Search results for: MESH MORPHING
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublicationOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics
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Molecular basis of TRF proteins and their interactions with peptides
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Structural analysis and predicting effects of natural mutations on telomerase
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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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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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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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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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Multi-objective design of miniaturized impedance transformers by domain segmentation
PublicationFast multi-objective design optimization of compact microstrip impedance transformers is discussed. Our approach exploits approximation models constructed using sampled coarse- mesh EM simulation data in a partitioned design space and response correction techniques for design refinement. Demonstra
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Architektura bezpieczeństwa systemu netBaltic
PublicationW artykule zaprezentowano założenia dotyczące zabezpieczania węzłów sieci realizowanej w ramach systemu netBaltic. Ze względu na dużą różnorodność rozważanych mechanizmów komunikacyjnych architektura bezpieczeństwa została podzielona na kilka elementów – infrastrukturę klucza publicznego (PKI), bezpieczeństwo systemowe węzłów, zabezpieczanie komunikacji w modelu samoorganizującej wieloskokowej sieci kratowej, a także sieci niewrażliwej...
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Research into flows in turbine blade seals. Part II: Numerical analysis
PublicationPrzedstawiono wyniki badań numerycznych programem Fluent przepływów w uszczelnieniu nadbandażowym stopnia turbinowego. Badania wykonano przy zastosowaniu różnych typów siatek obliczeniowych, różnych rodzajów "zszywek" oraz różnych metod obliczeniowych (Mixing Plane, Sliding Mesh, Multiple ReferenceFrame).
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Structures for parameterization, meshing and data exchange of topologically related surfaces of a ship hull
PublicationThis paper presents proposal of data structures for storage and processing of a parametric three-dimensional model of a midship hull sections. The model consists of coarse surfaces like: decks, frames, girders, stiffeners, brackets, partitions etc. bounded by topological relations. All workshop details are omitted as the model is intended for numeric calculations. Proposed data structures are prepared to facilitate changes in the...
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Orthotropic membrane as a mechanical model of surgical implant in abdominal hernia repair
PublicationEven though the incisional hernia repair surgery is a well known procedure, mechanical properties of the tissue-implant system are unknown so the implantation of the repairing mesh is quite intuitive and, recurrences of the illness still take place. The main objective of the study is to define an operated hernia model that can be used for surgery planning and the assessment of the repair persistence. The load applied to the structure...
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Mechanika analityczna, W, M, sem. 01, lato 21/22 (PG_00057017)
e-Learning Coursesmech analit
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Mechanika analityczna, W, MTR, sem. 01, lato 22/23 (PG_00057017)
e-Learning Coursesmech analit
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Mechanika analityczna, W, MTR, II st., sem. 01, letni 23/24, (PG_00057017)
e-Learning Coursesmech analit
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Biomechanical causes for failure of the Physiomesh/Securestrap system
PublicationThis study investigates the mechanical behavior of the Physiomesh/Securestrap system, a hernia repair system used for IPOM procedures associated with high failure rates. The study involved conducting mechanical experiments and numerical simulations to investigate the mechanical behavior of the Physiomesh/Securestrap system under pressure load. Uniaxial tension tests were conducted to determine the elasticity modulus of the Physiomesh...
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Virtual spring damper method for nonholonomic robotic swarm self-organization and leader following
PublicationIn this paper, we demonstrate a method for self-organization and leader following of nonholonomic robotic swarm based on spring damper mesh. By self-organization of swarm robots we mean the emergence of order in a swarm as the result of interactions among the single robots. In other words the self-organization of swarm robots mimics some natural behavior of social animals like ants among others. The dynamics of two-wheel robot...
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A concept of measurement system based on the Z-Wave standard
PublicationIn the paper a new concept of measurement system based on the Z-Wave standard is presented. This standard is dedicated to use mainly in home automation systems, but its properties enable to use it in dispersed measurement systems and support wireless communication between measurement nodes in a mesh-type network. In the paper basic metrological aspects of the Z-Wave standard and an example of impedance measurement system are discussed.
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Mechanizmy bezpieczeństwa w strefie C systemu netBaltic
PublicationW artykule zaprezentowano rozwiązania zaimplementowane do zabezpieczania komunikacji w warunkach sporadycznej i nieciągłej łączności (Delay Tolerant Networking – DTN) w systemie netBaltic - charakterystycznej dla strefy C tego systemu. Ze względu na dużą różnorodność rozważanych mechanizmów komunikacyjnych, architektura bezpieczeństwa całego systemu została podzielona na kilka elementów – infrastrukturę klucza publicznego (PKI),...
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Multiscale model for blood flow after a bileaflet artificial aortic valve implantation
PublicationCardiovascular diseases are the leading cause of mortality in the world, mainly due to atherosclerosis and its consequences. The article presents the numerical model of the blood flow through artificial aortic valve. The overset mesh approach was applied to simulate the valve leaflets motion and to realize the moving mesh, in the aortic arch and the main branches of cardiovascular system. To capture the cardiac system’s response...
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Recent Advances in Polymer Nanocomposites: Unveiling the Frontier of Shape Memory and Self-Healing Properties—A Comprehensive Review
PublicationShape memory and self-healing polymer nanocomposites have attracted considerable attention due to their modifiable properties and promising applications. The incorporation of nanomaterials (polypyrrole, carboxyl methyl cellulose, carbon nanotubes, titania nanotubes, graphene, graphene oxide, mesoporous silica) into these polymers has significantly enhanced their performance, opening up new avenues for diverse applications. The...
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Analysis of the Impact of Charging Electric Cars on the Power System Load
PublicationThe paper presents ways of integrating electric cars with the power system. In connection with this, daily load curves in the average working day have been developed in the G2V (Grid-to-Vehicle) and V2G (Vehicle-to-Grid) variants. The G2V solution consists in unidirectional energy flow from the power system to a vehicle’s battery. The V2G solution consists in bi-directional energy exchange between the power system and electric...
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Numerical Modeling and Simulation of Vehicular Crashes into Three-Bar Metal Bridge Rail
PublicationAdvanced finite element (FE) modeling and simulations were performed on vehicular crashes into a three-bar metal bridge rail (TMBR). The FE models of a sedan, a pickup truck, and a TMBR section were adopted in the crash simulations subject to Manual for Assessing Safety Hardware (MASH) Test Level 2 (TL-2) and Test Level 3 (TL-3) requirements. The test vehicle models were first validated using full-scale physical crash tests conducted...
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Modelling of Geared Multi-Rotor System
PublicationIn the paper the method of modelling a speed-varying geared rotor system is presented. The proposed approach enables us to obtain an accurate low-order lumped parameter representation of the investigated system. The final model consists of reduced modal models of an undamped beam/torsional shaft system as well as a spatially lumped model of other linear and nonlinear phenomena including gear mesh interaction.
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Example of Using Particle Swarm Optimization Algorithm with Nelder–Mead Method for Flow Improvement in Axial Last Stage of Gas–Steam Turbine
PublicationThis article focuses principally on the comparison baseline and the optimized flow efficiency of the final stage of an axial turbine operating on a gas–steam mixture by applying a hybrid Nelder– Mead and the particle swarm optimization method. Optimization algorithms are combined with CFD calculations to determine the flowpaths and thermodynamic parameters. The working fluid in this study is a mixture of steam and gas produced...
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The selected roof covering technologies in the aspect of their life cycle costs
PublicationIn the article is presented an analysis of the life cycle costs calculation for selected roof coverings. The scope of research includes costs of construction, maintenance and demolition of the roof covering structure for two alternative technologies – the traditional and new generation. On the presented example of an industrial building with a roof area of 1000 m², the above costs are taken to consideration for the roof covering...
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Integration of thermographic data with the 3D object model
PublicationThe aim of the paper is to present new method for merging the 3D model data of the measured object with thermograms. Our technique is based on the combination of visual 3D imaging technique and thermal imaging technique, which maps the 2D thermograms on to 3D anatomical mesh model. The combination of these imaging modalities allows the generation of combined 3D and thermal data from which thermal signatures can be verified and...
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Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublicationObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublicationCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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COMPUTER-AIDED DESIGN OF ORGANOPHOSPHORUS INHIBITORS OF UREASE
PublicationBased on the structure of the most potential inhibitor diamidophosphate, various novel groups of inhibitors were developed by knowledge-based design approach with covalent carbon-phosphorus or carbon-phosphorus-carbon bond to improve hydrolytic stability to inhibit the microbial ureases. Designed compounds were evaluated with 10 (LigScore1, LigScore2, PLP1, PLP2, JAIN, PMF, PMF04, LUDI_1, LUDI_2 and LUDI_3) different scoring functions...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Tris(1,10-phenanthroline-k2N,N')iron(II) dichloride methanol hexasolvate
PublicationTytułowy związek składa się z kompleksowego kationu, w którym do żelaza(II) oktaedrycznie koordynują trzy bidentne ligandy fenantrolinowe oraz dwóch jednoujemnych agregatów: [Cl(MeOH)2](-) i [Cl(MeOH)4](-), gdzie jony chlorkowe i cząsteczki metanolu są powiązane wiązaniami wodorowymi.
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Numeryczna analiza hydrauliki toru kajakarstwa górskiego w Drzewicy
PublicationW artykule zaproponowano wykorzystanie do analizy hydrodynamiki toru kajakarstwa górskiego symulacji numerycznej, wykorzystującej dwuwymiarowe równania ruchu wody w warunkach przepływu szybkozmiennego. Rozwiązanie równań hydrodynamiki wykonano samodzielnie z zastosowaniem metody objętości skończonych. Jako przykład zastosowania zaproponowanej metody przedstawiono analizę przepływu wzdłuż istniejącego, poddanego modernizacji toru...
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Resilient Routing in Communication Networks
PublicationThis important text/reference addresses the latest issues in end-to-end resilient routing in communication networks. The work highlights the main causes of failures of network nodes and links, and presents an overview of resilient routing mechanisms, covering issues related to the Future Internet (FI), wireless mesh networks (WMNs), and vehicular ad-hoc networks (VANETs). For each of these network architectures, a selection of...
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Koncepcja układu do monitorowania i diagnozowania układu hydraulicznegopodbijarki torowej. W: Badanie, konstrukcja, wytwarzanie i eksploatacja układów hydraulicznych. Red. merytoryczna E. Palczak. Gliwice: Centr. Mech. Górn. KONMAG 2002 s. 105-118, 13 rys. bibliogr. 5 poz. Referaty zamieszczone w niniejszej monografii były przedmiotem publicznej prezentacji podczas dwunastej ogólnopolskiej konferencji CYLINDER 2002 wdniach 23-25.09.2002 r. Szczyrk.
PublicationW artykule scharakteryzowano układ hydrauliczny podbijarki torowej realizu-jący złożone funkcje. Dążąc do zapewnienia niezawodnej pracy maszyny, obni-żenia kosztów eksploatacji i ywkrywania zużytych elementów opracowano konce-pcje układu do monitorowania i diagnozowania najważniejszych podzespołów. Domonitorowania pomp i silników hydraulicznych przewiduje się wykorzystanie metody termodynamicznej oraz pomiar prędkości ruchu...
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Possibility of thermal imaging use in studies of natural convection heat transfer on the example of an isothermal vertical plate.
PublicationA new method of infrared (IR) camera use in convective heat transfer studies has been presented. Until now, IR cameras were utilized for temperature field visualizations of flat heated surfaces of solid objects only. Because liquids and gasses do not emit radiation in the infrared range of wave lengths, detection of temperature field in the air was conducted with the use of plastic mesh, which, after heating by hot air, emits infrared...
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Hydrogenation process ofTiO2/BiVO4/PEDOT:PSS observed by XPS method
Open Research DataTitania nanotubes synthesis was based on a two-stage anodization process at water/ethylene glycol (5%/95%) electrolyte containing 0.27 M NH4F and 1 M H3PO4 described previously. Anodization process was performed in two-electrode cell compartment using platinum mesh as a cathode. The distance between electrodes was about 2 cm. The anodization voltage...
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Home Sweet Home. Connecting the dots for healthy evening residential illumination
PublicationDuring the twentieth century, lighting designers would commonly use incandescent light sources for residential homes as they provided a visual comfort, with high quality colour rendering properties, along with relaxing ambient atmosphere. Unfortunately, it’s now difficult to buy incandescent light sources because they have been banned in many countries (https://bit.ly/2GwN2Wv). This article addresses some of the challenges in regards...
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Biomechanics of the front abdominal wall as a potential factorleading to recurrence with laparoscopic ventral hernia repair
PublicationThis study investigated the front abdominal wallto describe its elasticity in vivo and searched for elongationsthat possibly stretched an implanted mesh, therebycausing fixation failure and subsequent recurrence.To measure front abdominal wall elongations, amodel of fascia movements was created. Eight healthyvolunteers were measured during exercise to determine theextent of elongations in their front abdominal wall. Videoswere...
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Integracja międzywarstwowa protokołów RM-AODV Multicast DNS i IPv6 Neighbor Discovery w środowisku sieci standardu IEEE 802.11s
PublicationWraz z rozwojem bezprzewodowych technik transmisyjnych oraz wzrostem liczby i zasobów urządzeń mobilnych, wzrasta również popularność sieci bezprzewodowe o architekturze mesh, które znajdują rozliczne zastosowania w systemach dostępowych i dystrybucyjnych. W artykule przedstawiono krótką analizę efektywności działania protokołów IPv6 Neighbor Discovery oraz Multicast DNS w środowisku sieci IEEE 802.11s oraz propozycję metody jej...
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EXPERIMENTS AND SIMULATIONS FOR LAPAROSCOPICVENTRAL HERNIA REPAIR IMPROVEMENT
PublicationThe authors conducted a wide experimental and numerical study in order to determine effective approaches in the laparoscopic VH repair. At first the study covered identification of mechanical properties of the abdominal fascia, implants, tacks and transabdominalsutures. Basis on these data, the one and two-dimensional mathematical models were formulated and a number of numerical static and dynamic analyses were carried out. Then...
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Metoda Elementów Skończonych - Projekt (PG_00057399), MwBM sem1. zima 24/25
e-Learning CoursesCelem projektu jest zapoznanie studentów z tworzeniem programów MES , W ramach projektu studenci tworzą własne oprogramowanie MES do analizy konstrukcji belkowych i ramowych.
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3d Visualization of Seabed from Multibeam Sonar Records Using TriangularIrregular Mesh. W: [CD-ROM] Forum Acusticum Sevilla 2002. 3rd European Con-gres on Acoustics. XXXIII Spanish Congress on Acoustics-TECNIACUSTICA 2002.European and Japanese Symposium on Acoustics. Sevilla, Spain 16-20 Septem- ber 2002. Madrid: Soc. Espanola de Acustica**2002 vol. 33, [6 s.] 4 rys. bibliogr. 6 poz. ISBN: 84-87985-06-8 Special Issue of the Journal Revista de Acustica, vol.33, ano 2002. Trójwym. wizual.dna mors. z danych pochodz. z echosond wielowiąz. z wykorz.niergul.siat.TIN.
PublicationPrzedstawiono sposób trójwymiarowej wizualizacji dna morskiego przy wyko-rzystaniu siatki nieregularnej (TIN) otrzymanej w wyniku triangularyzacjioraz porównano otrzymane wyniki z rzeczywistymi pomiarami batymetrycznymidna Bałtyku Południowego.