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Search results for: qm/mm calculations
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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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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublicationThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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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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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublicationSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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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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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Analiza porównawcza metod zwiększania nośności i sztywności stalowych, doczołowych węzłów śrubowych.
PublicationInnowacyjna, w porównaniu z dotychczas stosowanym sposobem, metoda obliczania nośności stalowych węzłów została wdrożona wraz z normami europejskimi. Pozwala ona dokładniej odwzo-rować rzeczywistą pracę poszczególnych części węzła, gdyż wynik obliczeń uzależniony jest od znacznie większej liczby zmiennych. Dzięki postępowi technologicznemu w zakresie metalurgii oraz badaniom naukowym obecnie możliwe jest wzmacnianie połączeń...
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Earthwork calculations in various field conditions
PublicationThe article characterizes the continuation of ongoing work on the MUGO computer program. The analyzes refer to the modernization of railway lines and directly to the earthwork calculations. The methodology of calculating the earthwork size in the areas of fills and cuts is discussed in detail.
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TERMODYNAMIC CALCULATIONS OF TURBINE STEAM PARAMETERS
PublicationIn this work a heat balance was made for the nominal conditions of a block working with 18K370 turbine. For the parameters obtained, the thermal-flow calculations of the steam turbine were performed, maintaining the actual geometry of its flow system. Based on the nominal values obtained, iterative thermal and flow calculations were made for both the heat cycle of the power plant block and the steam turbine itself, seeking to obtain...
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Badania składu chemicznego materiału rury 323,90x12,70 mm
PublicationWykonano badania składu chemicznego materiału rury i dokonano oceny zgodności z atestem i normą.
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Ekspertyza przyczyn korozji złącza spawanego rury ze szwem 129x3,0 mm z instalacji flokulatora
PublicationCelem pracy było ustalenie przyczyn korozji złącza spawanego rury ze szwem 130x3,0 mm z instalacji flokulatora. Instalacja była wykonana ze stali nierdzewnej AISI 316L. Zakres pracy obejmował: wykonanie analizy EDX składu chemicznego spoiny oraz nalotów obecnych na rurociągu, wykonanie badań próbek metalograficznych wraz z określeniem mikrostruktury
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The hydrodynamic pressure field of the ship Zodiak, measurements and calculations
PublicationThe article presents the results of measurements of the slowly changing hydrodynamic pressure field HPF generated by the movement of the ship, Zodiak, in the Bay of Gdansk. The measurement results have been obtained in the framework of the program of the work in Siramis, under the auspices of the European Defence Administration of the EU, by the research team of the Naval Academy in Gdynia. The measurement results were compared with...
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Flow boiling of R1233zd(E) in a 3 mm vertical tube at moderate and high reduced pressures
PublicationThe results of flow boiling of R1233zd(E) in a 3 mm vertical stainless steel tube are presented at moderate and high saturation temperatures. Integral flow characteristics in the form of pressure drop and heat transfer coefficient are discussed for saturation temperatures ranging from 115 to 145 °C (corresponding reduced pressures from 0.2 to 0.7), mass velocity of 800 kg/m2s and heat flux of 20 kW/m2. All of the obtained heat...
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Discrete random variables in reliability calculations of a reticulated shell
PublicationImplementation of the Point Estimation Method (PEM) in the reliability analysis of a three-dimensional truss structure is presented in the paper. The influence of geometric and material random parameters on the truss load-carrying capacity was investigated. The analysis was performed for different combinations of basic variables. Symmetric and asymmetric cases of snow load were taken to assess the structural reliability. Sensitivity...
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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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Static and dynamic concrete calculations: Breakable aggregates in DEM model
PublicationThe paper deals with the calculations of a 3-point bending beam under static and dynamic loads. The real microstructure was obtained from laboratory tests using micro-tomography images. The quasi-static results were compared directly with experimental data at both macro and micro levels. Subsequently, higher strain rates were applied to investigate dynamic effects. The study focused on the influence of dynamic loading on the macroscopic...
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DESIGN AND STRENGTH CALCULATIONS OF THE TRIPOD SUPPORT STRUCTURE FOR OFFSHORE POWER PLANT
PublicationThe support structure being the object of the analysis presented in the article is Tripod. According to the adopted assumptions, it is a foundation gravitationally set in the water region of 60 m in depth, not fixed to the seabed, which can be used for installing a 7MW wind turbine. Due to the lack of substantial information on designing and strength calculations of such types of structures in the world literature, authors have...
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On the design of planar high directivity proximity couplers in the mm-wave range
PublicationPrzedyskutowano problemy projektowania sprzęgaczy zbliżeniowych wykonywanych w technologii planarnej i przeznaczonych do pracy w zakresie fal milimetrowych. Zasadniczym celem badań było zaprojektowanie, wykonanie i przebadanie układu sprzęgacza o wysokiej kierunkowości i umiarkowanym poziomie sprzężenia pracującego w zakresie 40-50GHz. Przedyskutowano i zamodelowano różne konfiguracje sprzęgaczy. Stwierdzono, że znane zasady projektowania...
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Towards modelling of the environmental fate of pharmaceuticals using the QSPR-MM scheme
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1D Model Callibration on the Basis on 3D calculations for Tesla Turbine
PublicationThe paper presents the system of equations for axisymmetriclaminar flow, after averaging, through the width of interdisk slit ofTesla turbine. Coefficients were introduced, as a result ofaveraging, that improve the efficiency of 1D model. The minimalnumber of such coefficients was determined. The 1D modelmakes it possible to attain analytical solutions to an accuracylimited by these coefficients. Calibration of 1D model depends...
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Calculations of Short-Circuit Current Flows in Earth Wires of HV Lines
PublicationThis paper presents a method which enables calculating flows of short-circuit currents in earth wires of high voltage transmission lines, and its implementation in the form of a computer programme. The algorithm enables performing calculations for a double-fed line and starconnected lines (three terminal lines). The developed programme enables verifying dimensioning of earth wires in the context of their short-circuit thermal withstand...
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Large hydrodynamic thrust bearing: Comparison of the calculations and measurements
PublicationHydrodynamic thrust bearings, used to carry axial loads in heavily loaded shafts of water power plants hydro turbines, can reach outer diameters even exceeding 5 m. In such large objects scale effect could be observed. According to this, allowable bearing specific load assuring safe operation of the bearings has to be decreased, which increases thrust bearing dimensions. This effect is caused by excessive thermal deflections of...
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Survivin expression in invasive pituitary gland adenomas with a diameter exceeding 20 mm
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Structural properties of hypothetical CeBa2Cu3O7 compound from LSDA+DMFT calculations
PublicationThe hypothetical stoichiometric CeBa2Cu3O7 (Ce123) compound, which has not been synthesized as a single phase yet, was studied by the density functional theory (DFT). We utilized a method which merges the local spin density approximation (LSDA) with the dynamical mean-field theory (DMFT) to account for the electronic correlations. The LSDA+DMFT calculations were performed in the high-temperature range. The particular emphasis was...
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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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Electron-scattering cross sections for selected alkyne molecules: Measurements and calculations
PublicationWe report cross-section results from experimental and theoretical studies on electron collisions with 1-butyne (HC≡C–CH2CH3) and acetylene (HC≡CH) molecules and from computations for a propyne (HC≡C–CH3) molecule. Absolute grand -total electron-scattering cross sections (TCSs) were measured at impact energies ranging from about 0.5 to 300 eV using the linear electron-transmission method. The TCS energy curve for 1-butyne has a...
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Badania składu chemicznego i własności mechanicznych materiału rury fi 323,85x12,7 mm
PublicationWykonano badania składu chemicznego i właściwości mechanicznych materiału (stal nierdzewna typu 316L)
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Ab initio and density functional theory calculations of proton affinities for volatile organic compounds
PublicationThe Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets and the density function theory-B3LYP have been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for volatile organic compounds. Calculated values of proton affinities are compared with experimental data.
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Computed vibrational excitation ofCF4by low-energy electrons and positrons: Comparing calculations and experiments
PublicationQuantum calculations for the excitation of the asymmetric modes of the CF4 target gas, ν3 and ν4, by impact of low-energy electrons and positrons are carried out in the energy range around 1 eV and are compared with recent experimental findings. The similarities and differences between the two types of projectiles, and the two different modes, are analyzed and discussed vis à vis the present accord with the experimental results.
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Computer-Aided Calculations of Earth Potential Rise in High Voltage Overhead Lines
PublicationHigh voltage overhead power lines with earth wires comprise towers made of conductive material. Some towers are in locations where people can be expected to be either for a long time or for a short time but very frequently. Evaluation of shock hazard near such towers requires calculation of line-to-earth short-circuit current, earth current and especially earth potential rise. Number of towers in high voltage power lines can exceed...
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JMATRIX - a package for relativistic J-matrix calculations in elastic scattering of electrons from model potentials
PublicationWe present a software package JMATRIX, consisting of two computer codes written in FORTRAN 95 and parallelized with OpenMP, implementing the so-called J-matrix method, applied to elastic scattering of electrons on the radial potential, vanishing faster than Coulomb one. In the J-matrix method, physical scattering problem is replaced by using well-defined model, which is solved analytically. Presented software implements both non-relativistic...
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublicationPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Displacements of chimney in the light of computer calculations and surveying
PublicationThe article presents the numerical analysis of reinforced concrete chimney displacements, which was carried out geodetic measurements.
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LattE- first-principles lattice energy calculations
PublicationCrystal engineering is currently attracting much interest. Its aim is to create materials of predefined properties fulfilling the requirements imposed by the applications. There are several parameters describing crystal structures, but the most important one is probably the energy of a crystal lattice. It is the energy released by the system when crystalline solid is formed out of molecules or ions in gaseous phase. Approximate...
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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First-principles calculations of the lattice dynamics of CuInSe2
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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublicationInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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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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Design of mm-wave MIC frequency multiplayers and mixers using simple microstrip high-pass filters
PublicationPrzedyskutowano podstawowe wymagania dotyczące impedancji elementów półprzewodnikowych wykorzystywanych w mieszaczach i powielaczach częstotliwości projektowanych dla zakresu fal milimetrowych. Określono typy układów filtrujących niezbędnych w różnych częściach układów, podkreślając znaczenie filtrów górnoprzepustowych. Mikropaskowy filtr ze zwartym brzegiem został wykonany i zaimplementowany w mieszaczu pracującym w zakresie 20-40GHz.
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Rozkład naprężeń mechanicznych w łyżce o szerokości 500 mm, przeznaczonej do koparki podsiębiernej
PublicationW artykule zaprezentowano optymalizację kształtu łyżki koparki przedsiębiernej z wykorzystaniem analizy wytrzymałościowej. Analizę oparto na trójwymiarowym modelu konstrukcji łyżki z zastosowaniem metody elementów skończonych (MES). Opracowanie wspomnianej metody pozwoliło na modyfikację konstrukcji łyżki, która dała w efekcie obniżenie naprężeń złożonych w newralgicznych obszarach konstrukcji łyżki. Przedstawiona analiza okazała...
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Nondestructive methods complemented by FEM calculations in diagnostics of cracks in bridge approach pavement
PublicationNondestructive methods of road pavement diagnostics are an alternative to traditional approach to pavement failure investigation. The article presents a detailed multidisciplinary inspection carried out using ground-penetrating radar (GPR), laser scanning technology and finite element method (FEM) calculations. It was done in order to assess the factors that contributed to occurrence of premature cracks of a bridge approach pavement....
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Calculations of notch stress factor of a thin-walled spreader bracket fillet weld with the use of a local stress approach
PublicationPresence of geometric notches in welded joints causes concentration of strains and stresses, therefore reducing fatigue strength of such joints. This article presents an analysis of stress concentrations in a fillet weld of a spreader mounting bracket on a small sailing yacht. The aim of this article is to direct the attention of designers, manufacturers and regulatory bodies to issues of fatigue cracks that form in brackets fastening...
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Cost-Effective and Sufficiently Precise Integration Method Adapted to the FEM Calculations of Bone Tissue
PublicationThe technique of Young’s modulus variation in the finite element is not spread in biomechanics. Our future goal is to adapt this technique to bone tissue strength calculations. The aim of this paper is to present the necessary studies of the element’s integration method that takes into account changes in material properties. For research purposes, a virtual sample with the size and distribution of mechanical properties similar...