A new microcomputer program for processing data in neutron activation analysis

A new utility program for processing data in neutron activation analysis (NAA) has been developed for use on MS-DOS microcomputers. Peak areas are read from ASCII data files of gamma-ray spectra which have been processed by a Gaussian peak fitting program, GAMANAL-PC. Elemental concentrations are then calculated by this new program, QUACANAL, via a semi-absolute algorithm that uses pre-determined activation constants. User-defined ASCII library files are employed to specify the elements of interest required for analysis, and (n, p) and (n, ) interferences are taken into account. The program has been written in turbo PASCAL, is menu driven and contains options for processing data from cyclic NAA. An interactive philosophy has been used in designing the program.Sabbatical address for 1991/1992.     

Computer-aided calculation of the molecular size of nondenatured proteins in pore-gradient gel electrophoresis.

A computer program written in Turbo C is described, which uses the two-step mathematical procedure published recently (Rothe, G. M., Electrophoresis 1988, 9, 307-316) to evaluate the molecular mass, Stokes' radius, spherical radius, and frictional coefficient of nondenatured proteins. The program runs on any IBM-PC or 100% compatible IBM-PC, provided the disk operating system MS-DOS or PC-DOS 3.0 or later has been installed. Functions that are permanently in use are accessible by menu. Storage and loading of data from disk and help instructions can be called by use of function keys. The program provides several tables into which inserted and calculated data is automatically integrated. Each table can be printed out, provided a printer with IBM character set is connected to the computer.     

CINA — A program for complete instrumental neutron activation analysis with a PC-type minicomputer

A program has been developed to use a PC-type minicomputer for instrumental neutron activation analysis. The program has the capacity for photopeak search, peak area computation, and element concentration determination using the single comparator method. Analysis time for a 4096-channel spectrum containing 20 photopeaks is about 4 minutes.     

MoWeD, a computer program to rapidly deconvolute low resolution electrospray liquid chromatography/mass spectrometry runs to determine component molecular weights

A computer program is described that can rapidly process low-resolution electrospray liquid chromatography/mass spectrometry (LC/MS) for peptides and proteins and assign molecular weights for observed components. The program first analyzes individual scans using a deconvolution algorithm similar to that previously described by Zhang and Marshall. Results for the entire run are then sorted by mass and those values found in adjacent scans are grouped together. The list of found components can also be compared to a user defined list of target molecular weight values making it easy to compare the results from different analyses. The program also has the capability to process a rolling average of scans that improves the performance when analyzing high molecular weight components. Other program features facilitate closer examination of selected spectra or regions of the chromatogram to check the MoWeD mass assignments. The utility of the program was demonstrated by the analysis of LC/MS data derived from a complex mixture of proteins derived from a bacterial whole cell lysate that had previously been analyzed manually. The MoWeD analysis was 30 times faster and provided a more comprehensive list of the components present.     

Single photon radioisotope emission computed tomography image using gamma camera (author's transl)]

Single photon radioisotope computed tomography (RCT) images were obtained using the following devices such as conventional gamma camera, data processer for exclusive use of nuclear medicine (C.D.S.-4096), magnetic tape and medium size electronic computer FACOM 230-28S (48K) for multipurposes, which are routinely used for clinical purpose. To reconstruct the RCT image we made absorption correction by geometric mean of opposing counts considering the thickness of source and used the convolution integral method. The reconstructed images of phantom study resolved one centimeter clearly and were very similar to original. The RCT image of patient was acquired by the rotation of patients using the revolving chair and the handmade implement which settles the center of patient's head. Three dimensional informations were obtained by one examination with a gamma camera which collects two dimensional images. When using a gamma camera, therefore, not only a transaxial but an arbitraly RCT image will be important to contribute for diagnosis.     

Isoelectric membrane simulator: a computational approach for isoelectric immobiline membranes.

Isoelectric membrane simulator (IMS) is a computer program meant for computation of pH, buffering power (beta), ionic strength (I) and dissociation degree (a) of a mixture of up to 3 buffering and 1 titrant Immobilines, for generating in a reproducible manner isoelectric membranes. Such membranes, of precise isoelectric point, are then used for large-scale protein purification by isoelectric focusing in multicompartment electrolyzers. IMS can be used, in a more general application, for titrating mixtures of buffers to a desired pH value. This versatile program is written in M.Q.BASIC rel. 2.5 and it runs on any IBM hardware or compatible machine supported by MS-DOS. An example of purification of superoxide dismutase in a multicompartment electrolyzer with a set of fixed pI membranes of widely differing composition is shown.     

Biochemical data-processing with microcomputers : Part 3. On-line data acquisition from a continuous flow analyzer

A program, written in BASIC, is described which allows data acquisition from a continuous flow analyzer. The program was developed for a readily available microcomputer, but should be easily modified for use on similar machines. Once the peak height has been measured, the concentration of the analyte is calculated by reference to a previously defined calibration. The program is designed to handle data from more than one channel, although there is a practical limit of 3–4 simultaneously active channels. The results of the separate assays are collated and printed as a group for each specimen, even when the analytical methods require different times for completion.     

Computer program for neutron activation analysis with the SLOWPOKE reactor

A FORTRAN computer program for automatic neutron activation analysis is presented. The program locates and identifies peaks in a gamma-ray spectrum, calculates peak areas and the concentrations of the elements of interest in the sample. This program was specifically designed for the SLOWPOKE reactor, it uses a semi-absolute method and does not need standards or flux monitors. The program was written so as to minimize the computation time, and a typical 4096-channel spectrum is processed in five seconds by an IBM 360/75 computer.     

Mathematical Simulation of Plasma-Chemical Coal Conversion

A mathematical model that describes the conversion of a coal-dust flow in a cylindrical plasma reactor is presented. The model describes a two-phase (coal particles + air) chemically reacting flow, which propagates in a channel with or without an internal heat source (an electric arc, a plasmatron torch, or exothermic chemical reactions). The model is based on the assumption that the process is quasi-stationary and one-dimensional; coal particles are taken isothermal, and ash is assumed an inert component. The model represents the composition of coals by their organic and mineral constituents. The model was implemented as a program for personal computers; calculations performed with the use of this program are in satisfactory agreement with experimental data.     

Ultrafast energy transfer dynamics of a bioinspired dyad molecule

A caroteno-purpurin dyad molecule was studied by steady-state and pump-probe spectroscopies to resolve the excited-state deactivation dynamics of the different energy levels as well as the connecting energy flow pathways and corresponding rate constants. The data were analyzed with a two-step multi-parameter global fitting procedure that makes use of an evolutionary algorithm. We found that following ultrafast excitation of the donor (carotenoid) chromophore to its S2 state, the energy flows via two channels: energy transfer (70%) and internal conversion (30%) with time constants of 54 and 110 fs, respectively. Additionally, some of the initial excitation is found to populate the hot ground state, revealing another limitation to the functional efficiency. At later times, a back transfer occurs from the purpurin to the carotenoid triplet state in nanosecond timescales. Details of the energy flow within the dyad as well as species associated spectra are disentangled for all excited-state and ground-state species for the first time. We also observe oscillations with the most pronounced peak on the Fourier transform spectrum having a frequency of 530 cm(-1). The dyad mimics the dynamics of the natural light-harvesting complex LH2 from Rhodopseudomonas acidophila and is hence a good model system to be used in studies aimed to further explain previous work in which the branching ratio between the competing pathways of energy loss and energy transfer could be manipulated by adaptive femtosecond pulse shaping.     

Formation of a Criegee intermediate in the low-temperature oxidation of dimethyl sulfoxide

Dimethyl sulfoxide (DMSO) is the major sulfur-containing constituent of the Marine Boundary Layer. It is a significant source of H2SO4 aerosol/particles and methane sulfonic acid via atmospheric oxidation processes, where the mechanism is not established. In this study, several new, low-temperature pathways are revealed in the oxidation of DMSO using CBS-QB3 and G3MP2 multilevel and B3LYP hybrid density functional quantum chemical methods. Unlike analogous hydrocarbon peroxy radicals the chemically activated DMSO peroxy radical, [CH3S(=O)CH2OO*]*, predominantly undergoes simple dissociation to a methylsulfinyl radical CH3S*(=O) and a Criegee intermediate, CH2OO, with the barrier to dissociation 11.3 kcal mol(-1) below the energy of the CH3S(=O)CH2* + O2 reactants. The well depth for addition of O2 to the CH3S(=O)CH2 precursor radical is 29.6 kcal mol(-1) at the CBS-QB3 level of theory. We believe that this reaction may serve an important role in atmospheric photochemical and irradiated biological (oxygen-rich) media where formation of initial radicals is facilitated even at lower temperatures. The Criegee intermediate (carbonyl oxide, peroxymethylene) and sulfinyl radical can further decompose, resulting in additional chain branching. A second reaction channel important for oxidation processes includes formation (via intramolecular H atom transfer) and further decomposition of hydroperoxide methylsulfoxide radical, *CH2S(=O)CH2OOH over a low barrier of activation. The initial H-transfer reaction is similar and common in analogous hydrocarbon radical + O2 reactions; but the subsequent very low (3-6 kcal mol(-1)) barrier (14 kcal mol(-1) below the initial reagents) to beta-scission products is not common in HC systems. The low energy reaction of the hydroperoxide radical is a beta-scission elimination of *CH2S(=O)CH2OOH into the CH2=S=O + CH2O + *OH product set. This beta-scission barrier is low, because of the delocalization of the *CH2 radical center through the -S(=O) group, to the -CH2OOH fragment in the transition state structure. The hydroperoxide methylsulfoxide radical can also decompose via a second reaction channel of intramolecular OH migration, yielding formaldehyde and a sulfur-centered hydroxymethylsulfinyl radical HOCH2S*(=O). The barrier of activation relative to initial reagents is 4.2 kcal mol(-1). Heats of formation for DMSO, DMSO carbon-centered radical and Criegee intermediate are evaluated at 298 K as -35.97 +/- 0.05, 13.0 +/- 0.2 and 25.3 +/- 0.7 kcal mol(-1) respectively using isodesmic reaction analysis. The [CH3S*(=O) + CH2OO] product set is shown to form a van der Waals complex that results in O-atom transfer reaction and the formation of new products CH3SO2* radical and CH2O. Proper orientation of the Criegee intermediate and methylsulfinyl radical, as a pre-stabilized pre-reaction complex, assist the process. The DMSO radical reaction is also compared to that of acetonyl radical.     

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.     

Introducing HYPERMET-PC for automatic analysis of complex gamma-ray spectra

In short time activation analysis prompt gamma-activation analysis and in high rate -ray spectroscopy in general, the shape parameters for peaks and back ground usually vary, rendering spectrum evaluation codes based on a fixed shape calibration unsuitable. An interactive version of the well-known, fully automatic -ray spectrum analysis code HYPERMET has been developed in C ++ for the IBM-PC. It runs under MS-DOS, in conventional memory, and can handle up to 16k-channel spectra, recorded with CANBERRA's System 100 and AccuSpec and with ORTEC's ACE plug-in MCA cards. A Windows-like graphics environment is provided with mouse controlled pull-down menus, pop-up windows and rubber band expansion. All basic features of HYPERMET such as fully automatic peak search, nonlinear fitting of multiplets with automatically adjusted Gaussian peak widths exponential tails and a complex background function have been retained. All details of the fitting procedure are recorded in a data base, hence any fitted region can be retrieved and modified interactively, even after a fully automatic spectrum evaluation. The program also provides an output peak list in SAMPO90 format for further processing. The latter format is widely used in a number of sample analysis programs such as KAYZERO a software package fork ₀ standardization in neutron activation analysis.     

Inorganic Crystal Structure Data to be Presented in a Form More Useful for Further Studies

To make inorganic structure data more useful for further studies a five-point list of simple procedures to be followed by authors of crystal structure papers is proposed. 1. A crystal structure should be described with the space group corresponding to its true symmetry. 2. A new structure proposal should be tested, if it is realistic in principle. 3. A structure should be described with a space group in a setting given in the International Tables. 4. For a comparison with other structures the structure data should be standardized with the program STRUCTURE TIDY. 5.“New” structure data should be checked in the databases, Chemical Abstracts or on-line intemet resources, if they are really new. The list is supplemented with many explanations, commentaries, examoles and references.     

Collision-induced dissociation of HS-(HCN): unsymmetrical hydrogen bonding in a proton-bound dimer anion

The energy-resolved competitive collision-induced dissociation of the proton-bound complex [HS.H.CN](-) is studied in a guided ion beam tandem mass spectrometer. H(2)S and HCN have nearly identical gas-phase acidities, and therefore, the HS(-) + HCN and the CN(-) + H(2)S product channels exhibit nearly the same threshold energies, as expected. However, the HS(-) + HCN channel has a cross section up to a factor of 50 larger than CN(-) + H(2)S at higher energies. The cross sections are modeled using RRKM theory and phase space theory. The complex dissociates to HS(-)+ HCN via a loose transition state, and it dissociates to CN(-) + H(2)S via a tight transition state. Theoretical calculations show that the proton-transfer potential energy surface has a single minimum and that the hydrogen bonding in the complex is strongly unsymmetrical, with an ion-molecule complex of the form HS(-)..HCN rather than CN(-)..H(2)S or an intermediate structure. The requirement for proton transfer before dissociation and curvature along the reaction path impedes the CN(-) + H(2)S product channel.     

Electron transfer dynamics from organic adsorbate to a semiconductor surface: zinc phthalocyanine on TiO2(110)

The femtosecond time evolutions of excited states in zinc phthalocyanine (ZnPC) films and at the interface with TiO2(110) have been studied by using time-resolved two-photon photoelectron spectroscopy (TR-2PPE). The excited states are prepared in the first singlet excited state (S1) with excess vibrational energy. Two different films are examined: ultrathin (monolayer) and thick films of approximately 30 A in thickness. The decay behavior depends on the thickness of the film. In the case of the thick film, TR-2PPE spectra are dominated by the signals from ZnPC in the film. The excited states decay with tau = 118 fs mainly by intramolecular vibrational relaxation. After the excited states cascaded down to near the bottom of the S1 manifold, they decay slowly (tau = 56 ps) although the states are located at above the conduction band minimum of the bulk TiO2. The exciton migration in the thick film is the rate-determining step for the electron transfer from the film to the bulk TiO2. In the case of the ultrathin film, the contribution of electron transfer is more evident. The excited states decay faster than those in the thick film, because the electron transfer competes with the intramolecular relaxation processes. The electronic coupling with empty bands in the conduction band of TiO2 plays an important role in the electron transfer. The lower limit of the electron-transfer rate was estimated to be 1/296 fs(-1). After the excited states relax to the states whose energy is below the conduction band minimum of TiO2, they decay much more slowly because the electron-transfer channel is not available for these states.     

Automatic classification of chemical structure databases using a highly parallel array processor

This article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis-Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.     

A tool for evaluating the Kovats index from the retention time of a substance in gas chromatography

A computer program based on a mathematical simulation of gas chromatography was developed for the identification of components during the course of the chromatographic analysis of molecular mixtures. The source data for the program are natural parameters that characterize the stationary phase (certified characteristics) and easy-to-specify operational parameters of chromatograph units. An example of calculating the retention time of a component under specified conditions from a specified Kovats index or, vice versa, calculating the Kovats index from the elution time of a component peak is given.     

Intramolecular energy transfer through charge transfer state in lanthanide compounds: a theoretical approach

A theoretical approach for the intramolecular energy transfer process involving the ligand-to-metal charge transfer (LMCT) state in lanthanide compounds is developed. Considering a two-electron interaction, both the direct Coulomb and exchange interactions are taken into account, leading to expressions from which selection rules may be derived and transfer rates may be calculated. These selection rules show that the direct Coulomb and exchange mechanisms are complementary, in the same way as obtained in previous works for the case of ligand-lanthanide ion energy transfer processes. An important result from numerical estimates is that the channel ligand-LMCT state is by far the dominant case, leading to transfer rates higher than for the channel lanthanide ion-LMCT state by several orders of magnitude. The analysis of the emission quantum yield as a function of the relative energy position of the LMCT state in a typical Eu(3+) compound allows the identification of two quenching regions, the most pronounced one occurring close to the lower ligand triplet level.     

Capillary liquid chromatography-microchip atmospheric pressure chemical ionization-mass spectrometry

A miniaturized nebulizer chip for capillary liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (capillary LC-microchip APCI-MS) is presented. The APCI chip consists of two wafers, a silicon wafer and a Pyrex glass wafer. The silicon wafer has a DRIE etched through-wafer nebulizer gas inlet, an edge capillary insertion channel, a stopper, a vaporizer channel and a nozzle. The platinum heater electrode and pads for electrical connection were patterned on to the Pyrex glass wafer. The two wafers were joined by anodic bonding, creating a microchip version of an APCI-source. The sample inlet capillary from an LC column is directly connected to the vaporizer channel of the APCI chip. The etched nozzle in the microchip forms a narrow sample plume, which is ionized by an external corona needle, and the formed ions are analyzed by a mass spectrometer. The nebulizer chip enables for the first time the use of low flow rate separation techniques with APCI-MS. The performance of capillary LC-microchip APCI-MS was tested with selected neurosteroids. The capillary LC-microchip APCI-MS provides quantitative repeatability and good linearity. The limits of detection (LOD) with a signal-to-noise ratio (S/N) of 3 in MS/MS mode for the selected neurosteroids were 20-1000 fmol (10-500 nmol l(-1)). LODs (S/N = 3) with commercial macro APCI with the same compounds using the same MS were about 10 times higher. Fast heat transfer allows the use of the optimized temperature for each compound during an LC run. The microchip APCI-source provides a convenient and easy method to combine capillary LC to any API-MS equipped with an APCI source. The advantages and potentials of the microchip APCI also make it a very attractive interface in microfluidic APCI-MS.