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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Approximate analytical boundary conditions for efficient finite difference frequency domain simulations in cylindrical coordinates
PublikacjaW artykule zaprezentowano prostą technikę analizy rezonatora otwartego. Algorytm łączy w sobie metodę różnic skończonych i rozwinięć funkcyjnych , umożliwiając implementację warunków brzegowych symulujących otwartą przestrzeń. Metoda testowana była w analizie rezonatorów o różnych wymiarach,a otrzymane wyniki dobrze zgadzały się z rezultatami innych metod.
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Applications of calcium electroporation to effective apoptosis induction in fibrosarcoma cells and stimulation of normal muscle cells
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P-666 Detecting gene variants correlated with MII oocytes developed during ovarian stimulation
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublikacjaAmphotericin 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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Measurements of glucose content in scattering media with time-of-flight technique: comparison with Monte Carlo simulations.
PublikacjaZbadano 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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FEM simulations applied to the failure analysis of RC structure under the influence of municipal sewage pressure
PublikacjaThe paper discusses a failure mechanism of reinforced concrete (RC) structure with steel cover that failed under the influence of municipal sewage pressure. To explain the reasons of failure, in-situ measurements, laboratory experiments and comprehensive Finite Element Method (FEM) computations were performed. Non-destructive in-situ scanning tests were carried out to determine quantity and cover thickness of embedded reinforcement...
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Experimental and numerical simulations of flow and heat transfer in heatexchanger elements using liquid crystal thermography.
PublikacjaPrzedstawienie 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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Improved-Efficacy EM-Based Antenna Miniaturization by Multi-Fidelity Simulations and Objective Function Adaptation
PublikacjaThe 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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Surrogate modeling of impedance matching transformers by means of variable‐fidelity electromagnetic simulations and nested cokriging
PublikacjaAccurate 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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Rapid Yield Optimization of Miniaturized Microwave Passives by Response Features and Variable-Fidelity EM Simulations
PublikacjaThe 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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Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations
PublikacjaThe 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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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublikacjaExascale 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
PublikacjaHydrated 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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Direct electrical stimulation of the human brain has inverse effects on the theta and gamma neural activities
PublikacjaObjective: 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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LS-DYNA simulations of the impacts of a 38-ton Heavy Goods Vehicle into a road cable barrier
PublikacjaNowadays, 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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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE 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
PublikacjaThe 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
PublikacjaThis 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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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublikacjaIn 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
PublikacjaIn 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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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe 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
PublikacjaThe 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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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublikacjaThe 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
PublikacjaIn 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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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublikacjaThis 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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FE-simulations of dynamic shear localization in granular bodies using an Arbitrary Lagrangian-Eulerian formulation.
PublikacjaW 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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Effects of FSW Tool Plunge Depth on Properties of an Al-Mg-Si Alloy T-Joint: Thermomechanical Modeling and Experimental Evaluation
PublikacjaOne of the main challenging issues in friction stir welding (FSW) of stiffened structures is maximizing skin and flange mixing. Among the various parameters in FSW that can affect the quality of mixing between skin and flange is tool plunge depth (TPD). In this research, the effects of TPD during FSW of an Al-Mg-Si alloy T-joint are investigated. The computational fluid dynamics (CFD) method can help understand TPD effects on FSW...
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WRF forecasting data of severe weather event in Central Europe on 11 August 2017
Dane BadawczeThis 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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CD NIWA jako platforma współpracy biznesu i nauki
PublikacjaArtykuł prezentuje koncepcję Centrum Doskonałości Naukowej Infrastruktury Wytwarzania Aplikacji: CD NIWA, które jest środowiskiem przetwarzania w chmurze obliczeniowej, źródłem stale doskonalonych aplikacji i usług oraz platformą współpracy użytkowników. Interaktywność współdziałania nauki i biznesu jest głównym założeniem i celem Centrum Doskonałości NIWA, które ma też służyć budowaniu społeczności współpracującej w zakresie realizacji...
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THE POTENTIAL OF DIFFERENT VARIETIES OF WHITE CABBAGE IN PHYTOREMEDIATION OF ZN AND CD
PublikacjaThe species belong to the botanical family Brassi- caceae are considered to be useful for phytoremediation of soil contaminated with heavy metals. Problems with use the plants recognized as hyperacumulators is that, the plants need to be harvested shortly after the plants become mature, which causes problems of disposal of obtained biomass. When these plants are dried, they easily crumble and flake off, greatly reducing the yield obtained,...
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Gradient-based optimization of filters using FD-TD software
PublikacjaW artykule opisane jest nowe podejście do zagadnienia optymalizacji filtrów mikrofalowych pasmowo-przepustowych. Optymalizacja prowadzona jest z wykorzystaniem metody gradientowej poszukiwania minimum wartości funkcji celu oraz przy założeniu pełnofalowej symulacji obwodów metodą różnic skończonych w dziedzinie czasu. W artykule pokazane jest, że stosując zaawansowane techniki cyfrowego przetwarzania sygnałów możliwa jest optymalizacja...
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Low-order models from FD-TD time samples
PublikacjaNiniejszy artykuł zawiera opis szeregu kryteriów pozwalających na automatyczne tworzenie wysokiej jakości modeli sygnałów czasowych uzyskanych w drodze symulacji obwodów wysokiej częstotliwości metodą różnic skończonych w dziedzinie czasu. Podany jest szczegółowy opis selekcji kluczowych parametrów modeli takich jak wybór długości ciągu użytego do konstrukcji modeli, współczynnika decymacji silnie nadpróbkowanego przebiegu w dziedzinie...
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Simulation of the weight averaging of pulse frequency modulated sensor output signal
Dane BadawczeThe aim of the research is investigation of the efficiency of weight averaging of pulse frequency modulated signal. It was shown that from the point of view of the reduction of the sampling error the best are polynomial weighing functions, for which the maximum of this component error decreases proportionally to the appropriate power of the number of...
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Long-term hindcast simulation of water temperature and salinity in the Baltic Sea
Dane BadawczeThe 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
Dane BadawczeThe 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
Dane BadawczeThe 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
Dane BadawczeThe 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
Dane BadawczeThe 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
Dane BadawczeThe 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...
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International Journal of Simulation Modelling
Czasopisma -
Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublikacjaBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
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A surface-exposed DraD protein of uropathogenic Escherichia coli bearing Dr fimbriae may be expressed and secreted independently from DraC usher and DraE adhesin
PublikacjaOperon dra uropatogennych szczepów Escherichia coli Dr+ odpowiedzialny jest za proces bakteryjnej adhezji i inwazji. Operon dra kodujący fimbrie Dr zawiera sześć otwartych ramek odczytu - draA, draB, draC, draD, draP oraz draE. Fimbrie Dr zlokalizowane na powierzchni komórki bakteryjnej, zbudowane są z podjednostek białka DraE. Niewiele wiadomo na temat powierzchniowej ekspresji białka DraD oraz jego roli w procesie biogenezy fimbrii...
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Molecular aspects of biogenesis of Escherichia coli Dr Fimbriae: characterization of DraB-DraE complexes
PublikacjaHemaglutynina Dr uropatogennych szczepów Escherichia coli jest fimbrialnym homopolimerem zbudowanym z podjednostek białkowych DraE kodowanych przez operon dra. Operon dra zawiera geny draB i draC, kodujące białka homologiczne do białek (białko opiekuńcze-białko kanałotwórcze) zaangażowanych w procesie biogenezy struktur polimerycznych eksprymowanych powierzchniowo. Białko DraB jest jednym z białek periplazmatycznych, należącym...
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The chaperone-usher pathway of bacterial adhesin biogenesis - from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design
PublikacjaSystem chaperone-usher (białko opiekuńcze-białko kanałotwórcze) warunkuje biogenezę powierzchniowych struktur adhezyjnych, odpowiedzialnych za wirulencję wielu bakterii gram-ujemnych. Powyższy mechanizm został zbadany na poziomie strukturalnym w przypadku różnych gatunków bakterii patogennych. Celem powyższej pracy było przedstawienie molekularnego mechanizmu biogenezy struktur adhezyjnych na bazie systemu chaperone-usher. Otrzymane...
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Application of SSB-like protein from Thermus aquaticus in multiplex PCR of human Y-STR markers identification
PublikacjaW tej publikacji prezentujemy zastosowanie białka SSB-podobnego Thermus aquaticus (TaqSSB) w reakcji multiplex PCR w celu identyfikacji markerów ludzkiego Y-STR. Wykorzystanie termostabilnego białka TaqSSB chroni lub redukuje tworzenie przez startery struktur dimerycznych, które powodują hamowanie hybrydyzacji starterów do badanego DNA i redukują ilość starterów dostępnych w reakcji PCR.
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Moving out of CF3‐Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF5) Group
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Electrochemically assisted deposition of hydroxyapatite on Ti6Al4V substrates covered by CVD diamond films — Coating characterization and first cell biological results
PublikacjaAlthough titaniumand its alloys are widely used as implant material for orthopedic and dental applications they show only limited corrosion stability and osseointegration in different cases. The aim of the presented research was to develop and characterize a novel surface modification system from a thin diamond base layer and a hydroxyapatite (HAp) top coating deposited on the alloy Ti6Al4V widely used for implants in contact with bone....
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The generalized Suzuki model of the multipath fading channel
Dane BadawczeThe dataset contains the results of simulations that are part of the research on modelling the multipath fading in the communication channel. The generalized Suzuki fading envelope is generated using the Monte-Carlo simulation (MCS) in the LabVIEW programming environment.