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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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The Mechanism of a Retro-Diels–Alder Fragmentation of Luteolin: Theoretical Studies Supported by Electrospray Ionization Tandem Mass Spectrometry Results
PublicationThe mechanisms of retro-Diels–Alder fragmentation of luteolin are studied theoretically using the Density Functional Theory method (B3LYP hybrid functional) together with the 6-311++G(d,p) basis set and supported by electrospray ionization tandem mass spectrometry (ESI-MS) results. The reaction paths leading to the formation of 1,3A and 1,3B fragment ions observed as the main spectral features in the ESI-MS spectrum are described...
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Influence of laser processing of the low alloy medium carbon structural steel on the development of the fatigue crack
PublicationThe paper contains the results of the structural analysis, hardness tests and fatigue tests conducted for the medium carbon structural steel with low content of Cr and Ni after its processing with CO2 laser beam. Pre-cracks were made in the round compact tension (RCT) specimen used for fatigue test. Next, four paths, parallel to each other, were melted on both sides of the samples using a laser beam. The paths were perpendicular...
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Rapid development of the photoresponse and oxygen evolution of TiO2 nanotubes sputtered with Cr thin films realized via laser annealing
PublicationRecently, earth abundant transition metal oxides have gained particular attention as potential catalyst candidates due to their availability and low-cost comparing to substrates containing precious Pt or Au species. Herein, we present characterization of morphology, structure and electrochemical properties of pulsed 532 nm laser treated TiO2 nanotubes (NT) sputtered by the thin film of chromium. Scanning electron microscopy enables...
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Load Testing of GFRP Composite U-Shape Footbridge
PublicationThe paper presents the scope of load tests carried out on an innovative shell composite footbridge. The tested footbridge was manufactured in one production cycle and has no components made from materials other than GFRP laminates and PET foam. The load tests, performed on a 14-m long structure, were the final stage of a research program in the Fobridge project carried out in cooperation with: Gdańsk University of Technology (leader),...
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Potentials of Water Usage in urban Neighbourhood Structures
PublicationThis paper will treat about water influence and possibility of its usage in the urban neighborhood structures (e.g. districts, real estate properties, town parts) in the context of actual regional environmental problems and according to directories determined by European targets. It is not rare yet in the basic stage of urban design that water is treated as a threat, not a chance. In result planned structures are often built,...
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Poroelastic Road Surfaces - State of The Art
PublicationPoroelastic Road Surfaces (PERS) constitute a specific group of pavements containing a great amount of crumbled rubber. In most cases rubber aggregate constitutes about 20% of the mixture (by weight) and a polyurethane resin is used as a binder. As a result, PERS is characterized by a much higher elasticity than asphalt and a high porosity typical for drainage pavements. Due to this, tire/road noise is greatly reduced and on top...
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Influence of statistical errors on damage detection based on structuralflexibility and mode shape curvature
PublicationDamage detection procedures based on measured natural frequencies and building structure mode shapes are discussed in this paper. Modal curvature and structural flexibility approaches are tested. Attention is paid to the modal identification errors that influence damage detection. This problem is studied using a computer simulation of a simple supported beam. For practical cases, the peak picking methodand its statistical errors...
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Antagonist adhesion effects due to variable substrate surface
PublicationThe effects of variability of intrinsic adhesion within a joint have been studied using a single cantilever beam (SCB) test. Fracture energy was found not to be a simple function of relative areas of 2 surface pre-treatments: a 'weak' zone decreased strength more than expected from simple, additive considerations. By severing the adhesive along the strong-weak transition, fracture energy increased.The prior antagonist effect appears...
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Vibration of the bridge under moving singular loads - theoretical formulation and numerical solution
PublicationThe paper presents the results of the numerical analysis of a simple vehicle passing over a simply supported bridge span. The bridge is modelled by a Euler-Bernoulli beam. The vehicle is modelled as a linear, visco-elastic oscillator, moving at a constant speed. The system is described by a set of differential equations of motion and solved numerically using the Runge-Kutta algorithm. The results are compared with the solution...
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Polarization interferometer using a Liquid Crystalline Polymer waveplate for wavelength measurement
PublicationA two-beam polarization interferometer for measuring wavelength changes of a tunable semiconductor laser was designed, built and tested. This interferometer uses a λ/8 waveplate made from Liquid Crystalline Polymer in order to generate two output signals in quadrature. The λ/8 waveplate can be manufactured either on a beamsplitter face or on the mirror surface, reducing the cost and complexity of the optomechnical assembly. Experiment...
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Special forms of echo visual representation in an ahead looking sonar.
PublicationThe paper discusses ways to organise visual representation in a multi-beam ahead looking sonars whose function is to detect objects on the bottom and in pelagic zones. Forms of visual representation are shown and illustrated on the basic screen (panoramic representation and setting, alarms) and on the auxiliary screen (type A, B and special). Special forms of visual representation are mainly used in detecting objects in difficult...
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Dissection of σE‐dependent cell lysis in Escherichia coli: roles of RpoE regulators RseA, RseB and periplasmic folding catalyst PpiD
PublicationTo understand the mechanism of sigma(E)-dependent cell lysis, we examined the consequences of deletion derivatives of rpoE regulators rseA, rseB and rseC on sigma(E) transcription, on levels of free versus membrane-bound sigma(E) and on OMP-biogenesis limiting factor(s) that could impact cell lysis. RT-PCR showed that individual nonpolar DeltarseA and DeltarseB increased the rpoE expression to varying extents, with pronounced induction...
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Weak Solutions within the Gradient-Incomplete Strain-Gradient Elasticity
PublicationIn this paper we consider existence and uniqueness of the three-dimensional static boundary-value problems in the framework of so-called gradient-incomplete strain-gradient elasticity. We call the strain-gradient elasticity model gradient-incomplete such model where the considered strain energy density depends on displacements and only on some specific partial derivatives of displacements of first- and second-order. Such models...
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Buckling analysis of a non-concentric double-walled carbon nanotube
PublicationOn the basis of a theoretical study, this research incorporates an eccentricity into a system of compressed double-walled carbon nanotubes (DWCNTs). In order to formulate the stability equations, a kinematic displacement with reference to the classical beam hypothesis is utilized. Furthermore, the influence of nanoscale size is taken into account with regard to the nonlocal approach of strain gradient and the van der Waals interaction...
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The Influence of Shear Deformation in analysis of plane frames
PublicationThe focus of the paper is to investigate the influence of shear deformation effect on the distribution of internal forces and frame deformation. To estimate shear deformation effect, the Timoshenko beam theory and the concept of shear deformation coefficients are used. Analysis of example frames gives the possibility to evaluate what have the most impact on size of shear deformation and in which type of frames the shear deformation...
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Influence of an applied bearing system on behaviour of multi-span footbridge
PublicationThe cycle overpass in Gdynia is a box structure over 300 metres long, 10-span. It was opened for bicycle traffic in the second half of 2013. At the end of its construction, there was failure due to excessive horizontal displacement of the system. A number of bearings exceeded the range of permissible transverse shifts thus it was necessary to temporarily protect the spans from slipping. The FEM analysis of the original solution...
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Proton transfer reactions for ionized water clusters
PublicationCalculations of formation energies of the ionized water clusters and energies of reactions between small (including less than eight water molecules) neutral and positively ionized water clusters are presented. Moreover, we discuss some reaction paths between neutral and positively charged dimers, trimers and tetramers and proton transfer reactions (PTR) between cyclic clusters and H3O+ ions which can appear in beam experiments...
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Stability of an imperfect truss loaded by wind
PublicationThe present paper is devoted to the numerical research of stability of a truss loaded by wind and stiffened by elastic supports located at the top chord. The lateral braces or lateral and torsional braces were taken into account. In this paper, the linear buckling analysis re- sults for the beam and shell model were presented. Two different shapes of initial geometric imperfections were considered in the non-linear static analysis...
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Vibrational excitation of acetylene by positron impact
PublicationVibrationally inelastic quantum calculations are carried out at low collision energies for the scattering of a beam of positrons off acetylene gaseous molecules. The normal mode analysis is assumed to be valid and the relative fluxes into the C–C and C–H symmetric vibrational modes are computed within a Body-Fixed (BF) formulation of the dynamics by solving the relevant vibrational Coupled Channels (VCC) equations. The clear dominance...
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Analysis of sloping brace stiffness influence on stability and load bearing capacity of a truss
PublicationThe paper is focused on the numerical study of stability and load bearing capacity of a truss with side elastic braces. The structure is made in reality. The rotational and sliding brace stiffnesses were taken into account. Linear buckling analysis and non-linear static analysis with geometric and material nonlinearity were performed for the beam and shell model of the truss with respect to the angle of sloping braces. As a result...
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How Do Ionic Liquids Affect the Surface Structure of Titania Photocatalyst? An Electron-Trap Distribution-Analysis Study
PublicationTitanium(IV) oxide, titania, photocatalyst particles were prepared from titanium alkoxide in the presence of several kinds of ionic liquids, and it was clarified that a group of samples exhibited photocatalytic activity for phenol degradation under the irradiation of light of wavelength >400 nm higher than those of the other group of samples. Although the conventional structural analytical results could not be related to the activity,...
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Low energy differential elastic electron scattering from acetonitrile (CH3CN)
PublicationMeasurements of elastic differential cross sections for electron scattering from acetonitrile (CH3CN) have been performed utilizing a crossed electron-molecular beam experiment and with the relative flow method, for the incident electron energy range of 0.7 eV–30 eV and the scattering angle range of 10◦–130◦. These differential cross sections have been used to calculate the elastic integral and momentum- transfer cross sections,...
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Stability of roof trusses stiffened by trapezoidal sheeting and purlins
PublicationIn the article linear buckling analysis of a set of steel trusses braced by purlins and trapezoidal sheeting are conducted. The buckling load factor due to the height of a corrugated sheeting profile is investigated in parametric studies. The minimal height of trapezoidal sheeting required for preventing the sheeting and chords of the trusses against the buckling is obtained. Two groups of models are considered: “axial” model as...
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Pomiary grubości cienkich warstw metodą modulacji chromatycznej.
PublicationTematem artykułu jest pomiar grubości struktur cienkowarstwowych szerokostosowanych w optoelektronice, transparentnych warstw dielektrycznych. Grubość jest najistotniejszym parametrem warstwy i determinuje jej właściwościoptyczne. Metoda pomiaru grubości cienkich warstw powinna być bezkontaktowa, nieniszcząca, niekosztowna oraz odporna na zakłócenia
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Implementation of Hermite-Ritz method and Navier’s Technique for Vibration of Functionally Graded Porous Nanobeam Embedded in Winkler-Pasternak Elastic Foundation Using bi-Helmholtz type of nonlocal elasticity
PublicationPresent study is devoted to investigating the vibration characteristics of Functionally Graded (FG) porous nanobeam embedded in an elastic substrate of Winkler-Pasternak type. Classical beam theory (CBT) or Euler-Bernoulli beam theory (EBT) has been incorporated to address the displacement of the FG nanobeam. Bi-Helmholtz type of nonlocal elasticity is being used to capture the small scale effect of the FG nanobeam. Further, the...
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Experimental Study on the Effectiveness of Polyurethane Flexible Adhesive in Reduction of Structural Vibrations
PublicationThe aim of the present study is to consider the idea of using polyurethane flexible adhesive in to reduce the vibrations in structures exposed to dynamic loads and evaluate their damping properties in relation to large deformations. Firstly, two aluminium cantilever beams, simulating structural elements (without and with polyurethane layer in the form of tape), were analysed, in order to check the damping of the unconstrained polymer...
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Mechanical Properties and Residual Stress Measurements of Grade IV Titanium and Ti-6Al-4V and Ti-13Nb-13Zr Titanium Alloys after Laser Treatment
PublicationNowadays, surface engineering focuses on research into materials for medical applications. Titanium and its alloys are prominent, especially Ti-6Al-4V and Ti-13Nb-13Zr. Samples made of pure grade IV titanium and the titanium alloys Ti-6Al-4V and Ti-13Nb-13Zr were modified via laser treatment with laser beam frequency f = 25 Hz and laser beam power P = 1000 W during a laser pulse with duration t = 1 ms. Subsequently, to analyze...
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Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublicationThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
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Electrical Simulations of the SIS100 Superconducting Dipole and Quadrupole Circuits: Transients, Earthing and Failure Modes
PublicationThe 100 Tm superconducting synchrotron SIS100 is the main accelerator of the international Facility for Antiproton and Ion Research (FAIR) currently under advanced construction in Darmstadt, Germany. The SIS100 dipole circuit which creates the magnetic field required to bend the beam, consists of 108 dipoles distributed over six arc sections of the ring. The magnetic field for the beam focusing is generated by three individual...
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Dynamic analysis of temporary steel grandstand subjected to human-induced excitations due to jumping
PublicationSteel grandstands are structures that are frequently used during sport games and many other non-sporting events, such as festivals, music concerts, or even politicians rallies, with participation of a large number of attendees. Unfortunately, the presence of unexpected excessive dynamic loads due to unpredictable behaviour of spectators (e.g. synchronized harmonic jumping or swaying) may lead to...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Sensitivity analysis of a composite footbridge
PublicationThis work include an example of sensitivity analysis for the design of a composite footbridge. A sandwich structure is used, consisting two high-strength skins separated by a core material. The analysis was conducted for two numerical models. The first one is a simple, single-span beam of a composite cross-section (laminate and foam), with different Young’s modulus for each material. Calculations were made by means of a MATLAB-based...
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Development and application of asphalt binder relaxation test in different dynamic shear rheometers
PublicationIn this study, a novel relaxation test is proposed to evaluate asphalt binder low temperature properties using a Dynamic Shear Rheometer (DSR) with parallel plates of 4 mm in diameter. Three rheometers from three different manufacturers are used to analyze seven asphalt binders. Different material parameters are derived which are useful to evaluate and discriminate different asphalt binders. Test results of all three instruments...
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Free Vibration of Flexomagnetic Nanostructured Tubes Based on Stress-driven Nonlocal Elasticity
PublicationA framework for the flexomagneticity influence is here considered extending the studies about this aspect on the small scale actuators. The developed model accommodates and composes linear Lagrangian strains, Euler-Bernoulli beam approach as well as an extended case of Hamilton’s principle. The nanostructured tube should subsume and incorporate size effect; however, for the sake of avoiding the staggering costs of experiments,...
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Influence of Dielectric Overlay Permittivity on Size and Performance of Miniaturized ESPAR Antenna
PublicationIn this paper, influence of dielectric overlay permittivity on miniaturized ESPAR antenna parameters is presented. ESPAR antenna is a low-cost and energy-efficient way to implement beam steering capability to a node and improve network performance. The antenna size reduction is obtained by embedding its active and passive elements in ABS based materials of relative permittivity equal to 4, 5.5 and 7.5 in order to achieve network...
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Two tests for adhesive bonding long term characterization: principles and applications
PublicationThis article describes recent refinement of the traditional wedge test technique used to characterize durability of the adhesive joints. We propose two types of measuring protocols to monitor precisely and continuously the propagation of an "effective" crack during long term mode I fracture mechanic test. First method is directly derived from the traditional wedge test technique and consist in monitoring the surface strain of adherent...
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Stability of a truss under upward wind loading
PublicationThe present paper is devoted to the numerical investigations of stability of a truss under upward wind load. The truss is braced at its the upper cord. A structural variant including lateral braces, or lateral and torsional braces is considered. The research presents the problems of linear buckling and non-linear static analysis of the truss shell and beam model with geometric and material non-linearity are presented. The initial...
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Modal analysis of temporary steel grandstand equipped with different bracing systems
PublicationThe aim of this paper is to present the results of numerical analysis focused on temporary steel scaffolding grandstand. The investigation has been devoted to modal analysis where modes of free vibrations and corresponding natural frequencies have been estimated and compared. The structure was equipped with different types of stiffener members. One on them is a typical tubular stiffener, while the second one is spe-cially designed...
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As- built inventory of the office building with the use of terrestrial laser scanning
PublicationTerrestrial Laser Scanning (TLS) is an efficient tool for building inventories. Based on the red- laser beam technology it is possible to provide the high accuracy data with complete spatial information about a scanned object. In this article, authors present the solution of use a TLS in as-built inventory of the office building. Based on the provided data, it is possible to evaluate the correctness of built details of a building...
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The modelling method of discrete-continuous systems
PublicationThe paper introduces a method of discrete-continuous systems modelling. In the proposed method a three-dimensional system is divided into finite elements in only two directions, with the third direction remaining continuous. The thus obtained discrete-continuous model is described by a set of partial differential equations. General difference equations of discrete system are obtained using the rigid finite element method. The limit...
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Nonlinear strain gradient and micromorphic one-dimensional elastic continua: Comparison through strong ellipticity conditions
PublicationWe discuss the strong ellipticity (SE) conditions for strain gradient and micromorphic continua considering them as an enhancement of a simple nonlinearly elastic material called in the following primary material. Recently both models are widely used for description of material behavior of beam-lattice metamaterials which may possess various types of material instabilities. We analyze how a possible loss of SE results in the behavior...
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Failure characterisation of sandwich beams using integrated acoustic emission and digital image correlation techniques
PublicationThe paper presents the experimental study of the failure behaviour of sandwich beams subjected to bending. The samples examined are sandwich beams made of polyethylene terephthalate foam core and glass fibre-reinforced polymer laminate face sheets. In a series of experiments, it has been proposed to integrate diagnostic techniques with acoustic emission and digital image correlation to accurately track the cracking process on the...
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On a 3D material modelling of smart nanocomposite structures
PublicationSmart composites (SCs) are utilized in electro-mechanical systems such as actuators and energy harvesters. Typically, thin-walled components such as beams, plates, and shells are employed as structural elements to achieve the mechanical behavior desired in these composites. SCs exhibit various advanced properties, ranging from lower order phenomena like piezoelectricity and piezomagneticity, to higher order effects including flexoelectricity...
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On time-dependent nonlinear dynamic response of micro-elastic solids
PublicationA new approach to the mechanical response of micro-mechanic problems is presented using the modified couple stress theory. This model captured micro-turns due to micro-particles' rotations which could be essential for microstructural materials and/or at small scales. In a micro media based on the small rotations, sub-particles can also turn except the whole domain rotation. However, this framework is competent for a static medium....
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Dissociative electron attachment to benzoic acid (C7H6O2)
PublicationThe dissociative electron attachment (DEA) to benzoic acid (C6H5COOH) has been studied using an experimental crossed beam setup of a quadrupole mass spectrometer and a trochoidal electron monochromator. Relative partial cross sections for the DEA to produce negative ion fragments show the main channels for dissociation. The comparison of the present results with the ultraviolet photoelectron spectrum of benzoic acid [J. Meeks,...
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generation of the vorticity mode by sound in a bingham plastic
PublicationThis study investigates interaction between acoustic and non-acoustic modes, such as vorticity mode,in some class of a non-newtonian fluid called Bingham plastic. The instantaneous equations describinginteraction between different modes are derived. The attention is paid to the nonlinear effects in the fieldof intense sound. The resulting equations which describe dynamics of both sound and the vorticity modeapply to both periodic...
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An influence of the ship's block coefficient implementation on the evaluation of it's hull girder bending
PublicationAn influence of the three different ways of implementation ship's block coefficient δ (three geometrical models) on the stresses due to wave bending moment have been investigated. Two models have been applied and compared: beam one (description of the shape usingparameters) and FEM shell model (direct representation of the shape). The outcomes have been compared to Polish Register of Shipping (PRS) rules. The results show that...
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Improved jamming resistance using electronically steerable parasitic antenna radiator
PublicationThis paper presents an idea of using an Electronically Steerable Parasitic Antenna Radiator (ESPAR) for jamming suppression in IEEE 802.11b networks. Jamming (intentional interference) attacks are known to be effective and easy to perform, which may impose connectivity problems in applications concerning Internet of Things (IoT). In our paper, theoretical considerations are presented and the results of experiments performed in...