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Search results for: TRYTON
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Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
PublicationW ostatnich latach zaproponowano szereg modeli typu implicit solvent, ktore bazują na bezpośrednim rozwiązaniu niejednorodnego równania Poissona w przestrzeni rzeczywistej. Modele te charakteryzują się elegancją, ponieważ wnęka, w której umieszczona jest molekuła substancji rozpuszczanej zdefiniowana jest bezpośrednio w funkcji gęstości elektronowej, a rozkład ładunku jest w sposób samouzgodniony polaryzowany dzięki reakcji dielektryka,...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
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The Influence of Casein Coatings on the Corrosion Behavior of Mg-Based Alloys
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublicationAb initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces...
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Optimization of the femtosecond laser impulse for excitation and the Spin-Orbit mediated dissociation in the NaRb Dimer
PublicationWe study the dynamics of multiple coupled states under the influence of an arbitrary time-dependent external field to investigate the femtosecond laser-driven excitation and the spin-orbit mediated dissociation in the NaRb dimer. In this process, the dimer is excited from the ground triplet state 1^3Sigma+ to the 1^3Pi state using the femtosecond laser impulse and the spin-orbit coupling between the 1^3Pi and 2^1Sigma+ states results...
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Born–Oppenheimer potential energy curves of NaK from the optimised atomic basis sets
PublicationThe article presents adiabatic potential energy curves of the ground and excited electronic states for the diatomic NaK molecule. The calculations were made using the ab initio computational methods to include electron correlation. The studied molecule was calculated as the effective two-electron problem, in which only the valence electrons of the molecule are explicitly taken into account. The remaining electrons with atomic nuclei...
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Dissociative electron attachment and anion-induced dimerization in pyruvic acid
PublicationWe report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions....
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Configurational and Conformational Preferences in Stereoselective Acylations of N-Methyl-1,3-diaminopropane with Acyl Chlorides
PublicationEvidence for a stereoinduction profile of the reaction of N-methyl-1,3-diaminopropane with acyl chlorides was provided. A possibility to engage in intramol. CH2···HN and Cl···H-N interactions and the proton migration process to the methylamino group leads to the E secondary amides carrying the N···H+···N or N-H···N bridges, that show unusual spectroscopic images. Empirical relations between the ΔδC chem. shift differences,...
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T1 RELAXATION TIME CALLIBRATION IN MAGNETIC RESONANCE IMAGING USING NANODIAMOND PHANTOMS
PublicationMRI is increasingly used in radiation treatment planning because of the excellent soft tissue contrast in the obtained images. It allows more precise definition of the boundaries between healthy tissues and those affected by cancerous lesions. To obtain good image quality, the difference in signal between two types of tissue must be significant despite the noise so it must be properly calibrated. This calibration includes...
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Cation sensing by diphenyl-azobenzocrowns
PublicationMetal cations complexation and proton binding by 13- and 16-membered diphenyl-azobenzocrowns and diphenyl-hydroxyazobenzocrowns were studied in acetonitrile using spectroscopic methods: UV–vis spectroscopy, spectrofluorimetry, and 1H NMR spectroscopy. Phenyl moieties in benzene rings were found to affect binding strength alkali and alkaline earth metal cations and hydrogen ion, and affect tautomeric equilibrium of hydroxyazobenzocrowns....
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Usuwanie hydrofobowych zanieczyszczeń ropopochodnych z gleby metodą odmywania za pomocą roztworów związków powierzchniowo czynnych = Washing out of hydrophobic organic pollutants from soil using surfactants solutions
PublicationBadano efektywność oczyszczania gleby zanieczyszczonej substancjami ropopochodnymi. W badaniach wykorzystano surfaktanty niejonowe z grupy oksyetylenowanych alkoholi tłuszczowych i alkilopoliglukozydów oraz biosurfaktant z grupy ramnolipidów. Efektywność odmycia gleby w zależności od rodzaju surfaktantów wahała się od 67 do 78% przy stężeniu surfaktantu 3 g/L. Wraz ze wzrostem stężenia surfaktantu w roztworze obserwowano wzrost...
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Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
PublicationFormation of the excited NH(A 3Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A 3Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom...
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Innowacyjna powłoka poprawiająca własności mechaniczne oraz biokompatybilne stopów tytanu Ti6Al4V i Ti13Zr13Nb przeznaczonych na implanty wewnetrzne
PublicationOstatnie badania nad materiałami tytanowymi przeznaczonymi na implanty wewnętrzne pokazują iż dotychczas uznawany za bezinwazyjny tytan odkłada się w organizmie. Nie wiadomo jeszcze jakie konsekwencje są tego procesu dla organizmu żywego. W artykule przedstawiono idee wytworzenia nowej, biokompatybilnej powłoki, która ma na celu zminimalizowanie przenikania jonów metalu do organizmu ludzkiego oraz ułatwienie porastania implantu...
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Effect of osmoprotectants on the survival of bacterial endophytes in lyophilized beet roots
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The structure and mechanical properties of AlMg5Si2Mn alloy after surface alloying by the use of fiber laser
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Application of the Finite Element Method for Modelling of the Spatial Distribution of Residual Stresses in Hybrid Surface Layers
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Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
PublicationStatistical block copolymers, composed of donor (D) and acceptor (A) blocks, are a novel type of material for organic photovoltaics (OPVs) devices. In particular a new series of polymers based on PBTZT-stat-BDTT-8, recently developed by Merck, offers high solubility in different solvents, and a high power conversion efficiency (PCE) in different device architectures. Although it is known that the electronic properties of these...
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Extracellular proteolytic activity of Deinococcus geothermalis
PublicationProduction of extracellular protease by extremophilic bacteria Deinococcus geothermalis cultivated in liquid media containing 0.1% (w/v) of peptone K, 0.1% yeast extract and 0.2% marine salt reached a maximum in 14 h of the cell growth at 45°C and pH 8.0. The enzyme was purified by a two-step procedure using fractionation by a graded ammonium sulphate precipitation technique and gel filtration on Sephadex G-100 column. Protease...
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Preparation and characterization of monometallic (Au) and bimetallic (Ag/Au) modified-titania photocatalysts activated by visible light
PublicationThe Au-TiO2 and Ag/Au-TiO2 nanoparticles have been prepared using a water-in-oil microemulsion system of water/AOT/cyclohexane and water/Triton X-100/cyclohexane. The obtained photocatalysts were subsequently characterized by a BET method, DRS spectroscopy, X-ray photoelectron emission spectroscopy (XPS), scanning transmission electron microscopy (STEM) and X-ray powder diffraction analysis (XRD). For gold-doped titanium (IV) oxide...
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Spectroscopic, thermal and equilibrium characterization of U(VI) ions sorption on inulin in the presence of phosphates
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Inwestycje w surowce w połączeniu z polskim rynkiem kapitałowym, analiza ryzyka i efektywności
PublicationW artykule przedstawiono główne kategorie i rodzaje inwestycji w surowce. Cel opracowania to zbadanie czy inwestycja w Warszawski Indeks Giełdowy stanowi główny składnik optymalnego tj. cechującego się minimalnym ryzykiem portfela inwestycyjnego. Ponadto ustalono czy wspomniana inwestycja tradycyjna stanowi najważniejszy element portfela inwestycyjnego odznaczającego się najwyższą efektywnością. Stwierdzono, że wszystkie z 29 analizowanych...
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EKSPERYMENTALNE I NUMERYCZNE BADANIA ALUMINIOWEJ BELKI WSPORNIKOWEJ Z WARSTWĄ MASY POLIMEROWEJ PODDANEJ ODDZIAŁYWANIOM DYNAMICZNYM
PublicationW pracy przedstawione zostały wyniki badań eksperymentalnych i numerycznych dotyczące wyznaczenia parametrów dynamicznych metalowego elementu wspornikowego poddanego oddziaływaniom dynamicznym. Przedmiotem badań była aluminiowa belka wspornikowa z podklejoną od dołu warstwą masy polimerowej. Badania polegały na uderzeniu w środku rozpiętości metalowego elementu młotkiem modalnym. Liczby tłumienia oraz częstotliwości drgań własnych...
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A XAS study of a highly diluted Pt electrocatalyst operating in PEM fuel cells
PublicationWe present an X-ray absorption spectroscopy (XAS) study of a low Pt content catalyst layer(Pt loading 0.1 mg c2) operating at the cathode of a proton exchange membrane fuel cell(PEMFC). This catalyst is based on the use of a mesoporous inorganic matrix as a support forthe catalyst Pt nanoparticles. Due to the high Pt dilution, in situ measurements of itsstructural properties by XAS are challenging and suitable experimental strategies...
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Ciekawy przypadek wiaduktu sprężonego, którego nie wzmocniono.
PublicationW ramach ekspertyzy dotyczącej nośności zarysowanych bloków oporowych nowego wiaduktu sprężonego, wykonano sprawdzające obliczenia statyczne rzeczywistej konstrukcji z uwzględnieniem wpływu sposobu modelowania przęseł na jego teoretyczne wytężenie. Wykonano również numeryczną analizę nośności konstrukcji bloków oporowych oraz przeprowadzono badania wiaduktu ''in situ''. W wyniku przeprowadzonych analiz i badań stwierdzono wystarczjającą...
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Konsekwencje sposobu modelowania mostu na przykładzie drogowego wiaduktu sprężonego.
PublicationW ramach projektu próbnego obciążenia nowego wiaduktu sprężonego wykonano obliczenia statyczne rzeczywistej konstrukcji. Rozbieżności pomiędzy założeniami projektowymi a wynikami własnymi, skłoniły do przeprowadzenia analizy wpływu sposobu modelowania przęseł na jego teoretyczne wytężenie. Analizowano cztery modele MES, rusz belkowy, model powłokowo-belkowy, model powłokowo-bryłowy oraz model bryłowy. Rezultaty odniesiono do wyników...
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Complexing and Chelating Agents Immobilized on Silica Gel and Related Materials and Their Application for Sorption of Inorganic Species
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Metodyka pomiaru jachtów regatowych przy pomocy skanowania laserowego 3D
PublicationPrzedstawiono metodykę pomiaru klasowego za pomocą skanera laserowego 3D, dostepne rzowiązania techniczne i oprogramowanie oraz przykłady zastosowania.
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Wpływ napięcia takielunku na odkształcenia kadłuba jachtu regatowego na przykładzie jednostki klasy Omega
PublicationPrzedstawiono problem deformacji kadłuba pod wpływem sił generowanych przez takielunekj, w kontekście przepisów klasowych oraz pożądanych i niepożądanych własności konstrukcyjnych kadłuba.
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Positron-electron correlation-polarization potentials for the calculation of positron collisions with atoms and molecules
PublicationWe present correlation-polarization potentials for the calculation of scattering cross sections of positrons with atoms and molecules. The potentials are constructed from a short-range correlation term and a long-range polarization term. For the short-range correlation term we present four different potentials that are derived from multi-component density functionals. For the long-range polarization term we employ a multi-term...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils
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The Influence of ZnO Oxide Layer on the Physicochemical Behavior of Ti6Al4V Titanium Alloy
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Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces
PublicationDensity functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign (“jellium”). This artificial neutralization does not occur in reality, where a different...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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Eksperymentalne i numeryczne badania parametrów dynamicznych trybuny stalowej
PublicationTrybuny stalowe to konstrukcje, które odnajdują swoje zastosowanie głównie podczas wydarzeń sportowych, koncertów muzycznych oraz innych wydarzeń, którym towarzyszą rytmiczne aktywności widzów i głośna muzyka. Ze względu na smukłość oraz lekkość elementów z jakich wykonana jest konstrukcja trybuny jest ona bardzo łatwo wzbudzana przez ludzi do drgań. Z przeprowadzonej w pracy [4] analizy modalnej wynika, że masa ludzi prowadzi...
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Do positrons measure atomic and molecular diameters?
PublicationWe report on density functional calculations (DFT) of elastic integral scattering cross-sections for positron collisions with argon, krypton, nitrogen and methane. The long-range asymptotic polarization potential is described using higher-order terms going much beyond an induced dipole potential (−α / r 4) while the short-range interaction is modeled by two different forms of electron – positron correlation potential (Boroński-Nieminen...
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A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublicationChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
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Transport properties of microemulsions with ionic liquid apolar domains as a function of ionic liquid content
PublicationThe specific conductivity, dynamic viscosity and apparent diffusion coefficient of each of four aqueous ionic liquid microemulsions (IL-MEs) were measured as a function of ionic liquid (IL) content. The investigated systems were composed of water, hydrophobic ILs (1-butyl-3-methylimidazolium hexafluorophosphate or bis(trifluoromethanesulphonyl)imide) and the nonionic surfactant Triton X-100 or its mixture with cosurfactant (butanol)....
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Electronic structure and rovibrational predissociation of the 2^1Π state in KLi
PublicationAdiabatic potential energy curves of the 3^1Σ^+, 3^3Σ^+, 2^1Π and 2^3Π states correlating for large internuclear distance with the K(4s) + Li(2p) atomic asymptote were calculated. Very good agreement between the calculated and the experimental curve of the 2^1Π state allowed for a reliable description of the dissociation process through a small (∼20 cm−1 for J = 0) potential energy barrier. The barrier supports several rovibrational...
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Quasirelativistic potential energy curves and transition dipole moments of NaRb
PublicationWe report on extensive calculations of quasi-relativistic potential energy curves and, for the first time, transition dipole moments including spin-orbit and scalar-relativistic effects of the NaRb molecule. The calculated curves of the 0+, 0-, 1, 2 and 3 molecular states correlate for large internuclear separation with the fourteen lowest atomic energies up to the Na(3s ^2S_{1/2}) + Rb(7s ^2S_{1/2}) atomic limit. Several new features...
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Anionic states of C6Cl6 probed in electron transfer experiments
PublicationThis is the first comprehensive investigation on the anionic species formed in collisions of fast neutral potassium (K) atoms with neutral hexachlorobenzene (C6Cl6) molecules in the laboratory frame range from 10 up to 100 eV. In such ion-pair formation experiments, we also report a novel K+ energy loss spectrum obtained in the forward scattering giving evidence of the most accessible electronic states. The vertical electron affinity...
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Processing of Satellite Data in the Cloud
PublicationThe dynamic development of digital technologies, especially those dedicated to devices generating large data streams, such as all kinds of measurement equipment (temperature and humidity sensors, cameras, radio-telescopes and satellites – Internet of Things) enables more in-depth analysis of the surrounding reality, including better understanding of various natural phenomenon, starting from atomic level reactions, through macroscopic...
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Choosing source of microorganisms and processing technology for next generation beet bioinoculant
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Tuning the work function of graphite nanoparticles via edge termination
PublicationGraphite nanoparticles are important in energy materials applications such as lithium-ion batteries (LIBs), supercapacitors and as catalyst supports. Tuning the work function of the nanoparticles allows local control of lithiation behaviour in LIBs, and the potential of zero charge of electrocatalysts and supercapacitors. Using large scale density functional theory (DFT) calculations, we find that the surface termination of multilayer...
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Complex Corrosion Properties of AISI 316L Steel Prepared by 3D Printing Technology for Possible Implant Applications
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Prediction of the properties of PVD/CVD coatings with the use of FEM analysis
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