of the matrix. When no response can be found for the analyte of interest at all, the system Xemic works like an expert in the field and searches chemically similar substances and offers a series of substances the physicochemical properties of which are close to the followed analyte with respect to the behavior in the electric field, and shows working conditions for their analysis. Thus, the analyst puts only the order in the form of a given analyte in a given matrix and obtains a recommendation of a separation system that should enable to perform a successful separation. The system is not rigid and enables the operator to change the importance of individual attributes used in similarity search so as to obtain a broader or narrower group of similar components. With a certain probability the analyte of interest can be successfully analyzed under separation conditions that suited for the analysis of the most similar substances in the given matrix.     

Automated sample preparation method for suspension arrays using renewable surface separations with multiplexed flow cytometry fluorescence detection

In this paper, we describe a new method of automated sample preparation for multiplexed biological analysis systems that use flow cytometry fluorescence detection. In this approach, color-encoded microspheres derivatized to capture particular biomolecules are temporarily trapped in a renewable surface separation column to enable perfusion with sample and reagents prior to delivery to the detector. This method provides for separation of the biomolecules of interest from other sample matrix components as well as from labeling solutions. After sample preparation, the beads can be released from the renewable surface column and delivered to a flow cytometer for direct on-bead analysis one bead at a time. Using mixtures of color-encoded beads derivatized for various analytes yields suspension arrays for multiplexed analysis. Development of this approach required a new technique for automated capture and release of the color-encoded microspheres within a fluidic system. We developed a method for forming a renewable filter and demonstrate its use for capturing microspheres that are too small to be easily captured in previous flow cells for renewable separation columns. The renewable filter is created by first trapping larger beads in the flow cell, and then smaller beads are captured either within or on top of the bed of larger beads. Both the selective microspheres and filter bed are automatically emplaced and discarded for each sample. A renewable filter created with 19.9 μm beads was used to trap 5.6 μm optically encoded beads with trapping efficiencies of 99%. The larger beads forming the renewable filter did not interfere with the detection of color-encoded 5.6 μm beads by the flow cytometer fluorescence detector. The use of this method was demonstrated with model reactions for a variety of bioanalytical assay types including a one-step capture of a biotinylated label on Lumavidin beads, a two-step sandwich immunoassay, and a one-step DNA binding assay. A preliminary demonstration of multiplexed detection of two analytes using color-encoded beads was also demonstrated. The renewable filter for creating separation columns containing optically encoded beads provides a general platform for coupling renewable surface methods for sample preparation and analyte labeling with flow cytometry detectors for suspension array multiplexed analyses.     

Diagrammatic kinetic theory for a lattice model of a liquid. I. Theory

We present a diagrammatic formalism for the time correlation functions of density fluctuations for an excluded volume lattice gas on a simple d-dimensional hypercubic lattice. We consider a multicomponent system in which particles of different species can have different transition rates. Our theoretical approach uses a Hilbert space formalism for the time dependent dynamical variables of a stochastic process that satisfies the detailed balance condition. We construct a Liouville matrix consistent with the dynamics of the model to calculate both the equation of motion for multipoint densities in configuration space and the interactions in the diagrammatic theory. A Boley basis of fluctuation vectors for the Hilbert space is used to develop two formally exact diagrammatic series for the time correlation functions. These theoretical techniques are generalizations of methods previously used for spin systems and atomic liquids, and they are generalizable to more complex lattice models of liquids such as a lattice gas with attractive interactions or polymer models. We use our formalism to construct approximate kinetic theories for the van Hove correlation and self-correlation function. The most simple approximation is the mean field approximation, which is exact for the van Hove correlation function of a one component system but an approximation for the self-correlation function. We use our first diagrammatic series to derive a two site multiple scattering approximation that gives a simple analytic expression for the spatial Fourier transform of the self-correlation function. We employ our second diagrammatic series to derive a simple mode coupling type approximation that provides a system of equations that can be solved for the self-correlation function.     

Electrocatalysis by ad-atoms: Part IV. Enhancement of the oxidation of formic acid on Pt-Au(subs) and Au-Pt(subs) electrodes by bismuth ad-atoms

The roles of surface and bulk for electrocatalysis have been investigated. Bi ad-atoms enhance a platinum electrode to a great extent for HCOOH oxidation. In order to examine whether bulk platinum atoms are necessary for the electrocatalysis, monolayer or submonolayer amounts of platinum atoms were made to deposit on a gold electrode which is quite inactive for the oxidation. The deposition of a complete monolayer of platinum atoms on a gold electrode makes the electrode as active as a platinum electrode itself. Bi ad-atoms enhance this electrode to the same extent as they do a platinum electrode for the oxidation. Thus surface atoms, Pt and Bi atoms, having no bulk atoms on a quite inactive electrode work effectively for the electrocatalysis, the platinum atoms for the adsorption of the main reactant and the Bi atoms for blocking of the sites against the formation of poison. It is the adsorptive property of the surface that controls the electrocatalytic activity.     

The use of cation exchange matrix separation coupled with ICP-MS to directly determine platinum group element (PGE) and other trace element emissions from passenger cars equipped with diesel particulate filters (DPF)

Inductively coupled plasma-mass spectrometry coupled with cation exchange matrix separation has been optimised for the direct determination of platinum group element (PGE) and trace element emissions from a diesel engine car. After matrix separation method detection limits of 1.6 ng g(-1) for Pd, 0.4 ng g(-1) for Rh and 4.3 ng g(-1) for Pt were achieved, the method was validated against the certified reference material BCR 723, urban road dust. The test vehicle was fitted with new and aged catalytic converters with and without diesel particulate filters (DPF). Samples were collected after three consecutive New European Driving Cycle (NEDC) of the particulate and "soluble" phases using a home-made sampler optimised for trace element analysis. Emission factors for the PGEs ranged from 0.021 ng km(-1) for Rh to 70.5 ng km(-1) for Pt; when a DPF was fitted, the emission factors for the PGEs actually used in the catalysts dropped by up to 97% (for Pt). Trace element emission factors were found to drop by a maximum of 92% for Ni to a minimum of 18% for Y when a DPF was fitted; a new DPF was also found to cause a reduction of up to 86% in the emission of particulate matter.     

Theory of docking scores and its application to a customizable scoring function

In general, the docking scoring tends to have a size dependence related to the ranking of compounds. In this paper, we describe a novel method of parameter optimization for docking scores which reduce the size dependence and can efficiently discriminate active compounds from chemical databases. This method is based on a simplified theoretical model of docking scores which enables us to utilize large amounts of data of known active and inactive compounds for a particular target without requiring large computational resources or a complicated procedure. This method is useful for making scoring functions for the identification of novel scaffolds using the knowledge of active compounds for a particular target or a customized scoring function for an interesting family of drug targets.     

Fluorine-NMR competition binding experiments for high-throughput screening of large compound mixtures

High-throughput ligand-based NMR screening with competition binding experiments is extended to (19)F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the (19)F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the (19)F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented.     

Retrieving definitional content for ontology development

Ontology construction requires an understanding of the meaning and usage of its encoded concepts. While definitions found in dictionaries or glossaries may be adequate for many concepts, the actual usage in expert writing could be a better source of information for many others. The goal of this paper is to describe an automated procedure for finding definitional content in expert writing. The approach uses machine learning on phrasal features to learn when sentences in a book contain definitional content, as determined by their similarity to glossary definitions provided in the same book. The end result is not a concise definition of a given concept, but for each sentence, a predicted probability that it contains information relevant to a definition. The approach is evaluated automatically for terms with explicit definitions, and manually for terms with no available definition.     

Projection between basis sets: A means of defining the electronic structure of functional subunits

The general problem of the transfer of the representation of a set of orthonormal functions from one basis to a different, nonequivalent one is considered and specialized to a matrix formulation convenient for use in molecular electronic structure calculations. A procedure is suggested for treating problems where the transfer of representation breaks into a subset of most interest and one of less interest as for example the occupied and virtual orbitals of a Hartree-Fock SCF calculation. These techniques are then applied to obtain a representation of a methyl group from an SCF wave function for methane.     

Simple and rapid analysis for quantitation of the most important volatile flavor compounds in yogurt by headspace gas chromatography-mass spectrometry

The aim of this experiment is to develop a rapid, simplified, direct gas chromatographic (GC) method for the analysis of volatile flavor compounds in yogurt combining a headspace with constant heating temperature and GC with a mass spectrometric detect ion. Repeatability of the method is assessed. The relative standard deviation for individual flavor compounds range from 3.5% for acetaldehyde to 8.4% for acetone, with a total mean value of 52.4 +/- 2.2 mg/kg for all of the studied aroma components. Recovery for individual flavor compounds range from 63.7% for acetone to 82.4% for acetic acid.     

Dimensions of branched and linear polymer chains in solution: Modifications of flory's theory

It is pointed out that a theory proposed by Vrij for the expansion of a linear polymer chain in solution beyond its unperturbed size is also applicable formally to branched chains. The theory predicts the temperature at which the chain obeys random-flight statistics to be lower for a branched chain than for a linear one (for a polymer–solvent system exhibiting the usual upper critical consolute point). Vrij's derivation follows a well-known procedure of Flory, but refines it to take account of the variation of the time-averaged segment density with distance from the center of mass of the chain. This modification in combination with a somewhat different derivation is shown to lead to a similar result. Yet another scheme for “correcting” Flory's theory is outlined. Some reasons are advanced for questioning the physical significance of these small modifications of Flory's theory, all of which depend on the retention of previously ignored terms in power series expansions.     

Fragility of supercooled liquids from differential scanning calorimetry traces: theory and experiment

Starting from the Debye model for frequency-dependent specific heat and the Vogel-Fulcher-Tammann (VFT) model for its relaxation time, an analytic expression is presented for the heat capacity versus temperature trace for differential scanning calorimetry (DSC) of glass transitions, suggesting a novel definition of the glass transition temperature based on a dimensionless criterion. An explicit expression is presented for the transition temperature as a function of the VFT parameters and the cooling rate, and for the slope as a function of fragility. Also a generalization of the results to non-VFT and non-Debye relaxation is given. Two unique ways are proposed to tackle the inverse problem, i.e., to extract the fragility from an experimental DSC trace. Good agreement is found between theoretically predicted DSC traces and experimental DSC traces for glycerol for different cooling rates.     

Electric field-derived point charges to mimic the electrostatics in molecular crystals

Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.     

Development of a custom high-throughput preparative liquid chromatography/mass spectrometer platform for the preparative purification and analytical analysis of compound libraries

Solution-phase parallel synthesis has had a profound impact on the speed of compound synthesis delivering relatively pure compounds (>80%) in short order. However, to develop structure activity relationships (SAR) for a compound series, each library member should preferably be >95% pure. Historically, achieving and quantifying such high-purity criteria for each library member proved to be the slow step for most lead discovery groups. To address this issue, significant modifications have been made to a commercial Agilent preparative LC/MS system to allow for the general mass-guided purification of diverse compound libraries. The custom modifications include (1) the "DMSO slug" approach for the purification of samples with poor solubility; (2) an active splitter to reduce system back-pressure, reduce the delay volume, and allow for a variable split ratio; (3) a sample loading pump for the quick purification of large, dilute samples; (4) a preparative column-selection valve to quickly change column selectivity or sample loading; and (5) an analytical injector with a separate flow path for crude reaction or fraction analyses.     

Quantum mechanical criteria for choosing appropriate voltage stabilization additives for polyethylene

One of the major application fields for solid dielectric polymers is their use as insulating materials for power cables. Since the electrical aging of the insulating polymeric materials is one of the most important factors affecting the service lifetime of power cables, developing a model which can be used to design materials with an improved resistance to electrical degradation would be highly beneficial. We developed a model for the electrical field within the polymer material contaminated with a sharp conducting defect (a metallic needle) and defined a parameter characterizing the resistance of polymer to electrical treeing. The model was used to analyse data for the electrical degradation of polyethylene stabilized with polycyclic aromatic hydrocarbons. Based on quantum mechanically calculated electron affinities and ionisation potentials of the stabilizer molecules, we discovered that if a molecule is to be considered for voltage stabilization use it has to have a specific combination of the ionisation potential and adiabatic electron affinity. The model allows for a choice of appropriate voltage stabilizers based on theoretical calculations only and can help to facilitate any experimental study for choosing appropriate voltage stabilizer additives.     

Rate constant for diffusion-influenced ligand binding to receptors of arbitrary shape on a cell surface

The theory of ligand binding to receptors on a cell surface suggested by Berg and Purcell and generalized by Zwanzig and Szabo uses the assumption that receptors are circular absorbing disks on an otherwise reflecting sphere. One of the key ingredients of this theory is a solution for the rate constant for ligand binding to a single circular receptor on a reflecting plane. We give an exact solution for the rate constant for binding to a single elliptic receptor and an approximate solution for binding to a single receptor of more general shape. The latter was tested by Brownian dynamics simulations. We found that the approximate formula predicted the rate constant with better than 10% accuracy for all studied receptor shapes. Using our solutions one can find the rate constant for ligand binding to a cell covered by N noncircular receptors by means of the Zwanzig-Szabo formula.     

Toward sensitive, quantitative point-of-care testing (POCT) of protein markers: miniaturization of a homogeneous time-resolved fluoroimmunoassay for prostate-specific antigen detection

Point-of-care testing (POCT) systems which allow for a sensitive, quantitative detection of protein markers are extremely useful for the early detection and therapy progress monitoring of cancer. However, currently commercially available POCT devices are mainly limited to the qualitative detection of protein markers. In this study we demonstrate the successive miniaturization of a sensitive and fast assay for the quantitative detection of prostate-specific antigen (PSA) using a well established and clinically approved homogeneous time-resolved fluoroimmunoassay technology (TRACE?) on a commercial plate-reader system (KRYPTOR?). Regarding the initial requirements for the development of POCT devices we applied a 30-fold assay volume reduction (150 μL to 5 μL) to achieve a reasonable lab-on-a-chip volume and a 24-fold and 120-fold excitation pulse energy reduction to achieve reasonable pulse energies for low-cost miniature excitation sources. Due to highly efficient optimization of key POCT parameters our miniaturized PSA assay achieved a 30% increased sensitivity and a 2-fold improved limit of detection compared to the standard plate-reader method. Our results demonstrate the successful implementation of key parameters for a significant miniaturization and for cost reduction in the clinically approved KRYPTOR? platform for protein detection. The technological alterations required are easy-to-implement and can be immediately adapted for more than 30 diagnostic protein markers already available for the KRYPTOR? platform. These features strongly recommend our assay format to be utilized in innovative, sensitive, quantitative POCT of protein markers.     

GRAPHICAL ESTIMATION OF CROSS SECTIONS FROM FLUENCE-RESPONSE DATA

Abstract— Light-induced absorbance changes have been studied by several investigators as a potential assay for the blue-light receptor pigments in numerous organisms. These studies involve a flavin-mediated photoreduction of a cytochrome. Here we consider several alternative models for the photochemical kinetics linking the flavin excitation to the cytochrome absorbance change. Straightforward approximations from these models form the basis of a simple graphical procedure which, when applied to fluence-response data, leads to an estimate of the quantum efficiency for the production of the absorbance change. Such estimates are helpful in evaluating the relevance of this spectrophotometric effect to the physiological responses. Efficiencies of order unity are indicated for results on Neurospora and corn compared to a much lower efficiency for a mycelial preparation of Phycomyces.