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Search results for: computation
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Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers
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Region-Specific Methylation Profiling in Acute Myeloid Leukemia
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Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent-Copalyl Diphosphate Synthase
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Natural articular cartilage: A smart biointerface
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Asymptotic Expansion Method with Respect to Small Parameter for Ternary Diffusion Models
PublicationTernary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs).
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Fast Antenna Optimization Using Gradient Monitoring and Variable-Fidelity EM Models
PublicationAccelerated simulation-driven design optimization of antenna structures is proposed. Variable-fidelity electromagnetic (EM) analysis is used as well as the trust-region framework with limited sensitivity updates. The latter are controlled by monitoring the changes of the antenna response gradients. Our methodology is verified using three compact wideband antennas. Comprehensive benchmarking demonstrates its superiority over both...
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Low-Cost Surrogate Modeling of Miniaturized Microwave Components Using Nested Kriging
PublicationIn the paper, a recently reported nested kriging methodology is employed for modeling of miniaturized microwave components. The approach is based on identifying the parameter space region that contains high-quality designs, and, subsequently, rendering the surrogate in this subset. The results obtained for a miniaturized unequal-power-split rat-race coupler and a compact three-section impedance transformer demonstrate reliability...
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Nested Kriging Surrogates for Rapid Multi-Objective Optimization of Compact Microwave Components
PublicationA procedure for rapid EM-based multi-objective optimization of compact microwave components is presented. Our methodology employs a recently developed nested kriging modelling to identify the search space region containing the Pareto-optimal designs, and to construct a fast surrogate model. The latter permits determination of the initial Pareto set, further refined using a separate surrogate-assisted process. As an illustration,...
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ON DYNAMICS OF ELASTIC NETWORKS WITH RIGID JUNCTIONS WITHIN NONLINEAR MICRO-POLAR ELASTICITY
PublicationWithin the nonlinear micropolar elasticity we discuss effective dynamic (kinetic) properties of elastic networks with rigid joints. The model of a hyperelastic micropolar continuum is based on two constitutive relations, i.e., static and kinetic ones. They introduce a strain energy density and a kinetic energy density, respectively. Here we consider a three-dimensional elastic network made of three families of elastic fibers connected...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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3D Computer Model of the Hip Joint Cartilage
PublicationThis paper presents 3D computer model of the hip joint cartilage in the ANSYS program. Model is made on the basis of anatomy and collected data on the material constants of bone and cartilage components. Analysis and comparison of biochemical model, viscoelastic and molecular mixed - aggregation serves to facilitate the creation of the next model of reality, which could be used in the design of joint prostheses. The correctness...
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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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Adjustment for shape restoration and force control of cable arch stayed bridges
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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GaMRed – adaptive filtering of high-throughput biological data
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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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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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On the importance of volume of eroded material for cavitation erosion
PublicationW pracy przedstawiono model matematyczny opisujący wpływ objętości erodowanego materiału na przebieg krzywych erozji kawitacyjnej
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Computer aided materials design of PM duplex stainless steels
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Modelling of heat and mass transfer through wooden buildings
PublicationThe aim of this review paper is to examine the most recent available studies dealing with theoretical, numerical and experimental aspects related to modelling of heat and mass transfer through wooden buildings. The main thermophysical, mechanical and hygrometric properties of wood are firstly discussed. Then, the basic governing equations of heat and mass transfer phenomena are presented. A detailed description of the physical...
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A Regular Expression Matching Application with Configurable Data Intensity for Testing Heterogeneous HPC Systems
PublicationModern High Performance Computing (HPC) systems are becoming increasingly heterogeneous in terms of utilized hardware, as well as software solutions. The problems, that we wish to efficiently solve using those systems have different complexity, not only considering magnitude, but also the type of complexity: computation, data or communication intensity. Developing new mechanisms for dealing with those complexities or choosing an...
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E-cohomological Conley index
PublicationIn this thesis we continue with developing the E-cohomological Conley index which was introduced by A.Abbondandolo. In particular, we generalize the index to non-gradient flows, we show that it an possesses additional multiplicative structure and we prove the continuation principle. Then, using continuation principle, we show how the computation of the E-cohomological Conley index can be reduced to the computation of the classical...
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Coherent-wave Monte Carlo method for simulating light propagation in tissue
PublicationSimulating propagation and scattering of coherent light in turbid media, such as biological tissues, is a complex problem. Numerical methods for solving Helmholtz or wave equation (e.g. finite-difference or finite-element methods) require large amount of computer memory and long computation time. This makes them impractical for simulating laser beam propagation into deep layers of tissue. Other group of methods, based on radiative...
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Virtual team collaboration - Spring'24
e-Learning CoursesObjectives of the course include introducing non-algorithmic distributed computation models, indicating new trends in IT driving the development of the information society and demonstrating in practice several applications which represent basic classes of distributed interactive systems.
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Virtual team collaboration - Spring'24
e-Learning CoursesObjectives of the course include introducing non-algorithmic distributed computation models, indicating new trends in IT driving the development of the information society and demonstrating in practice several applications which represent basic classes of distributed interactive systems.
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Reconstruction of 3D structure of positive corona streamer by local methods
PublicationThe computer algorithms were used for reconstruction of streamer 3D structure. We propose the 3D tree structure model of corona discharge streamer composed with nodes and edges between chosen couples of nodes, which enables easy computation of some important parameters ofstreamers. The 3D model can be derived directly from two projection images by global methods like evolutionary searching or particle simulations. In this paper...
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The consideration to the dynamic systems parameter identification
PublicationIn this paper, a concept for continuous-time dynamic systems parameter identification using modulating function approach is presented. It refers to linear as well as selected non-linear systems. It shows the possibility of direct application without converting differential equation. In particular cases direct application can decrease the amount of computation in non-linear system identification, which generally requires Fourier...
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Efficient signal processing in spectroscopic optical coherence tomography
PublicationSpectroscopic optical coherence tomography (SOCT) is an extension of a standard OCT technique, which allows to obtain depth-resolved, spectroscopic information on the examined sample. It can be used as a source of additional contrast in OCT images e.g. by encoding certain features of the light spectrum into the hue of the image pixels. However, SOCT require computation of time-frequency distributions of each OCT A-scan, what is...
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High performance filtering for big datasets from Airborne Laser Scanning with CUDA technology
PublicationThere are many studies on the problems of processing big datasets provided by Airborne Laser Scanning (ALS). The processing of point clouds is often executed in stages or on the fragments of the measurement set. Therefore, solutions that enable the processing of the entire cloud at the same time in a simple, fast, efficient way are the subject of many researches. In this paper, authors propose to use General-Purpose computation...
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Simplified Distribution Grid Modelling for Connection Analyses
PublicationThis paper considers the modelling of medium and low voltage grids for the purpose of connection studies by distribution grid operators. Possible simplifications in grid modelling are discussed, which are acceptable from the viewpoint of the final result. The main driver of the modelling simplification is the MS Excel environment used as the computation platform, and the limitation of time for grid modelling.
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Waveform design for fast clutter cancellation in noise radars
PublicationCanceling clutter is an important, but computation-ally intensive part of signal processing in noise radars. It is shown that considerable improvements can be made to a simple least squares canceler if minor constraints are imposed onto noise waveform. The proposed scheme is potentially capable of canceling clutter in real-time, even for high sampling rates.
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Implementation of discrete convolution using polynomial residue representation
PublicationConvolution is one of the main algorithms performed in the digital signal processing. The algorithm is similar to polynomial multiplication and very intensive computationally. This paper presents a new convolution algorithm based on the Polynomial Residue Number System (PRNS). The use of the PRNS allows to decompose the computation problem and thereby reduce the number of multiplications. The algorithm has been implemented in Xilinx...
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Direct detection of quantum entanglement
PublicationBasing on positive maps separability criterion we propose the experimentally viable, direct detection of quantum entanglement. It is efficient and does not require any a priori knowledge about the state. For two qubits it provides a sharp (i.e., “if and only if”) separability test and estimation of amount of entanglement. We view this method as a new form of quantum computation, namely, as a decision problem with quantum data structure.
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Application of Analytic Signal and Smooth Interpolation in Pulse Width Modulation for Conventional Matrix Converters
PublicationThe paper proposes an alternative and novel approach to the PWM duty cycles computation for Conventional Matrix Converters (CMC) fed by balanced, unbalanced or non–sinusoidal AC voltage sources. The presented solution simplifies the prototyping of direct modulation algorithms. PWM duty cycles are calculated faster by the smooth interpolation technique, using only vector coordinates, without trigonometric functions and angles. Both...
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Evidence for SrHo2O4 and SrDy2O4 as model J1- J2 zigzag chain materials
PublicationNeutron diffraction and inelastic spectroscopy is used to characterize the magnetic Hamiltonian of SrHo2O4 and SrDy2O4. Through a detailed computation of the crystal-field levels we find site-dependent anisotropic single-ion magnetism in both materials, and diffraction measurements show the presence of strong one-dimensional spin correlations.Our measurements indicate that competing interactions of the zigzag chain, combinedwith...
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Comprehensive compensation of grid current distortion by shunt active power filters
PublicationThe paper presents a comprehensive approach to the compensation of grid current distortion in shunt active power filter systems. Four sources of current distortion are addressed: imperfect grid synchronization caused by the distortion in the grid voltages, time delays in the evaluation of grid voltages and computation of compensating currents, fluctuations of the dc bus voltage, and the distortion of inverter output voltages due...
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Efficient quadrature for fast oscillating integralof paraxial optics
PublicationThe study concerns the determination of quadrature for the integral solutionof the paraxial wave equation. The difficulty in computation of the integral isassociated with the rapid change of the integrand phase. The developed quadraturetakes into account the fast oscillating character of the integrand. The presentedmethod is an alternative to the commonly used methods based on the use of theFourier transform. The determination...
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LINEAR CHARACTERISTICS OF THE SLOSHING PHENOMENON FOR THE PURPOSE OF ON-BOARD SHIP'S STABILITY ASSESSMENT
PublicationThe paper presents results of experimental research and numerical simulations of the sloshing phenomenon. The research was focused on computation of the heeling moment affecting stability of a vessel. The proposed linearisation enables application of the results to the assessment of the ship's stability. The dependence of the heeling moment upon localisation of a tank in the ship's hull is analysed. The heeling moment obtained...
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The Concept of Geodetic Analyses of the Measurement Results Obtained by Hydrostatic Leveling
PublicationThe article discusses the issue of hydrostatic leveling. Its application is presented in structural health monitoring systems in order to determine vertical displacements of controlled points. Moreover, the article includes a complete computation scheme that utilizes the estimation from observation differences, allowing the elimination of the influence of individual sensors’ systematic errors. The authors suggest two concepts of...
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An Enhanced Reduced Basis Method for Wideband Finite Element Method Simulations
PublicationIn this paper, we present a novel strategy for selecting expansion points in the reduced basis method. A single computation of the error estimator is used to select a few expansion points in the multi-parameter space simultaneously. The number of selected points is determined adaptively, based on the accuracy of the current reduced model. The reliability and efficiency of this proposed approach are illustrated by numerical tests...
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The Experimental Determination of Bearings Dynamic Coefficients in a Wide Range of Rotational Speeds, Taking into Account the Resonance and Hydrodynamic Instability
PublicationMethods for the experimental determination of dynamic coefficients are commonly used for the analysis of various types of bearings, including hydrodynamic, aerodynamic and foil bearings. There are currently several algorithms that allow estimating bearing dynamic coefficients. Such algorithms usually use various excitation techniques applied to rotor–bearings systems. So far only a small number of scientific publications show how...
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Testing the impact of simplifications adopted in models describing wave loads on ship
PublicationThe wave-ship system in naval architecture is generally assumed to be a linear one. This allows for the computation of a transfer function of ship response to waves including wave loads on ship. The transfer function and the wave spectral density function enable the development of the stochastic process of wave loads on ship, corresponding to the irregular wave generating that loads. If the mathematical models of wave load transfer...
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Testing the impact of simplifications adopted in models describing wave loads on ship
PublicationThe wave-ship system in naval architecture is generally assumed to be a linear one. This allows for the computation of a transfer function of ship response to waves including wave loads on ship. The transfer function and the wave spectral density function enable the development of the stochastic process of wave loads on ship, corresponding to the irregular wave generating that loads. If the mathematical models of wave load transfer...
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Software for calculation of noise maps implemented on the supercomputer
PublicationThis paper presents investigation results relevant to the implementation of the algorithms for the calculation of noise maps. The aim of the implementation of the algorithms on the computer cluster is explained. Selected implementation details of the software called the noise propagation model are described. The interaction of the software with the data acquisition system is presented. Noise maps obtained by exploitation of the...
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Usage of the Gstreamer framework for generation, analysis, processing and visualization of sonar signal
PublicationIn this paper a novel method of the bearing estimation in a passive sonar system with a towed array is introduced. The classical approach of the bearing estimation based on the spatial spectrum is extended by using the synchrosqeezing method that is a part of the reassignment method introduced by Kodera et al. The usage of this method leads to the precise bearing estimation. The proposed method requires a relatively small amount...
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THE SYNCHROSQUEEZING METHOD IN BEARING ESTIMATION OF STATIONARY SIGNALS FOR PASSIVE SONAR WITH TOWED ARRAY
PublicationIn this paper, a novel method of bearing estimation in a passive sonar system with a towed array is introduced. The classical approach of bearing estimation based on the spatial spectrum [1] is extended by using the synchrosqeezing method that is a part of the reassignment method introduced by Kodera et al. [2]. Using this method leads to a precise bearing estimation. The proposed method requires a relatively small amount of computation,...
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Rainscreen panels deformations mods
PublicationIn rainscreen panels designing simplified calculation models are used. For plate computation simply supported panels or panels with fixed edges are commonly used. Such approximations are subjected to large errors that lead to inefficient rainscreen panels design. In order to develop a method for determining the optimal geometry of the rainscreen panels, that would take into consideration the real stiffness of both continuous and...
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Reconstruction of 3D image of corona discharge streamer
PublicationIn this paper, the method of reconstruction of the 3D structure of streamers in DC positive corona discharge in nozzle-to-plate electrode configuration is presented. For reconstructing of 3D image of corona discharge streamer we propose a stereographical method, where streamers are observed from several directions simultaneously. The multi-directional observation enabled to obtain fine positional coordinates of streamers for a...
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Marek Czachor prof. dr hab.
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Internetowe systemy przetwarzania rozproszonego typu grid w zastosowaniach biznesowych
PublicationSkoncentrowano się na możliwościach wykorzystania oraz integracji rozproszonych mocy obliczeniowych komputerów Internautów w globalnej sieci www. Zaprezentowano paradygmaty sieciowego przetwarzania typu grid computing oraz volunteer computing. Podkreślono istotność tego typu przetwarzania w zagadnieniach wymagających bardzo dużych mocy obliczeniowych. Zaprezentowano przykłady rozwiązań systemowych tego typu: system BOINC, będący...