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Search results for: MOLECULAR-ORBITAL METHODS
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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublicationAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
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Methods of selenium supplementation. Bioavability and determination of selenium compounds
PublicationIn This paper the method of supplementation of selenium in the environment and analytical methods of determining selenium were described
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Machine-Learning Methods for Estimating Performance of Structural Concrete Members Reinforced with Fiber-Reinforced Polymers
PublicationIn recent years, fiber-reinforced polymers (FRP) in reinforced concrete (RC) members have gained significant attention due to their exceptional properties, including lightweight construction, high specific strength, and stiffness. These attributes have found application in structures, infrastructures, wind power equipment, and various advanced civil products. However, the production process and the extensive testing required for...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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OVERALL SET OF BANDSAW TEETH VERSUS METHODS OF MEASUREMENTS
PublicationThis article deals with the impact of the manual methods of measurement on the overall set measurement results. It describes the results of the measurement of bandsaw teeth kerf with the use of a micrometer and a digital calliper. It is commonly known that the cutting process causes the wear of cutting tools. The wear of the cutting edge depends on the cutting conditions as well as on the mechanical properties of the processed...
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublicationExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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The Verification of the Usefulness of Electronic Nose Based on Ultra-Fast Gas Chromatography and Four Different Chemometric Methods for Rapid Analysis of Spirit Beverages
PublicationSpirit beverages are a diverse group of foodstuffs. They are very often counterfeited which cause the appearance of low quality products or wrongly labelled products on the market. It is important to find a proper quality control and botanical origin method enabling the same time preliminary check of the composition of investigated samples, which was the main goal of this work. For this purpose, the usefulness of electronic nose...
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Identification of ship’s hull mathematical model with numerical methods
PublicationThe modern maritime industry is moving toward the development of technology that will allow for full or partial autonomy of ship operation. This innovation places high demands on ship performance prediction techniques at the design stage. The researchwork presented in the article is related to the design stage of the ship and concerns methods for prognosis and evaluation of the specific operational condition of the ship, namely...
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ANALYSIS OF EFFECTIVENESS AND COMPUTATIONAL COMPLEXITY OF TREND REMOVAL METHODS
PublicationThe paper presents a method of processing measurement data due to remove slowly varying component of the trend occurring in the recorded waveforms. Comparison of computational complexity and trend removal efficiency between some commonly used methods is presented. The impact of these procedures on probability distribution and power spectral density is shown. Effectiveness and computational complexity of these methods depend essentially...
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Novel analysis methods of dynamic properties for vehicle pantographs
PublicationTransmission of electrical energy from a catenary system to traction units must be safe and reliable especially for high speed trains. Modern pantographs have to meet these requirements. Pantographs are subjected to several forces acting on their structural elements. These forces come from pantograph drive, inertia forces, aerodynamic effects, vibration of traction units etc. Modern approach to static and dynamic analysis should...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Analytical Methods for Causality Evaluation of Photonic Materials
PublicationWe comprehensively review several general methods and analytical tools used for causality evaluation of photonic materials. Our objective is to call to mind and then formulate, on a mathematically rigorous basis, a set of theorems which can answer the question whether a considered material model is causal or not. For this purpose, a set of various distributional theorems presented in literature is collected as the distributional...
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Prediction of Weld Deformations by Numerical Methods - Review
PublicationThe welding process is the basic technique of joining in the shipbuilding industry. This method generates welding distortions that cause a lot of problems during the manufacturing process due to both the time and cost of straightening as well as their influence on later stages of production. Proper preparation of welding processes plays a growing role in the shipbuilding industry and the development of calculating tools is being...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublicationThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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METHODS OF TEACHING NOISE PROTECTION AT ENVIRONMENTAL ENGINEERING
PublicationNoise strongly influences both our health and behavior in everyday life and as employees or employers. The lost of hearing and other effects of noise on humans result not only in a significant decrease in the quality of life or work efficiency but have also have economic consequences. As noise can be preventable in part by the Environmental Engineers, but it is necessary to introduce them noise issues during their education process....
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Measurement methods for assessing insulation condition of underground pipelines
PublicationThe paper discusses the most frequently applied measurement methods for assessing the quality of external insulation along pipelines and detecting defect locations in the protective coating. The quality of coating along a given pipeline section under investigation is assessed by determining unitary resistance of the coating, which is calculated on the basis of measurement results obtained along a pipeline subjected to cathodic...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Spectroscopic, molecular docking and molecular dynamic simulation studies on the complexes of β-lactoglobulin, safranal and oleuropein
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Review of Selected Methods for Prediction of Added Resistance in Following Waves
PublicationThe added resistance in waves is a mean value of non-linear, second order reaction of a ship to incoming waves. In the beginning of the 20th century, the experimental methods for investigation of ship hydrodynamics at model scale were developed. They allowed the evaluation of added resistance by measurements in irregular waves (directly) or by measurements in regular waves (in-direct method). The main goal was to find more precise...
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Applicability of Emotion Recognition and Induction Methods to Study the Behavior of Programmers
PublicationRecent studies in the field of software engineering have shown that positive emotions can increase and negative emotions decrease the productivity of programmers. In the field of affective computing, many methods and tools to recognize the emotions of computer users were proposed. However, it has not been verified yet which of them can be used to monitor the emotional states of software developers. The paper describes a study carried...
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Employing economical methods for pavement defects estimation
PublicationIt is a common practise that measurements of road surface conditions are made using professional and expensive apparatus. Typically a van or a truck equipped with a set of professional sensors i.e. laser scanners of surface is used, therefore the measurement update period is often quite long. Two alternative low-cost methods for estimating road pavement defects and failures were proposed and investigated by the authors. The first...
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Convergence of rational multistep methods of of Adams-Padé type
PublicationRational generalizations of multistep schemes, where the linear stiff part of a given problem is treated by an A-stable rational approximation, have been proposed by several authors, but a reasonable convergence analysis for stiff problems has not been provided so far. In this paper we directly relate this approach to exponential multistep methods, a subclass of the increasingly popular class of exponential integrators. This natural,...
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Economical methods for measuring road surface roughness
PublicationTwo low-cost methods of estimating the road surface condition are presented in the paper, the first one based on the use of accelerometers and the other on the analysis of images acquired from cameras installed in a vehicle. In the first method, miniature positioning and accelerometer sensors are used for evaluation of the road surface roughness. The device designed for installation in vehicles is composed of a GPS receiver and...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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A review of phosphorus recovery methods at various steps of wastewater treatment and sewage sludge management. The concept of “no solid waste generation” and analytical methods
PublicationPhosphorus deposits around the world are rapidly depleting, therefore phosphorus recovery methods are gaining more and more interest both in science and industry. This article presents the main methods of phosphorus recovery from sewage sludge. The described approaches are divided in two groups: phosphorus recovery from sewage sludge and leachate, and recovery of phosphorus from sewage sludge ashes. The latter seems to have more...
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Computational Methods for Liver Vessel Segmentation in Medical Imaging: A Review
PublicationThe segmentation of liver blood vessels is of major importance as it is essential for formulating diagnoses, planning and delivering treatments, as well as evaluating the results of clinical procedures. Different imaging techniques are available for application in clinical practice, so the segmentation methods should take into account the characteristics of the imaging technique. Based on the literature, this review paper presents...
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Displacement piles - classification and methods for the calculation of bearing capacity.
PublicationDisplacement piles belong to a group of technologies whose main idea is to install or make a pile without extracting ground material. According to definition, contained in PN-EN:1997-1:2008, displacement piles should be considered as driven, pressed in using vibrators and made with the use of spread augers. The classification of piles used so far with regard to the technology of execution is modified. An additional element is the...
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Affective computing and affective learning – methods, tools and prospects
PublicationEvery teacher knows that interest, active participation and motivation are important factors in the learning process. At the same time e-learning environments almost always address only the cognitive aspects of education. This paper provides a brief review of methods used for affect recognition, representation and processing as well as investigates how these methods may be used to address affective aspect of e-education. The paper...
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Use of Sensory Analysis Methods to Evaluate the Odor of Food and Outside Air
PublicationSensory analysis is applied in many areas of daily life. It is used to carry out the sensory evaluation of foodstuffs or other products and to evaluate the properties of odors present in the environment. The authors attempt to summarize the knowledge on the classification and application of sensory analysis methods to evaluate the odor nuisance of air, which allows the identification of sensory impressions and determination of...
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Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
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Methods of Assessing Degradation of Supercapacitors by Using Various Measurement Techniques
PublicationThis article presents the qualitative analyses of the construction of supercapacitor samples. The analyses are based on the suggested thermographic measurements as well as the technique of testing the inherent noise of the investigated element. The indicated assessment methods have been referred to the currently used parameters for the qualitative evaluation of supercapacitors. The approach described in this paper, which introduces...
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Quaternion encryption methods for multimedia transmission, a survey of existing approaches
PublicationIn this paper we review quaternion encryption methods for multimedia transmission. We explain their weak and strong properties as well as suggest possible modifications. Our main focus is an algorithm QFC presented in paper by Dzwonkowski et al. (2015). All encryption methods, presented in this paper, use special properties of quaternions to perform rotations of data sequences in 3D space. Each method uses a common key generation...
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New Peptide Based Fluconazole Conjugates with Expanded Molecular Targets
PublicationInfections of Candida spp. etiology are frequently treated with azole drugs. Among azoles, the most widely used in the clinical scenario remains fluconazole (FLC). Promising results in treatment of dangerous, systemic Candida infections demonstrate the advantages of combined therapies carried out with combinations of at least two different antifungal agents. Here, we report five conjugates composed of covalently linked FLC and...
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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Study on Methods to Control Interstory Deflections
PublicationOne of the possibilities to prevent building pounding between two adjacent structures is to consider appropriate in-between separation distance. Another approach might be focused on controlling the relative displacements during seismic excitations. Although the majority of building codes around the world recommend the use of some equations of various distances between structures to avoid pounding; a lot of reports after earthquakes...
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Revision of Biological Methods for Determination of EDC Presence and Their Endocrine Potential
PublicationEndocrine-disrupting compounds (EDC) are chemicals responsible for disturbances in the hormonal balance of organisms. This group of chemicals includes both egzogenic and endogenic substances or their mixtures that impact functioning of natural hormones in organisms. In the available literature one can find information on the application of chromatographic and related techniques in the analysis of environmental samples for detection,...
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Interactions of N-alkyl-N-methylmorpholinium based ionic liquids with acetonitrile studied by density and velocity of sound measurements and molecular dynamics simulations
PublicationMorpholinium-based ionic liquids (ILs) and their mixtures with polar co-solvents are an interesting class of emerging electrolytes in electrochemistry that is relatively poorly studied. In this work, densities and sound velocities of four ILs, N-ethyl-N-methylmorpholinium tetrafluoroborate, N-butyl-N-methylmorpholinium tetrafluoroborate, N-octyl-N-methylmorpho-linium tetrafluoroborate and N-decyl-N-methylmorpholinium tetrafluoroborate...
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublicationThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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The Examination of the Upper Layers of the Seabed by the Means of the Acoustic Methods
PublicationPropagation of acoustic waves in the sea, in particular in shallow sea, depends on several factors. The basic of them are source power and frequency of acoustic waves, spatial distribution inhomogeneous medium in which acoustic wave propagates, and distributions of speed of sound and density of seawater. The coastal conditions, which limit water medium from above (free surface of the sea) and from bottom (the seabed), are no less...
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Reconstruction of 3D structure of positive corona streamer by local methods
PublicationThe computer algorithms were used for reconstruction of streamer 3D structure. We propose the 3D tree structure model of corona discharge streamer composed with nodes and edges between chosen couples of nodes, which enables easy computation of some important parameters ofstreamers. The 3D model can be derived directly from two projection images by global methods like evolutionary searching or particle simulations. In this paper...
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Hip endhoprothesis development using rapid prototyping methods
PublicationIntegrated product development based on Rapid Prototyping methods, connected with computer aided 3D design and computer aided engineering enables fast and full new product verification and validation. A case study derived from clinical and technological practice using hip implant construction is also included.
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublicationPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Classification methods and criteria
PublicationKlasyfikacja akustyczna dna morskiego jest najnowszą metodologią zaprojektowaną w celu zdalnego wykrywania rozmaitych charakterystyk dna morskiego z informacji zawartych w echch od dna akustycznych impulsów transmitowanych z różnego typu sonarów. Poza szególnymi chrakterystykami sprzętowymi każdego systemu ASC, istotą każdej metody jest klasyfikacja modułu, który wyciąga serie cech z echa sygnału i przetwarza je aby posortować...