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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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On dynamic modeling of piezomagnetic/flexomagnetic microstructures based on Lord–Shulman thermoelastic model
PublicationWe study a time-dependent thermoelastic coupling within free vibrations of piezomagnetic (PM) microbeams considering the flexomagnetic (FM) phenomenon. The flexomagneticity relates to a magnetic field with a gradient of strains. Here, we use the generalized thermoelasticity theory of Lord–Shulman to analyze the interaction between elastic deformation and thermal conductivity. The uniform magnetic field is permeated in line with...
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Expedited Variable-Resolution Surrogate Modeling of Miniaturized Microwave Passives in Confined Domains
PublicationDesign of miniaturized microwave components is largely based on computational models, primarily, full-wave electromagnetic (EM) simulations. EM analysis is capable of giving an accurate account for cross-coupling effects, substrate and radiation losses, or interactions with environmental components (e.g., connectors). Unfortunately, direct execution of EM-based design tasks such as parametric optimization or uncertainty quantification,...
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Transformation of Energy Markets: Description, Modeling of Functioning Mechanisms and Determining Development Trends
PublicationOne of the key contemporary economic and social issues today is the global energy transition. Energy transition processes are having a significant impact on the development of world economies, increasing their TFP and leading to an increase in their level of innovation through the transfer of myriad new technologies. These processes also contribute to an increase in foreign direct investment and, consequently, an increase in the...
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Antenna Modeling Using Variable-Fidelity EM Simulations and Constrained Co-Kriging
PublicationUtilization of fast surrogate models has become a viable alternative to direct handling of fullwave electromagnetic (EM) simulations in EM-driven design. Their purpose is to alleviate the difficulties related to high computational cost of multiple simulations required by the common numerical procedures such as parametric optimization or uncertainty quantification. Yet, conventional data-driven (or approximation) modeling techniques...
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Recent advances in high-frequency modeling by means of domain confinement and nested kriging
PublicationDevelopment of modern high-frequency components and circuits is heavily based on full-wave electromagnetic (EM) simulation tools. Some phenomena, although important from the point of view of the system performance, e.g., EM cross-coupling effects, feed radiation in antenna arrays, substrate anisotropy, cannot be adequately accounted for using simpler means such as equivalent network representations. Consequently, the involvement...
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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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Discrete modeling of micro-structure evolution during concrete fracture using DEM
PublicationW artykule pokazano wyniki dyskretne DEM dla betonu poddanego ściskaniu i rozciąganiu jednoosiowemu. Wyniki siła-przemieszczenie i zarysowania porównano z doświadczeniami. Szczególną uwagę zwrócono na zjawiska mikrostrukturalne podczas zarysowania na poziomie kruszywa.
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Modeling of bearing capacity of footings on sand within stochastic micro-polar hypoplasticity.
PublicationAnalizowano numerycznie efekt wstępnego rozkładu wskaźnika porowatości na wytrzymałość i strefy ścinania w problemach fundamentów na piasku w skali modelowej. Obliczenia wykonano przy zastosowaniu stochastycznej metody elementów skończonych i mikropolarnego modelu hipoplastycznego. Wskaźnik porowatości miał formę skorelowanych pól stochastycznych. Dodatkowo obliczono efekt skali dla 3 różnych szerokości fundamentów.
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Multi-fidelity EM simulations and constrained surrogate modelling for low-cost multi-objective design optimisation of antennas
PublicationIn this study, a technique for low-cost multi-objective design optimisation of antenna structures has been proposed. The proposed approach is an enhancement of a recently reported surrogate-assisted technique exploiting variable-fidelity electromagnetic (EM) simulations and auxiliary kriging interpolation surrogate, the latter utilised to produce the initial approximation of the Pareto set. A bottleneck of the procedure for higher-dimensional...
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Comparison of the exponential thermal transient parameterization methods with the SMTP method in the unipedicled DIEP flap computer modelling and simulation
PublicationThe aim of this paper is to compare the spatial contrast of the image descriptors obtained via three different thermal transient parameterization methods in Active Dynamic Thermography. The thermal constants and amplitude values of the one- and two- exponential parametrization are compared to the Simplified Magnitude-Temporal Parametrization method (SMTP). The comparison is performed using the data obtained by simulating the cold...
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Modelling of Objects Behaviour for Their Re-identification in Multi-camera Surveillance System Employing Particle Filters and Flow Graphs
PublicationAn extension of the re-identification method of modeling objects behavior in muti-camera surveillance systems, related to adding a particle filter to the decision-making algorithm is covered by the paper. A variety of tracking methods related to a single FOV (Field of Vision) are known, proven to be quite different for inter-camera tracking, especially in case of non-overlapping FOVs. The re-identification methods refer to the...
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Modelling assisted phytoremediation of soils contaminated with heavy metals – Main opportunities, limitations, decision making and future prospects
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Physical aspect of application and usefulness of semi-Markovian processes for modelling the processes occurring in operational phase of technical objects.
PublicationW artykule zasygnalizowano przydatność teorii procesów semimarkowskich do tworzenia modeli procesów rzeczywistych, zachodzących w fazie eksploatacji różnych obiektów technicznych. Przydatność tej teorii została wykazana w wyniku przedstawienia: specyfiki procesów semimarkowskich oraz fizykalnych aspektów stosowania procesów semimarkowskich jako modeli procesów zachodzących w fazie eksploatacji wspomnianych obiektów. Specyfika została...
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Molecular modelling of transition state analogue inhibitors of glucosamine-6-P synthase and glucose-6-P isomerase.
PublicationStruktura kompleksu 2-amino-2-deoksy-D-glucitolo-6-P (ADGP) z centrum aktywnym syntazy GlcN-6-P z E. coli została wykorzystAna jako punkt wyjścia do modelowania molekularnego analogów ADGP. Używając programu GROMOS96 wygenerowano konformacje analogów o najniższych energiach wewnętrznych, które następnie ''dokowano'' w centrum aktywnym enzymu. Dokonano syntezy wybranych związków i określono parametry kinetyczne i termodynamiczne...
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Least square spline modelling along with tin decimation for 3D seafloor mapping from multibeam sonar data.
PublicationPrzedstawiono wyniki prac związane z zastosowaniem algorytmu aproksymacyjnego minimalnokwadratowego do wizualizacji danych wysokorozdzielczych pochodzących z sonaru wielowiązkowego. Metoda pozwala na redukcję danych oraz łatwą ich modyfikację.
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Modelling of high temperature air/steam gasification of biomassand solid wastes in view of hydrogen-rich gas production
PublicationPrzedstawiono zaawansowane technologie produkcji gazu bogatego w wodór z biomasy i odpadów komunalnych. Przeprowadzono badania eksperymentalne na stanowisku pomiarowym wykonanym w skali półprzemysłowej. Otrzymano obiecujące rezultaty podczas zgazowania palet drewnianych gazem o różnej zawartości pary wodnej.
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Estimation of Potential Leakage from Dumped Chemical Munitions in the Baltic Sea Based on Two Different Modelling Approaches
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Modelling relation between oxidation resistance and tribological properties of non-toxic lubricants with the use of artificial neural networks
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part I: studies in water
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Modelling and experimental investigation of the phenomenon of brekdown of the liquid layer formed by an impinging two-phase air-water jet
PublicationW pracy przedstawiono analizę teoretyczną i badania eksperymentalne badania zjawiska rozrywania warstwy cieczy powstałej z uderzającej strugi
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Modelowanie procesów migracji zanieczyszczeń organicznych w środowisku wodnym = Modelling of migration of organic xenobiotics in aquatic environment
PublicationPrzedstawiono zagadnienia związane z modelowaniem migracji związków chemicznych w środowisku. Zamieszczono także sposób konstruowania modeli i przegląd najważniejszych typów modeli migracji wraz z przykładami oraz wyniki, jakie można uzyskać za pomocą poszczególnych grup modeli. W pracy zawarto również podział modeli migracji ze względu na sposób przedstawienia transportu zanieczyszczeń, poziom kompilacji i zakres obszaru modelowania....
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Application of Monte-Carlo method to modelling influence of selected soil heterogeneity on macrodispersion of pollutants in unsaturated soil medium
PublicationThe influence of soil heterogeneity on miscible solute transport in soil is analyzed. The transport process is simulated numerically using the Monte-Carlo method. This paper shows how different types of soil heterogeneity influence the process of contaminant spreading. If independent flow paths exist in the soil, the degree of the mixing of pollutants in the outflow from the soil profile is larger. If the preferential flow paths...
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Application of reversed-phase thin layer chromatography and QSRR modelling for prediction of protein binding of selected β-blockers
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MODELLING OF TOXIC COMPOUNDS EMISSION IN MARINE DIESEL ENGINE DURING TRANSIENT STATES AT VARIABLE PRESSURE OF FUEL INJECTION
PublicationTransient states are an important part of the spectrum of engine loads, especially the traction engines. In the case of marine diesel engines, transient states are of particular importance in reducing the analysis of motion units for special areas and maneuvering in port, the participation of transient states in the load spectrum significantly increases, also, the emission of toxic compounds from this period increases proportionally....
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Modelling the impact of the agricultural holdings and land-use structure on the quality of inland and coastal waters with an innovative and interdisciplinary toolkit
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The Presidential Campaign of Małgorzata Kidawa-Błońska in Media Discourse: Analysis Based on Statistical Corpus Analysis and Topic Modelling
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Deterministic versus stochastic modelling of unsaturated flow in a sandy field soil based on dual tracer breakthrough data
PublicationThe 216 km2 Neuenhagen Millcreeck catchment can be characterized as a drought sensitive landscape in NE Germany. It is therefore a fundamental human interest to understand how water that fell as precipitation moves through the unsaturated soils and recharges groundwater. Additionally, a better knowledge of nutrient transport from soil to groundwater is important also, especially in landscapes with light sandy soils. For a better...
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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublicationInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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Modelling the impact of the agricultural holdings and land-use structure on the quality of inland and coastal waters with an innovative and interdisciplinary toolkit
PublicationThe changes taking place in the marine coastal zones are extremely important, as about 40% of the human population currently lives in the coastal areas (within 100 kilometres of the coastline) increasing anthropogenic pressure on the marine ecosystems. Agriculture is a significant source of nutrients to the marine environment that increase hypoxia, eutrophication and may pose a threat to the services provided by ecosystems. In...
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Modelling of Ship’s Heeling and Rolling for the Purpose of Gantry Control Improvement in the Course of Cargo Handling Operations in Sea Ports
PublicationThe paper presents two proposals of models of interaction between a ship and cargo being loaded or discharged by a gantry in port, in terms of heeling and rolling of the vessel. The main purpose of such modelling is the need for improvement of gantry control with regard to faster operations thanks to more accurate estimation of level and moment of cargo release from a gantry hook or spreader. The study may be the contribution to...
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Low-cost data-driven modelling of microwave components using domain confinement and PCA-based dimensionality reduction
PublicationFast data-driven surrogate models can be employed as replacements of computationally demanding full-wave electromagnetic simulations to facilitate the microwave design procedures. Unfortunately, practical application of surrogate modelling is often hindered by the curse of dimensionality and/or considerable nonlinearity of the component characteristics. This paper proposes a simple yet reliable approach to cost-efficient modelling...
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Integrated plant-wide modelling for evaluation of the energy balance and greenhouse gas footprint in large wastewater treatment plants
PublicationModern wastewater treatment plants (WWTPs) should maintain a balance between three combined sustainability criteria, including effluent quality, energy performance and greenhouse gas (GHG) emissions. All of these criteria were considered in the integrated plant-wide model developed in this study. The proposed model incorporates new features, including: (i) the addition of associated facilities to the overall energy balance and...
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Volterra series usefulness in modelling of the time-domain cross-talk phenomena in coupled microstrip lines with nonlinear termination
PublicationW pracy przedyskutowano możliwość wykorzystania szeregów Volterry do analizy zjawiska przesłuchu w sprzężonych liniach mikropaskowych z nieliniowym obciążeniem. Apracowano algorytm metody, zaś uzyskane wyniki numeryczne zweryfikowano poprzez porównania z wynikami badań eksperymentalnych linii obciążonych w torze transmisyjnym diodą Schottky'ego.
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Modelling of shear localization during granular flow within non-local hypoplasticity using material point method
PublicationArtykuł omawia wyniki numeryczne dotyczące powstawania lokalizacji odkształceń stycznych w materiałach granulowanych Obliczenia wykonano dla ściskania dwuosiowego i przypływu silosowego stosując hipoplastyczny model konstytutywny rozszerzony o długość charakterystyczną w ramach nielokalnej teorii. Zastosowano podejście punktów materialnych w celu uniknięcia nadmiernej deformacji elementów skończonych.
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Modelling of shear zones during quasi-static granular silo flow using material point method (MPM)
PublicationThe paper focuses on confined silo flow of cohesionless sand. The problem considered is a quasi-static flow in a plane strain model silo with parallel walls simulated with the material point method (MPM). The simulation used a non-local hypoplastic constitutive model. Initially, the paper validated the implemented numerical approach with basic element tests and a plane strain compression test. The subsequent MPM calculations for...
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The HRCT image analysis for quantitative description of peripheral airways remodelling.
PublicationPrzedstawiono analizę obrazów HRCT dla ilościowego opisu remodelingu dróg oddechowych. Zaproponowano metodologię postępowania w przypadku przekształceń geometrycznych celem uzyskania dokładnych wartości parametrów opisujących kształt.
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Moddeling urban processes based on requirements ofself-organization theory.
PublicationW artykule przedstawiono ogólne podstawy symulacji rozwoju urbanistycznego w oparciu o modele komórkowe. Nowa teoria, wykorzystująca aparat matematyczny stworzony do badań i modelowania dynamiki układów nieliniowych, rozszerza również możliwości poznawcze i wykorzystanie systemów GIS w szeroko pojmowanym planowaniu przestrzennym. Jej szybki rozwój w ostatnich latach i niezwykłe osiągnięcia w poznaniu procesów rządzących podstawową...
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Numerical Modeling of Water and Ice Dynamics for Analysis of Flow Around the Kiezmark Bridge Piers
PublicationThis paper presents the results of a numerical model study on the effect of ice on the proposed bridge piers in the Vistula River outlet and its effect on flow conditions in the river. The model DynaRICE is used in this study, which is a two-dimensional hydro-ice dynamic numerical model developed for dynamic ice transport and jamming in rivers. To simulate river hydrodynamics in the vicinity of the bridge piers, 2-dimensional numerical...
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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Decisional DNA for modeling and reuse of experiential clinical assessments in breast cancer diagnosis and treatment
PublicationClinical Decision Support Systems (CDSS) are active knowledge resources that use patient data to generate case specific advice. The fast pace of change of clinical knowledge imposes to CDSS the continuous update of the domain knowledge and decision criteria. Traditional approaches require costly tedious manual maintenance of the CDSS knowledge bases and repositories. Often, such an effort cannot be assumed by medical teams, hence...
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Novel approach to modeling spectral-domain optical coherence tomography with Monte Carlo method
PublicationNumerical modeling Optical Coherence Tomography (OCT) systems is needed for optical setup optimization, development of new signal processing methods and assessment of impact of different physical phenomena inside the sample on OCT signal. The Monte Carlo method has been often used for modeling Optical Coherence Tomography, as it is a well established tool for simulating light propagation in scattering media. However, in this method...
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Genre-Based Music Language Modeling with Latent Hierarchical Pitman-Yor Process Allocation
PublicationIn this work we present a new Bayesian topic model: latent hierarchical Pitman-Yor process allocation (LHPYA), which uses hierarchical Pitman-Yor pr ocess priors for both word and topic distributions, and generalizes a few of the existing topic models, including the latent Dirichlet allocation (LDA), the bi- gram topic model and the hierarchical Pitman-Yor topic model. Using such priors allows for integration of -grams with a topic model,...
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<title>Modeling of broadband light source to use with optical coherent tomography system</title>
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Computational modeling of molecularly imprinted polymers as a green approach to the development of novel analytical sorbents
PublicationThe development of novel molecularly imprinted polymers (MIP) sorbents for specific chemical compounds require a lot of tedious and time-consuming laboratory work. Significant quantities of solvents and reagents are consumed in the course of the verification of appropriate configurations of polymerization reagents. Implementation of molecular modeling in the MIP sorbent development process appears to provide a solution to this...
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Uniform sampling in constrained domains for low-cost surrogate modeling of antenna input characteristics
PublicationIn this letter, a design of experiments technique that permits uniform sampling in constrained domains is proposed. The discussed method is applied to generate training data for construction of fast replacement models (surrogates) of antenna input characteristics. The modeling process is design-oriented with the surrogate domain spanned by a set of reference designs optimized with respect to the performance figures and/or operating...
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Mathematical Modeling of the Impact Range of Sewage Discharge on the Vistula Water Quality in the Region of Włocławek
PublicationThe paper presents results of analysis of the industrial sewage discharge influence at km 688 + 250 of the Vistula River on water quality. During the analysis, two-dimensional models of flow, impurities and temperature transport were used. Hydrological conditions of the analyzed section of the river, characteristic flows and bathymetry of the riverbed in the first instance were defined. Calculations of velocity distribution at...
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Nonlinear planar modeling of massive taut strings travelled by a force-driven point-mass
PublicationThe planar response of horizontal massive taut strings, travelled by a heavy point-mass, either driven by an assigned force, or moving with an assigned law, is studied. A kinematically exact model is derived for the free boundary problem via a variational approach, accounting for the singularity in the slope of the deflected string. Reactive forces exchanged between the point-mass and the string are taken into account via Lagrange...
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MATHEMATICAL MODELING OF FLOOD MANAGEMENT SYSTEM IN THE CITY OF GDAŃSK, ORUŃSKI STREAM CASE STUDY
PublicationAim of the study This study analyses the efficiency of flood protection in a small urban catchment, based on a system of small reservoirs. Material and methods To assess the flood routing and surge reduction, a mathematical model of the river catchment was implemented. This was a lumped hydrological model, based on the SCS-CN method. Channel routing was performed, using kinematic wave equation. The sub-catchments have been determined...