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Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Modeling Volunteer Based Systems
PublicationThere are two main approaches to processing tasks requiring high amounts of computational power. One approach is using clusters of mostly identical hardware, placed in dedicated locations [1, 2, 3]. The other approach is outsourcing computing resources from large numbers of volunteers connected to the Internet [7]. This chapter presents an application of a mathematical model of the volunteer computing presented in Volume 1 of this...
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Usability of UML modeling tools
PublicationNarzędzia wspomagające modelowanie w UML pełnią istotną rolę w procesie wytwarzania i utrzymania oprogramowania. Badanie użyteczności tych narzędzi ma na celu poprawę produktywności oraz satysfakcji z ich użytkowania. W referacie zaprezentowano badania użyteczności za pomocą trzech metod: eksperymentalnego testowania efektywności, zapytań o aspekty użyteczności testowanych narzędzi oraz analitycznej metody GOMS (ang. Goals, Operators,...
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Mathematical Modeling of Ice Thrusting on the Shore of the Vistula Lagoon (Baltic Sea) and the Proposed Artificial Island
PublicationCoastal lagoons are inland and shallow water bodies, separated from the ocean by a barrier. In cold regions, ice phenomena in shallow water coastal lagoons occur every winter season. Ice is predominantly formed on the surface due to density stratification and surface cooling. The ice dynamics in such areas are dominantly affected by winds. Water dynamics also cause ice movement, but due to the large areal scale of lagoons, the...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublicationIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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Accurate Modeling of a Lossy Ferrite Circular Guide Section Magnetized Through a Rotary Four-Pole Magnetic Field
PublicationKorzystając z metody rodzajów sprzężonych opracowano model matematyczny umożliwiający określenie parametrów falowych i rozkładów pola em. fal występujących w ferrytowym falowodzie cylindrycznym magnesowanym czterobiegunowym polem magnetycznym. W oparciu o model określono macierz rozproszenia sekcji falowodu. Opracowane oprogramowanie pozwoliło na zbadanie charakterystyk częstotliwościowych sekcji ferrytowej i wskazanie możliwości...
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On Accuracy Modeling of Gas Turbine Cycles by the In-house COM-GAS Code
PublicationIn this paper, a comparison of accuracy modeling of gas turbine cycles between the basic (classical) model and the in-house COM-GAS code has been presented. The basic model uses a semi-perfect gas and well known projecting assumption. On the other hand, the computational flow mechanics (CFM) basis on a real gas by using thermodynamic tables. The thermodynamic analysis of thermal cycles, simply gas cycle GT8C and gas turbine cycle...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: Their in silico assessment as potential ligands for N-protein of SARS-CoV-2
PublicationIn view of recent global pandemic the 3-alkynyl substituted 2-chloroquinoxaline framework has been explored as a potential template for the design of molecules targeting COVID-19. Initial in silico studies of representative compounds to assess their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2 prompted further study of these molecules. Thus building of a small library of...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Modeling of truss with cold-formed section and positive eccentricity in the node
PublicationThis work is dedicated to establishing the load carrying capacity of tensed and compressed truss’ nodes made of cold-formed open cross sections. The occurrence of bending in the truss’ nodes is the result of a specific production technology for system lattice girders assumed by the designer and the producer. The aim of this research is to present the methodology of conduct for creation of computational models that best depict the...
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Cost-Efficient Two-Level Modeling of Microwave Passives Using Feature-Based Surrogates and Domain Confinement
PublicationA variety of surrogate modelling techniques has been utilized in high-frequency design over the last two decades. Yet, the curse of dimensionality still poses a serious challenge in setting up re-liable design-ready surrogates of modern microwave components. The difficulty of the model-ing task is only aggravated by nonlinearity of circuit responses. Consequently, constructing a practically usable surrogate model, valid across...
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Reduced-cost surrogate modeling of input characteristics and design optimization of dual-band antennas using response features
PublicationIn this article, a procedure for low-cost surrogate modeling of input characteristics of dual-band antennas has been discussed. The number of training data required for construction of an accurate model has been reduced by representing the antenna reflection response to the level of suitably defined feature points. The points are allocated to capture the critical features of the reflection characteristic, such as the frequencies...
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3D Hand Shape Modeling for Automatic Assessing Motor Performance in Parkinson's Disease
PublicationIn this paper a method for hand pattern processing to create a 3D hand model is presented. By applying a complete hand armature to the model obtained, an interpolation of three motor tests for an individual Parkinson's disease patient can be performed. To obtain the 3D hand model the top view of the hand from a web cam is analyzed. The hand contour is examined to find characteristic points that allows for dividing hand image into...
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Molecular dynamics-based model of VEGF-A and its heparin interactions
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Novel approach to modeling spectral-domain optical coherence tomography with Monte Carlo method
PublicationNumerical modeling Optical Coherence Tomography (OCT) systems is needed for optical setup optimization, development of new signal processing methods and assessment of impact of different physical phenomena inside the sample on OCT signal. The Monte Carlo method has been often used for modeling Optical Coherence Tomography, as it is a well established tool for simulating light propagation in scattering media. However, in this method...
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Building Information Modeling in Small and Middle Sized Buildings – Case Study
PublicationBuilding Information Modeling (BIM) is a technology designed to improve and integrate all engineering aspects in the construction design process. Tools that incorporate the idea of BIM are becoming more advanced and also more popular. Available software solutions have already reached an assumable high level of development, but still are not as widespread and used on nearly as many construction projects as could be expected. Therefore...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Processing of point cloud data retrieved from terrestrial laser scanning for structural modeling by Finite Element Method
PublicationFinite Element Method is one most popular contemporary method of strength analysis. The method is an advanced method for solving differential equations, based on discretization, which means that area is divided into finite elements. Each finite element has a solution of the equation approximated by specific functions and performing the actual calculations only for nodes of this division. Finite Element Method is widely used in...
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The experimental evaluation and modeling of SBR removing nutrients under varied aeration conditions
PublicationSequencing batch reactors (SBR) are mainly characterized by sequential process phases of fill, react, settle, decant and idle periods that allow considerable flexibility in the design and operation in different conditions. This flexibility and the unique features of SBRs used to wastewater treatment by activated sludge systems operated in laboratory scale, allow not only conducting experiments for the standard conditions but also...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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On dynamic modeling of piezomagnetic/flexomagnetic microstructures based on Lord–Shulman thermoelastic model
PublicationWe study a time-dependent thermoelastic coupling within free vibrations of piezomagnetic (PM) microbeams considering the flexomagnetic (FM) phenomenon. The flexomagneticity relates to a magnetic field with a gradient of strains. Here, we use the generalized thermoelasticity theory of Lord–Shulman to analyze the interaction between elastic deformation and thermal conductivity. The uniform magnetic field is permeated in line with...
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Understanding the Ukrainian Migrants Challenges in the EU: A Topic Modeling Approach
PublicationConfronted with the aggression against Ukraine in 2022, Europe faces one of the most important humanitarian challenges - the migration of war refugees from Ukraine, most of them women with children and the elderly. Both international institutions such as the European Union and the United Nations, but also national governments and, above all, local governments, which are the main providers of services and resources for refugees,...
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Operational Enhancement of Numerical Weather Prediction with Data from Real-time Satellite Images
PublicationNumerical weather prediction (NWP) is a rapidly expanding field of science, which is related to meteorology, remote sensing and computer science. Authors present methods of enhancing WRF EMS (Weather Research and Forecast Environmental Modeling System) weather prediction system using data from satellites equipped with AMSU sensor (Advanced Microwave Sounding Unit). The data is acquired with Department of Geoinformatics’ ground...
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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Modeling of the Two-Dimensional Flow Caused by Sea Conditions and Wind Stresses on the Example of Dead Vistula
PublicationThe article presents the results of two-dimensional modeling of flows caused by the sea conditions and wind stresses on the example of Dead Vistula. Based on the available bathymetric data, a numerical model of the river section was created, which was supplemented with data on the position of the water table depending on hydrometeorological conditions. To describe the flow field in steady conditions, a simplified model of two-dimensional...
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How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure–Property Relationship Modeling of Nanofluids
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Structure–activity relationships study on biological activity of peptides as dipeptidyl peptidase IV inhibitors by chemometric modeling
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Design-Oriented Two-Stage Surrogate Modeling of Miniaturized Microstrip Circuits with Dimensionality Reduction
PublicationContemporary microwave design heavily relies on full-wave electromagnetic (EM) simulation tools. This is especially the case for miniaturized devices where EM cross-coupling effects cannot be adequately accounted for using equivalent network models. Unfortunately, EM analysis incurs considerable computational expenses, which becomes a bottleneck whenever multiple evaluations are required. Common simulation-based design tasks include...
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Improved Modeling of Microwave Structures Using Performance-Driven Fully-Connected Regression Surrogate
PublicationFast replacement models (or surrogates) have been widely applied in the recent years to accelerate simulation-driven design procedures in microwave engineering. The fundamental reason is a considerable—and often prohibitive—CPU cost of massive full-wave electromagnetic (EM) analyses related to solving common tasks such as parametric optimization or uncertainty quantification. The most popular class of surrogates are data-driven...
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On Inadequacy of Sequential Design of Experiments for Performance-Driven Surrogate Modeling of Antenna Input Characteristics
PublicationDesign of contemporary antennas necessarily involves electromagnetic (EM) simulation tools. Their employment is imperative to ensure evaluation reliability but also to carry out the design process itself, especially, the adjustment of antenna dimensions. For the latter, traditionally used parameter sweeping is more and more often replaced by rigorous numerical optimization, which entails considerable computational expenses, sometimes...
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Molecular dynamics simulation of polymerization of p-xylylene
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Resonance microstrip structure with patch of arbitrary convex geometry with the use of field matching technique
PublicationAn analysis of the resonance frequency problem of planar microstrip structure with patch of arbitrary convex geometry is presented. A full-wave analysis is employed utilizing a combination of Galerkin’s moment method and field matching technique. In this approach, a field matching technique is adopted to calculate the patch surface current densities, and next the method of moments is utilized to calculate resonance frequencies...
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Dynamic Modeling of COVID-19 Disease with Impact of Lockdown in Pakistan and Malaysia
PublicationBeing researchers, it is an utmost responsibility to provide insight on social issues thus, this work addresses the dynamic modeling of first and most contagious disease named as COVID-19 caused by coronavirus. The first case of COVID-19 appeared in Pakistan was on 26th February 2020 and in Malaysia on 27th February 2020; both patients had foreign travel history. In the paper, the number of total affected cases and total deaths...
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Three-dimensional modeling and automatic analysis of the human nasal cavity and paranasal sinuses using the computational fluid dynamics method
PublicationPurpose The goal of this study was to develop a complete workflow allowing for conducting computational fluid dynam- ics (CFD) simulation of airflow through the upper airways based on computed tomography (CT) and cone-beam computed tomography (CBCT) studies of individual adult patients. Methods This study is based on CT images of 16 patients. Image processing and model generation of the human nasal cavity and paranasal sinuses...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Recent Advances in Accelerated Multi-Objective Design of High-Frequency Structures using Knowledge-Based Constrained Modeling Approach
PublicationDesign automation, including reliable optimization of engineering systems, is of paramount importance for both academia and industry. This includes the design of high-frequency structures (antennas, microwave circuits, integrated photonic components), where the appropriate adjustment of geometry and material parameters is crucial to meet stringent performance requirements dictated by practical applications. Realistic design has...
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Rigid finite elements and multibody modeling in analyses of a robot shaped elastic/plastic deformations of a beam
PublicationDynamics analysis of a system composed of a parallel manipulator and of an elastic beam is presented in the paper. Classic 3RRR parallel manipulator is considered and used to deform the beam. Elasto-plastic deformations are investigated. Rigid-finite-elements technique is employed to deal with dynamics of the beam. A multibody structure is associated with the introduced hybrid system in order to model its dynamics. Idea of the...
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Achieving Efficient and Stable Deammonification at Low Temperatures—Experimental and Modeling Studies
PublicationThe short-term effects of temperature on deammonification sludge were evaluated in a laboratory-scale sequencing batch reactor (SBR). Mathematical modeling was used for further evaluations of different intermittent aeration strategies for achieving high and stable deammonification performance at decreasing temperatures. As for the biomass cultivated at high temperatures (e.g., 30 C), a higher temperature dependency (the adjusted...
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The protocol for using elastic wall model in modeling blood flow within human artery
PublicationMedical diagnostic tools will play a major role in the future for an effective patient treatment and reduction their mortality, related to the cardiovascular system diseases (CVDs). There is an urgent need for developing diagnostic procedure to be robust, reliable, accurate and efficient, in the framework of a paradigm shift. Application of numerical techniques is seen as a perspective tool for such purpose. Nevertheless, existing...
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Optical method supported by machine learning for dynamics of C‐reactive protein concentrations changes detection in biological matrix samples
PublicationIn this article we present the novel spectroscopy method supported with machine learning for real-time detection of infectious agents in wastewater. In the case of infectious diseases, wastewater monitoring can be used to detect the presence of inflammation biomarkers, such as the proposed C-reactive protein, for monitoring inflammatory conditions and mass screening during epidemics for early detection in communities of concern,...
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Comparative molecular modelling of biologically active sterols
PublicationMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study
PublicationThe ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of...
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Weather Hazard Avoidance in Modeling Safety of Motor-Driven Ship for Multicriteria Weather Routing
PublicationWeather routing methods find the most suitable ocean?s route for a vessel, taking into account changeable weather conditions and navigational constraints. In the multicriteria approach based on the evolutionary SPEA algorithm one is able to consider a few constrained criteria simultaneously. The approach applied for a ship with hybrid propulsions has already been presented by one of the authors on previous TransNav?2009. This time...
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Rapid Design of 3D Reflectarray Antennas by Inverse Surrogate Modeling and Regularization
PublicationReflectarrays (RAs) exhibit important advantages over conventional antenna arrays, especially in terms of realizing pencil-beam patterns without the employment of the feeding networks. Unfortunately, microstrip RA implementations feature narrow bandwidths, and are severely affected by losses. A considerably improved performance can be achieved for RAs involving grounded dielectric layers, which are also easy to manufacture using...
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Modeling of Surface Roughness in Honing Processes by UsingFuzzy Artificial Neural Networks
PublicationHoning processes are abrasive machining processes which are commonly employed to improve the surface of manufactured parts such as hydraulic or combustion engine cylinders. These processes can be employed to obtain a cross-hatched pattern on the internal surfaces of cylinders. In this present study, fuzzy artificial neural networks are employed for modeling surface roughness parameters obtained in finishing honing operations. As...
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Modeling N2O behavior during denitrification with different carbon sources and electron acceptors
PublicationA mathematical model was developed for identification of the most important mechanism leading to nitrous oxide (N2O) accumulation in denitrifying activated sludge systems. The activated sludge model No. 2d (ASM2d) was extended to include intermediate three steps of the denitrification process. The formation and accumulation of nitric oxide (NO) was assumed to be very low in the performed laboratory experiments. These experiments...
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On dynamics of the question mark shell structure
PublicationW pracy prezentuje się problemy analizy dynamicznej nieregularnej konstrukcji powłokowej na przykładzie powłoki w kształcie znaku zapytania. Badania oparto na sześcioparametrowej nieliniowej teorii powłok, która pozwala na dyskretyzację modelu metodą elementów skończonych zawierających sześć stopni swobody w węźle. Ta teoria daje możliwość poprawnego modelowania nieregularności oraz rozgałęzień i ortogonalnych przecięć, jak również...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublicationWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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Modeling by finite element methods of impact of erosion on frequency of normal modes of L-0 blade
PublicationAfter some time of exploitation steam turbine rotors blades in energetic industry they are being eroded and also their frequency of normal modes is changed. Those changes can cause to unwanted shift of blades normal mode frequencies. It is necessary to find quick method of rating changes of frequency in connection of mass loss due erosion. The evaluation of this dependence was made by finite element modeling method using HyperWorks...