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Wyniki wyszukiwania dla: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Central-force decomposition of spline-based modified embedded atom method potential
PublikacjaCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
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Fabrication and Characterization of Flexible Medical-Grade TPU Filament for Fused Deposition Modeling 3DP Technology
PublikacjaThe possibility of using additive manufacturing (AM) in the medicine area has created new opportunities in health care. This has contributed to a sharp increase in demand for 3D printers, their systems and materials that are adapted to strict medical requirements. We described herein a medical-grade thermoplastic polyurethane (S-TPU) which was developed and then formed into a filament for Fused Deposition Modeling (FDM) 3D printers...
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Justyna Signerska-Rynkowska dr inż.
OsobySince 2021 visiting assistant professor in Dioscuri Centre in Topological Data Analysis (Institute of Mathematics of the Polish Academy of Sciences, IMPAN) Since 2016 assistant professor at Gdańsk University of Technology, Faculty of Applied Physics and Mathematics, Department of Differential Equations and Mathematics Applications 2020 - 2023 Principal Investigator in "SONATA" grant “Challenges of low-dimensional...
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Molecular biology GT
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Modeling nutrient removal and energy consumption in an advanced activated sludge system under uncertainty
PublikacjaActivated sludge models are widely used to simulate, optimize and control performance of wastewater treatment plants (WWTP). For simulation of nutrient removal and energy consumption, kinetic parameters would need to be estimated, which requires an extensive measurement campaign. In this study, a novel methodology is proposed for modeling the performance and energy consumption of a biological nutrient removal activated sludge system...
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Rotating Magnetic Field-Assisted Reactor Enhances Mechanisms of Phage Adsorption on Bacterial Cell Surface
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Modeling and experimental investigation of the small UPQC systems
PublikacjaIn this paper the basis of analytical modelling of the UPQC arrangements (Unified Power Quality Conditioner) in d-q rotating coordinates, as well as select results of investigations conducted on the simplified small power laboratory model were talked over. In short form power balance as well as fundamental dependences and analytic model with regard of decoupling circuits were investigated. Applied method for DC link capacity selection...
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Modeling of the internal combustion engine cooling system
PublikacjaThe article concerns computer modelling of processes in cooling systems of internal combustion engines. Modelling objectives and existing commercial programs are presented. It also describes Author’s own method of binding graphs used to describe phenomena in the cooling system of a spark ignition engine. The own model has been verified by tests on the engine dynamometer. An example of using a commercial program for experimental...
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Modeling and experimental investigation of the small UPQC systems
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Modeling of acoustics of hearing aid earmold systems
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Modeling knee joint endoprosthesis mode of deformation
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Waveguide modeling as a tool for fitting a hearing aid
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Fading Modeling in Maritime Container Terminal Environments
PublikacjaIn this paper, an analytical model for slow and fast fading effects in maritime container terminals is derived, from fitting distributions to the results of measurements performed in an actual operational environment. The proposed model is composed of a set of equations, enabling to evaluate fading statistical distribution parameters for different system and environments conditions, as a function of frequency, base station antenna...
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Multilevel pharmacokinetics-driven modeling of metabolomics data
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Computer modeling of the solution conformation of cyclic enkephalins
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Thermodynamic vs. extrathermodynamic modeling of chromatographic retention
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Modeling and Simulation Method of Precision Grinding Processes
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Selected reflections on formal modeling in Industry 4.0
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Three-dimensional CFD modeling of a steam ejector
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Modeling Study and Performance Investigation of a Thermoelectric Refrigerator
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Modeling of photovoltaic properties of bilayer organic systems
PublikacjaPraca prezentuje teoretyczny opis charakterystyki prądowo-napięciowej i efektu fotowoltaicznego układu zbudowanego z dwóch warstw organicznych i elektrod. Rozpatrywane jest przybliżenie stałego pola elektrycznego oraz wpływ pułąpkowania nośników ładunku.
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Modeling of polarimetric sensors using LabVIEW environment
PublikacjaW artykule przedstawiono program do modelowania światłowodowych sensorów polarymetrycznych. Program ten, stworzony w środowisku LabVIEW, wyznacza odpowiedź nieidealnego światłowodowego sensora polarymetrycznego na siłę działającą na przetwornik pomiarowy. Omówiono problemy występujące w procesie tworzenia oprogramowania do modelowania zjawisk fizycznych w graficznym środowisku programistycznym. Przedstawiono wybrane wyniki modelowania.
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Modeling of Axial Flux Permanent Magnet Generators
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Modeling of the process of selected fire signaling systems
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Modeling of active fiber Bragg grating sensors
PublikacjaW artykule omówiono działanie przetwornika hydrofonu wykorzystującego profilowaną membranę sprzężoną z aktywną światłowodową siatką Bragga. W wyniku modelowania, wykonanego Metodą Elementów Skończonych, stwierdzono występowanie gradientów naprężeń wzdłuż siatki. Opracowano program do modelowania pasywnych i aktywnych światłowodowych siatek Bragga wykorzystujący metodę modów sprzężonych. Przedstawiono charakterystyki widmowe pasywnych...
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Modeling and simulation of thin-walled beams and frames
PublikacjaPrzedstawiono koncepcję zastosowania superelementów węzłowych do modelowania połączeń słupów i rygli ram zbudowanych z prętów cienkościennych oraz stężeń konstrukcyjnych w belkach cienkościennych. Przeprowadzono analizę pracy ramy stalowej zbudowanej z prętów cienkościennych ze szczególnym uwzględnieniem problemu przekazywania bimomentu poprzez węzeł takiej ramy.
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Modeling of event trees for the rapid scenario development
PublikacjaThe paper concerns the safety of ships in abnormal/damage conditions. Some conclusions following from the research associated with development of a method for safety assessment of ships in abnormal/damage conditions is presented in the paper. The method called SSAMADC (Ship Safety Assessment Method in Abnormal/Damage Conditions) is a risk-based method and is connected with application of the quantitative risk assessment QRA approach....
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Thermal ablation modeling via bioheat equation
PublikacjaWe consider Pennes’ bioheat equation and discuss an implicit numerical scheme which has better stability properties than other approaches. Our discussion concerns Carthesian geometry problems, however it carries over to spherical geometry models and more complicated shapes.
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Quality Modeling in Grid and Volunteer-Computing Systems
PublikacjaA model of computational quality in large-scale computing systems was presented in the previous chapter of this book. This model describes three quality attributes: performance, reliability and energy efficiency. We assumed that all processes in the system are incessantly ready to perform calculations and that communication between the processes occurs immediately. These assumptions are not true for grid and volunteer computing...
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Modeling of Ice Phenomena in the Mouth of the Vistula River
PublikacjaThe mouth of the Vistula River, which is a river outlet located in tideless area, is analyzed. The Vistula River mouth is a man-made, artificial channel which was built in the 19th century in order to prevent the formation of ice jams in the natural river delta. Since the artificial river outlet was constructed, no severe ice-related flood risk situations have ever occurred. However, periodic ice-related phenomena still have an impact...
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Continuous and discontinuous modeling of cracks in concrete elements
PublikacjaW artykule przedstawiono różne sposoby modelowania rys w elementach betonowych w warunkach mieszanego sposobu obciążenia przy zastosowaniu modeli ciągłych i nieciągłych. Symulacje wykonano przy zastosowaniu 3 różnych modeli ciągłych: modelu sprężysto-plastycznego, modelu w ramach mechaniki zniszczeniowej i modelu rys rozmytych z rysami obracającymi się oraz 1 modelu nieciągłego przy zastosowaniu stref kontaktu..
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublikacjaIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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User-assisted methodology targeted for building structure interpretable QSPR models for boosting CO2 capture with ionic liquids
PublikacjaTask-specific ionic liquid (IL) is an emerging class of compounds that may be environmentally friendly. Properly selected, these compounds may be green alternative to amine solutions and can replace them in post-combustion carbon dioxide (CO2) capture processes on an industrial scale. However, owing to the vast diversity of ions and their possible combinations, laboratory research is time consuming and expensive. Therefore, computational...
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Selected Problems of Machine Dynamics
Kursy OnlineThe 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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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Modeling the impact of rotor movement on non-linearity of motor currents waveforms in high-speed PMSM drives
PublikacjaMotor current measurement techniques as well as predictive control algorithms for electric drives rely on an assumption of linear motor currents changes resulting from constant inverter output voltages. Recent research has reported that this assumption does not hold in motors with short electrical time constant, and in drives whose rotor position advances substantially during a control period. This paper proposes a simulation model...
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Copper containing protein sites - structure, properties and models
PublikacjaEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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Modeling of traffic safety indictors on Polish national road network
PublikacjaAlthough decreased from 2001 to 2013, Poland’s road deaths improved at a slower rate than the rest of the EU, leaving Poland as one of the worst road safety performing countries in the EU. The national road network in Poland, despite the dynamic transformation and development, still does not conform to the EU safety standards. Similar situation exists in other EU countries, particularly those in Central and Eastern Europe. Safety...
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Isocyanate-Free Polyurethanes
PublikacjaIsocyanate-free polyurethanes (also called non-isocyanate polyurethanes, or NIPUs) are alternatives to the conventional (commercially used) polyurethanes synthesized using di- or polyisocyanates, polyols, and chain extenders with low molecular weight. The major routes of NIPUs’ synthesis involve polyaddition of cyclic carbonates and di- or polyamines, polycondensation of carbamates, and diols. The most important intermediates are...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Molecular-dynamics simulation of clustering processes in sea-ice floes
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Cation diffusion coefficients in CuAgI via molecular dynamics simulations
PublikacjaPraca prezentuje wyniki analizy strukturalnej otrzymane poprzez symulacje dynamiczno-molekularne (zespół NpT, dwuciałowy potencjał Vashisty-Rahmana) superjonowego związku o składzie (1-x)Cu-xAg-I, x = 0.0, 0.25, 0.5, 0.75, 1.0). Wyznaczono wartość współczynnika dyfuzji kationów i energii aktywacji w funkcji składu szkła i temperatury. Otrzymane rezultaty porównano z danymi literaturowymi.
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Hunting for the Magnesium(I) Species: Formation, Structure, andReactivity of some Donor-Free Grignard Compounds
PublikacjaMagnesium bromide radicals have to be prepared as high-temperature molecules and trapped as a metastable solution because a seemingly simple reduction of donor-free Grignard compounds failed. However, the essential role of magnesium(I) species during the formation of Grignard compounds could be demonstrated experimentally.
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Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublikacjaA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
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Bounding approach to parameter estimation without prior knowledge on modeling error and application to quality modeling in drinking water distribution systems
PublikacjaW artykule rozważana jest estymacja parametrów modelu autoregresji z ruchoma średnią i sygnałem wejściowym (ARMAX) z wykorzystaniem przedziałowego modelu błędu. Zakłada się, że granice błędu struktury modelu są nieznane, bądź znane, ale bardzo konserwatywne. Dla zmniejszenia tego konserwatyzmu proponowane jest idea modeli punktowo-parametrycznych, w której występują zbiory parametrów i błędu modelu odpowiadające wszystkim wejściom....
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Numerical Estimation of Hull Hydrodynamic Derivatives in Ship Maneuvering Prediction
PublikacjaPrediction of the maneuvering characteristics of the ship at the design stage can be done by means of model tests, computational simulations or a combination of both. The model tests can be realized as direct simulation of the standard maneuvers with the free running model, which gives the most accurate results, but is also the least affordable as it requires very large tank or natural lake, as well as complex equipment of the...
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Periodic and chaotic dynamics in a map‐based neuron model
PublikacjaMap-based neuron models are an important tool in modeling neural dynamics and sometimes can be considered as an alternative to usually computationally costlier models based on continuous or hybrid dynamical systems. However, due to their discrete nature, rigorous mathematical analysis might be challenging. We study a discrete model of neuronal dynamics introduced by Chialvo in 1995. In particular, we show that its reduced one-dimensional...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublikacjaThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...