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Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Atomic-Scale Finite-Element Modeling of Elastic Mechanical Anisotropy in Finite-Sized Strained Phosphorene Nanoribbons
PublicationNanoribbons are crucial nanostructures due to their superior mechanical and electrical properties. This paper is devoted to hybrid studies of the elastic mechanical anisotropy of phosphorene nanoribbons whose edges connect the terminals of devices such as bridges. Fundamental mechanical properties, including Young’s modulus, Poisson’s ratio, and density, were estimated from first-principles calculations for 1-layer, 3-layer, and...
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POM/EVA Blends with Future Utility in Fused Deposition Modeling
PublicationPolyoxymethylene (POM) is one of the most popular thermoplastic polymers used in the industry. Therefore, the interest in its potential applications in rapid prototyping is understandable. Nevertheless, its low dimensional stability causes the warping of 3D prints, limiting its applications. This research aimed to evaluate the effects of POM modification with ethylene-vinyl acetate (EVA) (2.5, 5.0, and 7.5 wt.%) on its processing...
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Elimination of Impulsive Disturbances From Stereo Audio Recordings Using Vector Autoregressive Modeling and Variable-order Kalman Filtering
PublicationThis paper presents a new approach to elimination of impulsive disturbances from stereo audio recordings. The proposed solution is based on vector autoregressive modeling of audio signals. Online tracking of signal model parameters is performed using the exponential ly weighted least squares algo- rithm. Detection of noise pulses an d model-based interpolation of the irrevocably distorted sampl es is realized using an adaptive, variable-order...
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Towards the Application of Structure-Property Relationship Modeling in Materials Science: Predicting the Seebeck Coefficient for Ionic Liquid/Redox Couple Systems
PublicationThis work focuses on determining the influence of both ionic liquid (IL) type and redox couple concentration on Seebeck coefficient values of such a system. The quantitative structure property relationship (QSPR) and read-across techniques are proposed as methods to identify structural features of ILs (mixed with LiI/I2 redox couple), which have the most influence on the Seebeck coefficient (Se) values of the system. ILs consisting...
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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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CFD-based evaluation of current-carrying capacity of power cables installed in free air
PublicationEvaluation of current-carrying capacity of power cables and selection of cross-sectional area of their conductors are mainly performed in accordance with requirements of EN, IEC or IEEE standards. However, these standards do not provide all methods of cables installation and location which occur in practice. Thus, in some cases, performance of advanced modeling of various thermal phenomena, affecting power cables current-carrying...
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Modeling, simulation, and validation of a TB41 crash test of the H2/W5/B concrete vehicle restraint system
PublicationThe paper addresses numerical simulations of a concrete vehicle restraint system. The model is described in detail. The advanced material law of the continuous surface cap model was used to analyze the damage locations in concrete barrier segments. The results were validated against the TB41 full-scale crash test. The test was conducted in compliance with European standard EN 1317, and the validation was performed in accordance...
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Modeling the photodynamic effect in 2D versus 3D cell culture under normoxic and hypoxic conditions
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Interpretation and modeling of emotions in the management of autonomous robots using a control paradigm based on a scheduling variable
PublicationThe paper presents a technical introduction to psychological theories of emotions. It highlights a usable ideaimplemented in a number of recently developed computational systems of emotions, and the hypothesis thatemotion can play the role of a scheduling variable in controlling autonomous robots. In the main part ofthis study, we outline our own computational system of emotion – xEmotion – designed as a key structuralelement in...
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Modeling hydrolysis of slowly biodegradable organic compounds in biological nutrient removal activated sludge systems
PublicationHydrolysis is an important process in biological wastewater treatment and is known to be the ratelimiting step in organic carbon removal from municipal or industrial wastewater. The influence of the readily biodegradable chemical oxygen demand fraction in biological wastewater treatment systems has been extensively investigated, but little is known about the effects of slowly biodegradable substrate (XS) on denitrification and...
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AFM-assisted investigation of conformal coatings in electronics
PublicationPurpose – This paper aims to presents a new method of investigation of local properties of conformal coatings utilized in microelectronics. Design/methodology/approach – It is based on atomic force microscopy (AFM) technique supplemented with the ability of local electrical measurements, which apart from topography acquisition allows recording of local impedance spectra, impedance imaging and dc current mapping. Potentialities...
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Machine learning-based prediction of seismic limit-state capacity of steel moment-resisting frames considering soil-structure interaction
PublicationRegarding the unpredictable and complex nature of seismic excitations, there is a need for vulnerability assessment of newly constructed or existing structures. Predicting the seismic limit-state capacity of steel Moment-Resisting Frames (MRFs) can help designers to have a preliminary estimation and improve their views about the seismic performance of the designed structure. This study improved data-driven decision techniques in...
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International Journal of Modeling Simulation and Scientific Computing
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International Journal of Information System Modeling and Design
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SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL
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5G/6G optical fronthaul modeling: cost and energy consumption assessment
PublicationIn fifth generation (5G) and the future beyond 5G (6G) radio access networks (RANs), the cost of fronthaul deployment is a main challenge for mobile network operators. Depending on different constraints, there are various solutions to deploy an efficient fronthaul. Fiber-optic-based fronthaul offers long-term support with regard to a rapid increase in capacity demands. When fiber connections, either point-to-point (P2P) or point-to-multipoint...
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Evaluation of ferrofluid-coated rotating magnetic field-assisted bioreactor for biomass production
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Adolfo Poma
PeopleI am the group leader of the computational modelling of biomolecules divison at the institute of Fundamental Technological Research Polish Academy of Sciences in Poland. My group was hosted between 2021-2022 by International Centre for Research on Innovative Bio-based Materials (ICRI-BioM). In 2008, I got a Master degree in computational physics from the State University of Campinas, Brazil. Then I moved to Germany and under the...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Design-oriented modeling of antenna structures by means of two-level kriging with explicit dimensionality reduction
PublicationThe employment of full-wave electromagnetic (EM) analysis is a practical necessity in the design of contemporary antenna structures. This is because simpler models are generally not available or of limited accuracy. At the same time, EM-based design is computationally expensive. Consequently, the ways of accelerating tasks such as parametric optimization or uncertainty quantification have to be sought. A possible workaround that...
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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ELECTIVE PROJECT II _sem 5_Green Story - Free Time Space
e-Learning CoursesThe topic of the course - Green Story - Free Time Space, joins green architecture and a place to spend free time - inside and outside – to read, to eat, to relax. The idea is to design green – to give back the greenery to the public square – to make a city space more friendly for users and more friendly to the environment. You can design a story, to make a space more attractive. You can design a Green Story, to make people more...
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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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Knowledge Exchange Between KIBS Firms and Their Clients: Case Study Analysis
PublicationPurpose: This paper aims to analyse knowledge exchange between KIBS firms and their clients, and their potential determinants (e.g. client’s education, type of the service offered, channel of the knowledge exchange, and willingness of the customer to accept the knowledge). The paper is based on a literature analysis and a case study research, examining 5 KIBS firms located in the Pomeranian region in Poland. Methodology: On the...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublicationThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Transient modeling in common DC link of power converters
PublicationПредмет исследования. Представлена математическая модель силовых преобразователей электропривода, питающихся от общего звена постоянного тока, на примере тяговых электроприводов карьерного самосвала БЕЛАЗ-90 мощностью 280 кВт. Модель выполнена в пакете MATLAB/Simulink. Новизна предложенной модели заключается в применении новой топологии силовой схемы для исследования работы двух инверторов, под- ключенных к одному звену постоянного...
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EFFECTS OF BOUNDARY CONDITION EVALUATION ON DESIGN WAVE MODELING
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Modeling variable curvature on the turnout diverging track length
PublicationThe paper presents three variants of variable curvature application on the entire length of the turnout diverging track. One linear and two nonlinear curvature cases: described the function of C1 and C0 class were considered. It turned out that both linear curve and the function of C1 class requires a significant (even twice) length of diverging track extending with respect to the base turnout. The curvature described by the function...
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Modeling changes of the ionospheric potential due to lightning and sprites
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Quantum chemical modeling of electrochromism of tungsten oxide films
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Modeling Online Buyers’ Preferences Related to Webpages Layout
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Diffusion process modeling by using fractional-order models
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Modeling and Simulation of Electric Motors Using Lightweight Materials
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AAM toolkit: a system for visual object appearance modeling
PublicationAktywne modele wyglądu (AAM) mogą być traktowane jako zaawansowana metoda analizy informacji multimedialnych, pozwalająca na lokalizowanie i rozpoznawanie obiektów w obrazach statycznych i sekwencjach wideo. Pomimo tego że ukazało się wiele publikacji dotyczących AAM, przejście od koncepcji teoretycznych do działającej implementacji stanowi nadal duże wyzwanie. W pracy przedstawiono przygotowany przez autorów pakiet oprogramowania...
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Modeling organic nitrogen conversions in activated sludge bioreactors
PublicationOpracowano model przemian azotu organicznego (Norg)jako rozszerzenie Modelu Osadu Czynnego Nr 2d (ASM2d). Nowy model zawiera trzy frakcje Norg: rozpuszczoą, koloidalną i zawesinową. Każda frakcja została podzielona na dwie podfrakcje - rozkładalną i nierozkładalną. Model został zweryfikowany w oparciu o wyniki badań eksperymentalnych w oczyszczalni ścieków Gdańsk-Wschód.
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Numerical modeling of ice jam formation in the Włocławek reservoir
PublicationArtykuł opisuje zjawisko powstawania zatoru lodowego w zbiorniku przepływowym przy użyciu dwuwymiarowego modelu DynaRICE. Analizowany proces został przeanalizowany na przykładzie zatoru lodowego, który utworzył się na zbiorniku Włocławek w syczniu 1982 roku. Przeprowadzone obliczenia pokazały, że zator utworzyła się z lodu powierzchniowego. Efekt termiczny i tworzenie się śryżu w zbiorniku został pominięty jako drugorzędny. Wyniki...
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Numerical modeling of the nonlinear wave propagation in a bubble layer
PublicationRozważano zagadnienie propagacji fali wewnątrz warstwy z pęcherzykami. Omówiono model matematyczny, przedstawiono przykładowe wyniki badań teoretycznych. Analizowano zmiany ciśnienia wewnątrz warstwy, falę odbitą i bieżącą w ośrodku otaczającym, badano gęstość widmową mocy. Badania teoretyczne przeprowadzono dla różnych grubości warstwy, koncentracji pęcherzyków i wartości parametrów fali padającej.
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Modeling of behavior of organic pollutants in aquatic and related ecosystems
PublicationW pracy omówiono możliwości wykorzystania różnych modeli do opisu zjawisk migracji oraz przemian w środowisku wodnym ksenobiotyków z grupy trwałych zanieczyszczeń organicznych (TZO). Przedstawiono charakterystykę zarówno modeli otwartych, jak i zamkniętych w warunkach ustalonych, jak i w warunkach nierównowagowych.
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Modeling for Detection of Degraded Zones in Metallic and Composite Structures
PublicationW pracy przedstawiono przegląd metod modelowania uszkodzeń w postaci pęknięć i delaminacji wystepujących w elementach konstrukcyjnych
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Design and modeling of switched reluctance motor for scooter application
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<title>Control system modeling for superconducting accelerator</title>
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Modeling of unsaturated water flow in highly heterogeneous soils.
PublicationTematem pracy jest modelowanie przepływu wody w gruntach nienasyconych o podwójnej porowatości, które charakteryzują się obecnością dwóch podobszarów porowatych o skontrastowanych parametrach hydraulicznych. Jako punkt wyjścia przyjęto, że w skali lokalnej przepływ w obu podobszarach jest opisany równaniem Richardsa. Przedstawiono wyprowadzenie dwóch modeli przepływu w skali makroskopowej przy użyciu metody homogenizacji asymptotycznej....
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Modeling of cut layer's thickness for circular saw blade
PublicationW pracy omówiono sposób modelowania grubości warstwy skrawanej na podstawie wyprowadzonych zależności matematycznych.
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Modeling of substrate noise block properties for early rediction.
PublicationZaproponowano nowe podejscie do modelowania zakłóceń podłozowych we wczesnym etapie projektowania systemów na wspólnym podłożu krzemowym. Modelowanie zakłóceń oparto na założeniu, że głównym źródłem zakłóceń podłożowych jest sieć zasilająca. W oparciu o przeprowadzone symulacjie wykazano słusznosć takiej metody.
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Substrate noise modeling in early floorplanning of MS-SOCs.
PublicationW pracy zaproponowano model częstotliwościowy bloków analogowych wrażliwych na zakłócenia oraz bloków cyfrowych generujących zakłócenia w systemach mieszanych realizowanych na wspólnym podłożu krzemowym. Zaproponowane modele zostały wykorzystane w oprogramowaniu optymalizującym rozmieszczenie bloków funkcjonalnych na struktórze krzemowej. Dzieki użyciu procedur optymalizacyjnych uzyskano znaczącą redukcje poziomu zakłóceń przy...
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Modeling of damage in a circular plate subjected to dynamic excitation
PublicationSzereg różnych dziedzin nauki zajmuje się problemem zniszczenia ciśnieniowych metalowych zbiorników (mechanika, termodynamika, mechanika płynów). Tylko niektóre prace ujmują wszystkie aspekty analizy. W prezentowanej pracy przedstawiono numeryczna analizę metalowej płyty poddanej obciążeniu dynamicznemu, aż do momentu zniszczenia. Do analizy zastosowano program MSC.Marc, element powłokowy, i prawo sprężysto lekoplastyczne uwzględniające...
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Computer modeling of perceptual masking and its audiology applications
PublicationW referacie zaprezentowano podstawy perceptualne słyszenia pozwalające na stworzenie nowych modeli kodowania dźwięku, w szczególności do zastosowania w protezach słuchu.
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Temperature modeling in activated sludge systems: a case study
PublicationPrzedstawiono model dynamiki temperatury jako część ogólnego modelu komory osadu czynnego. Transport ciepła opisano za pomocą jednowymiarowego równania adwekcyjno-dyspersyjnego z członem źródłowym opisującym teoretyczny bilans ciepła dla komory. Model został zweryfikowany w oczyszczalni ścieków Rock Creek w stanie Oregon (USA) w oparciu o dane eksploatacyjne oraz pomiary meteorologiczne z pobliskiej stacji meteorologicznej. Wyniki...