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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublikacjaXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Numerical analysis of the flow rig for UWS spray examination in exhaust system-relevant conditions
PublikacjaIn the present study, a flow rig with optical access intended for spray investigations in exhaust system-relevant conditions was analysed in terms of flow and temperature in the spray area using numerical simulations. The operation of the rig was examined for a wide range of exhaust mass flow rates, temperatures and various forms of UWS (urea-water solution) spray plumes. The locations of the injector and thermocouple were verified....
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Parallel Implementation of the Discrete Green's Function Formulation of the FDTD Method on a Multicore Central Processing Unit
PublikacjaParallel implementation of the discrete Green's function formulation of the finite-difference time-domain (DGF-FDTD) method was developed on a multicore central processing unit. DGF-FDTD avoids computations of the electromagnetic field in free-space cells and does not require domain termination by absorbing boundary conditions. Computed DGF-FDTD solutions are compatible with the FDTD grid enabling the perfect hybridization of FDTD...
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Updating Finite Element Model of a Wind Turbine Blade Section Using Experimental Modal Analysis Results
PublikacjaThis paper presents selected results and aspects of themultidisciplinary and interdisciplinary research oriented for the experimental and numerical study of the structural dynamics of a bend-twist coupled full scale section of awind turbine blade structure.Themain goal of the conducted research is to validate finite elementmodel of themodified wind turbine blade section mounted in the flexible support structure accordingly to the...
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Two-Step Model Based Adaptive Controller for Dissolved Oxygen Control in Sequencing Wastewater Batch Reactor
PublikacjaDissolved Oxygen (DO) concentration is a crucial parameter for efficient operation of biological processes taking place in the activated sludge Wastewater Treatment Plant (WWTP). High-quality DO control is difficult to achieve because of complex nonlinear behavior of the plant and substantial influent disturbances. A method to improve the Direct Model Reference Adaptive Control (DMRAC) technology in application to DO tracking for...
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How to provide fair service for V2I communications in VANETs?
PublikacjaIn this paper, we focus on fairness issues of Vehicle-to-Infrastructure (V2I) communications. In particular, we show that under a common technique of selection of RSUs by OBUs based on the received signal strength, a vast variability of a number of OBUs connected to RSUs can be observed leading to inefficient/unfair service provided by RSUs. To overcome this problem, we propose an algorithm for RSU selection called RSEL to obtain...
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Damaged plasticity model - seismic analysis of structure of the Petronas Twin Towers (Kuala Lumpur) in Malaysia
PublikacjaThe article presents numerical simulations for the modelling of seismic impact on the structure of Petronas Twin Towers (Kuala Lumpur) in Malaysia with application of two methods. The Response Spectrum method, in which a spectrum of the structure's responses to an earthquake's impact is generated and the Acceletogram (BETA) method, in which we generate dynamic load in the form of a diagram of the connection between acceleration...
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Separation of the effects of notch and macro residual stress on the MFL signal characteristics
PublikacjaMagnetic flux leakage (MFL) distribution for three configurations of samples has been investigated in order to study the influence of notch and plastic deformation separately as well as together. Samples have been made of S355 steel. The MFL signal measurements were carried out along the longest dimension of the sample over a length of 120 mm. Two components of magnetic field were measured: 1) tangential to the main axis and 2)...
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New First - Path Detector for LTE Positioning Reference Signals
PublikacjaIn today's world, where positioning applications reached a huge popularity and became virtually ubiquitous, there is a strong need for determining a device location as accurately as possible. A particularly important role in positioning play cellular networks, such as Long Term Evolution (LTE). In the LTE Observed Time Difference of Arrival (OTDOA) positioning method, precision of device location estimation depends on accuracy...
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Low-Cost Multi-Objective Optimization Yagi-Uda Antenna in Multi-Dimensional Parameter Space
PublikacjaA surrogate-based technique for fast multi-objective optimization of a multi-parameter planar Yagi-Uda antenna structure is presented. The proposed method utilizes response surface approximation (RSA) models constructed using training samples obtained from evaluation of the low-fidelity antenna model. Utilization of the RSA models allowsfor fast determination of the best possible trade-offs between conflicting objectives in multi-objective...
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Multiple output differential OTA with linearizing bulk-driven active-error feedback loop for continuous-time filter applications
PublikacjaA CMOS circuit realization of a highly linear multiple-output differential operational transconductance amplifier (OTA) has been proposed. The presented approach exploits a differential pair as an input stage with both the gate and the bulk terminals as signal ports. For the proposed OTA, improved linearity is obtained by means of the active-error feedback loop operating at the bulk terminals of the input stage. SPICE simulations...
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Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models
PublikacjaMulti-objective optimization of antenna structures is a challenging task due to high-computational cost of evaluating the design objectives as well as large number of adjustable parameters. Design speedup can be achieved by means of surrogate-based optimization techniques. In particular, a combination of variable-fidelity electromagnetic (EM) simulations, design space reduction techniques, response surface approximation (RSA) models,...
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Wave Method for Structural Health Monitoring: Testing Using Full-Scale Shake Table Experiment Data
PublikacjaAn algorithm of the wave method for structural health monitoring (SHM) is tested and calibrated using shake table experiment data of a full-scale, seven-story, reinforced-concrete building slice. The method is based on monitoring changes in the velocity of waves propagating vertically through the structure, identified by least-squares (LSQ) fit of beam models. The experiment was conducted by a team from the University of California,...
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Traffic model for evaluation of call processing performance parameters in IMS-based NGN
PublikacjaIn the modern world requirements for accurate and fast information distribution are becoming more and more important, which creates a strong necessity for appropriate telecommunication network architecture. Proposition of such an architecture is the Next Generation Network (NGN) concept, which in order to guarantee Quality of Service (QoS), should be correctly designed and dimensioned. For this reason proper traffic models must...
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Why is TASK Quarterly a Significant Journal to Publish Your Article? —A Bibliometric Analysis of a Scientific and Technical Journal
PublikacjaA bibliometric analysis of TASK Quarterly in the years 1997-2021 in terms of various bibliometric indicators was performed to celebrate the 25th anniversary of the publication of the first issue of the journal. The number of publications and citations increased over the mentioned span of years. The leading countries in terms of the greatest number of papers published in TASK Quarterly are Poland, Italy, Germany, Ukraine, USA and...
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Adaptive Sampling for Non-intrusive Reduced Order Models Using Multi-Task Variance
PublikacjaNon-intrusive reduced order modeling methods (ROMs) have become increasingly popular for science and engineering applications such as predicting the field-based solutions for aerodynamic flows. A large sample size is, however, required to train the models for global accuracy. In this paper, a novel adaptive sampling strategy is introduced for these models that uses field-based uncertainty as a sampling metric. The strategy uses...
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Experimental and theoretical study on high-temperature creep of VT6 titanium alloy under multi-axial loading conditions
PublikacjaIn the framework of damage mechanics, we discuss a new mathematical model that describes the kinetics of the stress–strain state and damage accumulation during material degradation by the mechanism of long-term strength under complex multiaxial stress state. An experimental and theoretical technique is proposed for determination of material parameters and scalar constitutive functions for damaged media based on specially set experiments...
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Direction-of-Arrival Estimation Using an ESPAR Antenna with Simplified Beam Steering
PublikacjaIn this paper, it has been shown, how electronically steerable parasitic array radiator (ESPAR) antenna, in which beam steering is done in a simple way, can be used for directionof- arrival (DoA) estimation of an unknown signal impinging the antenna. The concept is based on an ESPAR antenna having twelve parasitic elements, in which beam switching is realized by RF switches providing required loads to its parasitic elements. Numerical...
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Study of Metrological Properties of Voltammetric Electrodes in the Time Domain
PublikacjaMetrological properties of voltammetric electrodes, in the situation where on their surface an electrochemical reaction of oxidizing/reduction takes place, were analyzed in this chapter. The properties of electrodes on which a reaction controlled by ion transport process takes place were taken into consideration. Also, it was analyzed how the electrode’s shape and the voltage polarizing the electrode influence this electrode’s...
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Estimation of Vehicle Energy Consumption at Intersections Using Microscopic Traffic Models
PublikacjaThis paper addresses issues related to modeling energy consumption and emissions using microscopic traffic simulations. This paper develops a method in which a traffic model is used to calculate the energy needed to travel through selected types of intersections. This paper focuses on energy consumption and derived values of calculated energy, which can be, for example, carbon dioxide emissions. The authors present a review of...
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Modelling and Analysis of the Positioning Accuracy in the Loading Systems of Mobile Cranes
PublikacjaIn this work, the authors analyse the influence of the order and range of sequential movements of a crane's working members on the accuracy of the final cargo positioning. The analysis was conducted on the basis of a specially developed method in which the authors proposed the introduction of a geometrical indicator of positioning the load in the intermediate positions (after completing each movement sequence) and in the target...
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Parametrized Local Reduced-Order Models With Compressed Projection Basis for Fast Parameter-Dependent Finite-Element Analysis
PublikacjaThis paper proposes an automated parametric local model-order reduction scheme for the expedited design of microwave devices using the full-wave finite-element method (FEM). The approach proposed here results in parameterized reduced-order models (ROMs) that account for the geometry and material variation in the selected subregion of the structure. In each subregion, a parameter-dependent projection basis is generated by concatenating...
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Rapid redesign of multiband antennas with respect to operating conditions and material parameters of substrate
PublikacjaThis work addresses geometry parameter scaling of multi-band antennas for Internet of Things applications. The presented approach is comprehensive and permits re-design of the structure with respect to both the operating frequencies and material parameters of the dielectric substrate. A two-step procedure is developed with the initial design obtained from an inverse surrogate model constructed using a set of appropriately prepared...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublikacjaThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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The Impact of Thermal Stresses on Volume Resistivity: Performance Comparison between TR-XLPE and XLPE Cables
PublikacjaMost failures in electric power cables are attributed to the development of water trees inside the insulating materials. Thus, the development and utilization of Tree Retardant Cross-Linked Polyethylene (TR-XLPE) based cables have recently been given great attention to overcome the treeing issues. TR-XLPE cables use low-density polyethylene compounds suppressing the formation of water trees while retaining excellent electrical,...
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Thermal boundary conditions to simulate friction layers and coatings at sliding contacts
PublikacjaA brief review of the thermal boundary conditions specified at sliding interfaces was performed. New thermal boundary conditions were derived aimed at solving problems of sliding with account of surface layers representing friction layers and tribological coatings. Based on the assumption of linear temperature distributions in the surface layers, the proposed conditions enable one to simplify simulations by eliminating the surface...
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublikacjaFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Modelling reinforced concrete beams under mixed shear-tension failure with different continuous FE approaches
PublikacjaThe paper presents quasi-static numerical simulations of the behaviour of short reinforced concrete beams without shear reinforcement under mixed shear-tension failure using the FEM and four various constitutive continuum models for concrete. First, an isotropic elasto-plastic model with a Drucker-Prager criterion defined in compression and with a Rankine criterion defined in tension was used. Next, an anisotropic smeared crack...
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NUMERYCZNE MODELOWANIE HYDRODYNAMIKI JAKO NARZĘDZIE WSPOMAGANIA PROJEKTOWANIA REKREACYJNYCH I SPORTOWYCH OBIEKTÓW WODNYCH
PublikacjaW artykule opisano zastosowanie obliczeń numerycznych w procesie projektowania, analizy działania oraz oceny bezpieczeństwa użytkowania wodnych obiektów rekreacyjnych i sportowych. Użytkownicy aquaparków, sportowcy, a szczególnie kibice, oczekują wyjątkowych doznań na obiektach wodnych z jednoczesną gwarancją bezpieczeństwa. Na te kwestie duży wpływ ma hydrodynamika przepływu. Aby właściwie dobrać parametry geometryczne i hydrauliczne...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne 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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Impact of dyes isomerization effect on the charge transfer phenomenon occurring on the dye/nanosemiconductor interface
PublikacjaThe present work aimed to find the answer how does the isomerization of the Ru based dyes affect the overall photon-to-current efficiency of the DSSCs and to explain the charge transfer phenomenon occurring on the dye/ nanosemiconductor interface. Therefore, electronic and optical properties of three bipyridine derivatives anchored on the TiO2 electrode were investigated by computational simulations based on quantum chemistry codes...
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Reduced-Cost Constrained Modeling of Microwave and Antenna Components: Recent Advances
PublikacjaElectromagnetic (EM) simulation models are ubiquitous in the design of microwave and antenna components. EM analysis is reliable but CPU intensive. In particular, multiple simulations entailed by parametric optimization or uncertainty quantification may considerably slow down the design processes. In order to address this problem, it is possible to employ fast metamodels. Here, the popular solution approaches are approximation...
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The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide
PublikacjaDimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations,...
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Quasi-Global Optimization of Antenna Structures Using Principal Components and Affine Subspace-Spanned Surrogates
PublikacjaParametric optimization is a mandatory step in the design of contemporary antenna structures. Conceptual development can only provide rough initial designs that have to be further tuned, often extensively. Given the topological complexity of modern antennas, the design closure necessarily involves full-wave electromagnetic (EM) simulations and—in many cases—global search procedures. Both factors make antenna optimization a computationally...
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Thermophysical study of the binary mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide – Experimental and theoretical approach
PublikacjaDensities at (293.15, 298.15, 303.15 and 308.15) K, and viscosities and ultrasonic velocities at 298.15 K of binary liquid mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide have been measured over the entire range of composition at p = 0.1 MPa. From the experimental data, values of excess molar volume, excess isentropic compressibility, viscosity deviation and excess Gibbs energy...
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Dynamic analysis of the railway bridge span under moving loads
PublikacjaThe first part of this paper provides a review of the state of knowledge of the dynamic behaviour of railway bridges under moving loads. Particular attention is paid to developments in modelling railway bridge loading and dynamic vehicle-span (structure) interaction. The most important aspects determining the advancements in this area of knowledge are identified. The contemporary techniques for defining bridge span finite element...
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Smart acoustic band structures
PublikacjaSmart acoustic band structures exhibit very interesting and non-standard physical properties due to the periodic nature of their certain characteristic on different scale levels. They manifest mostly in their frequency spectra as socalled frequency band-gaps or stop-bands, what has a great impact on the behaviour of these structures in relation to the propagation of vibro-acoustic signals that can be transmitted through the structures...
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Evaluation of the Influence of Farming Practices and Land Use on Groundwater Resources in a Coastal Multi-Aquifer System in Puck Region (Northern Poland)
PublikacjaThis study focuses on the modeling of groundwater flow and nitrate transport in a multi-aquifer hydrosystem in northern Poland, adjacent to Puck Bay (Baltic sea). The main goal was to investigate how changes in land use and farming practices may affect groundwater recharge and submarine groundwater discharge (SGD) to the sea and the associated N-NO3 fluxes. An integrated modelling approach has been developed, which couples the...
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Biomechanical properties of 3D-printed bone models
PublikacjaBone lesions resulting from large traumas or cancer resections can be successfully treated by directly using synthetic materials or in combination with tissue engineering methods (hybrid). Synthetic or hybrid materials combined with bone tissue’s natural ability for regeneration and biological adaptation to the directions of loading, allow for full recovery of its biological functions. Increasing interest in new production methods...
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Contact with coupled adhesion and friction: Computational framework, applications, and new insights
PublikacjaContact involving soft materials often combines dry adhesion, sliding friction, and large deformations. At the local level, these three aspects are rarely captured simultaneously, but included in the theoretical models by Mergel et al., (2019). We here develop a corresponding finite element framework that captures 3D finite-strain contact of two deformable bodies. This framework is suitable to investigate sliding friction even...
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Opportunities and challenges for exploiting drones in agile manufacturing systems
PublikacjaDrones have become an advanced supply chain implementation instrument, especially in connecting warehouses to outlet points or even individual customers. However, their potential application in an intra-logistics framework has not been studied, let alone explored so far. Modeling and simulations in virtual environments can help explore and evaluate the opportunities for practical and profitable applications of drones in manufacturing...
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Low-cost and reliable geometry scaling of compact microstrip couplers with respect to operating frequency, power split ratio, and dielectric substrate parameters
PublikacjaA technique for rapid re-design of miniaturised microstrip couplers with respect to operating conditions as well as material parameters of the dielectric substrate is proposed. The dimension scaling process is based on a set of pre-optimised reference designs, obtained for an equivalent circuit model of the coupler at hand. The reference designs are utilised to construct an inverse surrogate model which – upon suitable correction...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Detection and Imaging of Debonding in Adhesive Joints of Concrete Beams Strengthened with Steel Plates Using Guided Waves and Weighted Root Mean Square
PublikacjaStrengthening of engineering structures is an important issue, especially for elements subjected to variable loads. In the case of concrete beams or slabs, one of the most popular approaches assumes mounting an external reinforcement in the form of steel or composite elements by structural adhesives. A significant disadvantage of adhesive joints is the lack of access to the adhesive film for visual condition assessment, thus, there...
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Analysis of Validation and Simplification of Timber-Frame Structure Design Stage with PU-Foam Insulation
PublikacjaThe transition from experimental studies to the realm of numerical simulations is often necessary for further studies, but very difficult at the same time. This is especially the case for extended seismic analysis and earthquake-resistant design. This paper describes an approach to moving from the experimental testing of an elementary part of a wood-frame building structure to a numerical model, with the use of a commercial engineering...
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Role of cholesterol in substrate recognition by -secretase
Publikacja-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Local Nusselt number evaluation in the case of jet impingement
PublikacjaJet impingement still is one of demanding cases regarding computational fluid dynamics, due to its highly turbulent behaviour, with occurrence of turbulent-laminar transition. Even recently developed methods exhibit some drawbacks – RANS based simulations lack accuracy, LES and DNS based ones require too much computational time. Hybrid methods also exist, but their development and validation is in progress. Nevertheless, CFD application...
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A Ship Domain-Based Method of Determining Action Distances for Evasive Manoeuvres in Stand-On Situations
PublikacjaA ship encounter can be considered safe if neither of ships’ domains (defined areas around ships) is intruded by other ships. Published research on this includes optimising collision avoidancemanoeuvres fulfilling domain-based safety conditions.However, until recently there was no method, using ship’s domain to determine exact moment when a particular collision avoidance manoeuvre can still be successfully performed. The authors...
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Numerical Simulation of Catastrophic Flood: the Case Study of Hypothetical Failure of the Bielkowo Hydro–Power Plant Reservoir
PublikacjaThe numerical modeling of flood wave propagation following the hypo-thetical breaks of the embankments of the Bielkowo hydro–power plant storage reservoir (Kolbudy II Reservoir) on the Radunia River in Poland have been presented. The results of computations were used to estimate the parameters of the flood waves, which are indispensable for the flood zone determination and mapping and then for the flood risk analysis. When estimating...