Eigenvalues and eigenfunctions of the Laplace operator on an equilateral triangle

A boundary value problem for the Laplace equation with Dirichlet and Neumann boundary conditions on an equilateral triangle is transformed to a problem of the same type on a rectangle. This enables us to use, e.g., the cyclic reduction method for computing the numerical solution of the problem. By the same transformation, explicit formulae for all eigenvalues and all eigenfunctions of the corresponding operator are obtained.     

CHARMMing: a new, flexible web portal for CHARMM

A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP , 1O1O , and 1UFY . Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations.     

Water photodissociation in free ice nanoparticles at 243 nm and 193 nm

The photolysis of (H(2)O)(n) nanoparticles of various mean sizes between 85 and 670 has been studied in a molecular beam experiment. At the dissociation wavelength 243 nm (5.10 eV), a two-photon absorption leads to H-atom production. The measured kinetic energy distributions of H-fragments exhibit a peak of slow fragments below 0.4 eV with maximum at approximately 0.05 eV, and a tail of faster fragments extending to 1.5 eV. The dependence on the cluster size suggests that the former fragments originate from the photodissociation of an H(2)O molecule in the cluster interior leading to the H-fragment caging and eventually generation of a hydronium H(3)O molecule. The photolysis of surface molecules yields the faster fragments. At 193 nm (6.42 eV) a single photon process leads to a small signal from molecules directly photolyzed on the cluster surface. The two photon processes at this wavelength may lead to cluster ionization competing with its photodissociation, as suggested by the lack of H-fragment signal increase. The experimental findings are complemented by theoretical calculations.     

Biodegradation of a synthetic co-polyester by aerobic mesophilic microorganisms

The aerobic biological degradation of the synthetic aliphatic-aromatic co-polyester Ecoflex™ (BASF) by 29 strains of enzyme-producing soil bacteria, fungi and yeasts was investigated at moderate environmental conditions. Previous studies had shown that these materials could be degraded but these studies were done under thermophilic conditions. In this paper, a screening procedure was developed to assess the biodegradability of the co-polyester at ambient environmental conditions and to investigate the mechanism of biodegradation. Results showed that the aliphatic-aromatic co-polyester could be degraded by a number of different microorganisms. However, after 21 days exposure to even the most promising cultures of pure microorganisms, only partial degradation of the Ecoflex™ was accomplished and only a few samples showed visible signs of degradation as loosely defined by the mechanical weakening of the films. Weight loss was not as obvious as the visual degradation and suggested broader types of microbial attack. The bacteria studied preferentially degraded the bonds between aliphatic components of the copolymer and the rate of biodegradation of oligomers was appreciably faster than that for the polymer chains. Using GC-MS techniques, degradation intermediates were identified to be the monomers of the co-polyester. Gel permeation chromatography results suggested exo-enzyme type degradation, where the microbes hydrolysed the ester bonds at the termini of the polymeric chains preferentially.     

Emergence of charge-transfer-to-solvent band in the absorption spectra of hydrogen halides on ice nanoparticles: spectroscopic evidence for acidic dissociation

Extensive ab initio calculations complemented by a photodissociation experiment at 193 nm elucidate the nature of hydrogen halide molecules bound on free ice nanoparticles. Electronic absorption spectra of small water clusters (up to 5 water molecules) and water clusters doped with hydrogen fluoride, hydrogen chloride and hydrogen bromide were calculated. The spectra were modeled at the time-dependent density functional (TDDFT) level of theory with the BHandHLYP functional using the reflection principle. We observe the emergence of a charge-transfer-to-solvent (CTTS) band in the absorption spectra upon the acidic dissociation of the hydrogen halides. The CTTS band provides a spectroscopically observable feature for the acidic dissociation. The calculated spectra were compared with our new experimental photodissociation data for larger water clusters doped with HCl and HBr. We conclude that HCl and HBr dissociate to a large extent on the surface of ice nanoparticles at temperatures near 120 K and photoactive products are formed. The acidic dissociation of HX leads to an enhancement by about 4 orders of magnitude of the HCl photolysis rate in the 200-300 nm region, which is potentially relevant for the halogen budget in the atmosphere.     

Thallium fractionation in polluted environmental samples using a modified BCR three-step sequential extraction procedure and its determination by electrothermal atomic absorption spectrometry

Determination of thallium in polluted environmental samples and their extracts obtained by a modified BCR three-step sequential extraction procedure was used to study thallium distribution and mobility in the monitored polluted area affected by acidification (Šobov, Central Slovakia). The results of fractionation applied to 5 soil certified reference materials and 14 environmental samples show that the vast majority of thallium occurred in the residual fraction. This means that highly toxic thallium is strongly entrapped in the parent rock materials remains immobile and its environmental toxicity is therefore reduced. The limit of detection for thallium in the studied fractions was lower than 0.050 mg kg⁻¹, the precision (RSD) of the ultratrace determination of thallium in the studied fractions was better than 17 % and the accuracy of the used method was verified by analyzing certified reference materials. Presented at the XVIIIth Slovak Spectroscopic Conference, Spišská Nová Ves, 15–18 October 2006.     

Design and economics of industrial production of fructooligosaccharides

A process for industrial production of fructooligosaccharides (FOS’s) based on the conversion of sucrose by immobilized fructosyltransferase (FTase) from the cells of Aureobasidium pullulans CCY 27-1-94 was developed. Particular process operations and conditions were designed employing results of laboratory and semi-pilot scale experiments. The process flowsheet comprised three sections: FTase production, which included fermentation, isolation and purification of the enzyme, FTase immobilization and FOS’s production where a product with a high content of FOS’s was prepared by the removal of glucose, fructose and unreacted sucrose from the reaction mixture using simulated moving-bed chromatography. Two alternative process flowsheets were proposed for the annual production of 10 000 t of FOS’s: one for a powdery product and the second one for syrup. The economic analysis provided the costs for the production of immobilized FTase and FOS’s using two different price estimates for sucrose.     

Anomalous adsorptive properties of HIV protease: indication of two-dimensional crystallization?

Adsorption of HIV protease onto surfaces that are usually considered to be protein-resistant was studied quantitatively using surface plasmon resonance. Adsorption onto gold surfaces functionalized by OH-terminated alkyl chains was much stronger than onto oligo(ethylene glycol)-terminated surfaces. Equilibrium and kinetic adsorption constants were determined. An anomalous mutual attraction between adsorbate molecules was observed, indicating the possibility of two-dimensional crystallization of HIV protease. These results are applicable for the design of sensors/biosensors for HIV protease resistance detection and for proper manipulation of this enzyme in laboratory devices.     

ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics

In simplifying the evaluation and quantification of high-throughput label-free quantitative proteomic data, we introduce ProteinQuant Suite. It comprises three standalone complementary computer utilities, namely ProtParser, ProteinQuant, and Turbo RAW2MGF. ProtParser is a filtering utility designed to evaluate database search results. Filtering is performed according to different criteria that are defined by the end-user. ProteinQuant then utilizes this parsed list of peptides and proteins in conjunction with mzXML or mzData files generated from the raw files for quantification. This quantification is based on the automatic detection and integration of chromatographic peaks representative of the liquid chromatography/mass spectrometry (LC/MS) elution profiles of identified peptides. Turbo RAW2MGF was developed to extend the applicability of ProteinQuant Suite to data collected from different types of mass spectrometers. It directly processes raw data files generated by Xcalibur, a ThermoElectron data acquisition software, and generates a MASCOT generic file (MGF). This file format is needed since the protein identification results generated by the database search employing this file format include information required for the precise identification and quantification of chromatographic peaks. The performance of ProteinQuant Suite was initially validated using LC/MS/MS generated for a mixture of standard proteins as well as standard proteins spiked in a complex biological matrix such as blood serum. Automated quantification of the collected data resulted in calibration curves with R(2) values higher than 0.95 with linearity spanning over more than 2 orders of magnitude with peak quantification reproducibility better than 15% (RSD). ProteinQuant Suite was also applied to confirm the binding preference of standard glycoproteins to Con A lectin using a sample consisting of both standard glycoproteins and proteins.