Showing papers by "Wrocław University of Technology published in 2008"

cclib: A library for package‐independent computational chemistry algorithms

Abstract: There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Reporting Physisorption Data for Gas/Solid Systems

Abstract: The sections in this article are Introduction General Definitions and Terminology Methodology Methods for the Determination of Adsorption Isotherms Operational Definitions of Adsorption Experimental Procedures Outgassing the Adsorbent Determination of the Adsorption Isotherm Evaluation of Adsorption Data Presentation of Primary Data Classification of Adsorption Isotherms Adsorption Hysteresis Determination of Surface Area Application of the BET Method Empirical Procedures for Isotherm Analysis Assessment of Mesoporosity Properties of Porous Materials Application of the Kelvin Equation Computation of Mesopore Size Distribution Assessment of Microporosity Terminology Concept of Surface Area Assessment of Micropore Volume General Conclusions and Recommendations Keywords: physisorption data; IUPAC; adsorption isotherms; surface area; BET isotherm

How is protein aggregation in amyloidogenic diseases modulated by biological membranes

Abstract: The fate of proteins with amyloidogenic properties depends critically on their immediate biochemical environment. However, the role of biological interfaces such as membrane surfaces, as promoters of pathological aggregation of amyloidogenic proteins, is rarely studied and only established for the amyloid-β protein (Aβ) involved in Alzheimer’s disease, and α-synuclein in Parkinsonism. The occurrence of binding and misfolding of these proteins on membrane surfaces, is poorly understood, not at least due to the two-dimensional character of this event. Clearly, the nature of the folding pathway for Aβ protein adsorbed upon two-dimensional aggregation templates, must be fundamentally different from the three-dimensional situation in solution. Here, we summarize the current research and focus on the function of membrane interfaces as aggregation templates for amyloidogenic proteins (and even prionic ones). One major aspect will be the relationship between membrane properties and protein association and the consequences for amyloidogenic products. The other focus will be on a general understanding of protein folding pathways on two-dimensional templates on a molecular level. Finally, we will demonstrate the potential importance of membrane-mediated aggregation for non-amphiphatic soluble amyloidogenic proteins, by using the SOD1 protein involved in the amyotrophic lateral sclerosis syndrome.

Effect of cryogenic treatment on distribution of residual stress in case carburized En 353 steel

Abstract: The effect of cryogenic treatment on the distribution of residual stress in the case carburized steel (En 353) was studied using X-ray diffraction technique. Two types of cryogenic treatment: shallow cryogenic treatment (193 K) and deep cryogenic treatment (77 K) were adopted, as a supplement to conventional heat treatment. The amount of retained austenite in conventionally heat-treated, shallow cryogenically treated and deep cryogenically treated samples was found to be 28%, 22% and 14%, respectively. The conventionally heat-treated, shallow cryogenically treated and deep cryogenically treated samples in untempered condition had a surface residual stress of −125 MPa, −115 MPa and −235 MPa, respectively. After tempering the conventionally heat-treated, shallow cryogenically treated and deep cryogenically treated samples had a surface residual stress of −150 MPa, −80 MPa and −80 MPa, respectively. A comparative study of the three treatments revealed that there was an increase in the compressive residual stress in steel that was subjected to cryogenic treatment prior to tempering. The experimental investigation revealed that deep cryogenically treated steel when subjected to tempering has undergone a reduction in compressive residual stress. Such stress relieving behaviour was mainly due to the increased precipitation of fine carbides in specimens subjected to DCT with tempering.

Nonparametric system identification

Abstract: 1. Introduction 2. Discrete-time Hammerstein systems 3. Kernel algorithms 4. Semi-recursive kernel algorithms 5. Recursive kernel algorithms 6. Orthogonal series algorithms 7. Algorithms with ordered observations 8. Continuous-time Hammerstein systems 9. Discrete-time Wiener systems 10. Kernel and orthogonal series algorithms 11. Continuous-time Wiener system 12. Other block-oriented nonlinear systems 13. Multivariate nonlinear block-oriented systems 14. Semiparametric identification Appendices.

Biochemical bases for a widespread tolerance of cyanobacteria to the phosphonate herbicide glyphosate.

Abstract: Possible non-target effects of the widely used, non-selective herbicide glyphosate were examined in six cyanobacterial strains, and the basis of their resistance was investigated. All cyanobacteria showed a remarkable tolerance to the herbicide up to millimolar levels. Two of them were found to possess an insensitive form of glyphosate target, the shikimate pathway enzyme 5-enol-pyruvyl-shikimate-3-phosphate synthase. Four strains were able to use the phosphonate as the only phosphorus source. Low uptake rates were measured only under phosphorus deprivation. Experimental evidence for glyphosate metabolism was also obtained in strains apparently unable to use the phosphonate. Results suggest that various mechanisms may concur in providing cyanobacterial strains with herbicide tolerance. The data also account for their widespread ability to metabolize the phosphonate. However, such a capability seems limited by low cell permeability to glyphosate, and is rapidly repressed when inorganic phosphate is available.

Performance Improvement of Industrial Drives With Mechanical Elasticity Using Nonlinear Adaptive Kalman Filter

Abstract: This paper deals with the application of the adaptive control structure for torsional vibration suppression in the drive system with an elastic coupling The proportional-integral speed controller and gain factors of two additional feedback loops, from the shaft torque and load side speed, are tuned on-line according to the changeable load side inertia This parameter, as well as other mechanical variables of the drive system (load side speed, torsional and load torques), are estimated with the use of the developed nonlinear extended Kalman filter (NEKF) The initial values of the Kalman filter covariance matrices are set using the genetic algorithm Then, to ensure the smallest state and parameter estimation errors, the on-line adaptation law for the chosen element of the state covariance matrix of the NEKF is proposed The described control strategy is tested in an open and a closed-loop control structure The simulation results are confirmed by laboratory experiments

Circular Object Detection Using a Modified Hough Transform

Abstract: A practical modification of the Hough transform is proposed that improves the detection of low-contrast circular objects. The original circular Hough transform and its numerous modifications are discussed and compared in order to improve both the efficiency and computational complexity of the algorithm. Medical images are selected to verify the algorithm. In particular, the algorithm is applied to localize cell nuclei of cytological smears visualized using a phase contrast microscope.

Equivalence of the fractional Fokker-Planck and subordinated Langevin equations: the case of a time-dependent force.

Abstract: A century after the celebrated Langevin paper [C.R. Seances Acad. Sci. 146, 530 (1908)] we study a Langevin-type approach to subdiffusion in the presence of time-dependent force fields. Using a subordination technique, we construct rigorously a stochastic Langevin process, whose probability density function is equal to the solution of the fractional Fokker-Planck equation with a time-dependent force. Our model provides physical insight into the nature of the corresponding process through the simulated trajectories. Moreover, the subordinated Langevin equation allows us to study subdiffusive dynamics both analytically and numerically via Monte Carlo methods.

DeSUMOylating enzymes—SENPs

Abstract: Summary Modification of proteins by ubiquitin and SUMO (small ubiquitin-like modifiers) is a dynamic and reversible process. Similar to the ubiquitin pathway, where the action of deubiquitinating enzymes removes ubiquitin from ubiquitin-adducts, SUMO is also removed intact from its substrates by proteases belonging to the sentrin-specific proteases (SENPs) family. In addition to their isopeptidase activity, SENPs also execute another essential function as endopeptidases by removing the short C-terminal extension from immature SUMOs. The defining characteristics of SENPs are their predicted conserved molecular scaffold—defined as members of peptidase Clan CE, conserved catalytic mechanism, and their reported activity on SUMO or Nedd8 conjugated proteins (or the respective precursors). We discuss recent progress on the human SENPs and their substrates. 2008 IUBMB IUBMB Life, 60(11): 734–742, 2008

Photonic crystal fibers for sensing applications

Abstract: This paper discusses the sensing capabilities of the highly birefringent index-guided photonic crystal fibers (PCFs) such as dispersion characteristics of phase and group modal birefringence, polarization characteristics, sensitivity to hydrostatic pressures, temperature, and strain. Different types of applications including interferometric and polarimetric sensors of different physical parameters as well as evanescent field sensors for monitoring specific chemical compounds in gases and liquids are reported.

Inconsistency of knowledge and collective intelligence

Abstract: Is the intelligence of a collective larger than the intelligence of its members? How does one determine the knowledge of a collective on the basis of the knowledge of its members? In this paper, we try to answer these questions. Many examples show that the knowledge of a collective is not a usual union of the knowledge of its members. If we assume that the members of a collective possess their knowledge states about some common real world, and these states reflect to some degree the proper (real) state of the knowledge about the real world, then a question arises: How does one determine the knowledge of the collective, and what is its quality? In this paper, we use Consensus Theory to solve this problem and to show that, in many cases, the collective knowledge state is more proper than the knowledge states of the collective intelligence.

Simultaneous measurement of multiparameters using a Sagnac interferometer with polarization maintaining side-hole fiber.

Abstract: A Sagnac interferometer with a section of a polarization maintaining side-hole fiber for multiparameter measurement is proposed The sensor was experimentally demonstrated to be sensitive to torsion, temperature, and longitudinal strain, simultaneously The birefringence in the investigated side-hole fiber is induced simultaneously by the elliptical shape of a germanium-doped core and by field overlap with the air holes surrounding the core The latter effect is purely geometrical and causes high chromatic dispersion of the group birefringence in the long wavelength range, which results in a different period of spectral interference fringes A different wavelength response is obtained for each interference fringe peak when the fiber is subjected to torsion, temperature, or longitudinal strain A matrix equation for simultaneous measurement of the three parameters--torsion, temperature, and longitudinal strain--is also proposed

Heavy-tails and regime-switching in electricity prices

Abstract: In this paper we first analyze the stylized facts of electricity prices, in particular, the extreme volatility and price spikes which lead to heavy-tailed distributions of price changes. Then we calibrate Markov regime-switching (MRS) models with heavy-tailed components and show that they adequately address the aforementioned characteristics. Contrary to the common belief that electricity price models ‘should be built on log-prices’, we find evidence that modeling the prices themselves is more beneficial and methodologically sound, at least in case of MRS models.

Characterization of mechanical properties of suspension plasma sprayed TiO2 coatings using scratch test

Abstract: The study aimed at characterizing mechanical properties of TiO2 coatings obtained by the use of aqueous suspensions of fine rutile and anatase particles onto metal substrates. Thickness of the coatings was found with the use of optical microscope observations of metallographical cross-sections. The coatings morphology was found with scanning electron microscope (SEM) and their phase composition was determined by X-ray diffraction method. The mechanical properties were characterized using scratch test. The test enabled to characterize the adhesion of coatings by determination of critical force necessary to peel off the coatings from the substrate and, on the other hand, to estimate their cohesion by the measurement of the scratch hardness. The hardness was calculated using the width of the scratch and the value of force applied. The design of experiments (DOE) of spraying with the use of a 23 full factorial plan was applied to rutile powder. The coatings were sprayed onto aluminium substrate. The DOE enabled to find the effects of three principal parameters, i.e. electric power input to plasma, spray distance and suspension feed rate onto coating adhesion expressed by critical force. A preliminary data for anatase powder sprayed with one set of operational parameters onto stainless steel substrate are also shown.

Gold Recovery from HCl Solutions using Cyphos IL‐101 (a Quaternary Phosphonium Ionic Liquid) Immobilized in Biopolymer Capsules

Abstract: Tetraalkyl phosphonium chloride (Cyphos IL‐101), an ionic liquid (IL), was tested for gold recovery from HCl solutions: first in liquid/liquid extraction systems (using toluene and hexane as solvent) and in a second step, after being immobilized in a biopolymer composite matrix. SEM‐EDAX analysis was used for the characterization of the resins. The sorption capacity reached up to 140 mg Au(III) g−1 in 1 M HCl solutions. Base metals that do not form anionic chlorocomplexes and nitrate or chloride ions (at 5 g L−1) did not interfere with Au(III) binding. Gold binding probably occurs through the interaction of R3R'P+ with AuCl4 −. The kinetics of sorption was carried out varying agitation speed, metal concentration, IL content, and resin drying. Intraparticle diffusion played an important role on the control of sorption kinetics. Gold could be desorbed from the loaded IL‐impregnated resin using thiourea (in HCl solutions). The resin could be re‐used for at least 4 cycles. The resins are specially adapted for...

New Organoselenium Compounds Active against Pathogenic Bacteria, Fungi and Viruses

Abstract: Different N-substituted benzisoselenazol-3(2H)-ones, analogues of ebselen were designed as new antiviral and antimicrobial agents. We report their synthesis, chemical properties as well as study on biological activity against broad spectrum of pathogenic microorganisms (Staphylococcus aureus, Staphylococcus simulans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Candida albicans, Aspergillus niger) and viruses (herpes simplex virus type 1 (HSV-1), encephalomyocarditis virus (EMCV), vesicular stomatitis virus (VSV)), in vitro. Most of them exhibited high activity against viruses (HSV-1, EMCV) and gram-positive bacteria strains (S. aureus, S. simulans), while their activity against gram-negative bacteria strains (E. coli, P. aeruginosa, K. pneumoniae) was substantially lower. Some of tested compounds were active against yeast C. albicans and filamentous fungus A. niger.

Damping of Torsional Vibrations in Two-Mass System Using Adaptive Sliding Neuro-Fuzzy Approach

Abstract: In this paper, a new robust control system with the adaptive sliding neuro-fuzzy speed controller for the drive system with the flexible joint is proposed. A model reference adaptive control structure (MRAC) is used in this drive system. The torsional vibrations are successfully suppressed in the control structure with only one basic feedback from the motor speed. The damping ability of the proposed system has been confirmed for a wide range of the system parameters and compared with the other control concepts, like the adaptive Pi-type neuro-fuzzy controller and the classical cascade PI structure.

Partial substitution of lanthanum with silver in the LaMnO3 perovskite: Effect of the modification on the activity of monolithic catalysts in the reactions of methane and carbon oxide oxidation

Abstract: Partial substitution of lanthanum with silver in the LaMnO 3 perovskite deposited onto a monolithic metal support enhances catalytic activity in the oxidation of CH 4 and CO. The optimal silver content ( x ) in the La 1− x Ag x MnO 3 perovskite amounts to 0.2 and ranges from 0.1 to 0.3 for CH 4 combustion and CO oxidation, respectively. Methane conversion obtained over the monolithic catalyst with the most active perovskite (La 0.8 Ag 0.2 MnO 3 ) at 750 °C totals 98.9% and falls slightly (to 97.6%) after 130 h on stream. Ageing at 900 °C accounts for a distinct decline in methane conversion, which drops to 67% at 750 °C. The decrease in the activity of this catalyst during the run is attributable to the decreasing SSA and decreasing proportion of Ag + to Ag 0 and to the reduction of Mn 4+ to Mn 3+ on the perovskite surface. When the catalyst is aged at 900 °C, the processes are enhanced; the metallic silver that segregates onto the surface tends to form agglomerates, and the composition of the catalyst surface is similar to the composition of the LaMnO 3 perovskite.

New ANN-Based Algorithms for Detecting HIFs in Multigrounded MV Networks

Abstract: Application of two new ANN-based algorithms for arcing high impedance fault (HIF) detection in multigrounded medium-voltage (MV) distribution networks is presented in this paper. The paper provides an evaluation of two new structures of artificial neural networks (ANNs) that may be used for reliable HIF detection in multigrounded as well as isolated, compensated, and grounded via small resistance distribution grids. The results obtained by use of both neural nets are presented. The performance was tested using data obtained from staged HIFs in real MV network as well as from electromagnetic transients program-alternative transients program simulations. A small number of necessary neurons in developed ANNs, short measuring sliding data window, and easy interpretation of obtained output signals are the main advantages of the proposed approach. Satisfactory results of ANN performance were observed for all examined HIF cases in which the ground fault current was greater than 16 A. The selected ANNs of best performance show high reliability and immunity to transients resulting from switching operations in protected feeders and from capacitor bank switching.

Design, synthesis, and evaluation of novel organophosphorus inhibitors of bacterial ureases.

Abstract: A new group of organophosphorus inhibitors of urease, P-methyl phosphinic acids was discovered by using the structure based inhibitor design approach. Several derivatives of the lead compound, aminomethyl(P-methyl)phosphinic acid, were synthesized successfully. Their potency was evaluated in vitro against urease from Bacillus pasteurii and Proteus vulgaris. The studied compounds constitute a group of competitive, reversible inhibitors of bacterial ureases. Obtained thiophosphinic analogues of the most effective structures exhibited kinetic characteristics of potent, slow binding urease inhibitors, with Ki = 170 nM (against B. pasteurii enzyme) for the most active N-(N′-benzyloxycarbonylglycyl)aminomethyl(P-methyl)phosphinothioic acid.