Multicut-HDMR with an application to an ionospheric model

A new High Dimensional Model Representation (HDMR) tool, Multicut-HDMR, is introduced and applied to an ionospheric electron density model. HDMR is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high-dimensional input-output system behavior. HDMR describes an output [f(x)] in terms of its input variables (x = [x(1), x(2), em leader, x(n)]) via a series of finite, hierarchical, correlated function expansions. Various forms of HDMR are constructed for different purposes such as modeling laboratory or field data, or reproducing a complicated mathematical model. The Cut-HDMR technique, which expresses f(x) with respect to a specified reference point x in the input space, is appropriate when the input space is sampled in an orderly fashion. However, if the desired domain of the input space is too large, the HDMR function expansion may not converge, and Cut-HDMR will be unable to accurately approximate f(x). The new Multicut-HDMR technique addresses this problem through the use of multiple reference points in the input space.     

Thermooptical detection in microchips: from macro- to micro-scale with enhanced analytical parameters

In this paper, we compared the methods of photothermal spectroscopy used in different spatial scales, namely thermal-lens spectrometry (TLS) and thermal-lens microscopy (TLM) to enhance the performance parameters in analytical procedures. All of the experimental results were confirmed by theoretical calculation. It was proven that the design for both TLM and TLS, despite a different scale for the effect, is governed by the same signal-generating and probing conditions (probe beam diameter at the sample should be equal to the diameter of the blooming thermal lens), and almost does not depend on the nature of the solvent. Theoretical and experimental instrumental error curves for thermal lensing were coincident. TLM obeys the same law of instrumental error as TLS and shows better repeatability for the same levels of thermal-lens signals or absorbances. TLS is more advantageous for studying low concentrations in bulk, while TLM shows much lower absolute LODs due to better repeatability for low amounts. The behavior of the thermal-lens signal with different flow rates was studied and optimum conditions, with the minimum contribution to total error, were found. These conditions are reproducible, are in agreement with the existing theory of the thermal response in thermal lensing, and do not significantly affect the design of the optimum scheme for setups. TLM showed low LODs in solvent extraction (down to 10(-8) M) and electrokinetic separation (10(-7) M), which were shown to be governed by discussed instrumental regularities, instead of by microchemistry.     

An application of the zeeman effect to analytical atomic spectroscopy-II Background correction

A double-beam atomic-absorption spectrometer is described in which sample and reference beams are generated by Zeeman splitting of the source emission-line. The instrument was found to give satisfactory correction for lamp drift and for background scatter signals. The main advantage of the technique is the simplicity of the optical system used. Analytical sensitivity is found to be generally poorer than that given by single-beam measurements, largely because of the poor spectral characteristics of the lamps used here in comparison to their modern commercial hollow-cathode counterparts.     

An application of an homogenization method to a model of diffusion in glassy polymers

The sorption of gases in polymers below their glass-transition temperature T_g is known in many cases to be described by the “dual sorption” theory, according to which the gas is held in accordance with both the Langmuir and Henry's laws. Based on this theory, expressions for the “effective diffusion coefficient” in the glassy polymers have been obtained by investigators in the past, notably by Paul and Koros.² The present analysis regards the glassy polymers as inhomogeneous with regions on which the gas sorption follows the Langmuir law. Assuming that the linear dimensions of these regions, which are often referred to as “microvoids” (although they are not space filled by vacuum), are small compared to the macroscopic length of interest but large compared to the mean free path of the penetrant gas molecules, we derive a rigorous relation between the average flux and the concentration gradient in the polymer and show that this relation can be expressed in terms of an “effective diffusion coefficient” D_eff which depends on the details of the microstructure, i.e., the size, shape and spatial distribution of the “microvoids.” This expression for D_eff is shown to reduce to that of Paul and Koros² in two situations: (1) when the “voids” consist of slabs running parallel to the concentration gradient, and (2) when the “voids” are spherical and the temperature of the polymer is not too different from T_g. The results of the present study lead to an alternative procedure for interpreting the experimental data on sorption and permeation which may have some advantages over the procedure currently employed. Finally, the analysis presented here is also applicable to polymers containing adsorptive fillers.     

An analytical consistent pseudo-component delumping procedure for equations of state with non-zero binary interaction parameters

For mixtures with many components, some or most of the components are grouped into pseudo-components in order to reduce the dimensionality of the problem for phase equilibrium calculations, and therefore the computational effort. However, knowing the detailed fluid phase split may be important for a variety of applications. The detailed phase compositions resulting from a flash calculation performed on a lumped mixture can be predicted using a delumping (inverse lumping) procedure [C.F. Leibovici, E.H. Stenby, K. Knudsen, Fluid Phase Equilibr. 117 (1997) 225–232].If the mixture parameters of an equation of state (EoS) can be expressed as a linear combination of pure component parameters and the phase mole fractions, then the component fugacity coefficients can also be expressed as a linear combination of pure component parameters with coefficients only depending on mixture properties. As a result, the equilibrium coefficients are related only to component properties and EoS coefficients, independently on phase compositions.In this work, we show using a reduction method how to effectively obtain such an expression of the equilibrium constants even for non-zero binary interaction parameters (BIPs) in the EoS, and based on these results, we propose a totally consistent analytical procedure for the estimation of equilibrium constants of detailed mixtures from lumped information, which is an extension of Leibovici's delumping method.For several examples with non-zero BIPs between hydrocarbon components and classical contaminants, phase mole fractions and the vapor mole fraction of the delumped mixture are in excellent agreement with the exact values obtained by flashing the original mixture. The delumping procedure has multiple applications, mainly for reservoir simulation and distillation problems.     

On the calculation of circular dichroism spectra using quantum wave-packet dynamics with an application to molecular dimers

Circular dichroism (CD) spectra are calculated from the Fourier transform of a time-correlation function. The latter can efficiently be evaluated by wave-packet propagation methods. This approach is similar to the time-dependent evaluation of absorption or Raman spectra. As an application, correlation functions and CD spectra for a molecular dimer are determined and compared to the case of absorption.     

Modeling three-dimensional network formation with an atomic lattice model: application to silicic acid polymerization

We present an atomic lattice model for studying the polymerization of silicic acid in sol-gel and related processes for synthesizing silica materials. Our model is based on Si and O atoms occupying the sites of a body-centered-cubic lattice, with all atoms arranged in SiO(4) tetrahedra. This is the simplest model that allows for variation in the Si-O-Si angle, which is largely responsible for the versatility in silica polymorphs. The model describes the assembly of polymerized silica structures starting from a solution of silicic acid in water at a given concentration and pH. This model can simulate related materials-chalcogenides and clays-by assigning energy penalties to particular ring geometries in the polymerized structures. The simplicity of this approach makes it possible to study the polymerization process to higher degrees of polymerization and larger system sizes than has been possible with previous atomistic models. We have performed Monte Carlo simulations of the model at two concentrations: a low density state similar to that used in the clear solution synthesis of silicalite-1, and a high density state relevant to experiments on silica gel synthesis. For the high concentration system where there are NMR data on the temporal evolution of the Q(n) distribution, we find that the model gives good agreement with the experimental data. The model captures the basic mechanism of silica polymerization and provides quantitative structural predictions on ring-size distributions in good agreement with x-ray and neutron diffraction data.     

Chiral analytical method development of liquiritigenin with application to a pharmacokinetic study

Pharmacometric characterization studies of liquiritigenin have historically overlooked its chiral nature. To achieve complete characterization, an analytical method enabling the detection and quantification of the individual enantiomers of racemic (±) liquiritigenin is necessary. Resolution of the enantiomers of liquiritigenin was achieved using a simple high‐performance liquid chromatographic method. A Chiralpak® ADRH column was employed to perform baseline separation with UV detection at 210 nm.The standard curves were linear ranging from 0.5 to 100 µg/mL for each enantiomer. Limit of quantification was 0.5 µg/mL. The assay was applied successfully to stereoselective serum disposition of liquiritigenin enantiomers in rats. Liquiritigenin enantiomers were detected in serum as both aglycones and glucuronidated conjugates. Both unconjugated enantiomers had a serum half‐life of ~15 min in rats. The volume of distribution (V_d) for S‐ and R‐liquiritigenin was 1.49 and 2.21 L/kg, respectively. Total clearance (Cl_total) was 5.12 L/h/kg for S‐liquiritigenin and 4.79 L/h/kg for R‐liquiritigenin, and area under the curve (AUC_0‐inf) was 3.95 µg h/mL for S‐liquiritigenin and 4.23 µg h/mL for R‐liquiritigenin. The large volume of distribution coupled with the short serum half‐life suggests extensive distribution of liquiritigenin into tissues. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis of archaeal bipolar lipid analogues: a way to versatile drug/gene delivery systems

A synthetic route for the preparation of symmetrical and unsymmetrical archaeal tetraether-like analogues has been described. The syntheses are based upon the elaboration of hemimacrocyclic tetraether lipid cores from versatile building blocks followed by simultaneous or sequential introduction of polar head groups. Functionalizations of the tetraether lipids with neutral lactose or phosphatidylcholine polar heads and cationic glycine betaine moieties were envisaged both to increase membrane stability and to exhibit interactions with charged nucleic acids. Additionally, mannose and lactose triantennary clusters designed as multivalent ligands for selective interaction with lectin-type receptors were also efficiently synthesized for active cell/tissue targeting.     

An application of the zeeman effect to analytical atomic spectroscopy-I The construction of magnetically-stable spectral sources

A design is given for a d.c. discharge lamp which will maintain a stable plasma in a magnetic field. The lamp is of particular use for applications of the Zeeman effect to analytical atomic spectroscopy. Three designs of cathode are described, which cover three different temperature ranges for the m.p. of the elements concerned. The experimental behaviour of lamps at varying magnetic field strengths, filler pressures and operating currents is considered.     

An enolate claisen route to c-pyranosides : Development and application to an ionophore synthon

A new method for the stereoselective synthesis of dihydropyrans of various substitution patterns is described, involving the Ireland ester enolate Claisen rearrangements of 6-alkenyl-1,4-dioxan-2-ones. The method has been applied to an enantioselective synthesis of the “left-wing” tetrahydropyran portion 2 of the ionophore antibiotic indanomycin (1). The synthetic sequence employed for the production of 2 proceeded in greater than 29% overall yield in 12 steps from the allylic alcohol 26, thus underscoring the utility of the heterocycle synthesis described.     

D-MORPH regression: application to modeling with unknown parameters more than observation data

Diffeomorphic modulation under observable response preserving homotopy (D-MORPH) is a model exploration method, originally developed for differential equations. We extend D-MORPH to regression treatment of a model described as a linear superposition of basis functions with unknown parameters being the expansion coefficients. The goal of D-MORPH regression is to improve prediction accuracy without sacrificing fitting accuracy. When there are more unknown parameters than observation data, the corresponding linear algebraic equation system is generally consistent, and has an infinite number of solutions exactly fitting the data. In this case, the solutions given by standard regression techniques can significantly deviate from the true system structure, and consequently provide large prediction errors for the model. D-MORPH regression is a practical systematic means to search over system structure within the infinite number of possible solutions while preserving fitting accuracy. An explicit expression is provided by D-MORPH regression relating the data to the expansion coefficients in the linear model. The expansion coefficients obtained by D-MORPH regression are particular linear combinations of those obtained by least-squares regression. The resultant prediction accuracy provided by D-MORPH regression is shown to be significantly improved in several model illustrations.     

A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases

We present the theoretical evaluation of new AMBER force field parameters for 12 copper-based nucleases with bis(2-pyridylmethyl) amine, 2,2′-dipyridylamine, imidazole, N,N-bis(2-benzimidazolylmethyl) amine and their derivative ligands based on first-principles electronic structure calculations at the B3LYP level of theory. A three-point approach was developed to accurately and efficiently evaluate the force field parameters for the copper-based nucleases with the ligands. The protocol of RESP atomic charges has been used to calculate the atomic charge distributions of the studied copper-based nucleases. The evaluated force field parameters and RESP atomic charges have been successfully applied in the testing molecular mechanics calculations and molecular dynamics simulations on the nucleases and the nuclease–DNA complexes, respectively. It has been demonstrated that the developed force field parameters and atomic charges can consistently reproduce molecular geometries and conformations in the available X-ray crystal structures and can reasonably predict the interaction properties of the nucleases with DNA. The developed force field parameters in this work provide an extension of the AMBER force field for its application to computational modeling and simulations of the copper-based artificial nucleases associated with DNA.     

A contribution to the use of thorin as an analytical reagent: spectrophotometric study of its complexation with barium and application to sulphate determination in atmospheric particulates

The complexation of Ba(2+) by Thorin in the pH range 2-9 in aqueous ethanol medium has been investigated. The dissociation constants of Thorin in the ethanolic medium have been determined spectrophotometrically and the distribution of the protonated species has been used to explain the behaviour of the apparent complexation constant. On the basis of the apparent constants found, and mass-balances, the effect of sulphate on the absorbance has been calculated, and the best conditions for determination of sulphate have been established. Cation and anion interferences have been studied and means of overcoming them are proposed. The method developed has been applied to sulphate determination in atmospheric particulates. As little as 1 mug of sulphate can be measured.     

Neville elimination: an efficient algorithm with application to chemistry

Solving linear systems is often required in chemical problems. Besides, birth and death processes occur in many chemical phenomena and the matrices associated to these processes are totally positive, that is, all their minors are nonnegative. Neville elimination is an elimination procedure very useful when dealing with these matrices. Convergence and stability of iterative refinement using Neville elimination are analyzed, in particular when the coefficient matrix is totally positive. Other applications to chemistry are commented and numerical experiments are shown.     

Formation of core-shell Au@Ag nanorods induced by catecholamines: A comparative study and an analytical application

Gold nanorods (AuNRs) stabilized by cetyltrimethylammonium bromide (CTAB) were synthesized and an interaction of catecholamines (CAs) with silver ions in the presence of the obtained AuNRs was studied. The reaction results into formation of core-shell Au@Ag nanorods (Au@AgNRs) and leads to a hypsochromic shift of the long-wave surface plasmon resonance (SPR) band in the absorption spectrum of AuNRs. The influence of a CA structure, excess of CTAB, interaction time, pH, concentration of AuNRs, silver ions and CAs on this interaction was studied. Based on correlation of the NRs spectral characteristics with the concentration of CAs, a method for spectrophotometric determination of dobutamine, epinephrine, norepinephrine and dopamine with detection limits 27, 18, 16 and 13 μg L⁻¹, respectively, has been developed. The method can be applied to the analysis of medicines.     

An atomistic model of passive membrane permeability: application to a series of FDA approved drugs

We apply an atomistic model of passive membrane permeability to a series of weakly basic drugs. The computational model uses conformational sampling in combination with an all-atom force field and implicit solvent model to estimate relative passive membrane permeabilities. The model does not require the use of training data for rank-ordering compounds, and as such represents a different approach from the more commonly employed QSPR models. We compare the computational results to previously published experimental PAMPA and Caco-2 permeabilities.     

PCR-based detection of gene transfer vectors: application to gene doping surveillance

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.