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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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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions 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
PublicationMotor 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
PublicationEnzymy 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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Isocyanate-Free Polyurethanes
PublicationIsocyanate-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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Modeling of traffic safety indictors on Polish national road network
PublicationAlthough 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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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA 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
PublicationPraca 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
PublicationMagnesium 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
PublicationA 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
PublicationW 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
PublicationPrediction 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
PublicationMap-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
PublicationThree 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...
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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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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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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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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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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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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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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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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...
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EFFECTS OF BOUNDARY CONDITION EVALUATION ON DESIGN WAVE MODELING
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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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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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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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Diffusion process modeling by using fractional-order models
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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...