GESPECOR: A versatile tool in gamma-ray spectrometry

GESPECOR is a Monte Carlo based software developed for the computation of efficiency, of matrix effects and of coincidence summing effects in gamma-ray spectrometry. GESPECOR can be applied to coaxial and well-type HPGe or to Ge(Li) detectors and to various types of sources, including point, cylindrical, and spherical sources or Marinelli beakers. In this paper the structure of GESPECOR is presented and the procedures applied are described. The uncertainty of the results computed by GESPECOR is carefully analyzed. The analysis shows that GESPECOR is able to provide results with a well defined uncertainty, in a user friendly WINDOWS environment.     

Estimation of true coincidence corrections for voluminous sources

To analyze a voluminous radioactive source with the highest possible sensitivity, it is necessary to use both a high efficiency detector and an optimal measurement geometry. The optimal geometry implies positioning the source as close to the detector as possible. It also implies selection of the shape of the source in order to reach the highest efficiency possible (e.g., Marinelli beaker). Under such conditions of measurements, true coincidences may cause systematic errors that can reach levels of more than ten percent for some radionuclides. A method for estimation of the effect of these coincidences was developed. It is based on direct computation of the effect by means of integration of a function which involves the experimentally obtained detection efficiency for the place around the detector. It was found that for the tested detector with a relative efficiency of 15%, the so-called intrinsic peak-to-total calibration may be used in the course of such an integration: It has been shown that theP/T-ratio for the given energy in the working space around the detector may be considered a constant value. Some results from a peak-to-total calibration study in the presence of scattering material are also given.The main part of the material has been presented at the Third International Meeting Nuclear Methods for Protection of the Environment, May 1995, Dubna, Russia.     

Transmission of electronic effects of substituents in vinyl esters

To elucidate the transmission mechanism of electronic effects of substituents in vinyl esters on the optical parameters of the absorption bands in the IR spectra, a comparison was made of the frequencies of corresponding absorption bands in vinyl ethers, vinyl esters, alkyl esters of carboxylic acids, ketones, and acid anhydrides. Calculation of the - and -electron structure of the molecules by the Hückel and Del Re approximations was made. The results were compared with the spectral characteristics. The conclusion was reached that the ester oxygen atom in vinyl esters reduces interaction of the carbonyl and vinyl groups, although it is not removed completely. In vinyl esters of aromatic acids the effect of benzene ring substituents is displayed by a change of the -electron structure of the CH₂=CH-O-CO- fragment. In vinyl esters of aliphatic acids the electronic influence of radicals of the acid portion is transmitted by the ester oxygen, mainly inductively, which, in its turn, shows a change in the ability of this atom to conjugate with the vinyl group.The authors express their thanks to Yu. A. Kruglyak for allowing use of the programs for the computation and for helpful advice.     

On the calculation of arbitrary multielectron molecular integrals over Slater‐type orbitals using recurrence relations for overlap integrals. III. Auxiliary functions \documentclass{article}\pagestyle{empty}\begin{document}$Q_{nn'}^{q}$\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$G_{-nn'}^{q}$\end{document}

The auxiliary functions $Q_{nn'}^{q}(p,pt)$ and $G_{-nn'}^{q}(p_{a},p,pt)$ which are used in our previous paper [Guseinov, I. I.; Mamedov, B. A. Int J Quantum Chem 2001, 81, 117] for the computation of multicenter electron‐repulsion integrals over Slater‐type orbitals (STOs) are discussed in detail, and the method is given for their numerical computation. The present method is suitable for all values of the parameters p_a, p, and pt. Three‐ and four‐center electron‐repulsion integrals are calculated for extremely large quantum numbers using relations for auxiliary functions obtained in this paper. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Conductance equation of dilute mixed strong electrolytes. III. Electrophoresis

The electrophoretic velocity is computed through the order linear in concentration for a system containing any number of species of ions of any charges. The computation is based on the general theory of Fuoss and Onsager and the method for the generalization to mixed electrolytes developed by Chen and Onsager for the primitive model. The Boltzmann factor exp. (—e_{i ji}/kT) is retained explicitly through the computation to obtain a result consistent with earlier computations of the relaxation field. The equilibrium potential including a correction to Poisson-Boltzmann equation is used, which adds a linear term V _j ^c to the electrophoretic velocity in agreement with the result of Murphy and Cohen. The correction to the ionic distribution due to the solvent motion is considered, which results in a linear term inversely proportional to the square of the viscosity of the solution. The main contribution is V _j ^E , which is in agreement with the result for symmetrical electrolytes of Falkenhagen et al. with only a slight difference due mainly to the different approximation used in the computation of the local force.     

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S–S and C–S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S–S and C–S bond cleavages and, more importantly, can also identify fragments with the S–S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved.

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The anion radical of azobispyridin N-oxide

The anion radical of the fully aromatic di-N-oxide system of azobispyridine N-oxide was prepared and studied by ESR. Utilising computer simulation and CNDO computation the ESR spectrum was interpreted as follows: Using appropriate equations the spin densities were calculated at Ths semi-quinoidal nature of the radical suggests a possible use as a spin label.     

Comparison of commercially available genetic algorithms: GAs as variable selection tool

Many commercially available software programs claim similar efficiency and accuracy as variable selection tools. Genetic algorithms are commonly used variable selection methods where most relevant variables can be differentiated from less important variables using evolutionary computing techniques. However, different vendors offer several algorithms, and the puzzling question is: which one is the appropriate method of choice? In this study, several genetic algorithm tools (e.g. GFA from Cerius2, QuaSAR-Evolution from MOE and Parteks genetic algorithm) were compared. Stepwise multiple linear regression models were generated using the most relevant variables identified by the above genetic algorithms. This procedure led to the successful generation of Quantitative Structure–activity Relationship (QSAR) models for (a) proprietary datasets and (b) the Selwood dataset.     

MEPSIM: A computational package for analysis and comparison of molecular electrostatic potentials

Summary MEPSIM is a computational system which allows an integrated computation, analysis, and comparison of molecular electrostatic potential (MEP) distributions. It includes several modules. Module MEPPLA supplies MEP values for the points of a grid defined on a plane which is specified by a set of three points. The results of this program can easily be converted into MEP maps using third-parties graphical software. Module MEPMIN allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values, and all the geometrical relationships between them (distances, angles, and dihedral angles). Module MEPCOMP computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes the similarity. Module MEPCONF performs the same process as MEPCOMP, considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. The most recently developed module, MEPPAR, is another modification of MEPCOMP in order to compute the MEP similarity between two molecules, but only taking into account a particular plane. The latter module is particularly useful to compare MEP distributions generated by systems of aromatic rings. MEPSIM can use several wavefunction computation approaches to obtain MEP distributions. MEPSIM has a menu type interface to simplify the following tasks: creation of input files from output files of external programs (GAUSSIAN and AMPAC/MOPAC), setting the parameters for the current computation, and submitting jobs to the batch queues of the computer. MEPSIM has been coded in FORTRAN and its current version runs on VMS/VAX computers.     

Development of Advanced Software Tools for Computer‐Aided Design,Simulation, and Optimization of Polymerization Processes

A new software has been developed for the simulation, design, parameter and state estimation, optimization, and control of specific polymerization processes aiming at increasing plant efficiency, improving product quality, and reducing the impact to environment. It provides a user‐friendly interface, including a design environment that can be accessed from the engineer's desktop computer, allowing graphical interaction and expert system guidance on how to use the program or make engineering decisions. The software design allows the collection of models from different sources leading to an easy and comprehensive synthesis of process models. Recent advances regarding the development of software applications for three specific polymerization systems are presented.

     

Microwave Single Vessel Acid-Vapor Extraction: Effect of Experimental Parameters on Co and Fe Determination in Biological Samples

Characteristic parameters of a single vessel procedure were investigated for Co and Fe determination in biological samples using nitric acid-vapor extraction under atmospheric pressure. A laboratory-made PTFE support vessel suitable for four cups containing the samples was adapted to fit on the microwave glass vessel. Biological samples (30mg) were weighed directly into these PTFE cups and exposed to nitric acid vapor stemming from 15mL concentrated HNO₃ placed in the bottom of the glass vessel. Sample cups were positioned at 50, 80, 110, and 140mm from the support base. We evaluated the temperature, acidity, and residual carbon content of each sample cup, i.e. parameters that could influence the efficiency of vapor-phase acid digestion. The influence of sample particle size on digestion efficiency was also considered. It was demonstrated that temperature was the main parameter for efficient recovery of both Co and Fe in biological samples, and higher temperatures allowed lower residual carbon contents.     

C.A. Coulson's work on a contour-integral approach to the London theory of magnetic susceptibility of conjugated molecules

Mizoguchi has very recently cast London's theory of magnetic susceptibilities of conjugated molecules in terms of the Coulson contour-integral formulation of Hückel molecular-orbital theory. Since interest in this approach has been thus revived, we present here a previously unpublished document, dated May 16th, 1953, by the late Professor C.A. Coulson, FRS, in which he formulates the London theory in terms of his own contour-integral method. Coulson's treatment is based on bond-bond polarisabilities and it therefore provides an interesting parallel to certain aspects of the now-classic McWeeny polarisability method, advanced five years later. The Coulson polarisability formalism does not, however, provide for explicit computation of individual ring-current intensities, nor — since it preceded the experimental observations — for the direct calculation of ring-current secondary fields (and, hence,¹H-NMR chemical shifts).     

Preconcentration and determination of naphthalene in air and water using activated carbon adsorption,carbon disulfide extraction and gas chromatography

A new method for the determination of naphthalene in air and water has been developed. The naphthalene was preconcentrated using activated carbon adsorption with carbon disulfide extraction and determined by gas chromatography with flame ionization detection. The chromatographic peak of naphthalene was separated well from the potential interferents turpentine, terpenene, isoborneol, camphor and isobornyl acetate. The detection limit was 0.52 g/ml of CS₂, equivalent to 2.6 g/m³ of air or 0.05 g/ml in 50 ml of water. The precision for 10 g/ml naphthalene was 1.7%. The adsorption capacity, sampling efficiency and desorption efficiency of 100 mg of activated carbon for naphthalene in air were 8.8 mg, 98.8% and 95.2%, respectively. The extraction efficiency of 5 ml of carbon disulfide for naphthalene in water was 97.6%. The method was successfully applied to the determination of naphthalene in air and water from an industrial plant.     

Sol-Gel Derived TiO2/Lead Phthalocyanine Photovoltaic Cells

Transparent TiO2 films were deposited onto a base electrode comprising an InSnO2 glass substrate using the (alkoxide) sol-gel technique. Lead phthalocyanine was subsequently vacuum sublimed onto the TiO2 surface. The resulting InSnO2/TiO2/PbPc/Au heterojunction cell was investigated for its illuminated current density/voltage, and spectral characteristics. The ideality factor (m) and saturation current (Jo) were determined from current density/voltage J(V) measurements. Photoelectrical measurements were conducted under both simulated solar radiation and within a wavelength range of 300–900 nm. This allowed calculation of open circuit voltage Voc, short circuit current Jsc, fill factor FF, quantum efficiency Z and the overall conversion efficiency. Typical photovoltaic characteristics were obtained indicating the potential of the device for solar cell applications. The power conversion efficiency was 0.001%; improvements are therefore required.     

Consideration of data load time on modern processors for the Verlet table and linked-cell algorithms

Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short‐range pairwise interatomic potentials. These algorithms are based on the Verlet table (VT) and linked‐cell (LC) methods. It is widely believed that the VT is more efficient than the LC. The analysis of these methods shows that in case when the average number of interactions per particle is relatively large, or more specifically, the particle density ρ and skin radius r_skin meet the condition (4π/6) ρr/27 ? 1, which may be true for most simulations of liquids, the number of memory data load operations in the LC is much less than that in the VT. Because memory access on modern processors is a bottleneck, this advantage of the LC should be and was in fact used, and a code outperforming the VT by a factor of almost 2 was obtained. Some modifications of the VT were proposed to reduce its disadvantage concerning memory data loading. The key modifications included automated skin radius tuning during simulations and compression of the VT to minimize duplications of atom identifiers in its nearby rows. Although these modifications had improved the performance, the VT failed to regain the superiority over the LC. The methods were tested in the MOLKERN simulation software by using SIMD and multithreading. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Information theory of miniaturization advantages of column liquid chromatography for quantitative analysis

Summary The influences of decreasing column diameter and length on two analytical goals, the precision and solvent efficiency, in reversed-phase liquid-chromatography are studied. Low solvent consumption is one of analytical advantages of miniaturized columns and is shown to be quantitatively evaluated by the precision and solvent efficiency which are defined to be the total Shannon mutual information obtained from an assay and the information obtained in a unit solvent volume, respectively. Analysis of paraben food additives on a microbore column is taken as an example. In trace analysis, the relative standard deviation (RSD) of measurements theoretically derived from the precision is shown to approach to the observed ones.     

Action-FRET of a Gaseous Protein

Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question—and thus further develop mass spectrometry as a tool for structural biology—structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state—where a systematic decrease is observed—and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with methanol concentration is taken as evidence that the conformational ensemble of gaseous protein cations retains a memory of the solution phase conformational ensemble upon electrospray ionization.

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Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database (“suspect screening”) instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These “proof of principle” experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MS^E mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a “chopping” bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software.

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Multi-reference-state perturbation theory for computation of potential-energy surfaces

The implementation of multi-reference-state Rayleigh-Schrödinger perturbation theory for the evaluation of potential-energy surfaces is reviewed. The organization of the computation and the basic algorithms are outlined. A major difficulty is the quadratic increase in computing sources as the reference space is expanded. Truncating the space of nonreference determinants is suggested as a solution for the problem. The method applies a numerical cutoff criterion for the weights of the first-order wave function. The truncation reduces the computing time significantly with negligible sacrifice in the quality of the results.This paper was presented at the international conference on The Impact of Supercomputers on Chemistry, held at the University of London, London, UK, 13–16 April 1987