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Search results for: Molecular docking and simulation study
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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A numerical and experimental analysis of multi-hole orifice in turbulent flow
PublicationIn this research study, the comprehensive metrological analysis is investigated for a 4-hole orifice with module m = 0.25 installed in the pipeline with an internal diameter of 50 mm. A detailed numerical simulation was performed for the turbulence models: k-ε-realizable and k-ω-BSL. The novelties of the research include model validation by comparing the results of numerical studies with the experiment conducted in the area of...
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Constant vs. Variable Efficiency of Electric Drive in Train Run Simulations
PublicationTrain run simulations, which focus on various power- and energy-oriented aspects, should reflect the losses in the electric powertrain. In general, the powertrain efficiency varies with respect to load and speed. Including this relation in simulation requires knowledge about detailed drivetrain parameters, which are often unavailable. This paper verifies the possibility to approximate the drivetrain efficiency in train run simulations...
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Application of titanium dioxide thin films in fiber optic sensors
PublicationThe advance in the nanotechnology and fabrication of micro- and nanostructures has significant impact on development of new optical sensors. Presented study focuses on the applications of the titanium dioxide (TiO2) thin films in fiber optic sensors. The concept of a sensing fiber optic interferometer integrating TiO2 thin film is presented. The cavity of this interferometer is delimited by a 80 nm film fabricated on the end-face...
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Feasibility Study GaN Transistors Application in the Novel Split-Coils Inductive Power Transfer System with T-Type Inverter
PublicationA promising solution for inductive power transfer and wireless charging is presented on the basis of a single-phase three-level T-type Neutral Point Clamped GaN-based inverter with two coupled transmitting coils. The article focuses on the feasibility study of GaN transistor application in the wireless power transfer system based on the T-type inverter on the primary side. An analysis of power losses in the main components of the...
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Local response surface approximations and variable-fidelity electromagnetic simulations for computationally efficient microwave design optimisation
PublicationIn this study, the authors propose a robust and computationally efficient algorithm for simulation-driven design optimisation of microwave structures. Our technique exploits variable-fidelity electromagnetic models of the structure under consideration. The low-fidelity model is optimised using its local response surface approximation surrogates. The high-fidelity model is refined by space mapping with polynomial interpolation of...
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Earthquake-induced pounding between superstructure segments of isolated bridge
PublicationThe use of seismic isolation in bridges is considered as one of the most promising advanced technologies to enhance the structural safety during earthquakes. However, the method results in larger displacements of superstructure segments increasing the probability of pounding between them. Reports after severe ground motions show that the earthquake-induced structural pounding may lead to significant damage in isolated bridges....
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Comparison of Two Nonlinear Predictive Control Algorithms for Dissolved Oxygen Tracking Problem at WWTP
PublicationThe wastewater treatment plant is classified as a complex system, due to its nonlinear dynamics, large uncertainty of disturbance inputs, multiple time scales in the internal process dynamics, and multivariable structure. The aeration process, in turn, is an important and expensive part of wastewater treatment plant operation. All operating parameters of the aeration in biological processes are to be precisely controlled to provide...
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Cognitum Ontorion: Knowledge Representation and Reasoning System
Publication“If knowledge can create problems, it is not through ignorance that we can solve them.” (Isaac Asimov). Nevertheless, at any point of human activity, knowledge (besides practice) is a key factor in understanding and solving any given problem. Nowadays, computer systems have the ability to support their users in an efficient and reliable way. In this paper we present and describe the functionality of the Cognitum Ontorion system....
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Termination functions for evolutionary path planning algorithm
PublicationIn this paper a study of termination functions (stop criterion) for evolutionary path planning algorithm is presented. Tested algorithm is used to determine close to optimal ship paths in collision avoidance situation. For this purpose a path planning problem is defined. A specific structure of the individual path and fitness function is presented. For the simulation purposes a close to real tested environment is created. Five...
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Conducted emi identification in power electronic converters : modeling of EMI generation and propagation using circuit simulation and wiener filtering methods.
PublicationThis work presents the circuit simulations and the conventional signal processing technique (Wiener filtering) in order to reconstruct conducted ElectroMagnetic Interferences (EMI), generated and propagated in power electronics converters. In the simulation study, the most accurate presently available models of components of circuit have been used and improved. The proposed Wiener filtering method allows to identifying the transfer...
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Integrating modelling, simulation and data management tools to create a planning support system for the improvement of air quality by urban planning solutions
PublicationThe urbanization pressure requires urban planners, designers, and policy makers to be more responsive to the challenges related to improving the quality of the urban environment and the living conditions of the inhabitants. One of the many environmental issues that need to be taken into account is urban air pollution. As the process of urban ventilation and air pollution dis-persion is significantly affected by the urban layout,...
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Interpretation and modeling of emotions in the management of autonomous robots using a control paradigm based on a scheduling variable
PublicationThe paper presents a technical introduction to psychological theories of emotions. It highlights a usable ideaimplemented in a number of recently developed computational systems of emotions, and the hypothesis thatemotion can play the role of a scheduling variable in controlling autonomous robots. In the main part ofthis study, we outline our own computational system of emotion – xEmotion – designed as a key structuralelement in...
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Model Management for Low-Computational-Budget Simulation-Based Optimization of Antenna Structures Using Nature-Inspired Algorithms
PublicationThe primary objective of this study is investigation of the possibilities of accelerating nature-inspired optimization of antenna structures using multi-fidelity EM simulation models. The primary methodology developed to achieve acceleration is a model management scheme which the level of EM simulation fidelity using two criteria: the convergence status of the optimization algorithm, and relative quality of the individual designs...
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Full scale CFD seakeeping simulations for case study ship redesigned from V-shaped bulbous bow to X-bow hull form
PublicationIncreasing propulsion efficiency, safety, comfort and operability are of the great importance, especially for small ships operating on windy sites like the North Sea and the Baltic Sea. Seakeeping performance of ships and offshore structures can be analysed by different methods and the one that is becoming increasingly important is CFD RANS. The recent development of simulation techniques together with rising HPC accessibility...
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Numerical analysis of vacuum drying of a porous body in the integrated domain
Publicationn the present study, the vacuum drying process of an apple slice is numerically modeled based on a control volume method. Transient two-dimensional Navier– Stokes, energy, moisture, and Luikov equations are solved by numerical coding (Fortran) to simulate the simultaneous heat and mass transfer in the ambient and apple slice, respectively. The privilege of using Luikov's model is that the capillary forces are considered, and a...
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublicationCold active lipolytic enzymes are promising to replace the conventional enzymes processes of biotechnological industries. One of the most important feature of the cold-active lipases and esterases is that they offer economic benefits through energy saving. In general, they exhibit high activity at low temperatures and low thermostability at moderate temperatures. Lipolytic enzyme EstS9 was isolated from Pseudomonas sp. S9. A multiple...
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Relation of the polymorphism of cyp51A sequence and the susceptibility of Aspergillus fumigatus isolates to triazoles determined by commercial gradient test (Etest) and by reference methods
PublicationThe aim of this study was to evaluate the accuracy of commercial gradient test (Etest) in the detection of triazole resistant Aspergillus fumigatus isolates using reference microdilution methods and the analysis of sequences of the cyp 51A gene. The study was performed on twenty clinical isolates which were identified as Aspergillus fumigatus based on the DNA sequences of the ITS1-2 fragment of ribosomal DNA and the β-tubulin gene,...
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Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
PublicationThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives...
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Potential energy curves, transition and permanent dipole moments of KRb
PublicationWe present extensive calculations of 48 adiabatic potential energy curves of the KRb molecule. Efforts have been focused on preparing the appropriate basis sets. Compared to previous approaches, the set of new potential energy curves is extended to higher excitations, including the single-excited K(4s2S)+Rb(5d2D) and double-excited K(4p2P)+Rb(5p2P) atomic limits. Larger distances between nuclei are also taken into account. New...
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Dissociative ionization dynamics of dielectric gas C3F7CN
PublicationFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
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Non-volatile molecular composition and discrimination of single grape white of chardonnay, riesling, sauvignon blanc and silvaner using untargeted GC–MS analysis
PublicationThis study developed and applied a GC–MS method aiming at molecular fingerprinting of 120 commercial single grape white wines (Chardonnay, Riesling, Sauvignon Blanc and Silvaner) for possible authentication according to grape variety. The method allowed detection of 372 peaks and tentative identification of 146 metabolites including alcohols, organic acids, esters, amino acids and sugars. The grape variety effect explained 8.3%...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublicationThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Effect of Acetylation and Beta‐Amylase Treatment on Complexation of Debranched Starch with Naringenin
PublicationStarch inclusion complexation has been shown to improve solubility of water insoluble molecules. Potato starch and Hylon VII are acetylated at two levels and then debranched alone or combined with β‐amylase hydrolysis, and its complexes with naringenin are prepared in aqueous conditions and characterized in this study. Both soluble and insoluble complexes are formed with the soluble complex present in the supernatant and the insoluble...
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Aggregation of imidazoacridinones - spectroscopic and microcalorimetric approach
PublicationImidazoacridinones (IA) belong to a group of polycyclic heteroaromatic antitumor compounds. IA create the aggregated form in water solution. Self-association of substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules....
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Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin.
PublicationEnterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). Acquisition of resistance determinants not only seriously limits available therapeutic options but also increases available gene pool for other species. It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred...
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Simulation analysis of a production process with selected six sigma ratios
PublicationComputer technologies allow more and more to model as well as to perform simulation experiments of various processes. The simulation analysis provides a better understanding of the interdependencies between various stages of production processes.The results of simulation studies were presented, the aim of them was to show the opportunities of the analysis of the process according to the scenarios and variants developed in connection...
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Patch size setup and performance/cost trade-offs in multi-objective EM-driven antenna optimization using sequential domain patching
PublicationPurpose This paper aims to assess control parameter setup and its effect on computational cost and performance of deterministic procedures for multi-objective design optimization of expensive simulation models of antenna structures. Design/methodology/approach A deterministic algorithm for cost-efficient multi-objective optimization of antenna structures has been assessed. The algorithm constructs a patch connecting extreme Pareto-optimal...
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Simulation Environment in Python for Ship Encounter Situations
PublicationTo assess the risk of collision in radar navigation distance-based safety measures such as Distance at the Closest Point of Approach and Time to the Closest Point of Approach are most commonly used. Also Bow Crossing Range and Bow Crossing Time measures are good complement to the picture of the meeting situation. When ship safety domain is considered then Degree of Domain Violation and Time to Domain Violation can be applied. This...
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Neural modelling of dynamic systems with time delays based on an adjusted NEAT algorithm
PublicationA problem related to the development of an algorithm designed to find an architecture of artificial neural network used for black-box modelling of dynamic systems with time delays has been addressed in this paper. The proposed algorithm is based on a well-known NeuroEvolution of Augmenting Topologies (NEAT) algorithm. The NEAT algorithm has been adjusted by allowing additional connections within an artificial neural network and...
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Assessment of wastewater quality indicators for wastewater treatment influent using an advanced logistic regression model
PublicationInfluent quality indicators play a significant role in wastewater treatment plant performance due to their correlation with reactor operations and effluent quality. However, selecting a specific/best parameter indicator for predicting influent wastewater quality is one of the challenges in wastewa- ter treatment. This study, therefore, focused on determining suitable variables as influent quality indicators. For this purpose, a...
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Computer Supported Analysis of the Human Body Surface Area
PublicationRecent scientific studies show the growing importance of the coefficients: BSA and TBSA, as an alternative to the widely used BMI. The relevant indicators are widely used in medicine, including such areas as: the treatment of burns, chemotherapy, dermatology and toxicology; as benchmarks when calculating doses of drugs and fluids. The particular problems concerning this subject are: the change of the reference parameter value which...
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Modelling of residential sales price with kriging using different distance metrics in different correlation functions
PublicationThe modelling and estimation of sales prices based on economical conditions are important for housing sector especially in developing countries. Analysts are focused on the subject to analyze price movements and estimate the future trend of the sales prices for housing sector. In this study, we tried to generate a robust and efficient model related to the subject. Firstly, we investigated economic variables affecting housing sales...
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Cognitum Ontorion: Knowledge Representation and Reasoning System
PublicationAt any point of human activity, knowledge and expertise are a key factors in understanding and solving any given problem. In present days, computer systems have the ability to support their users in an efficient and reliable way in gathering and processing knowledge. In this chapter we show how to use Cognitum Ontorion system in this areas. In first section, we identify emerging issues focused on how to represent and inference...
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The process generation of WWTP models for optimization of activated sludge systems
PublicationThe objective of water and wastewater utilities, which are responsible for optimization of wastewater treatment plant operation, is threefold: environmental protection, saving money, and mitigation of pollutant emissions, both to water and air. The performed study aimed to assess the process generation of WWTP models that improve activated sludge systems operation, by means of new developed Mantis2 model. This model accounts for...
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Expedited Design Closure of Antennas By Means Of Trust-Region-Based Adaptive Response Scaling
PublicationIn the letter, a reliable procedure for expedited design optimization of antenna structures by means of trust-region adaptive response scaling (TR-ARS) is proposed. The presented approach exploits two-level electromagnetic (EM) simulation models. A predicted high-fidelity model response is obtained by applying nonlinear frequency and amplitude correction to the low-fidelity model. The surrogate created this way is iteratively rebuilt...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...
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A multiparameter simulation-driven analysis of ship response when turning concerning a required number of irregular wave realizations
PublicationThe growing implementation of Decision Support Systems on modern ships, digital-twin technology, and the introduction of autonomous vessels cause the marine industry to seek accurate modeling of vessel response. Despite the contemporary 6DOF models can be used to predict ship motions in irregular waves, the impact of their stochastic realization is usually neglected and remains under-investigated. Especially in the case of turning, differences...
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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublicationOver the past few years, metal halide perovskite solar cells have made significant advances. Currently, the single-junction perovskite solar cells reach a conversion efficiency of 25.7%. Perovskite solar cells with a wide band gap can also be used as top absorber layers in multi-junction tandem solar cells. We examined the dynamical and thermal stability, electronic structure, and optical features of In2PtX 6 (X = Cl, Br, and I)...
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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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Design of novel highly sensitive sensors for crack detection in metal surfaces: theoretical foundation and experimental validation
PublicationThe application of different types of microwave resonators for sensing cracks in metallic structures has been subject of many studies. While most studies have been focused on improving the sensitivity of planar crack sensors, the theoretical foundation of the topic has not been treated in much detail. The major objective of this study is to perform an exhaustive study of the principles and theoretical foundations for crack sensing...
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Particle Swarm Optimization Based Optimal Design of Six-Phase Induction Motor for Electric Propulsion of Submarines
PublicationAbstract: Recent research reveals that multi-phase motors in electric propulsion systems are highly recommended due to their improved reliability and efficiency over traditional three phase motors. This research presented a comparison of optimal model design of a six phase squirrel cage induction motor (IM) for electric propulsion by using Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). A six phase squirrel cage induction...
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The Effects of Pin Profile on HDPE Thermomechanical Phenomena during FSW
PublicationFriction stir welding (FSW) of polymeric materials has recently attracted significant attention. Herein, we present the effect of the tool pin profile on the FSW of high-density polyethylene (HDPE) joints through joint experimental analysis and thermomechanical simulations. For analysis of pin profile effects on the thermomechanical properties of HDPE joints, frustum (FPT), cubic (CPT), and triangular (TPT) pin shapes were selected...
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Simulation of the number of storm overflows considering changes in precipitation dynamics and the urbanisation of the catchment area: a probabilistic approach
PublicationThis paper presents a probabilistic methodology that allows the study of the interactions between changes in rainfall dynamics and impervious areas in urban catchment on a long- and short-term basis. The proposed probabilistic model predict future storm overflows while taking into account the dynamics of changes in impervious areas and rainfall. In this model, a logistic regression method was used to simulate overflow resulting...
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Combining X-ray tomogrpahy imaging and DEM simulations to investigate granular material flow during silo discharging
PublicationEven after few decades of research, the study of particle motion taking place during silo discharging hasn’t been fully addressed, both experimentally and numerically, because of nontrivial behaviors that occur during associated flow patterns. For instance, discrete element method (DEM) has shown good qualitative prediction potential of velocity profile, but, on the other hand, frequently failed to match quantitatively experimental...
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Research of Emergency Modes of Wind Power Plants Using Computer Simulation
PublicationThe aim of this study is to investigate changes in the wind power plant energy production parameters under the conditions of sudden wind changes and voltage drop. To achieve these goals, a simulation of operation of wind power plants was performed. Twelve wind turbines with variable rotational speed equipped with a Fuhrländer FL 2500/104 asynchronous double-fed induction generator (DFIG) were used, each with an installed capacity...
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Particle Swarm Optimization Based Optimal Design of Six-Phase Induction Motor for Electric Propulsion of Submarines
PublicationRecent research reveals that multi-phase motors in electric propulsion systems are highly recommended due to their improved reliability and efficiency over traditional three phase motors. This research presented a comparison of optimal model design of a six phase squirrel cage induction motor (IM) for electric propulsion by using Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). A six phase squirrel cage induction...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublicationThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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Silver(I) complexes with nitrile ligands: New materials with versatile applications
PublicationIn the present study, the structure, thermal stability, conductive properties, and antimicrobial activity of silver(I) complexes with nitrile ligands were investigated. For the construction of the materials, 2-cyanopyridine (2-cpy), 4-cyanopyridine (4-cpy), 1,2-dicyanobenzene (1,2-dcb), and 1,3-dicyanobenzene (1,3-dcb) were used in addition to the silver nitrite and nitrate. Four new compounds were isolated and structurally characterized:...