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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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Modeling hydrolysis of slowly biodegradable organic compounds in biological nutrient removal activated sludge systems
PublicationHydrolysis is an important process in biological wastewater treatment and has been known as the rate limiting step in organic carbon removal from municipal or industrial wastewater. The biodegradation of XS is initiated by hydrolysis which is an integral part of activated sludge models, such as the Activated Sludge Model no. 2d (ASM2d). The aim of this study was to evaluate different concepts of modeling the hydrolysis process...
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Helium-assisted, solvent-free electro-activation of 3D printed conductive carbon-polylactide electrodes
PublicationFused filament fabrication is one of the most rapidly developing 3D printing techniques, with numerous applications, including in the field of applied electrochemistry. Here, the utilisation of conductive carbon black polylactic acid (CB-PLA) for 3D printouts is the most promising. To use CB-PLA as an electrode material, an activation process must be performed, removing the polymer matrix and uncovering the electrically conductive...
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Remarks on steam condensation modeling related to steam turbine large output
PublicationIn the paper numerical simulations have been performed to predict the performance of the diferent steam models. All of the considered models of steam condensation have been validated on the base of benchmark experiment employing expansion in nozzle and next on the low pressure part of the steam turbine equipped with the so-called Baumann stage. For numerical analysis three models have been finally used - the ideal steam model without...
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Modeling the pH effects on nitrogen removal in the anammox-enriched granular sludge
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two kinetic parameters, including...
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MODELING THE pH EFFECTS ON NITROGEN REMOVAL IN THE ANAMMOX-ENRICHED GRANULAR SLUDGE
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched 10 granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the 11 granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature 12 T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two 13 kinetic parameters,...
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Nonlinear finite element modeling of vibration control of plane rod-type structural members with integrated piezoelectric patches
PublicationThis paper addresses modeling and finite element analysis of the transient large-amplitude vibration response of thin rod-type structures (e.g., plane curved beams, arches, ring shells) and its control by integrated piezoelectric layers. A geometrically nonlinear finite beam element for the analysis of piezolaminated structures is developed that is based on the Bernoulli hypothesis and the assumptions of small strains and finite...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
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Modeling and MANOVA studies on toxicity and endocrine potential of packaging materials exposed to different extraction schemes
PublicationThe stability of the linings of packaging that is in contact with the goods stored has been of major concern during decades of the development of packaging materials. In this work, an attempt was undertaken to assess the applicability of using two bioassays (Microtox® and XenoScreen YES/YAS) in estimating the stability of packaging (cans, caps, multilayer material) and the impact of their degradation on the toxicity of some simulated media....
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BUILDING INFORMATION MODELING - ANALIZA ZAKRESU I STANU IMPLEMENTACJI W POLSKIEJ BRANŻY BUDOWLANEJ
PublicationProblematyka BIM (Building Information Modeling) jest obecnie tematem wielu publikacji naukowych, ale także przedmiotem działań podejmowanych przez uczestników szeroko pojętego procesu budowlanego. Liczne zalety i szanse płynące ze stosowania technologii BIM w kolejnych etapach cyklu życia obiektu budowlanego, należy rozpatrywać z punktu widzenia inwestora/zamawiającego, architekta, projektanta konstrukcji i instalacji, dewelopera,...
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Mechanisms positioned in a neighbourhood of their singular positions - velocity amplification in the electromagnetic damping. Part 1 - Background of the mechanical structure modeling
PublicationW pracy przedstawiono metodę modelowania dynamiki drgającego hybrydowego układu mechanicznego złożonego z odkształcalnego podukładu ciągłego oraz z połączonego z nim mechanizmu. U układzie pojawiają się drgania części odkształcalnej. By je wytłumić, ich energia zamieniana jest w energię elektryczną (za pomocą prądnicy prądu stałego) i rozpraszana na oporności obecnej w układzie elektrycznym. Aby przyśpieszyć tłumienie, wprowadzony...
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Quantitative structure—retention relationship modeling of the retention behavior of selected antipsychotic drugs in normal-phase thin-layer chromatography
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GIS-based hydrodynamic modeling for urban flood mitigation in fast-growing regions: a case study of Erbil, Kurdistan Region of Iraq
PublicationFloods threaten urban infrastructure, especially in residential neighborhoods and fast-growing regions. Flood hydrodynamic modeling helps identify flood-prone locations and improve mitigation plans' resilience. Urban floods pose special issues due to changing land cover and a lack of raw data. Using a GIS-based modeling interface, input files for the hydrodynamic model were developed. The physical basin's properties were identified...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Improved Efficacy Behavioral Modeling of Microwave Circuits through Dimensionality Reduction and Fast Global Sensitivity Analysis
PublicationBehavioral models have garnered significant interest in the realm of high-frequency electronics. Their primary function is to substitute costly computational tools, notably electromagnetic (EM) analysis, for repetitive evaluations of the structure under consideration. These evaluations are often necessary for tasks like parameter tuning, statistical analysis, or multi-criterial design. However, constructing reliable surrogate models...
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Editorial for the special issue on advances in forward and inverse surrogate modeling for high-frequency design
PublicationThe design of modern‐day high‐frequency devices and circuits, including microwave/RF, antenna and photonic components, historically has relied on full‐wave electromagnetic (EM) simulation tools. Initially used for design verification, EM simulations are nowadays used in the design process itself, for example, for finding optimum values of geometry and/or material parameters of the structures of interest. In a growing number of...
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Low-Cost Flight Simulator with Possibility of Modeling of Flight Controls Failures
PublicationThe goal of this paper is to present a development of a low cost flight simulator, that allows to simulate flight controls failures. Cessna 172 has been chosen as an example of a general aviation aircraft and the flight model has been implemented in Simulink. The model allows for easy integration of an experimental autopilot, using various strategies. Aerodynamic coefficients have been calculated using software called DATCOM. Such...
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Central-force decomposition of spline-based modified embedded atom method potential
PublicationCentral-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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Machine learning-based prediction of residual drift and seismic risk assessment of steel moment-resisting frames considering soil-structure interaction
PublicationNowadays, due to improvements in seismic codes and computational devices, retrofitting buildings is an important topic, in which, permanent deformation of buildings, known as Residual Interstory Drift Ratio (RIDR), plays a crucial role. To provide an accurate yet reliable prediction model, 32 improved Machine Learning (ML) algorithms were considered using the Python software to investigate the best method for estimating Maximum...
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Fabrication and Characterization of Flexible Medical-Grade TPU Filament for Fused Deposition Modeling 3DP Technology
PublicationThe 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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Rotating Magnetic Field-Assisted Reactor Enhances Mechanisms of Phage Adsorption on Bacterial Cell Surface
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Modeling nutrient removal and energy consumption in an advanced activated sludge system under uncertainty
PublicationActivated 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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Modeling and experimental investigation of the small UPQC systems
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Modeling of photovoltaic properties of bilayer organic systems
PublicationPraca 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 the process of selected fire signaling 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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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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Quality Modeling in Grid and Volunteer-Computing Systems
PublicationA 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
PublicationThe 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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Modeling and experimental investigation of the small UPQC systems
PublicationIn 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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Fading Modeling in Maritime Container Terminal Environments
PublicationIn 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 of the internal combustion engine cooling system
PublicationThe 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 of Axial Flux Permanent Magnet Generators
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Modeling of event trees for the rapid scenario development
PublicationThe 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
PublicationWe 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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Modeling and simulation of thin-walled beams and frames
PublicationPrzedstawiono 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 active fiber Bragg grating sensors
PublicationW 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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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 polarimetric sensors using LabVIEW environment
PublicationW 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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Continuous and discontinuous modeling of cracks in concrete elements
PublicationW 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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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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