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Search results for: COMPUTATIONAL FLUID DYNAMICS
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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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Machine Dynamics Research
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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational methods for the identification of novel targets and to...
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COMPUTATIONAL MECHANICS
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Synthesis, spectroscopy and computational studies of some biologically important hydroxyhaloquinolines and their novel derivatives
PublicationA series crystalline compounds of methyl and phosphinyl derivatives of 2-methylquinolin-8-ol (1a) and related 5,7-dichloro-2-methylquinolin-8-ol (1b) were quantitatively prepared and characterized by microanalysis, IR, UV-vis and multinuclear NMR spectroscopy. Five of them have been characterized by single crystal X-ray diffraction method. The known compounds, 8-methoxy-2-methylquinoline (2a) and 8-methoxyquinoline (2d), were synthesised...
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Synthesis, spectroscopy and computational studies of some novelphosphorylated derivatives of quinoline-5,8-diones
PublicationThe neutral phosphorus nucleophiles such as R2P(=Y)M allowed the radical addition to 2-methyl-5,8-dioxo-5,8-dihydroquinoline-7-amine and N-(2-methyl-5,8-dioxo-5,8-dihydroquinolin-7-yl)acetamide giving exclusively O-phosphorylated products. All products were quantitatively prepared and characterized by microanalysis, and multinuclear NMR spectroscopy. Seven of them, have been characterized by single crystal X-ray diffraction method....
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Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis
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Gradient theories of ductile and brittle damage: a thermodynamical consistent framework and computational issues
PublicationPrzedstawiono termodynamicznie zgodny opis gradientowych teorii plastycznego i kruchego zniszczenia. Przyjęto, że propagujące mikro-zniszczenia posiadają bezwładność i ich ruch jest wywołany przez mikro-siły, które spełniają ich własne dynamiczne równania równowagi. Poza równaniami równowagi makro- i mikro-sił sformułowano pierwsze i drugie prawo termodynamiki na poziomie mikro i mezo. Zakładając ogólną formę równań konstytutywnych...
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A proposition of the computational model for the dynamic analysis of stress and strain distribution in the hip joint
PublicationCelem pracy jest sformułowanie zadania modelowania dynamiki odkształceń i rozkładu naprężeń stawu biodrowego, a w szczególności kości udowej, pod wpływem sił mięśniowych oraz zadanych sił zewnętrznych. Rozwiązanie tego zadania pozwoli wyjaśnić niektóre zjawiska np. jakie ruchy kości udowej oraz jakie materiały użyte do jej alloplastyki są przyczyną urazów i poważnych uszkodzeń. Omówiono problemy związane z zastosowaniem metody...
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Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
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Consensus models: Computational complexity aspects in modern approaches to the list coloring problem
PublicationArtykuł poświęcony jest nowym modelom konsensusowego kolorowania grafów. Artykuł zawiera omówienie trzech takich modeli, analizę ich złożoności obliczeniowej oraz wielomianowy algorytm dla częściowych k-drzew, dla tzw. modelu addytywnego.
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Scheduling of identical jobs with bipartite incompatibility graphs on uniform machines. Computational experiments
PublicationWe consider the problem of scheduling unit-length jobs on three or four uniform parallel machines to minimize the schedule length or total completion time. We assume that the jobs are subject to some types of mutual exclusion constraints, modeled by a bipartite graph of a bounded degree. The edges of the graph correspond to the pairs of jobs that cannot be processed on the same machine. Although the problem is generally NP-hard,...
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublicationIn nature, numerous biomolecules are implicated in charge transfer (CT) and energy transfer (ET) mechanisms crucial for fundamental processes such as photosynthesis. Unveiling these mechanisms is pertinent to multiple disciplines including chemistry, engineering and biochemistry. This letter presents a study involving two molecules forming a model system with efficient ET properties. Specifically, their complex exhibits dark quenching...
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Low-energy positron scattering from gas-phase tetrahydrofuran: A quantum treatment of the dynamics and a comparison with experiments
PublicationIn this paper we report new quantum calculations of the dynamics for low-energy positrons interacting with gaseous molecules of tetrahydrofuran. The new quantum scattering cross sections are differential and integral cross sections at collision energies between 1.0 and 25.0 eV and include a careful treatment of the additional effects on the scattering process brought about by the permanent dipole moment of the target molecule....
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FLUID PHASE EQUILIBRIA
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Independent dynamics of low, intermediate, and high frequency spectral intracranial EEG activities during human memory formation
PublicationA wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various frequency ranges are coordinated across the space of the human cortex and time of memory processing is inconclusive. They can either be coordinated together across the frequency spectrum at the same cortical site and time or induced independently in particular bands. We used a large dataset of human intracranial...
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The number of work permits issued (in thousands) and the dynamics of changes (%, year on year) in 2008-2018
Open Research DataThe number of work permits issued increased from 18,000 in 2008 to nearly 329 thousand in 2018, i.e. by 18 times. The largest increases in nominal terms occurred in 2015-2018, noting a change from 66 thousand in 2015, up to 127 thousand in 2016, 236,000 in 2017 and 329 thousand in 2018. The number of permits issued (in thousands) and the dynamics of...
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DISCRETE DYNAMICS IN NATURE AND SOCIETY
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Transportmetrica B-Transport Dynamics
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Journal of Spatial and Organizational Dynamics
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Dynamics of Partial Differential Equations
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International Journal of Dynamics and Control
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Journal of Applied Nonlinear Dynamics
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Nonlinear Dynamics and Systems Theory
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JOURNAL OF GUIDANCE CONTROL AND DYNAMICS
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Russian Journal of Nonlinear Dynamics
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STUDIES IN NONLINEAR DYNAMICS AND ECONOMETRICS
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Redundantly Actuated 3RRR Parallel Planar Manipulator - Numerical Analyses of its Dynamics Sensitivity on Modifications of its Platform’s Inertia Parameters
PublicationIn the paper, numerical analyses, as well as dynamics of a complex mechanism, are presented. Two objectives are crucial for the paper: inverse dynamic model is needed (dedicated to be use in the model predictive controller); an identification method is searched (some trajectory parameters are controlled, when specific trajectory is tracked under an open-loop model-based control), as selected parameters must be identified for the...
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Experimental research on effectiveness of the magnetic fluid seals for rotary shafts working in water
PublicationUszczelnianie wałów obrotowych, łożysk i innych zespołów mechanicznych, za pomocą cieczy magnetycznej, tworzącej przegrodę uszczelniającą utrzymywaną siłami pola magnetycznego jest techniką uszczelniania, stosowaną z powodzeniem w urządzeniach pracujących w środowisku gazowym przy ciśnieniu do około 1,0 MPa. Uszczelnienia te umożliwiają również skuteczne rozwiązywanie problemu szczelności przepustów stałych i ruchowych w urządzeniach...
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The Hydromechanics of Edema Fluid in Lymphedematous Lower Limb During Intermittent Pneumatic Compression
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A thermodynamic criterion for selection of working fluid for subcritical and supercritical domestic micro CHP
PublicationW pracy przedstawiono kryterium termodynamiczne doboru czynnika roboczego dla mikrosiłowni pracującej w warunkach podkrytycznych i nadkrytycznych. Przeanalizowano 20 płynów możliwych do wykorzystania w mikrosiłowni ORC. Z analizy wynika, że najlepszym płynem roboczym jest etanol, R123 oraz R141b.
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Working fluid selection for Organic Rankine Cycle applied to heat recovery systems
PublicationPrzedstawiono algorytm obliczeń sprawności systemu ORC na bazie dużej liczby cieczy organicznych.
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Human amniotic-fluid-derived stem cells: a unique source for regenerative medicine
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Selection of Materials Used in Viscous Clutch With ER Fluid Working in Special Conditions
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Three dimensional fluid equations from distribution function with discontinuity in velocity space
PublicationUkład równań typu hydrodynamicznego dla rozwarstwionego gazu w polu grawitacyjnym jest wyprowadzony z równania BKG przy użyciu metody kawałków ciągłej funkcji dystrybucji. Otrzymany układ równań uogólnia układ Naviera-Stokesa dla dowolnych liczb Knudsena.
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The Use of Liquid Crystal Thermography an Image Processing in Heat and Fluid-Flow Research
PublicationLiquid crystal thermography (LCT) have been used in many technical, industrial and biomedical applications [1]. During over 20 years it has been successfully applied in Department of Energy and Industrial Apparatus at Gdansk University of Technology for visualization of steady-state and transient temperature fields. In order to demonstrate feasibility of LCT techniques in practical heat transfer contexts, the authors have performed...
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Are firefighters able to perform intraosseous access and start fluid resuscitation in an anaphylactic patient?
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Fluid–Structure Interaction methods for the progressive anatomical and artificial aortic valve stenosis
PublicationCardiovascular system diseases, as aortic valve stenosis, are the main cause of mortality and morbidity among patients. There is still a room for enhancement of the diagnostic and therapeutic procedures, which will lead to improvement of the treatment. One of the remedies are the computer tools to support the medical diagnoses and prostheses design. The development of a procedure for modeling the aortic valves: anatomical tricuspid...
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Fluid Mechanics PG 00049759, Laboratorium, sem. 4, lato 2023
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Fluid Mechanics PG 00049759, Laboratorium, sem. 4, lato 2024
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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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Metodyka badań rozwojowych nowego typu silników i pomp satelitowych
PublicationResearch and development of new type satellite motors and satellite pumps SM with small geometrical displacement, from 5 to 73 cm3/rev, has been conducted in cooperation with Stosowanie Maszyn company from Katowice (manufacturer of motors and pump SM). The improvement of construction of those machines, especially construction of axial compensation and construction of fluid distribution channels have been the main problem of research...
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Natural Deep Eutectic Solvents as Agents for Improving Solubility, Stability and Delivery of Curcumin
PublicationPurpose Study on curcumin dissolved in natural deep eutectic solvents (NADES) was aimed at exploiting their beneficial properties as drug carriers. Methods The concentration of dissolved curcumin in NADES was measured. Simulated gastrointestinal fluids were used to determine the concentration of curcumin and quantum chemistry computations were performed for clarifying the origin of curcumin solubility enhancement in NADES. Results NADES...
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Numerical Study of the Impinging Jets Formed by an Injector with Different Nozzle Diameters
PublicationThe collision of two or more liquid jets may provide considerable atomisation and efficient mixing of injected substances at the same time. This phenomenon is used, among others, in rocket engines, where the fuel and oxidiser are introduced separately and almost immediately mixed through self-impingement. Depending on the injection and operating conditions, diverse configurations of impinging jets are used, such as doublets,...
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A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin
PublicationIn this study, we established a dynamic micromodel of urinary tract infection to analyze the impact of UT-segment-specific urinary outflow on the persistence of E. coli colonization. We found that the adherence of Dr+ E. coli to bladder T24 transitional cells and type IV collagen is maximal at lowest shear stress and is reduced by any increase in flow velocity. The analyzed adherence was effective in the whole spectrum of physiological...
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Alternative convolution approach to friction in unsteady pipe flow
PublicationIn the paper some aspects of the unsteady friction in pipe flow expressed by the convolution are analyzed. This additional term introduced into the motion equation involves the accelerations of fluid occurring in the past and a weighting function. The essence of such approach is to assume the appropriate form of weighting function. However, until now no fully reliable formula for this function has been found. To avoid some inconveniences...
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Comparative analysis of mechanical conditions in bone union following first metatarsophalangeal joint arthrodesis with varied locking plate positions: A finite element analysis
PublicationFirst metatarsophalangeal joint arthrodesis is a typical medical treatment performed in cases of arthritis or joint deformity. The gold standard for this procedure is arthrodesis stabilisation with the dorsally positioned plate. However, according to the authors’ previous studies, medially positioned plate provides greater bending stiffness. It is worth to compare the mechanical conditions for bone formation in the fracture callus...
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Thermal Energy Storage with PCMs in Shell-and-Tube Units: A Review
PublicationThe paper presents a survey of the experimental and numerical studies of shell-and-tube systems in which phase change material (PCM) is used. Due to the multitude of design solutions for shell-and-tube systems, the emphasis is placed on double-tube (DT), triplex-tube (TT), and multitube (MT) units. Additionally, only single-pass systems are considered. Particular attention is paid to the method of heat transfer intensification....
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A Concept for Safe and Less Expensive Acceleration of a Marine Steam Turbine Start-up
PublicationThis paper analyses the issue of accelerated start-up of a marine steam turbine, which is an important problem because the start-up of a steam machine involves the combustion of fuel that is not transformed into useful energy. To find novel technologies that offer improvements in this aspect is essential due to restrictions on reducing ship emissions. Thus, the shorter the start-up time, the better for the environment and economy....