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Search results for: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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ATOMIC DATA AND NUCLEAR DATA TABLES
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Pharmacological Profile and Molecular Modeling of Cyclic Opioid Analogues Incorporating Various Phenylalanine Derivatives
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Simulation of the derecho event in Poland of 11th August 2017 using the WRF model and GFS data as initial conditions
Open Research DataThis series contains datasets related to the forecasting of a severe weather event, a derecho, in Poland on 11 August 2017. The simulations were conducted using the Weather Research and Forecasting (WRF) model version 4.2.1 with initial and boundary conditions from Global Forecast System (GFS). Simulation was performed for two starting hours: at 00:00...
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Simulation of the derecho event in Poland of 11th August 2017 using the WRF model and ECMWF data as initial conditions
Open Research DataThis series contains datasets related to the forecasting of a severe weather event, a derecho, in Poland on 11 August 2017. The simulations were conducted using the Weather Research and Forecasting (WRF) model version 4.2.1 with initial and boundary conditions from European Centre for Medium-Range Weather Forecasts (ECMWF). Simulation was performed...
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Rich Bifurcation Structure in a Two-Patch Vaccination Model
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Modeling of Human Tissue for Medical Purposes
PublicationThe paper describes the possibilities offered for medicine by modeling of human tissue using virtual and augmented reality. It also presents three proposals of breast modeling for the use in clinical practice. These proposals are the result of arrangements of medical and computer scientists team (the authors) and will be pursued and implemented in the near future. There is included also a brief description of the most popular methods...
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Crystal and molecular structure of lithium iodide complex of 13-membered azoxycrown ether
PublicationPublikacja zawiera uzupełniające informacje do znalezionej wcześniej korelacji między typem kationu, rozmiarem makrocyklu i cechami struktury krystalicznej kompleksów a selektywnością elektrod membranowych dotowanych odpowiednimi azo- lub azoksykoronami. Ustalono strukturę krystaliczną i molekularną kompleksu 13-członowej azoksykorony (L13-O) z jodkiem litu. Stechiometria kompleksu jest 1:1. Kryształ zbudowany jest z hydratowanych...
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Bifunctional catalyst based on molecular structure: Spherical mesoporous TiO2 and gCN for photocatalysis
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Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in Tissues
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Janusz Kozak prof. dr hab. inż.
PeopleJanusz KOZAK Born 04.07.1953 Puck, Poland Intermediate school” Technikum Budowy Okrętów „Conradinum” Gdansk, 1973. Graduated on Faculty of Shipbuilding of Gdańsk University of Technology, Poland, 1978. Employed: From 1978 - Gdynia Shipyard 1978 as designer, from 1980 as a specialist in Chair of Technology in Faculty of Shipbuilding of Gdańsk University of Technology, 1993 as assistant, PhD (1993), “Method for assessment...
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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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Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models
PublicationMulti-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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Topological-numerical analysis of a two-dimensional discrete neuron model
PublicationWe conduct computer-assisted analysis of a two-dimensional model of a neuron introduced by Chialvo in 1995 [Chaos, Solitons Fractals 5, 461–479]. We apply the method of rigorous analysis of global dynamics based on a set-oriented topological approach, introduced by Arai et al. in 2009 [SIAM J. Appl. Dyn. Syst. 8, 757–789] and improved and expanded afterward. Additionally, we introduce a new algorithm to analyze the return times...
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Data Warehouses 2023/2024
e-Learning CoursesThe aim of the course is to familiarize students with the development process of data warehouses for BI systems. The course is prepared for students of Data Engineering.
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Modeling energy consumption of parallel applications
PublicationThe paper presents modeling and simulation of energy consumption of two types of parallel applications: geometric Single Program Multiple Data (SPMD) and divide-and-conquer (DAC). Simulation is performed in a new MERPSYS environment. Model of an application uses the Java language with extension representing message exchange between processes working in parallel. Simulation is performed by running threads representing distinct process...
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Sparse autoregressive modeling
PublicationIn the paper the comparison of the popular pitch determination (PD) algorithms for thepurpose of elimination of clicks from archive audio signals using sparse autoregressive (SAR)modeling is presented. The SAR signal representation has been widely used in code-excitedlinear prediction (CELP) systems. The appropriate construction of the SAR model is requiredto guarantee model stability. For this reason the signal representation...
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Molecular structures of two E-azobenzocrown ethers
PublicationRentgenowska analiza strukturalna monokryształów posłużyła do scharakteryzowania struktury izomerów E dwóch azobenzokoron: 13- i 16-członowej. Oba związki krystalizują w układzie jednoskośnym. W komórce elementarnej, w każdym przypadku znajdują się dwie niezależne cząsteczki, różniące się konformacją, szczególnie łańcucha eterowego. Porównując konformacje ''wolnych'' makrocykli z konformacjami ich kompleksów z jonami metali wskazano,...
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation
PublicationThe 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel...
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A model of occurrence of the situations endangering inland waterways passanger ships and the environment
PublicationZaproponowano czterostanowy semimarkowski model pojawiania się sytuacji zagrażających pasażerskim statkom śródlądowym. Model ten został opracowany w formie semimarkowskiego procesu dyskretnego w stanach i ciągłego w czasie, którego wartościami są rodzaje stanów, interpretowanych jako sytuacje: normalna, skomplikowana, niebezpieczna oraz awaryjna. Zobrazowano przykładową realizację procesu zmian sytuacji, jakie mogą pojawić się...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
e-Learning Courses{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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Polymeric materials in medicine – structure and desing 2023/24
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QoS-sensitive selfish behavior in ad hoc wireless lans: a stochastic game model
PublicationRozważany jest prosty model stacji sieci bezprzewodowej wprowadzają-cych ruch elastyczny przy wymaganiu minimalnej przepływności. Każda stacja, okresowo przełączając się na egoistyczną konfigurację MAC, próbuje wyeliminować inne stacje z ubiegania się o pasmo sieci. Dla powstającej w ten sposób gry zastosowano model gry markowowskiej i pokazano istnienie symetrycznego punktu równowagi strategicznej.
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A semi-Markov model of fuel combustion process in a Diesel engine
PublicationW artykule przedstawiono czterostanowy model procesu spalania w przestrzeniach roboczych (cylindrach) silników o zapłonie samoczynnym w formie procesu semimarkowskiego, dyskretnego w stanach i ciągłego w czasie. Wartościami tego procesu są stany odpowiadające powszechnie akceptowanym rodzajom spalania w tego rodzaju silnikach a mianowicie takie stany procesu jak: spalanie pełne (całkowite i zupełne), spalanie niezupełne, spalanie...
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Stability & Dynamics of Ship and Offshore Structures II W2021/22
e-Learning CoursesLecture and Lab classes - Stability & Dynamics of Ship and Offshore Structures II W2021/22
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Crystal structure, hydrogen bonds, and lattice dynamics in kanemite from first-principles calculations
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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OIL-ASSISTED THERMO-MECHANICAL RECLAMATION OF GROUND TIRE RUBBER
PublicationNowadays, it is crucial to seek for the methods of by-products and waste utilization, considering both environmental and economic factors. The example of waste material generated in the massive amounts, which requires the attention is ground tire rubber generated during recycling of post-consumer car tires. It can be applied as a filler into different polymer matrices, but to enhance its effectivity proper modifications should...
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A Model of Thermally Activated Molecular Transport: Implementation in a Massive FPGA Cluster
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Dimensionality-Reduced Antenna Modeling with Stochastically Established Constrained Domain
PublicationOver the recent years, surrogate modeling methods have become increasingly widespread in the design of contemporary antenna systems. On the one hand, it is associated with a growing awareness of numerical optimization, instrumental in achieving high-performance structures. On the other hand, considerable computational expenses incurred by massive full-wave electromagnetic (EM) analyses, routinely employed as a major design tool,...
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Data in Brief
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublicationIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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Numerical modeling of sound intensity distributions around acoustic transducer
PublicationThe aim of this research study is to measure, simulate and compare sound intensity distribution generated by the acoustic transducers of the loudspeaker. The comparison of the gathered data allows for validating the numerical model of the acoustic radiation. An accurate model of a sound source is necessary in mathematical modeling of the sound field distribution near the scattering obstacles. An example of such obstacle is a human...
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The Dynamics of Trade Relations between Ukraine and Romania: Modelling and Forecasting
PublicationThe article examines the monthly dynamics of exports, imports and balance of trade between Ukraine and Romania in the period from 2005 to 2021. Time series from 2015 to 2021 were used for modelling and forecasting (since the date the European Union–Ukraine Association Agreement took effect). Adequate models of the dynamics series of the Box-Jenkins methodology were built: additive models with seasonal component ARIMA (Autoregressive...
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Variable Data Structures and Customized Deep Learning Surrogates for Computationally Efficient and Reliable Characterization of Buried Objects
PublicationIn this study, in order to characterize the buried object via deep-learning-based surrogate modeling approach, 3-D full-wave electromagnetic simulations of a GPR model has been used. The task is to predict simultaneously and independent of each characteristic parameters of a buried object of several radii at different positions (depth and lateral position) in various dispersive subsurface media. This study has analyzed variable...
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Arbutin: Isolation, X-ray structure and computional studies
PublicationArbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were...
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Computationally Efficient Surrogate-Assisted Design of Pyramidal-Shaped 3D Reflectarray Antennas
PublicationReflectarrays (RAs) have been attracting considerable interest in the recent years due to their appealing features, in particular, a possibility of realizing pencil-beam radiation patterns, as in the phased arrays, but without the necessity of incorporating the feeding networks. These characteristics make them attractive solutions, among others, for satellite communications or mobile radar antennas. Notwithstanding, available microstrip...
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Modeling the Influence of Salts on the Critical Micelle Concentration of Ionic Surfactants
PublicationWe show for the first time that a phenomenological, augmented volume-based thermodynamics (aVBT) model is capable to predict the critical micelle concentrations of ionic surfactants, including ionic liquids, with added salts. The model also adjusts for the type of salt added by including its molecular volume, which might form a connection to the Hofmeister effect. The other physico-chemically relevant quantities included in the...
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A model of risk for assessment of ships in damaged conditions
PublicationW pracy omówiono problemy związane z modelowaniem zagrożeń, konsekwencji i ryzyka, w metodzie oceny bezpieczeństwa statków w stanie uszkodzonym. W celu dokonania oceny bezpieczeństwa statku, w metodzie zastosowano podejścia oparte na ocenie zachowania się statku i ocenie ryzyka. Podejście oparte na ocenie zachowania się statku związane jest z oceną charakterystyk hydromechanicznych statku w stanie uszkodzonych w warunkach zbliżonych...
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Lattice type fracture model for brittle materials
PublicationW artykule przedstawiono wyniki obliczeń propagacji rys w elementach betonowych przy zastosowaniu modelu dyskretnego opartego na ruszcie belkowym. Obliczenia wykonano dla różnych problemów brzegowych. W modelu przyjęto inne właściwości dla kruszywa, zaczynu cementowego oraz strefy kontaktu.
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2D lattice model for fracture in brittle materials
PublicationW artykule przedstawiono wyniki obliczeń propagacji rys w elementach betonowych przy zastosowaniu modelu dyskretnego opartego na ruszcie belkowym. Obliczenia wykonano dla różnych problemów brzegowych.
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Optimising approach to designing kernel PCA model for diagnosis purposes with and without a priori known data reflecting faulty states
PublicationFault detection plays an important role in advanced control of complex dynamic systems since precise information about system condition enables efficient control. Data driven methods of fault detection give the chance to monitor the plant state purely based on gathered measurements. However, they especially nonlinear, still suffer from a lack of efficient and effective learning methods. In this paper we propose the two stages learning...
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Data Analysis in Bridge of Data
PublicationThe chapter presents the data analysis aspects of the Bridge of Data project. The software framework used, Jupyter, and its configuration are presented. The solution’s architecture, including the TRYTON supercomputer as the underlying infrastructure, is described. The use case templates provided by the Stat-reducer application are presented, including data analysis related to spatial points’ cloud-, audio- and wind-related research.
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Dynamic Bayesian Networks for Symbolic Polyphonic Pitch Modeling
PublicationSymbolic pitch modeling is a way of incorporating knowledge about relations between pitches into the process of an- alyzing musical information or signals. In this paper, we propose a family of probabilistic symbolic polyphonic pitch models, which account for both the “horizontal” and the “vertical” pitch struc- ture. These models are formulated as linear or log-linear interpo- lations of up to fi ve sub-models, each of which is...
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Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations
PublicationThe fraction of absorbed photosynthetically active radiation (fAPAR) is a key parameter for estimating the gross primary production (GPP) of trees. For continuous, dense forest canopies, fAPAR, is often equated with the intercepted fraction, fIPAR. This assumption is not valid for individual trees in urban environments or parkland settings where the canopy is sparse and there are well-defined tree crown boundaries. Here, the distinction...
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Bounding approach to parameter estimation without priori knowledge on model structure error.
PublicationArtykuł przedstawia estymację parametrów modelu ARMA (Autoregresive moving average) metodą zbiorów ograniczonych. Założono brak wiedzy na temat ograniczeń na błąd struktury modelu lub, że wiedza ta jest bardzo konserwatywna. W celu redukcji tego konserwatyzmu, zaproponowano koncepcje modelu punktowo-parametrycznego. W podejściu tym zakłada się istnienie zbioru parametrów modelu oraz błędu struktury odpowiadających każdej z trajektorii...
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Domain segmentation for low-cost surrogate-assisted multi-objective design optimisation of antennas
PublicationAbstract: Information regarding the best possible design trade-offs of an antenna structure can be obtained through multiobjective optimisation (MO). Unfortunately, MO is extremely challenging if full-wave electromagnetic (EM) simulation models are used for performance evaluation. Yet, for the majority of contemporary antennas, EM analysis is the only tool that ensures reliability. This study introduces a procedure for accelerated...
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EBE: elastic blob ensemble for coarse human tracking
PublicationProponujemy nowy probabilistyczny algorytm śledzenia oparty na elastycznym zespole kropelkowym (EBE), który ma zastosowanie przy śledzeniu obiektów elastycznych. Wynikiem jest wskazówka nt. zgrubnego ruchu w postaci lokalizacji i orientacji obiektu wraz z lokalizacją kropelki. Głównym założeniem jest to, że orientacja całego obiektu nie zmienia się znacznie między sąsiednimi klatkami. Dyskretna przestrzeń rozwiązań jest tworzona...
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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