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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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Application of gas chromatographic data and 2D molecular descriptors for accurate global mobility potential prediction
PublicationMobility is a key feature affecting the environmental fate, which is of particular importance in the case of persistent organic pollutants (POPs) and emerging pollutants (EPs). In this study, the global mobility classification artificial neural networks-based models employing GC retention times (RT) and 2D molecular descriptors were constructed and validated. The high usability of RT was confirmed based on the feature selection...
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Integration and verification of meteorological observations and NWP model data for the local GNSS tomography
PublicationGNSS meteorology applies the Global Navigation Satellite Systems (GNSS) to derive information about the state of the atmosphere (particularly troposphere). The tomography is one of the methods used in GNSS meteorology. The input data of GNSS tomography are the signal troposphere delays, results of GNSS data processing and additionally meteorological observations and Numerical Weather Prediction (NWP) models data. Different types...
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Intelligent monitoring the vertical dynamics of wheeled inspection vehicles
PublicationThe problem of intelligent monitoring of the vertical dynamics of wheeled inspection vehicles is addressed. With the independent MacPherson suspension system installed, the basic analysis focuses on the evaluation of the parameters of the so-called quarter car model. To identify a physically motivated continuous description, in practice, dedicated integral-horizontal filters are used. The obtained discrete model, which retains...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
PublicationThe increasing interest in polyurethane materials has raised the question of the environmental impact of these materials. For this reason, the scientists aim to find an extremely difficult balance between new material technologies and sustainable development. This work attempts to validate the possibility of replacing petrochemical polyols with previously synthesized bio-polyols and their impact on the structure and properties...
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Combining Computational Fluid Dynamics with a Biokinetic Model for Predicting Ammonia and Phosphate Behavior in Aeration Tanks
PublicationThe aim of this study was to use computational fluid dynamics for predicting the behavior of reactive pollutants (ammonia and phosphate) in the aerobic zone of the bioreactor located at the Wschod wastewater treatment plant in Gdansk, Poland. The one-dimensional advection-dispersion equation was combined with simple biokinetic models incorporating the Monod-type expressions as source terms for the two pollutants. The problem was...
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Erratum to: Coarse-grained model of the native cellulose Iα and the transformation pathways to the Iβ allomorph
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Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids
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Simulation of the derecho event in Poland of 11th August 2017 using the WRF model and ERA5 data on model levels 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 ERA5 on model levels. Simulation was performed for two starting hours: at 00:00 and 12:00...
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The effect of high molecular weight bio-based diamine derivative of dimerized fatty acids obtained from vegetable oils on the structure, morphology and selected properties of poly(ether-urethane-urea)s
PublicationIn this work, the effect of the high molecular weight bio-based diamine on the chemical structure and selected properties of poly(ether-urethane-urea)s has been investigated. The ether-urethane prepolymer was cured using 1,4-butanediol and/or bio-based diamine. Mentioned chain extenders were used separately or in the mixture, and their different molecular weight and chemical structure resulted in obtaining materials with diversified...
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Position in global value chains and wages in Central and Eastern European countries
PublicationThis paper examines the relationship between the relative position of industries in Global Value Chains (GVC) and wages in 10 Central and Eastern European countries. We combine GVC measures of global import intensity of production, upstreamness and the length of the value chain with micro-data on workers. We find that the wages of Central and Eastern European countries workers are higher when their industry is at the beginning...
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Biopolyols obtained via microwave-assisted liquefaction of lignin: structure, rheological, physical and thermal properties
PublicationThe present study examined the application of polyols obtained via microwave-assisted liquefaction of lignin in the production of rigid polyurethane foam. Lignin was liquefed in crude glycerol and 1,4-butanediol at diferent temperatures (130–170 °C), without a catalyst and using various biomass concentrations (15 and 30 wt%). The physicochemical properties, process yield, and FTIR-based identifcation of the obtained polyols were...
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A Quality Model for UML tools
PublicationJakość narzędzi UML wpływa na efektywność wykonywania zadań związanych z modelowaniem systemów w procesie wytwarzania oprogramowania. Celem badań prezentowanych w tym referacie jest wyodrębnienie kryteriów jakości narzędzi UML. Omówiono rolę narzędzi UML w projekcie informatycznym, a następnie zaprezentowano szereg kryteriów jakości narzędzi UML wraz z aspektami oceny oraz opisem ankiety, która służy do oceny narzędzi względem...
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The elasto-viscoplstic Chaboche model
PublicationW artykule przedstawiono rozwoj i numeryczną aplikacje sprężysto-lepkoplastycznego modelu Chabocha. Przedstawione są także szczegółowe opisy kilkunastu wariantów modelu Chaboche'a wraz z parametrami materiałowymi.
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Testing the Effect of Bathymetric Data Reduction on the Shape of the Digital Bottom Model
PublicationDepth data and the digital bottom model created from it are very important in the inland and coastal water zones studies and research. The paper undertakes the subject of bathymetric data processing using reduction methods and examines the impact of data reduction according to the resulting representations of the bottom surface in the form of numerical bottom models. Data reduction is an approach that is meant to reduce the size...
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The impact of initial and boundary conditions on severe weather event simulations using a high-resolution WRF model. Case study of the derecho event in Poland on 11 August 2017
PublicationPrecise simulations of severe weather events are a challenge in the era of changing climate. By performing simulations correctly and accurately, these phenomena can be studied and better understood. In this paper, we have verified how different initial and boundary conditions affect the quality of simulations performed using the Weather Research and Forecasting Model (WRF). For our analysis, we chose...
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Numerical Simulations for Transonic Flow in Control Valve
PublicationResults of numerical simulations for transonic flow in control valve are presented. The valve is the main part of an adaptive pneumatic shock absorber. Flow structure in the valve domain and the influence of the flow non-uniformity in the valve on a mass flow rate is investigated. Numerical simulation results are compared with experimental data.
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Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
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Comparative 3D DEM simulations of sand–structure interfaces with similarly shaped clumps versus spheres with contact moments.
PublicationThree-dimensional simulations of a monotonic quasi-static interface behaviour between initially dense cohesionless sand and a rigid wall of different roughness during tests in a parallelly guided direct shear test under constant normal stress are presented. Numerical modelling was carried out by the discrete element method (DEM) using clumps in the form of convex non-symmetric irregularly shaped grains. The clumps had an aspect...
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Introductory modeling for decision-making using AMPL
e-Learning CoursesIntroductory modeling for decision-making using AMPL
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Modeling projects for decision-making using AMPL
e-Learning CoursesModeling projects for decision-making using AMPL
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Rapid dimension scaling of triple-band antennas by means of inverse surrogate modeling
PublicationGeometry scaling of antennas, i.e., finding optimum dimensions of the structure for given operating conditions and material parameters is an important yet challenging problem. In this paper, we discuss fast dimension scaling of triple-band antennas with respect to operating frequencies. We adopt the inverse surrogate modeling approach where the surrogate model is a function of the three operating frequencies of the antenna and...
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Polymerization and Structure of Opposing Polymer Brushes Studied by Computer Simulations
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Structures for parameterization, meshing and data exchange of topologically related surfaces of a ship hull
PublicationThis paper presents proposal of data structures for storage and processing of a parametric three-dimensional model of a midship hull sections. The model consists of coarse surfaces like: decks, frames, girders, stiffeners, brackets, partitions etc. bounded by topological relations. All workshop details are omitted as the model is intended for numeric calculations. Proposed data structures are prepared to facilitate changes in the...
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Count Data Modeling About Relationship Between Dubai Housing Sales Transactions and Financial Indicators
PublicationIn this study, illustrating and comparing the performances of count data models such as Poisson, negative binomial (NB), Hurdle and zero-inflated models for the determination of factors affected housing sales in Dubai. Model comparisons are made via Akaike’s information criterion (AIC), the Vuong test and examining the residuals. Main purpose of this study is building reliable statistical model for relationship between Dubai housing...
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The structure of knowledge resources supporting a model of IT technologies architecture = Struktury zasobów wiedzy wspierających model architektury technologii IT
PublicationThis paper introduces an abstract model for tools used in the software engineering process. The main goal of the research is to develop a universal model which allows a description of tools used in the process. The model supports a decision making process and gives an option to choose the best tooling for the situation. The model considers many factors including, but not exclusive to, the company structure, project environment...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Lattice dynamics of Mg2SiO4
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Selected Problems of Machine Dynamics II
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Selected Problems of Machine Dynamics - advances
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Selected Problems of Machine Dynamics - advances
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Paweł Możejko dr hab.
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Numerical Modeling of Hydrosystems 2023/2024
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Security information sharing for smart grids: Developing the right data model
PublicationThe smart grid raises new security concerns which require novel solutions. It is commonly agreed that to protect the grid the effective collaboration and information sharing between the relevant stakeholders is prerequisite. Developing a security information sharing platform for the smart grid is a new research direction which poses several challenges related to the highly distributed and heterogeneous character of the grid. In...
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Numerical Evaluation of Dynamic Response of a Steel Structure Model under Various Seismic Excitations
PublicationThe present paper reports the results of the study, which was designed to perform a numerical evaluation of dynamic response of a single-storey steel structure model. The experimental model was previously subjected to a number of different earthquake ground motions during an extensive shaking table investigation. The analyzed structure model was considered as a 1-DOF system with lumped parameters, which were determined by conducting...
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Simulations of wave propagation and attenuation in fields of colliding ice floes
Open Research DataThis dataset contains results of numerical smulations of sea ice-wave interactions, corresponding to laboratory experiments conducted at the Large Ice Model Basin (LIMB) at the Hamburg Ship Model Basin (HSVA) as part of the LS-WICE ("Loads on Structure and Waves in Ice"; https://zenodo.org/record/1067170#.XrLt_dhpxhE) project. THe simulations were conducted...
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Dynamics of Ice Jam Formation and Release
PublicationThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
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M-Split Estimation in Laser Scanning Data Modeling
PublicationPublikacja traktuje o wykorzystaniu estymacji M-Split do modelowania danych pozyskanych w wyniku skaningu laserowego. Autorzy prezentują rozwiązanie w oparciu o detekcję krawędzi dwóch płaszczyzn.
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Molecular Modeling of Interaction of the Vasopressin Analogs with Vasopressin and Oxytocin Receptors
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Molecular geometry of phenylboronic acid
Open Research DataData presents molecular geometry of the ground singlet state of phenylboronic acid. The geometry was obtained via DFT calculations using Becke–Lee–Yang–Parr density functional (B3LYP) with the balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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Cost-Efficient Surrogate Modeling of High-Frequency Structures Using Nested Kriging with Automated Adjustment of Model Domain Lateral Dimensions
PublicationSurrogate models are becoming popular tools of choice in mitigating issues related to the excessive cost of electromagnetic (EM)-driven design of high-frequency structures. Among available techniques, approximation modeling is by far the most popular due to its versatility. In particular, the surrogates are exclusively based on the sampled simulation data with no need to involve engineering insight or problem-specific knowledge....
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Coulomb-Assisted Dissociative Electron Attachment: Application to a Model Peptide
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Modelling gene expression of a self-regulating protein
PublicationWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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Rapid EM-driven antenna dimension scaling through inverse modeling
PublicationIn this letter, a computationally feasible technique for dimension scaling of antenna structures is introduced. The proposed methodology is based on inverse surrogate modeling where the geometry parameters of the antenna structure of interest are explicitly related to the operating frequency. The surrogate model is identified based on a few antenna designs optimized for selected reference frequencies. For the sake of computational...
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Numerical Simulations of Hydrodynamic Open-Water Characteristics of a Ship Propeller
PublicationThe paper presents the results of numerical simulations of ship propeller operation bearing the name of Propeller Open Water (POW) Tests. The object of tests was a sample ship propeller (PPTC1), the geometrical and kinematic data of which are available, along with the results of model tests, on the official page of the research centre involved in the measurements. The research aimed at verifying the correctness of results of numerical...
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The effect of sunscreen 4‐methylbenzylidene camphor in different and reproductive models, its bioaccumulation and molecular effects on ligand‐receptor interaction, and protein expression
Publication4-Methylbenzylidene camphor (4-MBC) is a photo-absorbing UV filter prevalently used in cosmetics, which can be absorbed into circulation and cause systemic effects. 4-MBC is continued to be released in the environment despite the growing knowledge about its bioaccumulation and endocrine disrupting effects. Previous reviews have mentioned UV-filter together but this review considers 4-MBC alone, due to its prevalence and concerning...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Simulations of flows in the coastal zone of the Baltic Sea
Open Research DataThe study area is located in the Southern Baltic, within Polish Marine Areas, adjacent to the coastline in the vicinity of Lubiatowo village, where The Coastal Research Station (CRS) – a field laboratory of the Institute of Hydro-Engineering of the Polish Academy of Sciences (IBW PAN) –is situated. The numerical reconstruction of the coastal flow was...
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Modeling of Electrified Transportation Systems Featuring Multiple Vehicles and Complex Power Supply Layout
PublicationThe paper proposes a novel approach to modeling electrified transportation systems. The proposed solution reflects the mechanical dynamics of vehicles as well as the distribution and losses of electric supply. Moreover, energy conversion losses between the mechanical and electrical subsystems and their bilateral influences are included. Such a complete model makes it possible to replicate, e.g., the impact of voltage drops on vehicle...