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Search results for: DYNAMICS
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Modelling of high frequency dynamic responses of engineering structures
PublicationModelling of high frequency dynamic responses of engineering structures, especially those related to wave propagation, is a real numerical challenge. Nowadays most of numerical models, used for that purpose, are based on the application of various finite element techniques. However, finite element discrete models may also be considered as possessing certain periodic structures, which may manifest themselves in particular scenarios....
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Tomasz Wąsowicz dr hab.
PeopleTomasz Wąsowicz's research was first related to high-resolution atomic spectroscopy and focused on measurements and analysis of the transition probabilities of the forbidden lines, the hyperfine and isotopic structure of spectral lines of heavy elements, Stark effect in the helium atom. Tomasz Wąsowicz currently studies physicochemical processes occurring during interactions of various forms of radiation with atoms and molecules...
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A robust sliding mode observer for non-linear uncertain biochemical systems
PublicationA problem of state estimation for a certain class of non-linear uncertain systems has been addressed in this paper. In particular, a sliding mode observer has been derived to produce robust and stable estimates of the state variables. The stability and robustness of the proposed sliding mode observer have been investigated under parametric and unstructured uncertainty in the system dynamics. In order to ensure an unambiguous non-linear...
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Simulation Studies of Control Systems for Doubly Fed Induction Generator Supplied by the Current Source Converter
PublicationThe control system for a Doubly Fed Induction Generator (DFIG) supplied by a grid-connected Current Source Converter (CSC) is presented in this paper. Nonlinear transformation of DFIG model to the multi-scalar form is proposed. The nonlinear control strategy of active and reactive power of DFIG is realized by feedback linearization. In the proposed control scheme, the DFIG model and CSI parameters are included. Two Proportional-Integral...
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Billiard in a rotating half-plane
PublicationThe main objective of this research is to study the properties of a billiard system in an unbounded domain with moving boundary. We consider a system consisting of an infinite rod (a straight line) and a ball (a massless point) on the plane. The rod rotates uniformly around one of its points and experiences elastic collisions with the ball. We define a mathematical model for the dynamics of such a system and write down asymptotic...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
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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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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Rotational state-changing collisions of C2H− and C2N− anions with He under interstellar and cold ion trap conditions: A computational comparison
PublicationWe present an extensive range of quantum calculations for the state-changing rotational dynamics involving two simple molecular anions that are expected to play some role in the evolutionary analysis of chemical networks in the interstellar environments, C2H− (X1Σ+) and C2N− (X3Σ−), but for which inelastic rates are only known for C2H−. The same systems are also of direct interest in modeling selective photo-detachment experiments...
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Janusz Cieśliński prof. dr hab. inż.
PeopleHe was born on April 15, 1954 in Slupsk. He graduated from the Faculty of Mechanical Engineering at Gdańsk University of Technology (1978). In 1986 he received the title of Doctor, in 1997 he obtained the title of Ph.D. with habilitation, and in 2006 he received the title of Professor. He worked as head of department and vice-dean for Education at the Faculty of Mechanical Engineering for two terms (2002-2008). His research interests...
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Comparative analysis of the theoretical models of ideal propulsor, ideal fluid brake, ideal screw propeller and ideal axial wind turbine
PublicationThe article presents a detailed discussion of four different fluid dynamics devices.These devices are presented with all relevant mathematical formulae regarding the forces, the power and the efficiency. It is demonstrated that application of the Betz theorem to axial wind turbines is not correct and it underestimates the maximujm achievable efficiency. This conclusion is supported by numerical calculations.
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Ampacity of power cables exposed to solar radiation – recommendations of standards vs. CFD simulations
PublicationThe aim of the paper is to evaluate the ampacity of a low-voltage single power cable according to: 1) recommendations of the standard IEC 60287, 2) a Computational Fluid Dynamics method, implemented in Ansys software; and comparison of the results obtained for these two cases. Moreover, limitations of recommendations of the above mentioned standard are indicated.
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The share of employment in individual cities in total employment in the BPO/SSC sector in Poland
Open Research DataEmployment in the sector in 2019 was almost three times higher than in 2013. Throughout the analyzed period, employment grew year on year. The dynamics of changes ranged from 10% in 2019 to nearly 43% in 2016, when the highest increase in employment in the sector in nominal terms was at the level of 64,000.BPO, SSC / GBS, IT, R&D centers generated...
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Comparison of the number of foreigners registered for retirement and disability pension insurance - at the end of the year
Open Research DataThe increase in the number of foreigners registered for retirement and disability insurance was characterized by the highest dynamics in the case of non-EU migrants, in particular Ukrainian citizens (26-time increase in the period 2008-2018; impressive nominal growth from 16.2 to 420.7 thousand economic migrants) and Georgia (a 37-time increase). Also...
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Wybrane elementy nieliniowej dynamiki struktur kratowych
PublicationW pracy jest dyskutowany problem nieliniowej dynamiki struktur kratowych. Zastosowano stacjonarny opis Lagrange'a (ang. Total Lagrange), pokazano silne i słabe sformułowanie dla pręta kratowego, jego aplikację do MES. W zakresie całkowania równań ruchu przedstawiono metodę Newmarka i metodę-a dla problemów liniowych i nieliniowych. Załączony przykład numeryczny ilustruje cechy przedstawionych metod.
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Karolina Krośnicka dr hab. inż. arch.
PeopleKarolina A. Krośnicka, Ph.D., D.Sc., Eng. Arch., is associated professor at Department of Urban Design and Regional Planning, Faculty of Architecture, Gdańsk University of Technology (Poland). For many years (1998 – 2016) she was employed at the Department of Transport and Logistics at the Faculty of Navigation at Gdynia Maritime University (Gdynia, Poland), where she was mostly involved in issues connected with seaports and port...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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An observability and detectability analysis for non-linear uncertain CSTR model of biochemical processes
PublicationThe problem of proving observability/detectability properties for selected non-linear uncertain model of biochemical processes has been addressed in this paper. In particular, the analysis of observability/detectability in the face of parametric and unstructured uncertainty in system dynamics transformed into unknown inputs, and unknown initial conditions has been performed. Various sets of system measured outputs were taken into...
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TIME-DOMAIN NUMERICAL EVALUATION OF SHIP RESISTANCE AND MOTION IN REGULAR WAVES BY USING THE CFD URANS METHOD
PublicationTaking into account the International Maritime Organisation’s (IMO) strategy to radically reduce the GHG emitted by the shipping industry towards zero emission operation, today's assessment of ship behaviour in waves, its seakeeping characteristics and resistance and their interrelation with fuel consumption and emissions are one of the most attended research subject. There are three methods to conduct this analysis, which are...
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Wavepacket of the Universe and its Spreading
PublicationWavepackets in quantum mechanics spread and the Universe in cosmology expands. We discuss a formalism where the two effects can be unified. The basic assumption is that the Universe is determined by a unitarily evolving wavepacket defined on space-time. Space-time is static but the Universe is dynamic. Spreading analogous to expansion known from observational cosmology is obtained if one regards time evolution as a dynamical process...
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A new assay for simultaneous identification and differentiation of Klebsiella oxytoca strains
PublicationBacterial strain typing, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics.
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The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
Open Research DataThe developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic...
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Obliczeniowa dynamika płynów w analizie zagadnień smarowaniahydrodynamicznego = CFD in analysis of hydrodynamic lubrication
PublicationW pracy przedstawiono wybrane problemy związane z wykorzystaniem obliczeniowej dynamiki płynów (ang. CFD - Computational Fluid Dynamics)do obliczeń łożysk hydrodynamicznych. Omówione zostało zagadnienie przyjmowania rodzaju przepływu w analizie łożyska oraz przyjmowania warunków brzegowych dotyczących wymiany ciepła oraz problem zbieżności obliczeń.
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On the use of a charge balancing method for low energy measurements
PublicationThe paper presents the method for the estimation of the energy consumption of the low-power microcontroller-based devices. Due to high dynamics of the changes of the supply current of the tested devices during the operational cycle, the consumed energy estimation is not easy. In order to avoid disadvantages of known methods, the charge balancing method was employed similarly like in some types of A/D converters.
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Model of aeration system at biological wastewater treatment plant for control design purposes
PublicationThe wastewater treatment plant (WWTP) is a dynamic, very complex system, in which the most important control parameter is the dissolved oxygen (DO) con-centration. The air is supplied to biological WWTP by the aeration system. Aera-tion is an important and expensive activity in WWTP. The aeration of sewage ful-fils a twofold role. Firstly, oxygen is provided as the main component for biolog-ical processes. Secondly, it supports...
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Chronographic Imprint of Age-Induced Alterations in Heart Rate Dynamical Organization
PublicationBeat-to-beat changes in the heart period are transformed into a network of increments between subsequent RR-intervals, which enables graphical descriptions of short-term heart period variability. Three types of such descriptions are considered: (1) network graphs arising from a set of vertices and directed edges, (2) contour plots of adjacency matrices A, representing the networks and transition matrices T, resulting from A, and (3)...
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Students, graduates and lecturers at non-public universities in 1997-2011
Open Research DataAt the beginning of the 2010/2011 academic year, there were 328 private universities educating 580.1 thousand students (i.e. 31.5% of all students). Compared to the previous year, there was a slight decrease in the number of non-public universities, moreover, the number of young people studying there decreased by 8.4%.
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Combined Single Neuron Unit Activity and Local Field Potential Oscillations in a Human Visual Recognition Memory Task
PublicationGOAL: Activities of neuronal networks range from action potential firing of individual neurons, coordinated oscillations of local neuronal assemblies, and distributed neural populations. Here, we describe recordings using hybrid electrodes, containing both micro- and clinical macroelectrodes, to simultaneously sample both large-scale network oscillations and single neuron spiking activity in the medial temporal lobe structures...
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Multiple-channel frequency-adaptive active vibration control using SONIC
PublicationSONIC (self-optimizing narrowband interference canceller) is an acronym of a new approach to rejection of sinusoidal disturbances acting at the output of a discretetime stable linear plant with unknown and possibly timevarying dynamics. The paper presents two frequency-adaptive extensions of the multivariate SONIC algorithm. The efficacy of the proposed solutions is tested using our laboratory-scale active vibration control plant.
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Estimation of wind pressure acting on the new palm house in Gdansk
PublicationThis paper deals with the problem of numerical simulations of wind loads acting on a Palm House with complex geometry. Flow simulations with aid of computational fluid dynamics procedures have been performed to check if the pressure distributions for the structure are greater than those calculated using the standard design codes with assumption that the Palm House horizontal cross sections are described by smooth cylinders.
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Study of Aliphatic Polyurethanes by the Low-Field 1H NMR Relaxometry Method with the Inversion of the Integral Transformation
PublicationIn this paper, the distributions of the 1H nuclear magnetic resonance (NMR) spin–lattice and spin–spin relaxation times are used to characterize the mobility of different sections of macromolecules of aliphatic polyurethanes and the cross-linking density of polymer chains. The NMR relaxometry method with inversion of integral transformation is applied to study the effect of poly (ethylene glycol) and glycerol phosphate calcium...
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Modelowanie bezpiecznika rozłącznikowego w układach formowania impulsów wielkiej mocy
PublicationProblem modelowania bezpieczników o dużej dynamice wyłączania prądu jest zagadnieniem szeroko opisywanym w literaturze. Układy takie mogą być wykorzystane w szczególności do formowania impulsów wysokiego napięcia o wartościach rzędu setek kV, charakteryzujących się czasem trwania rzędu ułamka μs. W niniejszej pracy przedstawiono empiryczny model bezpiecznika wielotopikowego, rozszerzony w oparciu o wyniki badań eksperymentalnych.
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Control of mass concentration of reagents by sound in a gas with nonequilibrium chemical reactions
PublicationThe weakly nonlinear dynamics of a chemically reacting gas is studied. Nonlinear interaction of acoustic and nonacoustic types of motion are considered. We decompose the base equations using the relationships of the gas-dynamic perturbations specific for every type of motion. The governing equation for the mass fraction of a reagent influenced by dominating sound is derived and discussed. The conclusions concern the equilibrium...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Unusual divergence of magnetoacoustic beams
PublicationTwo-dimensional magnetosonic beams directed along a line forming a constant angle h with the equilibrium straight magnetic field are considered. Perturbations in a plasma are described by the system of ideal magnetohydrodynamic equations. The dynamics of perturbations in a beam are different in the cases of fast and slow modes, and it is determined by h and equilibrium parameters of a plasma. In particular, a beam divergence may...
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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Real-time simulator of agricultural biogas plant
PublicationThis article presents a real-time simulator of an agricultural biogas plant. The project contains biogas and biomass circuits simulation, as well as heating circuit simulation with a complete control system and visualization interface of the whole process. The software tool used to simulate the plant work is CFD (Computational Fluid Dynamics), which enables a user to create and test simulation objects based on fundamental physical...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Visualization of short-term heart period variability with network tools as a method for quantifying autonomic drive
PublicationWe argue that network methods are successful in detecting nonlinear properties in the dynamics of autonomic nocturnal regulation in short-term variability. Two modes of visualization of networks constructed from RR-increments are proposed. The first is based on the handling of a state space. The state space of RR-increments can be modified by a bin size used to code a signal and by the role of a given vertex as the representation...
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Effect of power frequency on the stress state of disc actuator
PublicationThis paper presents the concept of determining the optimum frequency of coil supply in inductive-dynamic drive. As a criterion to obtain the sought frequency, the smallest value of reduced stress in the disc was assumed while maintaining the desired dynamics. The disc stress is determined on the basis of solution of vibrating thin plate equation. Magnetic pressure acting on the disc is obtained from a hybrid circumferentially-field...
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Robert Jankowski prof. dr hab. inż.
PeopleHe was born on December 26, 1968 in Gdynia. A graduate of the High School at the Consulate of Poland in Benghazi, Libya (1987), a student at the Gdańsk University of Technology (MSc studies, 1987-1991 and 1992-1993), University of Sheffield, England (BSc studies, 1991-1992), University of Roskilde, Denmark (MSc course, 1993) and University of Tokyo, Japan (PhD studies, 1994-1997). From the beginning of his professional career associated...
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Methodology of estimating temperature measurement uncertainty in a system for endurance tests.
PublicationThe team consisting of the article authors developed a non-invasive method and a system for measuring temperature during an endurance test. A thermocouple which provided the required accuracy of changes in temperature dynamics measurements was used for the purpose of the required research. The paper presents the methodology for estimating uncertainty of temperature measurement done with the presented system, using a method based...
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Measurement of the temperature change of PVCP tissue phantom illuminated by dermatological laser 1.series
Open Research DataApplication of laboratory set-up for characterization of thermal properties of optical tissue phantoms during laser irradiation is presented. The produced system utilizes a thermographic camera VIGOcam v50 and a dermatological laser system with a 975 nm diode laser module. The set-up was used to perform measurements of the temporal and spatial temperature...
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Estimation of Stresses in a Dry Sand Layer Tested on Shaking Table
PublicationTheoretical analysis of shaking table experiments, simulating earthquake response of a dry sand layer, is presented. The aim of such experiments is to study seismic-induced compaction of soil and resulting settlements. In order to determine the soil compaction, the cyclic stresses and strains should be calculated first. These stresses are caused by the cyclic horizontal acceleration at the base of soil layer, so it is important...
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On Explaining Intuitiveness of Software Engineering Techniques with User eXperience Concepts
PublicationW referacie zawarto próbę wyjaśnienia intuicyjności technik inżynierii oprogramowania za pomocą pojęć zaczerpniętych z obszaru doświadczenia użytkownika. Analizy dotyczą zarówno intuicyjności przy pierwszym zetknięciu się użytkownika z daną techniką, jak i dynamiki transformacji epizodycznych doświadczeń na doświadczenie skumulowane i powiązane z nim postrzeganie intuicyjności. Przedyskutowano potencjalne zastosowania modelu i...
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Non-Perfect Propagation of Information to a Noisy Environment with Self-Evolution
PublicationWe study the non-perfect propagation of information for evolving a low-dimensional environment that includes self-evolution as well as noisy initial states and analyse the interrelations between the degree of objectivization and environment parameters. In particular, we consider an analytical model of three interacting qubits and derive its objectivity parameters. The numerical analysis shows that the quality of the spectrum broadcast...
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Water Behavior Near the Lipid Bilayer
PublicationIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Experimental Verification of the CFD Model of the Squeeze Film Lifting Effect
PublicationAbstract: The presented study shows the results of the research into the squeeze film levitation phenomena. The system introduced in the investigation is composed of a vibrating surface, air squeeze film, and the surface of the body freely suspended over the film. The use of the CFD (Computational Fluid Dynamics) model used in the system allows us to determine the steady state, periodic behavior of the air film (described by Navier–Stokes,...