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Search results for: VARIABLEFIDELITY EM SIMULATIONS
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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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Novel strategies to enhance hydrodynamic cavitation in a circular venturi using RANS numerical simulations
PublicationHydrodynamic cavitation is a popular advanced oxidation technique and it has received wide range of applications from waste water treatment to the nanoparticles synthesis in recent years. The enhancement of the intensity of the hydrodynamic cavitation is always been an emerging field of research. Within this framework, we have proposed and investigated three distinct strategies to enhance the intensity of cavitation in a circular...
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A concept of heterogeneous numerical model of concrete for GPR simulations
PublicationThe Ground Penetrating Radar (GPR) method, which is increasingly being used in the non-destructive diagnostics of reinforced concrete structures, often needs more accurate interpretation tools for analysis of experimental data. Recently, there has been growing interest in developing of various numerical models for exhaustive understanding of GPR data. This paper presents the concept of a heterogeneous numerical model of concrete,...
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Computer simulations of hearing aid acoustical system performance
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NUMERICAL SIMULATIONS OF GAP FLOW ABOVE ROTATING DISK
PublicationA rotating disk can be considered a basic configuration for the investigati ons of the impact of various conditions on the flow through the clearance between the s hrouded turbine blade and the casing. Numerical calculations using Fine/Turbo Numeca were conducted to examine the influence of the rotational velocity and the pressure differ ence across the disk on the flow conditions, especially the mass flow through the clearance....
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Application of Numerical Simulations on 10GN2MFA Steel Multilayer Welding
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Numerical Simulations of X22CrMoV12-1 Steel Multilayer Welding
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Heat Source Models in Numerical Simulations of Laser Welding
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
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Broken-dam simulations using Smoothed Particle Hydrodynamics
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CFD Simulations and Tests of a Prototype Flow Control Valve
PublicationIn this paper a prototype of a flow control valve is described and numerically simulated. The flow control valve is used in hydraulic systems to maintain constant fluid flow despite changing loads of a receiver. The standard construction of this type of valves is modified mainly by eliminating the spring. The prototype consists the hydrostatically unloaded throttle valve and pressure ratio valve substituting pressure difference...
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Application of a cellular automaton to simulations of granular flow in silos
PublicationA cellular automaton based on a gas model of hydrodynamics was used to calculate the kinematics of non-cohesive granular materials during confined flow in a mass flow and funnel flow model silo. In the model, collisions of particles were taken into account during granular flow. In addition, a simplified automaton was used wherein granular flow was assumed as an upward propagation of holes through a lattice composed of cells representing...
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Discrete simulations of a triaxial compression test for sand by DEM.
PublicationArtykuł przedstawia wyniki symulacji dyskretnych dla ściskania trójosiowego stosując metodę elementów dyskretnych DEM. Symulacje wykonano dla piasku. Zastosowano kuli z momentami kontaktu do symulacji kształtu ziaren. Przeprowadzono analizy dla różnych zmiennych parametrów: średnica piasku, krzywa uziarnienia, kształt ziaren, wymiary próbki i warunki brzegowe.
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3D DEM simulations of fracture in reinforced concrete beams
PublicationArtykuł dotyczy zachowania się belki żelbetowej bez zbrojenia pionowego przy trzypunktowym zginaniu. Belka uległa zniszczeniu wskutek ścinania z powodu obecności nadmiernego zbrojenia podłużnego. Eksperymenty przeprowadzono w skali laboratoryjnej z wykorzystaniem systemu mikro-CT, a następnie odtworzono je w analizach numerycznych stosując metodą elementów dyskretnych 3D (DEM). Zastosowano 4-fazowy model betonu z mezostrukturą,...
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FE-simulations of a direct and a true simple shear test
PublicationPorównano dwa aparaty ścinania: aparat bezpośredniego ścinania i aparat prostego ścinania. Analizy pola naprężeń i odkształceń dokonano stosując metodę elementów skończonych i mikropolarne prawo hypoplastyczne. Analiza ta pokazała, że pole naprężeń i odkształceń jest niejednorodne w obu aparatach, szczególnie w aparacie bezpośredniego ścinania.
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FE-simulations of a direct wall shear box test.
PublicationW artykule przedstawiono wyniki numerycznej anlizy lokalizacji odkształceń stycznych w materiałach granulowanych podczas bezposredniego ścinania przy ścianie. Obliczenia przeprowadzono z mikropolarnym modelem hipoplastycznym. Obliczenia wykonano w płaskim stanie odkształcenia stosując metodę elementów skończonych. Wyniki numeryczne porównano z wynikami doświadczalnymi.
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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The Role of Molecular Structure in Monte Carlo Simulations of the Secondary Electron Yield and Backscattering Coefficient from Methacrylic Acid
PublicationIn this paper, we show the influence of the chemical structure of four different conformers on the secondary electron emission and backscattering of an electron beam from a gel of methacrylic acid. The conformers have different permanent dipole moments, which determines the cross sections for elastic collisions with electrons. The cross sections are used in Monte Carlo simulations of an electron beam, which enters the gel of methacrylic...
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Electrical Simulations of the SIS100 Superconducting Dipole and Quadrupole Circuits: Transients, Earthing and Failure Modes
PublicationThe 100 Tm superconducting synchrotron SIS100 is the main accelerator of the international Facility for Antiproton and Ion Research (FAIR) currently under advanced construction in Darmstadt, Germany. The SIS100 dipole circuit which creates the magnetic field required to bend the beam, consists of 108 dipoles distributed over six arc sections of the ring. The magnetic field for the beam focusing is generated by three individual...
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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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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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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
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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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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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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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Initializing the EM Algorithm for Univariate Gaussian, Multi-Component, Heteroscedastic Mixture Models by Dynamic Programming Partitions
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GPU-Accelerated Finite-Element Matrix Generation for Lossless, Lossy, and Tensor Media [EM Programmer's Notebook]
PublicationThis paper presents an optimization approach for limiting memory requirements and enhancing the performance of GPU-accelerated finite-element matrix generation applied in the implementation of the higher-order finite-element method (FEM). It emphasizes the details of the implementation of the matrix-generation algorithm for the simulation of electromagnetic wave propagation in lossless, lossy, and tensor media. Moreover, the impact...
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EM-Driven Multi-Objective Optimization of a Generic Monopole Antenna by Means of a Nested Trust-Region Algorithm
PublicationAntenna structures for modern applications are characterized by complex and unintuitive topologies that are difficult to develop when conventional experience-driven techniques are of use. In this work, a method for automatic generation of antenna geometries in a multi-objective setup has been proposed. The approach involves optimization of a generic spline-based radiator with adjustable number of parameters using a nested trust-region-based...
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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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Prediction of cast-in-place concrete strength of the extradosed bridge deck based on temperature monitoring and numerical simulations
PublicationThe work is devoted to the implementation of a monitoring system for high performance concrete embedded in the span of an extradosed bridge deck using a modified maturity method augmented by numerical simulations conducted by the authors’ FEM code. The paper presents all research stages of bridge construction and considers the conclusions drawn from the results of laboratory tests, field measurements, and numerical calculations....
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Reduction of Computational Complexity in Simulations of the Flow Process in Transmission Pipelines
PublicationThe paper addresses the problem of computational efficiency of the pipe-flow model used in leak detection and identification systems. Analysis of the model brings attention to its specific structure, where all matrices are sparse. With certain rearrangements, the model can be reduced to a set of equations with tridiagonal matrices. Such equations can be solved using the Thomas algorithm. This method provides almost the same values...
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Numerical Simulations of Laser and Hybrid S700MC T-Joint Welding
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Computational Techniques in Numerical Simulations of Arc and Laser Welding Processes
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Measurements and numerical simulations of laser hardening and remelting thermal cycles
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APPLICATION OF NUMERICAL SIMULATIONS ON X10CRWMOVNB9-2 STEEL MULTILAYER WELDING
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Numerical heat transfer model in skin burn depth simulations
PublicationW artykule przedstawiono numeryczny model wymiany ciepła zachodzącej w tkance skórnej . Wyniki symulacji na modelu zostały porównane z wynikami pomiarów In vivo na zwierzętach.
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Hydroacoustic signals simulations in workstation for training asw helicopter navigators
PublicationPolska Marynarka Wojenna użytkuje śmigłowce wyposażone w systemy pokładowe zmoderni-zowane w ostatnich latach a przeznaczone do wykrywania i śledzenia okrętów podwodnych: sonary z opuszczaną anteną, odbiorniki do nasłuchu i analizy sygnałów z radiohydroboi oraz magnetometry. W artykule przedstawiono pokrótce strukturę trenażera nawigatorów - operatorów tych systemów, wykorzystywanego również jako stanowisko do analizy danych zebranych...
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Polymerization and Structure of Opposing Polymer Brushes Studied by Computer Simulations
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Simulations of impact force spectrum for earthquake-induced structural pounding.
PublicationCelem artykułu jest analiza możliwości zastosowanie tzw. spektrum siły zderzenia przy projektowaniu sąsiadujących ze sobą konstrukcji budowlanych na terenach sejsmicznych, w przypadku zbyt małej przerwy dylatacyjnej między nimi. W artykule przedstawiono wyniki symulacji numerycznych przeprowadzonych dla różnych wartości parametrów dynamicznych konstrukcji.
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Representation of magnetic hysteresis in single-phase transformer for circuit simulations
PublicationThe paper presents a mathematical model for the hysteresis phenomenon in a multi-winding single-phase core type transformer. In the circuit transformer model, it is assumed that there is a flux common Φ to all windings as nonlinear and hysteretic function of the total currents Θ (Ampere turns) of all windings. To simulate magnetic behaviour of the iron core the feedback scalar Preisach model of hysteresis is developed. The Preisach...
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OpenGL accelerated method of the material matrix generation for FDTD simulations
PublicationThis paper presents the accelerated technique of the material matrix generation from CAD models utilized by the finite-difference time-domain (FDTD) simulators. To achieve high performance of these computations, the parallel-processing power of a graphics processing unit was employed with the use of the OpenGL library. The method was integrated with the developed FDTD solver, providing approximately five-fold speedup of the material...
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Simulations of fracture in concrete elements using continuous and discontinuous models
PublicationArtykuł przedstawia wyniki symulacji MES w elementach betonowych przy zastosowaniu modeli ciągłych i nieciągłych. Stosując modele ciągłe symulowano proces lokalizacji odkształceń. Stosując modele nieciągłe symulowano proces zarysowania. Obliczenia wykonano dla różnych typów obciążeń.
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Cation diffusion coefficients in CuAgI via molecular dynamics simulations
PublicationPraca prezentuje wyniki analizy strukturalnej otrzymane poprzez symulacje dynamiczno-molekularne (zespół NpT, dwuciałowy potencjał Vashisty-Rahmana) superjonowego związku o składzie (1-x)Cu-xAg-I, x = 0.0, 0.25, 0.5, 0.75, 1.0). Wyznaczono wartość współczynnika dyfuzji kationów i energii aktywacji w funkcji składu szkła i temperatury. Otrzymane rezultaty porównano z danymi literaturowymi.
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A material model of asphalt mixtures based on Monte Carlo simulations
PublicationThe paper aims to numerically reflect mineral-asphalt mixture structure by a standard FEM software. Laboratory test results are presented due to bending tests of circular notched elements. The result scatter is relatively high. An attempt was made to form a random aggregate distribution in order to obtain various results corresponding to laboratory tests. The material structure calibration, its homogenization and finite element...
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Electromagnetic Simulations with 3D FEM and Intel Optane Persistent Memory
PublicationAbstract—Intel Optane persistent memory has the potential to induce a change in how high-performance calculations requiring a large system memory capacity are conducted. This article presents what this change may look like in the case of factorization of large sparse matrices describing electromagnetic problems arising in the 3D FEM analysis of passive highfrequency components. In numerical tests, the Intel oneAPI MKL PARDISO was...
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Discrete simulations of shear zone pattern in earth pressure problems
PublicationW artykule przedstawiono wyniki dyskretnych symulacji naporu piasku na ściankę szczelną. Obliczenia wykonano stosując metodę elementów dyskretnych z kulami uwzględnieniem momentów kontaktu. Wyniki symulacji numerycznych porównano z wynikami doświadczalnymi.
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Numerical simulations of granular material flow in silos with and without insert
PublicationArtykuł omawia wyniki naporu materiału sypkiego podczas przepływu w silosach z i bez wkładek. Obliczenia wykonano wykorzystując sformułowanie ale na bazie prawa sprężysto-plastycznego według druckera-pragera. Zbadano wpływ kształtu i położenia wkładki na wielkość naporu i rodzaj przepływu.
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FE-simulations of size effects in granular and quasi-brittle materials
PublicationW artykule przedstawiono symulacje efektów skali w materiałach granulowanych i kruchych. Obliczenia wykonano dla ściskania dwuosiowego i fundamentu w przypadku materiałów granulowanych oraz belek zginanych w przypadku materiałów kruchych. Do obliczeń wykorzystano mikropolarne prawo hipoplastyczne i sprężysto-plastyczne prawo z nielokalnym osłabieniem.
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Simulations of the Behavior of Granular Bodies Using the Discrete Element Approach
PublicationZachowanie niespójnych ciał ziarnistych opisano metodą elementów dyskretnych (DEM) w warunkach quasi-statycznych dwu- i trójwymiarowych. Do symulacji nieregularnego kształtu granulatu wykorzystano kule z momentami kontaktowymi lub skupiska sztywnych kul. Początkowo badano dwa różne problemy dla zagęszczonego materiału ziarnistego: pasywne przemieszczanie ściany oporowej i ściskanie w płaskim stanie odkształceń pod stałym ciśnieniem...