Expert system for interpretation of the infrared spectra of environmental mixtures

A program for the identification of the principal components of mixtures through interpretation of the infrared mixture spectrum (IntIRpret) was developed. This program, which was developed as a preliminary screening tool for unknown organic mixtures, has five main subroutines: the interferogram processing and peak-selection subroutine (PUSHSUB), the automated knowledge-acquisition subroutine (AUTOGEN), the system optimization subroutine (STO), the interpretation subroutine (PAIRS), and final processing subroutine to subtract spectral similarity (PAIRSPLUS). Principal advantages of this system compared to earlier systems are speed, flexibility and accuracy.     

Ident--a radioisotope-identification subroutine for use with the gamma-ray spectrum analysis program sampo

A radioisotope-identification and mass-determination subroutine has been added to the gamma-ray spectrum analysis program SAMPO. The subroutine IDENT contains a nuclear data library of 750 gamma-rays that are likely to be encountered in thermal-neutron activation analysis. Peaks found by SAMPO are compared with the library peaks and possible isotope identifications are made. To maximize the degree of confidence in the isotope identification, the subroutine carries out a half-life check and also confirms that the most prominent gamma-ray of the isotope concerned is present. Using the library data, together with information on the neutron flux, duration of the irradiation, subsequent decay time, and gamma-detection efficiency, the subroutine calculates the masses of elements identified in the sample, and can handle spectra acquired during either simple or cyclic irradiation. As well as the calculated masses the output contains information on identifications rejected by certain criteria. The nuclear data library used by the subroutine is presented in this paper in a simplified tabular form, and, as such, may be used for direct isotope identification and elemental mass determination.     

AN INDIRECT METHOD FOR DETERMINATION OF PARAMETERS IN THE FORECAST MODEL

An indirect method for determining some parameters in a forecast model has been developed, by which the program of the original model with little modification can be used as a subroutine of the inversion system and the optimum estimate of the parameters can be obtained by calling the subroutine time after time. It is specially useful for the sophisticated numerical weather prediction model. It may also be utilized to improve the forecast timely in case of obvious differences between the recent observations and the forecasts. The effect of the method is verified by numerical simulation tests with simple models.     

Multistep reaction analysis. A numerical approach based on relaxation theory

A general numerical method and program for simulation of the kinetics of multistep reactions is described, with details for collation of data, construction of a mechanistic model, and simulation of reciprocal relaxation times and calculation of individual rate constants. The working scheme of the program includes an initial approximate simulation by adjustment of the rate constants followed by their optimization with a Powell minimization subroutine. The procedure is applied to aromatic nucleophilic addition.     

A modified program for computation of formation constants of synergetic extraction complexes with two-phase titrations by using the Marquardt-Fletcher algorithm

A modified computer program SCTPT for the computation of formation constants of extraction complexes with two-phase pH titration data by using the Marquardt-Fletcher algorithm is described. It can be used to deal with extraction systems which consist of a metal, an acidic extractant and a neutral synergistic reagent with no need of new subroutine. It has been applied successfully to the Pb-PMBP(1-phenyl-3-methyl-4-benzoyl-pyrazolone-5)-TBP (tributyl phosphate) system. The results obtained are in agreement with those published in the literature.     

苯乙烯基形状记忆聚合物热力学行为的有限元分析

对苯乙烯基形状记忆聚合物进行了拉伸实验研究,测定了该材料在25℃、30℃、40℃和50℃时的弹性模量和屈服极限.根据实验结果,建立了苯乙烯基形状记忆聚合物的材料参数方程,描述了苯乙烯基形状记忆聚合物在玻璃体转化过程中,材料参数和温度的关系.在假设形状记忆聚合物为各向同性材料的基础上,将Tobushi等建立的热力学本构方程从一维扩展到三维.基于有限元分析软件ABAQUS的二次开发功能,针对上述本构方程和材料参数方程,编写了可供ABAQUS调用的UMAT函数,并对苯乙烯基形状记忆聚合物实现形状记忆效应的高温变形、应力冻结和形状恢复等热力学过程,进行了有限元数值模拟分析.     

Computerunterstützte Identifizierung von Isotopenmustern in niederaufgelösten Massenspektren

The identification of isotopic patterns in low resolution mass spectra with the aid of a computer program is described. Those masses in the mass spectra which coincide with the isotopic patterns are printed out. As additional information, a criterion is given indicating the quality of correlation between the measured and calculated isotopic pattern. The program is written as a subroutine in FORTRAN IV and can be executed by small computers too.     

Multiparametric curve fitting-XI: POLET computer program for estimation of formation constants and stoichiometric indices from normalized potentiometric data

The FORTRAN computer program POLET(84) analyses a set of normalized potentiometric titration curves to find a chemical model, i.e., the number of species present and their stoichiometry, and to determine the corresponding stability constants log beta(pqrs) and unknown stoichiometric indices p, q, r, and s of up to quaternary M(p)L(q)Y(r)H(s) complexes. The program belongs to the ABLET family, based on the LETAG subroutine, and can use an algorithmic and/or heuristic minimization strategy, or a beneficial combination of both. The data, a set of potentiometric titration curves plotted as volume and potential, are converted into normalized variables (formation function, pH) and then a computer-assisted search for a chemical model by POLET(84) is applied. The procedure for efficient application of POLET(84) in an equilibrium analysis is described and the program is validated by use of literature and simulated data. The reliability of the chemical model and its parameters is established by the degree-of-fit achieved, and the closeness of the stoichiometric indices to integral values.     

The COLUMBUS Standard Integral File Structure: A proposed interchange format

The integral file structure used in the COLUMBUS Program System is described. This file structure is proposed for use as an interchange format for the exchange of information between various electronic structure codes. Access to the integral and density matrix arrays stored in the file structure is simplified by a supporting subroutine library. This library is portable across various computers and is readily available to programmers from the COLUMBUS distribution files. This library provides for the efficient processing of individual records, including the use of asynchronous I/O and the vectorized processing of packed orbital labels. The individual arrays are identified in a self-defining and extensible manner, allowing for the addition of new integral types as demanded by the application. The format of the individual records is also self-defining, allowing for the use of various packing and data compression methods within each record without burdening the calling program with unnecessary complications.     

Estimation of cracking risk of concrete at early age based on thermal stress analysis

The purpose of this study is to simulate the early age concrete behaviors and evaluate the cracking risk with the thermal and thermal stress analysis. A new finite element method program associated with ANSYS program is developed for the computation of thermal field and thermal stress field for early age concrete considering the following characters: degree of hydration, thermal properties (such as specific heat, thermal diffusivity), thermal boundary conditions, and mechanical properties (such as shrinkage, creep) which occur at early age. The results from simulation compared with experimental values found in the literature show a good agreement. Finally, based on this user-developed subroutine, the effects of hydration heat, ambient temperature, wind velocity, shrinkage, and length-height ratio on cracking risk were analyzed for a concrete wall which is one part of the structure of Maridal culvert in Norway. By which, the measures to control the cracking were provided for the engineering application.     

Rapid evaluation of the Voigt function and its use for interpreting X-ray photoelectron spectroscopic data

While the Voigt function is recognized as the best function to represent the photoelectron spectroscopic process, it is less frequently used because it cannot be represented as an analytical function and thus has to be evaluated numerically. This paper shows how the true Voigt function can be calculated rapidly with approximately the same speed as pseudo-Voigt functions by using approaches that have been used by the astronomical sciences community. The Voigt function is calculated using code previously published by Wells. The paper describes a method for calculating the function to generate photoelectron peaks for curve fitting X-ray photoelectron spectroscopic data. An appendix is provided with the listing of a Fortran 90 program which uses the subroutine HUMDEV published by Wells. Examples of using this approach for the fitting of experimental core X-ray photoelectron spectroscopic data are presented, and the fits compared with fits using a pseudo Voigt product function. The use of the true Voigt function in the calculation of spectra in the core and valence band region is also described and illustrated by comparing the calculated spectra with experimental spectra.     

Analysis and design of photobioreactors for microalgae production I: method and parameters for radiation field simulation

Having capabilities for the simulation of the radiation field in suspensions of microalgae constitutes a great asset for the analysis, optimization and scaling-up of photobioreactors. In this study, a combined experimental and computational procedure is presented, specifically devised for the assessment of the coefficients of absorption and scattering, needed for the simulation of such fields. The experimental procedure consists in measuring the radiant energy transmitted through samples of suspensions of microalgae of different biomass concentrations, as well as the forward and backward scattered light. At a microscopic level, suspensions of microalgae are complex heterogeneous media and due to this complexity, in this study they are modeled as a pseudocontinuum, with centers of absorption and scattering randomly distributed throughout its volume. This model was tested on suspensions of two algal species of dissimilar cell shapes: Chlorella sp. and Scenedesmus quadricauda. The Monte Carlo simulation algorithm developed in this study, when used as a supporting subroutine of a main optimization program based on a genetic algorithm, permits the assessment of the physical parameters of the radiation field model. The Monte Carlo algorithm simulates the experiments, reproducing the events that photons can undergo while they propagate through culture samples or at its physical boundaries.     

Tools and strategies for processing diffusion-ordered 2D NMR spectroscopy (DOSY) of a broad,featureless resonance: an application to methylaluminoxane (MAO)

DOSY has been extremely successful in many studies of molecular weight distributions, especially when the components are separable along the chemical shift axis. However, an unresolved NMR resonance yields the familiar problem of overlapping exponential decays. In a study of methylaluminoxane (MAO), a set of data processing and simulation tools were developed: read Bruker data files (Matlab); preliminary non-linear least-squares fit with f-test (Matlab); movie generation of the fits (Matlab); conversion of diffusion coefficients to molecular masses through molecular volumes (Gaussian-98); and simulation of DOSY data sets for various molecular mass distributions (Mathematica). These tools are presented here and briefly compared with other DOSY analysis methods.Electronic Supplementary Material Supplementary material is available in the online version of this article at . The following Matlab and Mathematica files are made available: Plot_Raw_DOSY.m, Fit_Two_Component.m (which calls One_Gaussian_LEASTSQ.m, Two_Gaussian_LEASTSQ.m, and pFTest.m), and DOSY_theory.nb. Note: Matlab v5.2 optimization toolbox, as supplied, lacked a confidence interval subroutine; upon our request, confint.m was provided to the authors by Mathworks, Inc. Newer versions of Matlab have a similar program already included in the optimization     

Iterative analysis of the 1H NMR spectra of naphthalene (AA′ A″ A‴ BB′ B″ B‴ system) and two of its derivatives

The ¹H NMR spectra of naphthalene as an eight spin system, and two of its derivatives, 2,4-dichloro- and 2,4-dinitro-1-naphthol, have been completely analysed. The Indor technique has been very useful in the determination of the signs and magnitudes of very small coupling constants. An improved version of the Laocoon 3 program has greatly facilitated the spectral analysis through, first, the knowledge of the dependence of each transition upon the spectral parameters; second, some modifications in the iterative loop which avoid failure of convergence, and, third, the use of a slightly modified diagonalization subroutine which saves 20% CPU computer time. Our data suggest a rather small substituent effect on intra-ring couplings of the unsubstituted ring. The inter-ring coupling constants display a negative or positive sign according to an even or odd number of intervening bound, except the all-trans ⁶J which is positive. No substituent effect on the inter-ring couplings has been observed, except a small effect for the all-trans ⁶J.     

A nonlinear least squares program, MULTI(FILT), based on fast inverse Laplace transform for microcomputers

A nonlinear curve fitting program MULTI(FILT) into which the fast inverse Laplace transform (FILT) is incorporated was developed on a microcomputer. FILT is an algorithm for the numerical inversion of Laplace-transformed equations (image equations) to generate the corresponding real time courses. The pharmacokinetic models can be defined in the form of Laplace-transformed equations as a subroutine in MULTI(FILT). MULTI(FILT) achieves the numerical inversion of the defined image equations according to FILT and the subsequent curve-fitting of the inverse-transformed time courses to the experimental data points to estimate the pharmacokinetic parameters by the nonlinear least-squares method. MULTI(FILT) has a function to impose constraints on the pharmacokinetic parameters. In order to verify the reliability of MULTI(FILT), the pharmacokinetic parameters estimated by MULTI(FILT) were compared with those by MULTI using 100 time courses which were artificially generated according to the Monte Carlo method, based on data for theophylline and bishydroxycoumarin. The estimated pharmacokinetic parameters by MULTI(FILT) agreed with those by MULTI. Thus, it is suggested that FILT, developed in the field of electronic technology, is also useful in the pharmacokinetic field.     

Visualisation and integration of G protein-coupled receptor related information help the modelling: Description and applications of the Viseur program

G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur program allows one to interactively visualise and/or modify the sequences, transmembrane areas, alignments, models and results of mutagenesis experiments in an integrated environment. This integration increases the ease of modelling GPCRs: visualisation and manipulation improvements enable easier databank interrogation and interpretation. Unique program features include: (i) automatic construction of 'Snake-like' diagrams or hyperlinked GPCR molecular models to HTML or VRML and (ii) automatic access to a mutagenesis data server through the Internet. The novel algorithms or methods involved are presented, followed by the overall complementary features of the program. Finally, we present two applications of the program: (i) an automatic construction of GPCR snake-like diagrams for the GPCRDB WWW server, and (ii) a preparation of the modelling of the 5HT receptor subtypes. The interest of the direct access to mutagenesis results through an alignment and a molecular model are discussed. The Viseur program, which runs on SGI workstations, is freely available and can be used for preparing the modelling of integral membrane proteins or as an alignment editor tool.     

A program for evaluation of NAA spectra

A program for qualitative and quantitative analysis of spectra obtained by comparative NAA method is described. It includes peak search, calculation of essential peak parameters, isotope identification and estimation of concentrations and/or detection limits of nuclides, corrected for cooling time and decay during measurement. Corrections for blank samples and peak interference are performed as well. Uncertainties estimation of final results are performed according to the error propagation law. The program is aimed to help an experienced user to calculate the results of analysis but the possibility for automatic mode for routine analysis is provided as well.Supported by International Atomic Energy Agency through the research contract 7268/RB.     

Monte-Carlo model for the hydrogenation of alkenes on metal catalyst

A Monte-Carlo model for the simulation of alkene hydrogenation on metallic catalysts has been developed and implemented in Fortran language. We describe the model employed for ethylene hydrogenation on platinum and show the flow chart of the program. Computational characteristics such as number of necessary calculations to reach steady state, running times on different platforms, and effect of the size of the catalyst matrix, are presented. Good correlation between simulated and experimental data was observed. A subroutine allows for visual observation of the reaction. This approach is very useful for obtaining a personal impression of the important factors governing the reaction. By using this example the advantages of Monte-Carlo simulation to test the level of understanding of catalytic phenomena are discussed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 396–403, 1998     

Development and parametrization of sindo1 for second-row elements

The semiempirical MO method SINDO 1 is extended to second-row atoms from sodium to chlorine. The basis set has a provision to include d orbitals. To retain rotational invariance in a d orbital set, a number of hybrid integrals has to be included that invalidate the zero differential overlap (ZDO ) assumption even in a symmetrically orthogonalized basis set. The inclusion of d orbitals rendered the set-up of integral calculation of the original INDO method impractical. Instead of one subroutine for each integral, all explicitly calculated integrals (overlap, core, electronic repulsion) are now contained in a single subroutine under unifying aspects. The parametrization scheme includes pseudopotentials and adjusts the total energy under inclusion of zero point energies to experimental heats of formation of ground states. The vibrational frequencies for the calculation of zero point energies are obtained from calculated force constants and G matrix elements by a scaling procedure. The results for geometries, energies, and dipole moments are compared with MNDO data.     

Assessment of dose measurement uncertainty using RisøScan

The dose measurement uncertainty of the dosimeter system RisøScan, office scanner and Risø B3 dosimeters has been assessed by comparison with spectrophotometer measurements of the same dosimeters. The reproducibility and the combined uncertainty were found to be approximately 2% and 4%, respectively, at one standard deviation. The subroutine in RisøScan for electron energy measurement is shown to give results that are equivalent to the measurements with a scanning spectrophotometer.