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Search results for: Molecular dynamics simulations
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Influence of magnetic interaction on lattice dynamics of FeBO 3
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Discrepancies of energy values in dynamics of three intersecting plates
PublicationW pracy analizuje się lot konstrukcji powłokowej złożonej z trzech przecinających się powłok. Obciążeniem jest przestrzenny układ sił o zadanym trójkątnym przebiegu w czasie. Po ustaniu obciążenia powłoka doświadcza swobodnego lotu. Celem pracy jest dyskusja różnic wartości energii całkowitej układu w locie swobodnym jakie znane są w literaturze przedmiotu. W pracy przedstawiono także przykład weryfikujący zastosowane algorytmy...
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Dynamics of ginsenoside biosynthesis in suspension culture of Panax quinquefolium
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Investigations on the the dynamics of motor vehicle driving in nighttime conditions
PublicationThe article describes investigations on vehicle driving in nighttime conditions
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On energy-conserving algorithms in the context of rigid body dynamics.
PublicationPraca dotyczy dynamiki ciała sztywnego. Opracowanie teoretyczne wsparte jest przykładami numerycznymi. Głównym celem artykułu jest opracowanie i analiza algorytmu zachowującego energię, który umożliwia całkowanie równań ruchu ciała sztywnego sformułowanego z uwzględnieniem grupy obrotów SO(3) w definicji jego przestrzeni konfiguracyjnej.
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Two-dimensional simulations of concrete fracture at aggregate level with cohesive elements based on X-ray lCT images
PublicationThe paper presents results of two-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 4-phase material composed of aggregate grains placed in the cement matrix, interfacial transitional zones (ITZs) and macro-voids. The particle distribution was taken from real concrete beams on the basis of X-ray lCT images. Comprehensive numerical analyses were carried...
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The impact of initial and boundary conditions on severe weather event simulations using a high-resolution WRF model. Case study of the derecho event in Poland on 11 August 2017
PublicationPrecise simulations of severe weather events are a challenge in the era of changing climate. By performing simulations correctly and accurately, these phenomena can be studied and better understood. In this paper, we have verified how different initial and boundary conditions affect the quality of simulations performed using the Weather Research and Forecasting Model (WRF). For our analysis, we chose...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Adolfo Poma
PeopleI am the group leader of the computational modelling of biomolecules divison at the institute of Fundamental Technological Research Polish Academy of Sciences in Poland. My group was hosted between 2021-2022 by International Centre for Research on Innovative Bio-based Materials (ICRI-BioM). In 2008, I got a Master degree in computational physics from the State University of Campinas, Brazil. Then I moved to Germany and under the...
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Optimization of hydrodynamic vortex separator for removal of sand particles from storm water by computational fluid dynamics
PublicationStorm water treatment has been gradually acknowledged for the removal of pollutants from urban areas using the hydro cyclone separation technique. The separation efficiency of the hydrodynamic vortex separator (HDVS) is a complex phenomenon. With the aim enhance the separation potency of HDVS for storm runoff to get rid of sand particles, the HDVS with different structural configurations was studied by computational fluid dynamics....
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Computational fluid dynamics simulation of heat transfer from densely packed gold nanoparticles to isotropic media
PublicationThis work aims to determine and compare heat generation and propagation of densely packed gold nanoparticles (Au NPs) induced by a resonant laser beam (532 nm) according to the Mie theory. The heat flux propagation is transferred into the materials, which here are: silica glass; soda-lime-silica glass; borosilicate glass; polymethyl methacrylate (PMMA); polycarbonate (PC); and polydimetylosiloxane (PDMS). This analysis aims to...
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Molecular Classification of Low-Grade Diffuse Gliomas
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Coherent electron transport in hydrocarbon molecular devices
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Hubbard operators approach to the transport in molecular junctions
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Molecular basis of TRF proteins and their interactions with peptides
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
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Multigap superconducting state in molecular metallic hydrogen
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A ferrocene-templated Pd-bearing molecular reactor
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Molecular Modelling of the Neurophysin II/Vasopressin Complex
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Molecular simulation study of cooperativity in hydrophobic association
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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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Professor Edward Borowski and molecular aspects of chemotherapy.
PublicationPrzedstawiono sylwetkę naukową i krótkie podsumowanie najważniejszych osiągnięć badawczych profesora Edwarda Borowskiego. Profesor Borowski jest autorem lub współautorem około 800 publikacji naukowych oraz 70 patentów, a jego prace były cytowane ponad 1100 razy. Do najważniejszych osiągnięć prof. Borowskiego i Jego zespołu naukowego należy zaliczyć: izolację i charakterystykę antybiotyków peptydowych, tetainy i edeiny oraz antybiotyków...
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Transcriptome Dynamics Underlying Planticine®-Induced Defense Responses of Tomato (Solanum lycopersicum L.) to Biotic Stresses
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Tuning of the plasmon resonance location in Au nanostructures coated with a ultrathin film of Al2O3 – Optical measurements and FDTD simulations
PublicationThe Au nanostructures have been coated with an ultra-thin films of amorphous aluminium oxide. Optical absorption spectra show the influence of the thickness of Al2O3 on plasmon resonance wavelength. The observed red-shift of the resonance location with the increase of the thickness of the Al2O3 film, can be explained by the change in the dielectric function of this film. It allows control of the optical spectra of the coated particles....
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NUMERICAL SIMULATIONS OF HONING PROCESS OF THIN WALL CYLINDER LINERS, WITH CONSTANT AND WITH VARIABLE THICKNESS OF WALL OF HONED PARTS
PublicationNumerical simulations of honing process of thin-wall cylinder liners, with constant and with variable thickness of the wall of honed workpieces can improve and can help to conduct the experimental research of honing process and can improve the honing process. A very valuable research assumption, before performing the numerical analysis of computer simulation of honing process, is the measurement of the real geometry of the honing...
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Molecular biaxiality determines the helical structure – infrared measurements of the molecular order in the nematic twist-bend phase of difluoro terphenyl dimer
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Quantitative assessment of the influence of tensile softening of concrete in beams under bending by numerical simulations with XFEM and cohesive cracks
PublicationResults of the numerical simulations of the size effect phenomenon for concrete in comparison with experimental data are presented. In-plane geometrically similar notched and unnotched beams under three-point bending are analyzed. EXtended Finite Element Method (XFEM) with a cohesive softening law is used. Comprehensive parametric study with the respect to the tensile strength and the initial fracture energy is performed. Sensitivity...
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Multi-fidelity EM simulations and constrained surrogate modelling for low-cost multi-objective design optimisation of antennas
PublicationIn this study, a technique for low-cost multi-objective design optimisation of antenna structures has been proposed. The proposed approach is an enhancement of a recently reported surrogate-assisted technique exploiting variable-fidelity electromagnetic (EM) simulations and auxiliary kriging interpolation surrogate, the latter utilised to produce the initial approximation of the Pareto set. A bottleneck of the procedure for higher-dimensional...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublicationBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
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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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An MOR Algorithm Based on the Immittance Zero and Pole Eigenvectors for Fast FEM Simulations of Two-Port Microwave Structures
PublicationThe aim of this article is to present a novel model-order reduction (MOR) algorithm for fast finite-element frequency-domain simulations of microwave two-port structures. The projection basis used to construct the reduced-order model (ROM) comprises two sets: singular vectors and regular vectors. The first set is composed of the eigenvectors associated with the poles of the finite-element method (FEM) state-space system, while...
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Molecular Catalysis
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 500 mm stroke subjected only to a mass load of 2570 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 63 mm piston diameter and 500 mm stroke subjected only to a mass load of 1640 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 63 mm piston diameter and 150 mm stroke subjected only to a mass load of 750 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 150 mm stroke subjected only to a mass load of 1100 g
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 150 mm stroke subjected only to a mass load of 1530 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 100 mm stroke subjected only to a mass load of 1650 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 63 mm piston diameter and 100 mm stroke subjected only to a mass load of 1640 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 300 mm stroke subjected only to a mass load of 1650 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 100 mm stroke subjected only to a mass load of 930 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 300 mm stroke subjected only to a mass load of 930 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 150 mm stroke subjected only to a mass load of 1650 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 100 mm stroke subjected only to a mass load of 450 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 500 mm stroke subjected only to a mass load of 1530 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 63 mm piston diameter and 300 mm stroke subjected only to a mass load of 1680 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 50 mm piston diameter and 150 mm stroke subjected only to a mass load of 930 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 63 mm piston diameter and 100 mm stroke subjected only to a mass load of 560 g
Open Research DataThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....