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Effect of Presowing Magnetic Field Stimulation on the Seed Germination and Growth of Phaseolus vulgaris L. Plants
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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublicationIn the paper experimental tests and numerical simulations of a full cross-section segment of ultimately designed foot-and cycle-bridge are presented. The experimental tests were conducted on element with length reduced to 3 m and unchanged (target) cross-section dimensions. The external skin of structure is GFRP laminate while internal core is PET foam. Several quasi-static tests were performed using hydraulic cylinder to generate...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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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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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublicationThis paper aimed at developing a new method of estimating the impact speed of a passenger car at the moment of a crash into a W-beam road safety barrier. The determination of such a speed based on the accident outcomes is demanding, because often there is no access to full accident data. However, accurate determination of the impact speed is one of the key elements in the reconstruction of road accidents. A machine learning algorithm...
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Rapid Yield Optimization of Miniaturized Microwave Passives by Response Features and Variable-Fidelity EM Simulations
PublicationThe operation of high-frequency devices, including microwave passive components, can be impaired by fabrication tolerances but also incomplete knowledge concerning operating conditions (temperature, input power levels) and material parameters (e.g., substrate permittivity). Although the accuracy of manufacturing processes is always limited, the effects of parameter deviations can be accounted for in advance at the design phase...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Improved-Efficacy EM-Based Antenna Miniaturization by Multi-Fidelity Simulations and Objective Function Adaptation
PublicationThe growing demands for integration of surface mount design (SMD) antennas into miniatur-ized electronic devices have been continuously imposing limitations on the structure dimen-sions. Examples include embedded antennas in applications such as on-board devices, picosatel-lites, 5G communications, or implantable and wearable devices. The demands for size reduction while ensuring a satisfactory level of the electrical and field...
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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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Simulations of freshwater lens recharge and salt/freshwater interfaces using the HYDRUS and SWI2 packages for MODFLOW
PublicationThe paper presents an evaluation of the combined use of the HYDRUS and SWI2 packages for MODFLOW as a potential tool for modeling recharge in coastal aquife rs subject to saltwater intrusion. The HYDRUS package for MODFLOW solves numerically the one-dimensional form of the Richards equation describing water flow in variably- saturated media. The code computes groundwater recharge to or...
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Communication and Load Balancing Optimization for Finite Element Electromagnetic Simulations Using Multi-GPU Workstation
PublicationThis paper considers a method for accelerating finite-element simulations of electromagnetic problems on a workstation using graphics processing units (GPUs). The focus is on finite-element formulations using higher order elements and tetrahedral meshes that lead to sparse matrices too large to be dealt with on a typical workstation using direct methods. We discuss the problem of rapid matrix generation and assembly, as well as...
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LS-DYNA simulations of the impacts of a 38-ton Heavy Goods Vehicle into a road cable barrier
PublicationNowadays, more and more attention is being paid to safety on roads and motorways. It is due to the continuous development of road and motorway network and a significant increase of the number of vehicles on roads. To meet the expectations of improving road safety in Poland, the Road Innovations Development (RID) research programme was implemented in 2016. The aim of the RID 3A - Road Safety Equipment (RoSE) project is a comprehensive...
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Surrogate modeling of impedance matching transformers by means of variable‐fidelity electromagnetic simulations and nested cokriging
PublicationAccurate performance evaluation of microwave components can be carried out using full‐wave electromagnetic (EM) simulation tools, routinely employed for circuit verification but also in the design process itself. Unfortunately, the computational cost of EM‐driven design may be high. This is especially pertinent to tasks entailing considerable number of simulations (eg, parametric optimization, statistical analysis). A possible...
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Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations
PublicationThe fraction of absorbed photosynthetically active radiation (fAPAR) is a key parameter for estimating the gross primary production (GPP) of trees. For continuous, dense forest canopies, fAPAR, is often equated with the intercepted fraction, fIPAR. This assumption is not valid for individual trees in urban environments or parkland settings where the canopy is sparse and there are well-defined tree crown boundaries. Here, the distinction...
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Direct electrical stimulation of the human brain has inverse effects on the theta and gamma neural activities
PublicationObjective: Our goal was to analyze the electrophysiological response to direct electrical stimulation (DES) systematically applied at a wide range of parameters and anatomical sites, with particular focus on neural activities associated with memory and cognition. Methods: We used a large set of intracranial EEG (iEEG) recordings with DES from 45 subjects with electrodes...
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations
PublicationIn this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas–liquid...
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Experimental and numerical simulations of flow and heat transfer in heatexchanger elements using liquid crystal thermography.
PublicationPrzedstawienie koncepcji badań eksperymentalnych i numerycznych oraz ich wyników podczas wymiany ciepła w modelach klasycznych i płytowych wymienników ciepła w warunków przepływów przejściowych i turbulentnych.
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Measurements of glucose content in scattering media with time-of-flight technique: comparison with Monte Carlo simulations.
PublicationZbadano możliwości pomiaru koncentracji glukozy w materiale silnie rozpraszającym światło z wykorzystaniem techniki czasu przelotu. Badania przeprowadzono wykorzystując ''Intralipid'' będącym fantomem tkanki. Stężenie glukozy wynosiło 100, 200, 300, 500, 1000, 2000,4000 lub 8000 mg/dl. Wyniki pomiarów porównano z wynikami uzyskanymi na drodze modelowania matematycznego.
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FE-simulations of dynamic shear localization in granular bodies using an Arbitrary Lagrangian-Eulerian formulation.
PublicationW artykule przedstawiono wyniki symulacji lokalizacji odkształceń w materiałach granulowanych. Obliczenia wykonano przy zastosowaniu nielokalnego modelu hipoplastycznego dla 2 różnych problemów: sciskania dwuosiowego i przepływu silosowego. W obliczeniach wykorzystano sformułowanie ALE.
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Michał Lech dr inż.
PeopleMichał Lech was born in Gdynia in 1983. In 2007 he graduated from the faculty of Electronics, Telecommunications and Informatics of Gdansk University of Technology. In June 2013, he received his Ph.D. degree. The subject of the dissertation was: “A Method and Algorithms for Controlling the Sound Mixing Processes by Hand Gestures Recognized Using Computer Vision”. The main focus of the thesis was the bias of audio perception caused...
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A Simulation-Optimization Model for Automated Parcel Lockers Network Design in Urban Scenarios in Pamplona (Spain), Zakopane, and Krakow (Poland)
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Comparison of Miller laryngoscope and UEScope videolaryngoscope for endotracheal intubation in four pediatric airway scenarios: a randomized, crossover simulation trial
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<title>Decomposition of MATLAB script for FPGA implementation of real time simulation algorithms for LLRF system in European XFEL</title>
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Co-simulation strategy of transient CFD and heat transfer in building thermal envelope based on calibrated heat transfer coefficients
PublicationThe paper presents a strategy to develop a fully transient numerical model of a heat transfer in building, using a transient CFD model of indoor air and a thermal envelope model, running in a co-simulation. The strategy relies on the utilization of RANS with a high-Re turbulence model and a wall function, which enables to use a coarse computational mesh limiting the computational time. Since wall functions give invalid heat transfer...
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Sano-Tachiya-Noolandi-Hong, Onsager and Braun models vs Monte Carlo simulation of charge photogeneration in organic solids
PublicationThe Sano-Tachiya-Noolandi-Hong (STNH), Onsager, and Braun models as well as Monte Carlo (MC) simulations of charge recombination/separation have been applied for the first time to reproduce the results of the electromodulated photoluminescence measurements in vacuum-evaporated films of fluorescent materials commonly used in optoelectronic devices. The values of the electron-hole pair final recombination speed in the monomer emitters:...
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An Attempt to Develop a Model Selection Algorithm of Computer Simulation during the Design Process of Mechanical Response of Any Mechanical Body
PublicationIn the literature, there are algorithms associated with the design of simulations of technological processes, in which the material model has always been defined previously. However, in none of the studies of computer simulation modelling of technological processes known to the authors of this article, is there a detailed description of how the algorithm, or the selection of plastic model used, is subject to this process. This...
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Influence of gas turbine controller adjustment on propulsion system behaviour in high sea conditions. Part 2. The simulation investigations.
PublicationDo badań przyjęto układ napędowy okrętowy z turbinami gazowymi napędzającymi poprzez przekładnię mechaniczną zębatą śrubę okrętową o zmiennym skoku.Przy użyciu programu komputerowego Matlab i jego nakładki Simulink wykonano symulację dynamiki układu napędowego statku pracującego na wzburzonym morzu.Zbadano wpływ nastaw i typu regulatora na pracę układu. Porównano nastawy układu regulacyjnego układu napędowego dla pracy...
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Construction of a simulation model of goods delivery in international road transportation taking into account the functioning efficiency of logistics supply chain
PublicationThe object of this study is the process of goods delivery in international road transport using various types of logistics chains. The problem being solved is due to the need to develop recommendations for exporters of goods to reformat or design new supply chains during wartime. The expediency of organizing foreign trade operations by the cargo owners' own forces or with the involvement of enterprises providing logistics consulting...
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Tailoring optical constants of few-layer black phosphorus coatings: Spectroscopic ellipsometry approach supported by ab-initio simulation
Publication2D black phosphorus (BP) has attracted extensive attention as an anisotropic platform for novel optoelectronic and polarizing optics applications. Insight into the factors that tune the optical and polarizing properties of 2D BP reveals their essential influence on BP-based photonic and optoelectronic devices. In this work, studies of the optical constants of few-layer black phosphorus coatings are studied and discussed, with particular...
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The coexistence and competition of canonical and comammox nitrite oxidizing bacteria in a nitrifying activated sludge system – Experimental observations and simulation studies
PublicationThe second step of nitrification can be mediated by nitrite oxidizing bacteria (NOB), i.e. Nitrospira and Nitrobacter, with different characteristics in terms of the r/K theory. In this study, an activated sludge model was developed to account for competition between two groups of canonical NOB and comammox bacteria. Heterotrophic denitrification on soluble microbial products was also incorporated into the model. Four 5-week washout...
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An attempt to develop a model selection algorithm of computer simulation during the design process of mechanical response of any mechanical body
Publicationn the literature, there are algorithms associated with the design of simulations of technological processes, in which the material model has always been defined previously. However, in none of the studies of computer simulation modelling of technological processes known to the authors of this article, is there a detailed description of how the algorithm, or the selection of plastic model used, is subject to this process. This article...
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Efficient Surrogate Modeling and Design Optimization of Compact Integrated On-Chip Inductors Based on Multi-Fidelity EM Simulation Models
PublicationHigh-performance and small-size on-chip inductors play a critical role in contemporary radio-frequency integrated circuits. This work presents a reliable surrogate modeling technique combining low-fidelity EM simulation models, response surface approximations based on kriging interpolation, and space mapping technology. The reported method is useful for the development of broadband and highly accurate data-driven models of integrated...
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Phase I and phase II metabolism simulation of antitumor-active 2-hydroxyacridinone with electrochemistry coupled on-line with mass spectrometry.
PublicationHere, we report the metabolic profile and the results of associated metabolic studies of 2-hydroxyacridinone (2-OH-AC), the reference compound for antitumor-active imidazo- and triazoloacridinones. Electrochemistry coupled with mass spectrometry was applied to simulate the general oxidative metabolism of 2-OH-AC for the first time. The reactivity of 2-OH-AC products to biomolecules was also examined. The usefulness of the electrochemistry...
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Hybrid stepless distribution transformer with four-quadrant AC/DC/AC converter at low voltage side - simulation tests
PublicationThe article presents the work of the stepless hybrid distribution transformer (HT), as an alternative to the so far applied Automatic Voltage Regulator (AVR) solutions, used to control the voltage in the power system in terms of the fundamental harmonic. The HT is a combination of a conventional distribution transformer and an AC/DC/AC converter connected in series with the transformers secondary winding. In the work the basic...
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WRF forecasting data of severe weather event in Central Europe on 11 August 2017
Open Research DataThis dataset is related to the forecasting of weather conditions in Central Europe on 11 August 2017. During that day, the severe and devastating weather phenomenon (derecho) occurred in Poland. The simulations were carried out using the Weather Research and Forecasting (WRF) model version 4.2.1 with the initial and boundary conditions from the Global...
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C-Reactive Protein and White Blood Cell Count in Non-Infective Acute Ischemic Stroke Patients Treated with Intravenous Thrombolysis
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Human poverty - measuring relative deprivation from basic achievements: a comparative study for 144 countries over the period 1990-2010
PublicationPoverty – differently defined and measured – still remains one the crucial parts of the world development debate. It`s broadly perceived as multidimensional phenomenon which deprives people from basic capabilities and freedoms, limits their opportunity to educate and fully participate in the labor market contributing to overall country`s socioeconomic performance. Referring to seminal works of Sen and many others(see e.g. Morris...
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Electrochemistry/mass spectrometry (EC/MS) for fast generation and identification of novel reactive metabolites of two unsymmetrical bisacridines with anticancer activity.
PublicationThe development of a new drug requires knowledge about its metabolic fate in a living organism, regarding the comprehensive assessment of both drug therapeutic activity and toxicity profiles. Electrochemistry (EC) coupled with mass spectrometry (MS) is an efficient tool for predicting the phase I metabolism of redox-sensitive drugs. In particular, EC/MS represents a clear advantage for the generation of reactive drug transformation...
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Inverse Nonlinear Eigenvalue Problem Framework for the Synthesis of Coupled-Resonator Filters With Nonresonant Nodes and Arbitrary Frequency-Variant Reactive Couplings
PublicationA novel, general circuit-level description of coupledresonator microwave filters is introduced in this article. Unlike well-established coupling-matrix models based on frequency-invariant couplings or linear frequency-variant couplings (LFVCs), a model with arbitrary reactive frequencyvariant coupling (AFVC) networks is proposed. The engineered formulation is more general than prior-art ones—with the only restriction that the coupling...
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Michał Mazur dr inż.
PeopleAktualne zainteresowania inżynieria mechaniczna, robotyka, drgania mechaniczne, analiza modalna, sterowanie, systemy czasu rzeczywistego Wybrane publikacje Kaliński K., Galewski M., Mazur M., Chodnicki M, 2017, Modelling and Simulation Of A New Variable Stiffness Holder for Milling Of Flexible Details, Polish Maritime Research, vol 24, ss. 115-124 Kaliński K. J., Mazur M.: Optimal control at energy performance index of the mobile...
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Long-term hindcast simulation of water temperature and salinity in the Baltic Sea
Open Research DataThe dataset contains the results of numerical modelling of water temperature and salinity over a period of 50 years (1958-2007) in the Baltic Sea. A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). The hydrodynamic...
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Simulation of perovskite-based CuI/CH3NH3PbI3/TiO2 solar cell performance
Open Research DataThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/TiO2 model structure (Model 1) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Simulation of perovskite-based CuI/CH3NH3PbI3/SnO2 solar cell performance
Open Research DataThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/SnO2 model structure (Model 2) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Simulation of perovskite-based CuI/CH3NH3PbI3/ZnO solar cell performance
Open Research DataThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/ZnO model structure (Model 3) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Simulation of ship turning circle test for ballast and full load conditions
Open Research DataThe data show the results of the turning circle spiral test for the simplified ship model, taking into account two states of loading: ballast and full load. During the circulation test, the manoeuvrability of the vessel is tested.
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ECG measurement in the bathtub - electrodes on the sides of the bathtub, bath simulation - women
Open Research DataThe measurement data shows the measurement of the ECG signal in water in the bathtub. The data includes the measurement time, the reference ECG signal from the chest, and the ECG signal measured by electrodes placed in the bathtub without contact with the human body. Using the presented data, it is possible to estimate the optimal arrangement of measuring...