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Search results for: Molecular dynamics simulations
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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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Fast Multi-Objective Aerodynamic Optimization Using Sequential Domain Patching and Multifidelity Models
PublicationExploration of design tradeoffs for aerodynamic surfaces requires solving of multi-objective optimization (MOO) problems. The major bottleneck here is the time-consuming evaluations of the computational fluid dynamics (CFD) model used to capture the nonlinear physics involved in designing aerodynamic surfaces. This, in conjunction with a large number of simulations necessary to yield a set of designs representing the best possible...
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Multi-objective optimization of the cavitation generation unit structure of an advanced rotational hydrodynamic cavitation reactor
PublicationHydrodynamic cavitation (HC) has been widely considered a promising technique for industrial-scale process intensifications. The effectiveness of HC is determined by the performance of hydrodynamic cavitation reactors (HCRs). The advanced rotational HCRs (ARHCRs) proposed recently have shown superior performance in various applications, while the research on the structural optimization is still absent. The present study, for the...
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Discrete identification of continuous non-linear and non-stationary dynamical systems that is insensitive to noise correlation and measurement outliers
PublicationThe paper uses specific parameter estimation methods to identify the coefficients of continuous-time models represented by linear and non-linear ordinary differential equations. The necessary approximation of such systems in discrete time in the form of utility models is achieved by the use of properly tuned `integrating filters' of the FIR type. The resulting discrete-time descriptions retain the original continuous parameterization...
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Modelling hydraulic and capillary-driven two-phase fluid flow in unsaturated concretes at the meso-scale with a unique coupled DEM-CFD technique
PublicationThe goal of the research was to demonstrate the impact of thin porous interfacial transition zones (ITZs) between aggregates and cement matrix on fluid flow in unsaturated concrete caused by hydraulic/capillary pressure. To demonstrate this impact, a novel coupled approach to simulate the two-phase (water and moist air) flow of hydraulically and capillary-driven fluid in unsaturated concrete was developed. By merging the discrete...
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Experimental and Computational Fluid Dynamics Studies on Straight and U-Bend Double Tube Heat Exchangers with Active and Passive Enhancement Methods
PublicationIn this work, the authors wanted to demonstrate the possibility to increase the heat transfer efficiency by using simple wire coil inserts to create turbulent flow in the boundary layer as well as air blowing into the annulus of the pipe. Experimental investigations were carried out for four heat exchanger constructions, i.e., plain double tube, turbulized double tube, plain U-bend double tube, U-tube with turbulator, plain double...
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A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism
PublicationThis work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa...
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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublicationOver the past few years, metal halide perovskite solar cells have made significant advances. Currently, the single-junction perovskite solar cells reach a conversion efficiency of 25.7%. Perovskite solar cells with a wide band gap can also be used as top absorber layers in multi-junction tandem solar cells. We examined the dynamical and thermal stability, electronic structure, and optical features of In2PtX 6 (X = Cl, Br, and I)...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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A Numerical Model Study on Ice Boom in a Coastal Lake
PublicationA numerical study on the effectiveness of the proposed ice boom to be installed near the entrance of Lake Notoro, Hokkaido, Japan to prevent sea ice moving into the lake is presented. A two-dimensional hydro–ice dynamics model was modified to allow for the treatment of ice-boom interaction with the effect of tidal current. The numerical model is a coupled hydrodynamic and ice dynamic model. The ice dynamic component uses a Lagrangian...
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Extended duration running and impulse loading characteristics of an acoustic bearing with enhanced geometry
PublicationThis paper presents performance during prolonged running of the acoustic bearing when PZTs are switched off and when they are switched on. The effect of active PZT on shaft’s displacements in X and Y directions is clearly demonstrated. Performance of the acoustic bearing was also assessed when an impulse force was applied to the running shaft at speed. Once again the benefits of having PZTs active are beyond doubt. The instability...
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Effect of power frequency on the stress state of disc actuator
PublicationThe paper presents the concept of determinig 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.
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A spline-based FE approach to modelling of high frequency dynamics of 1-D structures
PublicationIn this paper a computational methodology leading to the development of a new class of FEs, based on the application of continuous and smooth approximation polynomials, being splines, has been presented. Application of the splines as appropriately defined piecewise elemental shape functions led the authors to the formulation of a new approach for FEM, named as spFEM, where contrary to the well-known NURBS approach, the boundaries...
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Nonlinear phenomena of small-scale sound in a gas with exponential stratification
PublicationThe nonlinear dynamics of perturbations, quickly varying in space, with comparatively large characteristic wavenumbers k: k>1/H, is considered. H is the scale of density and pressure reduction in unperturbed gas, as the coordinate (H is the so-called height of the uniform equilibrium gas). Coupling nonlinear equations which govern the sound and the entropy mode in a weakly nonlinear flow are derived. They describe the dynamics...
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A Computational Analysis of the Aerodynamic and Aeromechanical Behavior of a Thermo-Well for Steam Temperature Measurement in a Steam Turbine
PublicationThe goal of the paper is twofold: firstly, it presents computational fluid dynamics analysis for finding maximum unsteady flow forces (and their frequencies) acting on a thermo-well for measuring steam temperature in a steam turbine control stage and secondly, it presents computational solid dynamics analysis of possibility of entry into resonance of the thermowell structure. There have been analyzed two cases of flow with changing...
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Wild oscillations in a nonlinear neuron model with resets: (II) Mixed-mode oscillations
PublicationThis work continues the analysis of complex dynamics in a class of bidimensional nonlinear hybrid dynamical systems with resets modeling neuronal voltage dynamics with adaptation and spike emission. We show that these models can generically display a form of mixed-mode oscillations (MMOs), which are trajectories featuring an alternation of small oscillations with spikes or bursts (multiple consecutive spikes). The mechanism by...
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A hierarchical observer for a non-linear uncertain CSTR model of biochemical processes
PublicationThe problem of estimation of unmeasured state variables and unknown reaction kinetic functions for selected biochemical processes modelled as a continuous stirred tank reactor is addressed in this paper. In particular, a new hierarchical (sequential) state observer is derived to generate stable and robust estimates of the state variables and kinetic functions. The developed hierarchical observer uses an adjusted asymptotic observer...
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Comparison of Two Nonlinear Predictive Control Algorithms for Dissolved Oxygen Tracking Problem at WWTP
PublicationThe wastewater treatment plant is classified as a complex system, due to its nonlinear dynamics, large uncertainty of disturbance inputs, multiple time scales in the internal process dynamics, and multivariable structure. The aeration process, in turn, is an important and expensive part of wastewater treatment plant operation. All operating parameters of the aeration in biological processes are to be precisely controlled to provide...
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OBTAINING FLUID FLOW PATTERN FOR TURBINE STAGE WITH NEURAL MODEL.
PublicationIn the paper possibility of applying neural model to obtaining patterns of proper operation for fluid flow in turbine stage for fluid-flow diagnostics is discussed. Main differences between Computational Fluid Dynamics (CFD) solvers and neural model is given, also limitations and advantages of both are considered. Time of calculations of both methods was given, also possibilities of shortening that time with preserving the accuracy...
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Nonlinear Control of a Doubly Fed Generator Supplied by a Current Source Inverter
PublicationNowadays, wind turbines based on a doubly fed induction generator (DFIG) are a commonly used solution in the wind industry. The standard converter topology used in these systems is the voltage source inverter (VSI). The use of reverse-blocking insulated gate bipolar transistor (RB-IGBT) in the current source inverter topology (CSI), which is an alternative topology, opens new possibilities of control methods. This paper presents...
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Interval estimator for chlorine monitoring in drinking water distribution systems under uncertain system dynamics, inputs and state measurement errors
PublicationThe design of interval observer for estimation of unmeasured state variables for application to drinking water distribution systems is described in this paper. In particular, it considers the design of such observer for estimation of water quality described by free chlorine concentration. An interval observer is derived to produce robust interval bounds on the estimated water quality state variables. The stability and robustness...
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Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT)
PublicationIntroduction: Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising...
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Newton’s Method for the McKendrick-von Foerster Equation
PublicationIn the paper we study an age-structured model which describes the dynamics of one population with growth, reproduction and mortality rates. We apply Newton’smethod to the McKendrick-von Foerster equation in the semigroup setting. We prove its first- and second-order convergence.
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Mathematical Modeling of Ice Thrusting on the Shore of the Vistula Lagoon (Baltic Sea) and the Proposed Artificial Island
PublicationCoastal lagoons are inland and shallow water bodies, separated from the ocean by a barrier. In cold regions, ice phenomena in shallow water coastal lagoons occur every winter season. Ice is predominantly formed on the surface due to density stratification and surface cooling. The ice dynamics in such areas are dominantly affected by winds. Water dynamics also cause ice movement, but due to the large areal scale of lagoons, the...
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Molecular geometry of hexachlorobenzene
Open Research DataPresented data shows molecular geometry of the ground singlet state of hexachlorobenzene and hexachlorobenzene with potassium atom in 10 angstrom distance. The geometry was obtained via MP2 and CCSD calculations using balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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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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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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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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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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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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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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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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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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At the Limits of Criticality-Based Quantum Metrology: Apparent Super-Heisenberg Scaling Revisited
PublicationWe address the question of whether the super-Heisenberg scaling for quantum estimation is indeed realizable. We unify the results of two approaches. In the first one, the original system is compared with its copy rotated by the parameter-dependent dynamics. If the parameter is coupled to the one-body part of the Hamiltonian, the precision of its estimation is known to scale at most as N−1 (Heisenberg scaling) in terms of the number...
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MOLECULAR PHYSICS
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Molecular geometry of phenylboronic acid
Open Research DataData presents molecular geometry of the ground singlet state of phenylboronic acid. The geometry was obtained via DFT calculations using Becke–Lee–Yang–Parr density functional (B3LYP) with the balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, 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. The part...
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Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublicationNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
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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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Analytical data on molecular umbrella: cispentacin and molecular umbrella: fluorescent probe conjugates
Open Research DataAnalytical data (NMR, MS, FTIR) for nine conjugates of molecular umbrella with cispentacin, Lys(Mca) or Nap-NH2. The conjugates have been rationally designed as potential antifungal agents. 1H NMR and 13C NMR spectra were obtained at 500 MHz Varian Unity Plus spectrometer and the deuterated solvents were used as internal locks. High-resolution mass...
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Advanced Theory and Simulations
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MACROMOLECULAR THEORY AND SIMULATIONS
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Scientific Modeling and Simulations
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Robert Bogdanowicz dr hab. inż.
PeopleRobert Bogdanowicz received his Ph.D. degree with honours in Electronics from the Gdansk University of Technology. He worked as a post-doc researcher in Ernst-Moritz-Arndt-Universität Greifswald Institut für Physik. He has initiated optical emission imaging of muti-magnetron pulsed plasma and contributed to the development of antibacterial implant coatings deposited by high-power impulse magnetron sputtering. He moved back to...
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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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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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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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Oddziaływania taboru na mosty kolejowe przy zmiennych parametrach ruchu
PublicationW pracy poruszono zagadnienia związane z identyfikacją oraz modelowaniem układu dynamicznego most-pojazd ruchomy. Za element szczególnie istotny uznano czynnik obciążający. Opracowano i wdrożono metodykę identyfikacji cech dynamicznych rzeczywistego pojazdu szynowego. Eksperyment badawczy przeprowadzono dla jednostki trakcyjnej EN57, jednak nie ma żadnych ograniczeń w stosowaniu metody dla innego, konwencjonalnego taboru szynowego....