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Search results for: Molecular docking and simulation study
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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublicationThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Adaptive Multiplex Resource Allocation Method for DAB+ Broadcast System
PublicationIn this paper an adaptive multiplex resource allocation method for the DAB+ broadcast system is presented. An analysis of content transmitted over different radio programs with respect to their profile is discussed. Simulation results of an adaptive multiplexer, as well as the technological demonstrator, fully compatible with the DAB+ standard, are described. The concept is verified by a subjective quality assessment study of real-time...
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Fractional Calculus Evaluation of Hyaluronic Acid Crosslinking in a Nanoscopic Part of Articular Cartilage Model System
PublicationThis work presents a study of the mechanism of physical crosslinking of hyaluronic acid in the presence of common phospholipids in synovial joint organ systems. Molecular dynamic simulations have been executed to understand the formation of hyaluronan networks at various phospholipid concentrations. The results of the simulations suggest that the mechanisms exhibit subdiffusion characteristics. Transportation quantities derive...
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Electron impact fragmentation of pyrrole molecules studied by fluorescence emission spectroscopy
PublicationThe fluorescence emission spectroscopy using electron impact excitation technique was employed to study fragmentation processes of the gas phase pyrrole molecules. The following excited fragmentation species were observed by detection of their fluorescence decay: the atomic hydrogen H(n), n = 4-7 and the diatomic CH(A2Δ), CN(B2Σ+), NH(A3Π) and C2(d3Πg) fragments. These atomic and molecular products differ from those previously...
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Multifunctional PID Neuro-Controller for Synchronous Generator
PublicationThis paper deals with a PID Neuro-Controller (PIDNC) for synchronous generator system. The controller is based on artificial neural network and adaptive control strategy. It ensures two functions: maintaining the generator voltage at its desired value and damping electromechanical oscillations. The performance of the proposed controller is evaluated on the basis of simulation tests. A comparative study of the results obtained with...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Optimal Rotating Receiver Angles Estimation for Multicoil Dynamic Wireless Power Transfer
PublicationThis study proposed an approach to dynamic wireless charging that uses a rotating receiver coil. Our simulation study focused on the verification of a novel way of increasing the coupling coefficient and power transfer stability by following the flux of the transmitting coils. To obtain the highest possible coupling by means of the FEM analysis, we studied the optimization of the trajectory of the angular velocity of the rotating...
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Monitoring of CRT by means of impedance multiple measurements - simulation studies
PublicationCardiac resynchronization therapy (CRT) is a very promising treatment for patients with congestive heart failure. An Impedance Cardiography (ICG) is used for evaluation of heart mechanical activity. A simulation study with the use of a FEM model was performed. The developed realistic model of the thorax, based on CT data obtained from examination of a 68-year-old man, consisted of 212 000 tetrahedral elements. Different configurations...
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Modified Inductive Multi-Coil Wireless Power Transfer Approach Based On Z-Source Network
PublicationThis article presents a non-conventional approach to a multi-coil wireless power transfer system based on a Z-source network. The novelty of the approach lies in the use of a Z-source as a voltage source for energy transmission through the wireless power transfer coils. The main advantage is in a reduced number of semiconductors. This paper provides the design approach, simulation and experimental study. Feasibility and possible...
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Fuzzy Divisive Hierarchical Clustering of Solvents According to Their Experimentally and Theoretically Predicted Descriptors
PublicationThe present study describes a simple procedure to separate into patterns of similarity a large group of solvents, 259 in total, presented by 15 specific descriptors (experimentally found and theoretically predicted physicochemical parameters). Solvent data is usually characterized by its high variability, dierent molecular symmetry, and spatial orientation. Methods of chemometrics can usefully be used to extract and explore accurately...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublicationThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Numerical Modeling of Water and Ice Dynamics for Analysis of Flow Around the Kiezmark Bridge Piers
PublicationThis paper presents the results of a numerical model study on the effect of ice on the proposed bridge piers in the Vistula River outlet and its effect on flow conditions in the river. The model DynaRICE is used in this study, which is a two-dimensional hydro-ice dynamic numerical model developed for dynamic ice transport and jamming in rivers. To simulate river hydrodynamics in the vicinity of the bridge piers, 2-dimensional numerical...
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Approach to security assessment of critical infrastructures' information systems
PublicationThis study presents an approach to the security assessment of the information systems of critical infrastructures. The approach is based on the faithful reconstruction of the evaluated information system in a computer security laboratory followed by simulations of possible threats against the system. The evidence collected during the experiments, stored and organised using a proprietary system InSAW, may later be used for the creation...
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Environmental exposure to cadmium in breast cancer – association with the Warburg effect and sensitivity to tamoxifen
PublicationThe association between cadmium and breast cancer remains unexplained due to inconsistent epidemiological data and unknown underlying mechanisms. This study aimed to assess the relationship between environmental exposure to cadmium and the Warburg effect in breast cancer and, thus, its possible interference with breast cancer treatment. The observational study in two groups of breast cancer patients indicated a positive correlation between...
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Early Stages of RNA-Mediated Conversion of Human Prions
PublicationPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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The use of mathematical models for diagnosis of activated sludge systems in WWTP
PublicationIn this study diagnosis of activated sludge systems in wastewater treatment plant (WWTP) was investigated. Diagnosis of technical objects can be realized in many ways. One of the divisions of the diagnostic methods include modelling with or without a model of the object. The first of these is the analysis of the symptoms for which, based on the parameter values, the abnormality in the diagnosed objects are sought. Another way is...
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ASYNCHRONICZNE METODY RADIOLOKALIZACYJNE
PublicationW pracy przedstawiono wybrane problemy lokalizowania obiektów w asynchronicznych sieciach radiowych. W pierwszej kolejności zostały zdefiniowane kryteria jakościowe do oceny efektywności pracy opracowanych metod oraz przedstawiono model symulacyjny, który został użyty do badań. W kolejnych trzech rozdziałach szczegółowo opisano trzy oryginalne asynchroniczne metody radiolokalizacyjne w różnych wariantach. Przeprowadzono analizę...
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Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures
PublicationDapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS:...
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Improving SBR Performance Alongside with Cost Reduction through Optimizing Biological Processes and Dissolved Oxygen Concentration Trajectory
PublicationAuthors of this paper take under investigation the optimization of biological processes during the wastewater treatment in sequencing batch reactor (SBR) plant. A designed optimizing supervisory controller generates the dissolved oxygen (DO) trajectory for the lower level parts of the hierarchical control system. Proper adjustment of this element has an essential impact on the efficiency of the wastewater treatment process as well...
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Accurate modeling of quasi-resonant inverter fed IM drive
PublicationIn this paper wide-band modeling methodology of a parallel quasi-resonant dc link inverter (PQRDCLI) fed induction machine (IM) is presented. The modeling objective is early-design stage prediction of conductive electromagnetic interference (EMI) emissions of the considered converter fed IM drive system. Operation principles of the selected topology of PQRDCLI feeding IM drive are given. Modeling of the converter drive system is...
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Effects of Noncontact Shoulder Tool Velocities on Friction Stir Joining of Polyamide 6 (PA6)
PublicationIn this study, the effects of the traverse and rotational velocities of the noncontact shoulder tool on the heat generation and heated flux during the friction stir joining of high-density polyamide 6 (PA6) polymer were investigated. The computational fluid dynamics (CFD) method was employed to simulate the thermomechanical phenomena during the friction stir joining (FSJ) process of PA6. A developed model was used to consider the...
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublicationIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublicationSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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Parameter and delay estimation of linear continuous-time systems
PublicationIn this paper the problem of on-line identification of non-stationary delay systems is considered. Dynamics of supervised industrial processes is described by ordinary differential equations. Discrete-time mechanization of their continuous-time representations is based on dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures implemented in recursive forms are applied for simultaneous identification...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublicationA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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A Model of Thermal Energy Storage According to the Convention of Bond Graphs (BG) and State Equations (SE)
PublicationThe main advantage of the use of the Bond Graphs method and State Equations for modeling energy systems with a complex structure (marine power plants, hybrid vehicles, etc.) is the ability to model the system components of different physical nature using identical theoretical basis. The paper presents a method of modeling thermal energy storage, which is in line with basic BG theory. Critical comments have been put forward concerning...
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Real-time PCR approach in dermatophyte detection and Trichophyton rubrum identification
PublicationDermatophytes are keratinophilic molds that infect human hair, nails and skin. Diagnosis of dermatophytosis is based on morphological, serological and biochemical features. However, identification is difficult and laborious due to similarities between microorganisms. Thus, there is considerable interest to develop mycological diagnostic procedures based on molecular biology methods. In this study, fast, two-step DNA extraction...
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Average Size of a Suffix Tree for Markov Sources
PublicationWe study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size of such a suffix tree is asymptotically equivalent to the average size of a trie built over n independentsequences from the same Markovian source. This equivalenceis only known for memoryless...
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Two Time-Scale Hierarchical Control of Integrated Quantity and Quality in Drinking Water Distribution Systems
PublicationThe paper considers a feedback optimising control of drinking water distribution systems (DWDS). Although the optimised pump and valves scheduling and disinfectant injection control attracted considerable attention over last two decades most of the contributions were limited to an open-loop optimisation repetitively performed during the DWDS operation. Also, while a strong interaction between the water quantity and quality exists...
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublicationThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
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Performance and Emission Modelling and Simulation of Marine Diesel Engines using Publicly Available Engine Data
PublicationTo analyse the behaviour of marine diesel engines in unsteady states for different purposes, for example to determine the fuel consumption or emissions level, to adjust the control strategy, to manage the maintenance, etc., a goal-based mathematical model that can be easily implemented for simulation is necessary. Such a model usually requires a wide range of operating data, measured on a test stand. This is a time-consuming process...
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Comparative Analysis of Salient and Non-Salient Pole Brushless Synchronous Generator for Application in Autonomous Electric Power System
PublicationThis paper presents a comparative study of two types of brushless synchronous generator for application in autonomous electric power systems (e.g. airplane power grid). Commercially used salient pole and a prototype non-salient pole high speed multi-pole brushless synchronous generator (BSG) have been presented. Comparative analysis of both types of the generator has been performed. Chosen simulation (using FEM and circuit models)...
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Study of prototype multi-pole non-salient field winding for high speed brushless synchronous generator
PublicationIn this paper a non-salient field winding for a brushless synchronous generator working with high speed in an autonomous energy generation system (e.g. airplane power grid) has been presented. A conception of a six-pole cylindrical-rotor with distributed field winding has been proposed. Comparison study of salient and prototype non-salient field winding has been carried out. Chosen simulation and measurement results of the generator...
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On–line Parameter and Delay Estimation of Continuous–Time Dynamic Systems
PublicationThe problem of on-line identification of non-stationary delay systems is considered. The dynamics of supervised industrial processes are usually modeled by ordinary differential equations. Discrete-time mechanizations of continuous-time process models are implemented with the use of dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures mechanized in recursive forms are applied for simultaneous...
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Multi-Transformer Flyback Converter for Supplying Isolated IGBT and MOSFET Drivers
PublicationA multi transformer flyback converter topology for supplying transistor drivers is presented. The topology presents some advantages over typical multi output single transformer, as reduction of effective leakage inductance, equal magnetic coupling between primary and secondary circuits and better isolation between outputs. Simulation study carried out in the LTSpice IV program and preliminary experimental results indicate high...
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Parameter and delay estimation of linear continuous-time systems
PublicationIn this paper the problem of on-line identification of non-stationary delay systems is considered. Dynamics of supervised industrial processes is usually described by ordinary differential equations. Discrete-time mechanization of their continuous-time representations is based on dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures implemented in recursive forms are applied for simultaneous...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Synthesis, structure and properties of novel poly(hydroxyurethane)s obtained by non-isocyanate route
PublicationNon-isocyanate polyurethanes (NIPUs) can be synthesized by polyaddition of five-membered bis(cyclic carbonate)s and primary diamines. NIPUs are an alternative for the commonly used (in the form of foams, elastomers, coatings or fibers) in the industry polyurethanes obtained using toxic and moisture sensitive diisocyanates, polyols and low-molecular weight chain extenders. The main aim of this work was to synthesize non-isocyanate...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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In-Reactor Polypropylene Functionalization─The Influence of Catalyst Structures and Reaction Conditions on the Catalytic Performance
PublicationTo unravel the relationship between silylene-bridged metallocene catalyst structures and polymerization conditions and their effect on the performance in in-reactor functionalization of polypropylene, the behaviors of rac-Me2Si(2-Me-4-Ph-Ind)2ZrCl2/MMAO, rac-Me2Si(Ind)2ZrCl2, rac-Me2Si(2-Me-4-Ph-Ind)2HfCl2, and rac-Me2Si(Ind)2HfCl2 in propylene/aluminum alkyl-passivated 10-undecen-1-ol copolymerization were compared. Kinetic analysis...
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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The Influence of the Co-Dopant Dexamethasone Phosphate on the Electrodeposition Process and Drug-Release Properties of Polypyrrole-Salicylate on Iron
PublicationIn this work, the influence of incorporation of two anti-inflammatory drugs dexamethasone phosphate and sodium salicylate on the electrodeposition process of polypyrrole (PPy) film on iron has been studied. The incorporation of the agents into PPy has been carried out in a one-step electropolymerization process on oxidizable iron. The role of each drug agent during the deposition process has been discussed. The morphological and...
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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Investigation of Thermoplastic Polyurethanes Synthesized via Two Different Prepolymers
PublicationThe man aim of this work was to investigate the effect of the molecular weight of polyols, mixture of prepolymers, and [NCO]/[OH] molar ratio used during the prepolymer chain extending step on the chemical structure, thermomechanical and mechanical properties, and thermal stability of thermoplastic poly(ether-urethane)s In this work thermoplastic poly(ether-urethane)s were synthesized by using polyols with a various molecular weight,...
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Weldability of pipe grade polyethylenes as realized from thermal and mechanical properties assessments
PublicationSince polyethylene (PE) has been widely accepted for the production of high-pressure fluid conveying pipelines, studies devoted to weldability of PE connections were always of major importance. In this study, two industrial PE grades designed for pipe production, namely PE80 and PE100, were injection molded, cut, and then welded as PE100-PE100, PE100-PE80, and PE80-PE80. The heat-welded joints were assessed by differential scanning...
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The advanced monitoring as a key factor for appropriate optimization and control of full-scale activated sludge systems – case study Debogorze WWTP.
PublicationComputer simulation has become a helpful tool in wastewater treatment systems performance and effectiveness analysis. Advanced monitoring, by using appropriate software, enables to create a mathematical model of a real wastewater treatment plant (WWTP), run a simulation and subsequently interpret results under various conditions. An operation of WWTP is usually controlled by global parameters such as flow, solids retention time,...
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Typing of Scopulariopsis and Microascus fungi by Random Amplified Polymorphic DNA (RAPD)
PublicationOBJECTIVES Scopulariopsis species and their teleomorphs of the genus Microascus are commonly isolated from soil, decaying plant material and indoor environments. Moreover, certain Scopulariopsis and Microascus species are recognised as opportunistic human pathogens. Although most species can be identified by detailed morphological study, phenotypic characters appear to overlap in several cases and morphology seems to be insufficient...