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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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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 of performance of an AUV stealth vehicle. Design for operation.
PublicationIn the paper some results of research connected with modelling of performance and risk assessment of an AUV stealth vehicle are presented. A general approach to design of the stealth AUV autonomous underwater vehicle under consideration is introduced. The basic stealth characteristics of the AUV stealth vehicle are briefly described. The method of research is introduced. The AUV stealth vehicle concept is presented including the...
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Modeling of Combined Phenomena Affecting an AUV Stealth Vehicle
PublicationIn the paper some results of research connected with modelling the basic stealth characteristics of an AUV vehicle are presented. First of all a general approach to design of the stealth AUV autonomous underwater vehicle under consideration is introduced. Then, the AUV stealth vehicle concept is briefly described. Next a method of modelling of the stealth characteristics is briefly described as well. As an example of the stealth...
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Energy Modeling of Single-Family Houses in the Conceptual Phase
PublicationThe aim of the article is to identify the potential impact of the latest commercial digital tools for building energy analysis on the everyday architectural practice in Poland in the context of typology and energy optimization of single –family houses. The reason for this survey is that “architect friendly” interfaces simulation results’ visualization and energy analysis tools are not given deserved attention in the architectural...
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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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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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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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<title>Control system modeling for superconducting accelerator</title>
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Modeling of the acoustic waves propagation in non-homogeneous medium
PublicationRozważano zagadnienie propagacji fal w ośrodku niejednorodnym. Przedstawiono model matematyczny i przykładowe wyniki badań numerycznych. Model matematyczny zbudowano w oparciu o równanie KZK. Do rozwiązania zagadnienia zastosowano metodę różnic skończonych. Badano zmiany ciśnienia i zmiany widma odpowiednio w ośrodku jednorodnym i niejednorodnym.
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Modeling of flow phenomena associated with polymer injection into a mold
PublicationPodczas wtrysku tworzywa do formy w strefie tworzywo-ścianka formy występują zjawiska, które są źródłem zwiększonej chropowatości powierzchni i wad wypraski. W pracy pisano powyższe zjawiska oraz zaprezentowano model numeryczny, umożliwiający symulację tych zjawisk. Symulację komputerową wykonano w CI TASK stosując program FIDAP. Wyniki badań symulacyjnych zweryfikowano badaniami doświadczalnymi, wykonując fotografie i profilogramy...
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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...
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Design and modeling of switched reluctance motor for scooter application
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Modeling and Simulation of Electric Motors Using Lightweight Materials
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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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Modeling of strain localization in granular and quasi-brittle materials
PublicationW artykule przedstawiono wyniki symulacji lokalizacji odkształceń w materiałach granulowanych i kruchych. Zasosowano różne modele w ramach mechaniki ośrodków ciągłych i dyskretnych. Wyniki obliczeń porównano z doswiadczeniami.
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Quantum structure in competing lizard communities
PublicationAlmost two decades of research on applications of the mathematical formalism of quantum theory as a modeling tool in domains different from the micro-world has given rise to many successful applications in situations related to human behavior and thought, more specifically in cognitive processes of decision-making and the ways concepts are combined into sentences. In this article, we extend this approach to animal behavior, showing...
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Modeling a Traffic Remapping Attack Game in a Multi-hop Ad Hoc Network
PublicationIn multi-hop ad hoc networks, selfish nodes may unduly acquire high quality of service (QoS) by assigning higher priority to source packets and lower priority to transit packets. Such traffic remapping attacks (TRAs) are cheap to launch, impossible to prevent, hard to detect, and harmful to non-selfish nodes. While studied mostly in single-hop wireless network settings, TRAs have resisted analysis in multi-hop settings. In this paper...
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Structure of the scalar field around unidirectional circular cylinders
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Reliable low-cost surrogate modeling and design optimisation of antennas using implicit space mapping with substrate segmentation
PublicationAbstract: In this work, a reliable methodology for fast simulation-driven design optimisation of antenna structures is proposed. The authors’ approach exploits implicit space mapping (ISM) technology. To adopt it for handling antenna structures, they introduce substrate segmentation with separate dielectric permittivity value assigned for each segment as ISM preassigned parameters. At the same time, the coarse model for space mapping...
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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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Lattice dynamics of Mg2SiO4
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Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
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Separation of variables in molecular-dynamics simulations: A criterion to estimate the quality of the approximation
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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Stress Relaxation Behaviour Modeling in Rigid Polyurethane (PU) Elastomeric Materials
PublicationPolyurethane (PU) has been used in a variety of industries during the past few years due to its exceptional qualities, including strong mechanical strength, good abrasion resistance, toughness, low-temperature flexibility, etc. More specifically, PU is easily “tailored” to satisfy particular requirements. There is a lot of potential for its use in broader applications due to this structure–property link. Ordinary polyurethane items...
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Release of Encapsulated Bioactive Compounds from Active Packaging/Coating Materials and Its Modeling: A Systematic Review
PublicationThe issue of achieving controlled or targeted release of bioactive compounds with specific functional properties is a complex task that requires addressing several factors, including the type of bioactive, the nature of the delivery system, and the environmental conditions during transportation and storage. This paper deals with extensive reporting for the identification of original articles using Scopus and Google Scholar based...
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Determination of free tyrosine in equestrian supplements by LC–MS/MS and comparison of its quantity with total free amino acids content in view of doping control
PublicationThe reports on the probable beneficial impact of tyrosine (TYR) supplementation on performance enhancement have contributed to the growth of interest in TYR in equestrian sports field and related industries, such as the manufacture of dietary and nutritional supplements. In this study, the first attempt to the assessment of horses exposure to TYR during nutritional supplementation was demonstrated by quantification of unbound TYR...
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Inverse Modeling and Optimization of CSRR-based Microwave Sensors for Industrial Applications
PublicationDesign optimization of multivariable resonators is a challenging topic in the area of microwave sensors for industrial applications. This paper proposes a novel methodology for rapid re-design and parameter tuning of complementary split-ring resonators (CSRRs). Our approach involves inverse surrogate models established using pre-optimized resonator data as well as analytical correction techniques to enable rapid adjustment of geometry...
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Decoherence-free communication over multiaccess quantum channels
PublicationIn this paper we consider decoherence-free communication over multiple access and k-user quantum channels. First, we concentrate on a hermitian unitary noise model U for a two-access bi-unitary channel and show that in this case a decoherence-free code exists if the space of Schmidt matrices of an eigensubspace of U exhibits certain properties of decomposability. Then, we show that our technique is also applicable for generic random unitary...
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Exchange-Traded Funds in Europe
PublicationExchange-Traded Funds in Europe provides a single point of reference on a diverse set of regional ETF markets, illuminating the roles ETFs can play in risk mitigation and speculation. Combining empirical data with models and case studies, the authors use diffusion models and panel/country-specific regressions—as well as graphical and descriptive analyses— to show how ETFs are more than conventional, passive investments. With new...
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What drives sustainable investing? Adoption determinants of sustainable investing exchange-traded funds in Europe
PublicationDespite the growing interest in various topics related to sustainable (ESG) investing, some issues remain understudied, such as the determinants of their utilization at the macro level. This paper contributes to the state of knowledge two-directionally. First, it shows the development of sustainable investing exchange-traded funds (ETFs) in European countries. Second, it traces the significant determinants of adopting sustainable...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Expedited Geometry Scaling of Compact Microwave Passives by Means of Inverse Surrogate Modeling
PublicationIn this paper, the problem of geometry scaling of compact microwave structures is investigated. As opposed to conventional structures (i.e., constructed using uniform transmission lines), re-design of miniaturized circuits (e.g., implemented with artificial transmission lines, ATSs) for different operating frequencies is far from being straightforward due to considerable cross-couplings between the circuit components. Here, we...
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Analysis of dynamics of a map-based neuron model via Lorenz maps
PublicationModeling nerve cells can facilitate formulating hypotheses about their real behavior and improve understanding of their functioning. In this paper, we study a discrete neuron model introduced by Courbage et al. [Chaos 17, 043109 (2007)], where the originally piecewise linear function defining voltage dynamics is replaced by a cubic polynomial, with an additional parameter responsible for varying the slope. Showing that on a large...
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublicationWe present the results of recent investigations of charge transfer processes in the collisions of C²⁺ ions with heterocyclic molecules of tetrahydrofuran.
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Genre-Based Music Language Modeling with Latent Hierarchical Pitman-Yor Process Allocation
PublicationIn this work we present a new Bayesian topic model: latent hierarchical Pitman-Yor process allocation (LHPYA), which uses hierarchical Pitman-Yor pr ocess priors for both word and topic distributions, and generalizes a few of the existing topic models, including the latent Dirichlet allocation (LDA), the bi- gram topic model and the hierarchical Pitman-Yor topic model. Using such priors allows for integration of -grams with a topic model,...
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Genre-Based Music Language Modeling with Latent Hierarchical Pitman-Yor Process Allocation
PublicationIn this work we present a new Bayesian topic model: latent hierarchical Pitman-Yor process allocation (LHPYA), which uses hierarchical Pitman-Yor pr ocess priors for both word and topic distributions, and generalizes a few of the existing topic models, including the latent Dirichlet allocation (LDA), the bi- gram topic model and the hierarchical Pitman-Yor topic model. Using such priors allows for integration of -grams with a topic...
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Enhanced uniform data sampling for constrained data‐driven modeling of antenna input characteristics
PublicationData-driven surrogates are the most popular replacement models utilized in many fields of engineering and science, including design of microwave and antenna structures. The primary practical issue is a curse of dimensionality which limits the number of independent parameters that can be accounted for in the modelling process. Recently, a performance-driven modelling technique has been proposed where the constrained domain of the...
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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...