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Search results for: DYNAMIC PARALLELISM
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Analytical method of determining dynamic properties of thermocouples used in measurements of quick – changing temperatures of exhaust gases in marine diesel engines
PublicationThe article presents selected issues of mathematical modeling of heat exchange between the thermocouple and the exhaust gas flowing them, in unsteady conditions. On the way of energy balancing consideration of thermodynamic processes developed differential equations describing the dynamic properties for three versions of the design sheathed thermocouples: with weld isolated from the sheath, with weld welded the sheath and with...
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Evaluation of citric acid corrosion inhibition efficiency and passivation kinetics for aluminium alloys in alkaline media by means of dynamic impedance monitoring
PublicationA novel approach is proposed for constructing the adsorption isotherm in corrosion studies, based on a well-known interaction between citric acid and aluminium in alkaline electrolytes. Our approach utilizes the instantaneous impedance measurements via Dynamic Electrochemical Impedance Spectroscopy in galvanostatic mode (g-DEIS). Unlike other common tools, g-DEIS delivers exact information about the concentration required for full...
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A dynamic vehicle-bridge model based on the modal identification results of an existing EN57 train and bridge spans with non-ballasted tracks
PublicationThis paper addresses the methodology of the bridge-vehicle dynamic model definition based on the free response measurements of an existing train and existing bridge spans. In the case of the railway vehicle, the methodology uses the impulse excitations of a single car by means of the wedge method. In the case of the bridge spans, free responses are collected after the passages of trains. The global modal parameters (frequencies...
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Effect of Pin Shape on Thermal History of Aluminum-Steel Friction Stir Welded Joint: Computational Fluid Dynamic Modeling and Validation
PublicationThis article studied the effects of pin angle on heat generation and temperature distribution during friction stir welding (FSW) of AA1100 aluminum alloy and St-14 low carbon steel. A validated computational fluid dynamics (CFD) model was implemented to simulate the FSW process. Scanning electron microscopy (SEM) was employed in order to investigate internal materials’ flow. Simulation results revealed that the mechanical work...
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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Combining Computational Fluid Dynamics with a Biokinetic Model for Predicting Ammonia and Phosphate Behavior in Aeration Tanks
PublicationThe aim of this study was to use computational fluid dynamics for predicting the behavior of reactive pollutants (ammonia and phosphate) in the aerobic zone of the bioreactor located at the Wschod wastewater treatment plant in Gdansk, Poland. The one-dimensional advection-dispersion equation was combined with simple biokinetic models incorporating the Monod-type expressions as source terms for the two pollutants. The problem was...
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Orientational Order and Dynamics of Nematic Multipodes Based on Carbosilazane Cores Using Optical and Dielectric Spectroscopy
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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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Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublicationW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.
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On dynamics of flexible branched shell structures undergoing large overall motion using finite elements
PublicationZaprezentowano autorski algorytm do analizy dynamicznej powłok sprężystych oparty na niejawnym schemacie Newmarka. Rozważania dotyczą całkowania po czasie dynamicznych równań ruchu sformułowanych w ramach nieliniowej sześcioparametrowej teorii powłok. Opracowanie zawiera pewne elementy analizy statycznej, poprzedzającej badania dynamiczne. Przykłady numeryczne prezentują zastosowanie algorytmu stanowią podstawową część pracy.
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublicationTime-dependent density functional theory calcula- tions combinedwith the Marcus theory of electron transfer (ET) were app lied on the molecular photocatalys t [(tbbpy) 2 Ru(tpph z)PdC l 2 ] 2 + in order to elucidate thelight-in- duced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational resultsshow that after the initial excitation, metal (Ru) to ligand (tpphz)chargetransfer...
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Aerodynamic shape optimization by variable-fidelity computational fluid dynamics models: a review of recent progress
PublicationA brief review of some recent variable-fidelity aerodynamic shape optimization methods is presented.We discuss three techniques that—by exploiting information embedded in low-fidelity computationalfluid dynamics (CFD) models—are able to yield a satisfactory design at a low computational cost, usu-ally corresponding to a few evaluations of the original, high-fidelity CFD model to be optimized. Thespecific techniques considered here...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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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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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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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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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Computational Fluid Dynamics Simulation of Gas–Liquid Multiphase Flow in T-junction for CO2 Separation
PublicationThe article presents the results of a computational fluid dynamics (CFD) analysis of gas-liquid multiphase flow. The simulation was conducted using CFD code and the Euler–Euler approach. The presented study relates to the non–reactive, steady-state, turbulent flow of water and carbon dioxide mixture in a 3D pipe. Separation phenomenon between phases is observed. The solution was obtained using a mixture model. Different values...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Formation of carbon monoxide by radiative association: a quantum dynamical study
PublicationRate coefficients for the formation of carbon monoxide (CO) by radiative association of carbon and oxygen atoms are computed using quantum dynamical simulations. At temperatures above 10 K CO radiative association is dominated by C(3P) and O(3P) approaching on the A1Π potential energy curve. The rate coefficient is estimated as k=A(T/300 K)αexp−β/T with A= 1.39 × 10−18 cm3 s−1, α=−0.016 and β= 92.2 for temperatures between 6 and...
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Identyfikacja dynamiki elektrowni wiatrowej na podstawie danych pomiarowych
PublicationW referacie przedstawiono wyniki badań symulacyjnych przeprowadzonychz wykorzystaniem standardowych modeli identyfikacyjnych programu Matlab. Zawarto opisbadanego obiektu, przebiegu procesu identyfikacji, wykorzystanych modeli, oraz wybrane wynikibadań. Uzyskane wyniki pozwoliły sformułować uwagi ogólne dotyczące przydatnościwspomnianych modeli do celów identyfikacji dynamiki elektrowni wiatrowej.
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Magnetically induced dynamical stability of a Fe monolayer on W(110)
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Dynamical properties of pnictide ZnSnP2 from ab initio calculations
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Frequency response based identification of fractional order dynamical systems
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Wykorzystanie strumienia masy w badaniach dynamiki napędów pneumatycznych
PublicationW pracy opisano zastosowanie znormalizowanego modelu masowego natężenia przepływu powietrza w symulacyjnych badaniach napędu pnaumatycznego.
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Model dynamiki sprężarki wirnikowej z regulowanymi łopatkami kierownicy
PublicationPrzedstawiono model dynamiki sprężarki wirnikowej turbiny gazowej współpracującej z siecią elektroenergetyczną. Model symuluje charakterystyki statyczne i dynamiczne sprężarki wirnikowej z regulowanym kątem nastawienia łopatek kierowniczych wlotowych. Za pomocą przedstawionego modelu dynamiki bloku elektroenergetycznego turbiny gazowej symulowano charakterystyki statyczne układu oraz charakterystyki dynamiczne. Odpowiedzi skokowe...
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Modelowanie dynamiki pojazdu w badaniach na hamowni silnikowej
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Dynamika bezzałogowego aparatu latającego w układzie czterowirnikowego pionowzlotu
PublicationDziałanie maszyn, w tym również pojazdów latających, jest nieodłącznie związane z przekazywaniem oddziaływań siłowych: statycznych i dynamicznych. Dynamika jest działem mechaniki zajmującym się makroskopowym ruchem ciał przy uwzględnieniu przyczyn wywołujących ten ruch. Pierwszym etapem analizy dynamiki konstrukcji są zwykle obliczenia wartości i postaci drgań własnych modelu konstrukcji. Drgania własne zwykle ulegają szybkiemu...
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Symulator szybkich procesów dynamiki reaktora jądrowego wodno ciśnieniowego
PublicationArtykuł przedstawia symulator dynamiki reaktora jądrowego (RJ) zbudowany w oparciu o punktowe modele matematyczne procesów reaktora typu wodnego ciśnieniowego (ang. Pressurized Water Reactor – PWR) i zaimplementowany w środowisku MATLAB/Simulink. Symulator wykorzystywany jest obecnie jako narzędzie pomocne w dydaktyce i wstępnych badaniach w zakresie energetyki jądrowej na Politechnice Gdańskiej. W pierwszej części artykuł Autorzy...
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Dynamika niskonapięciowego łuku zwarciowego przemieszczającego się wzdłuż szyn
Publicationw artykule przedstawiono zagadnienia związane z jednym z najpoważniejszych zakłóceń pracy urządzeń rozdzielczych, jakimi są zwarcia łukowe. szczególną uwagę poświęcono wpływowi znaczeniu zmian prędkości chwilowej przemieszczającego się łuku awaryjnego. w artykule zamieszczono opis prostego modelu ruchu niskonapięciowego łuku wielkoprądowego palącego się pomiędzy równoległymi, prostoliniowymi szynami swobodnie w powietrzu o ciśnieniu...
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Modelowanie i symulacja dynamiki ruchu trakcyjnego odbieraka prądu
PublicationW artykule przedstawiono dwa modele matematyczne kolejowych odbieraków prądu. Model podstawowy opracowano na podstawie analizy konstrukcji odbieraka ze stopniami swobody w ruchu obrotowym i postępowym. Drugi tzw. model zastępczy ma obydwa stopnie swobody w ruchu postępowym. Przedstawiono prosty sposób wyznaczenia wartości parametrów modelu zastępczego na podstawie wyników symulacji modelu odbieraka podstawowego. Model zastępczy,...
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Ekspertyza techniczna dot. uwarunkowań w zakresie dynamiki mostów
PublicationReferat jest pewnym przyczynkiem do dyskusji nad formalnymi uwarunkowaniami ujętymi w różnych dokumentach, a dotyczących wymagań z zakresu dynamiki mostów. W szczególności zapisu cyt.: ,,Stany graniczne użytkowania uważa się za przekroczone, jeżeli wymagania użytkowe dotyczące konstrukcji obiektu nie są dotrzymane. Oznacza to, że w konstrukcji obiektu nie powinny wystąpić: … 4) drgania własne o częstotliwości mniejszej niż 3 Hz”;...
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Znaczenie i dynamika efektuacji w działaniach zespołów projektowych IT
PublicationCel: Celem opracowania jest sprawdzenie, na ile wdrażanie zasad efektuacji jest korzystne dla efektywności zespołów projektowych pracujących nad innowacyjnymi rozwiązaniami i czy wpływa na ich satysfakcję. Metodyka badań: Badania ilościowe zrealizowano w studenckich zespołach projektowych z branży IT, opracowujących rozwiązania na zlecenie interesariuszy zewnętrznych. Do pomiaru zmiennych wykorzystano autorskie kwestionariusze....
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Multicast Traffic Throughput Maximization through Joint Dynamic Modulation and Coding Schemes Assignment, and Transmission Power Control in Wireless Sensor Networks
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Performance evaluation of an improved optical computed tomography polymer gel dosimeter system for 3D dose verification of static and dynamic phantom deliveries
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Fixed final time and free final state optimal control problem for fractional dynamic systems – linear quadratic discrete-time case
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Influence of gas turbine controller adjustment on propulsion system behaviour in high sea conditions. Part 1. The dynamic model of propulsion system.
PublicationDo badań przyjęto układ napędowy okrętowy z turbinami gazowymi napędzającymi poprzez przekładnię mechaniczną zębatą śrubę okrętową o zmiennym skoku. Nakład napędowy statku z turbinami gazowymi napędzającymi śrubę nastawną oddziałują wymuszenia zarówno od nastaw prędkości obrotowej wału śrubowego jaki skoku śruby napędowej, ale również istnieje silna reakcja od falowania morza (stanu morza) na pracę układu napędowego. Zbudowano...
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Increased inspiratory resistance alters the cardiac contribution to the dynamic relationship between blood pressure and pial artery pulsation oscillations in healthy subjects
PublicationThere is increasing evidence that heart performance directly influences cerebral perfusion. We hypothesised that increased inspiratory resistance will affect the cardiac contribution to the relationship between blood pressure and pial artery pulsation oscillations.
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Analysis of the Dynamic Height Distribution at the Estuary of the Odra River Based on Gravimetric Measurements Acquired with the Use of a Light Survey Boat—A Case Study
PublicationLaCoste) for determining the dynamic height along the Odra River, in northwest Poland. The gravity measurement campaign described in this article was conducted on a small, hybrid-powered survey vessel (overall length: 9.5 m). We discuss a method for processing the results of gravimetric measurements performed on a mobile platform affected by strong external disturbances. Because measurement noise in most cases consists of signals...
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Differential Quadrature Method for Dynamic Buckling of Graphene Sheet Coupled by a Viscoelastic Medium Using Neperian Frequency Based on Nonlocal Elasticity Theory
PublicationIn the present study, the dynamic buckling of the graphene sheet coupled by a viscoelastic matrix was studied. In light of the simplicity of Eringen's non-local continuum theory to considering the nanoscale influences, this theory was employed. Equations of motion and boundary conditions were obtained using Mindlin plate theory by taking nonlinear strains of von Kármán and Hamilton's principle into account. On the other hand, a...