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Wyniki wyszukiwania dla: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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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
PublikacjaThis 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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Fast bubble dynamics and sizing
PublikacjaSingle bubble sizing is usually performed by measuring the resonant bubble response using the Dual Frequency Ultrasound Method. However, in practice, the use of millisecond-duration chirp-like waves yields nonlinear distortions of the bubble oscillations. In comparison with the resonant curve obtained under harmonic excitation, it was observed that the bubble dynamic response shifted by up to 20 percent of the resonant frequency...
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From flow to jamming: Lattice Gas Automaton simulations in granular materials
PublikacjaWe introduce the first extension of a Lattice Gas Automaton (LGA) model to accurately replicate observed emergent phenomena in granular materials with a special focus on previously unexplored jamming transitions by incorporating gravitational effects, energy dissipation in particle collisions, and wall friction. We successfully reproduce flow rate evolution, density wave formation, and jamming transition observed in experiments....
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Four Degree-of-Freedom Hydrodynamic Maneuvering Model of a Small Azipod-Actuated Ship With Application to Onboard Decision Support Systems
PublikacjaThe main contribution of this paper is a numerical ship motion model of NTNU’s research vessel Gunnerus, capturing the surge, sway, roll, and yaw dynamics when sailing in uniform and steady currents. The model utilizes a crossflow drag formulation for the transverse viscous loads, and it includes a nonlinear formulation for the propulsion and steering loads provided by two azipod thrusters. A wide range of experimental data obtained...
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FDTD Simulations on Disjoint Domains with the Use of Discrete Green's Function Diakoptics
PublikacjaA discrete Green's function (DGF) approach to couple disjoint domains in the finite-difference time-domain (FDTD) grid is developed. In this method, total-field/scattered-field (TFSF) FDTD domains are associated with simulated objects whereas the interaction between them is modeled with the use of the DGF propagator. Hence, source and scatterer are simulated in separate domains and updating of vacuum cells, being of little interest,...
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How digital technology affects working conditions in globally fragmented production chains: Evidence from Europe
PublikacjaThis paper uses a sample of over 9 million workers from 22 European countries to study the intertwined relationship between digital technology, cross-border production links and working conditions. We compare the social consequences of technological change exhibited by three types of innovation: computerisation (software), automation (robots) and artificial intelligence (AI). To fully quantify work-related wellbeing, we propose...
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Arginine-, d-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublikacjaThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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The experimental evaluation and modeling of SBR removing nutrients under varied aeration conditions
PublikacjaSequencing batch reactors (SBR) are mainly characterized by sequential process phases of fill, react, settle, decant and idle periods that allow considerable flexibility in the design and operation in different conditions. This flexibility and the unique features of SBRs used to wastewater treatment by activated sludge systems operated in laboratory scale, allow not only conducting experiments for the standard conditions but also...
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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
PublikacjaW 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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The dynamics of the total output of the fishery sector: The case of Indonesia
PublikacjaThe purpose of this study is to analyze the dynamics of the total output of the Indonesian fishery industry when the changes of the final demand occur. This study employs a demand-pull Input-Output (IO) quantity model, one of the calculation tools in the IO analysis, as an analysis instrument. Two conditions are noticed in calculation and analysis parts, namely (1) “whole sector change”, and (2) “pure change”. An initial period...
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublikacjaIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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Modeling organic nitrogen conversions in activated sludge bioreactors
PublikacjaFor biological nutrient removal (BNR) systems designed to maximize nitrogen removal, the effluent total nitrogen (TN) concentration may range from 2.0 to 4.0 g N/m3 with about 25-50% in the form of organic nitrogen (ON). In this study, current approaches to modeling organic N conversions (separate processes vs. constant contents of organic fractions) were compared. A new conceptual model of ON conversions was developed and combined...
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Discrete-Element bonded-particle Sea Ice model DESIgn, version 1.3a – model description and implementation
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Uncertainty Quantification in Experimental Structural Dynamics Identification of Composite Material Structures
PublikacjaComposite materials are widely used in manufacture of aerospace and wind energy structural components. These load carrying structures are subjected to dynamic time-varying loading conditions. Robust structural dynamics identification procedure impose tight constraints on the quality of modal models estimates obtained from vibration experiments. Modal testing results are influenced by numerous factors introducing uncertainty to...
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Nonlinear planar modeling of massive taut strings travelled by a force-driven point-mass
PublikacjaThe planar response of horizontal massive taut strings, travelled by a heavy point-mass, either driven by an assigned force, or moving with an assigned law, is studied. A kinematically exact model is derived for the free boundary problem via a variational approach, accounting for the singularity in the slope of the deflected string. Reactive forces exchanged between the point-mass and the string are taken into account via Lagrange...
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublikacjaRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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Nested Kriging with Variable Domain Thickness for Rapid Surrogate Modeling and Design Optimization of Antennas
PublikacjaDesign of modern antennas faces numerous difficulties, partially rooted in stringent specifications imposed on both electrical and field characteristics, demands concerning various functionalities (circular polarization, pattern diversity, band-notch operation), but also constraints imposed upon the physical size of the radiators. Conducting the design process at the level of full-wave electromagnetic (EM) simulations, otherwise...
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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
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Performance‐driven modeling of compact couplers in restricted domains
PublikacjaFast surrogate models can play an important role in reducing the cost of EM-driven design closure of miniaturized microwave components. Unfortunately, construction of such models is challenging due to curse of dimensionality and wide range of geometry parameters that need to be included in order to make it practically useful. In this letter, a novel approach to design-oriented modeling of compact couplers is presented. Our method...
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On Reduced-Cost Design-Oriented Constrained Surrogate Modeling of Antenna Structures
PublikacjaDesign of contemporary antenna structures heavily relies on full-wave electromagnetic (EM) simulation models. Such models are essential to ensure reliability of evaluating antenna characteristics, yet, they are computationally expensive and therefore unsuitable for handling tasks that require multiple analyses, e.g., parametric optimization. The cost issue can be alleviated by using fast surrogate models. Conventional data-driven...
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublikacjaToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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Effect of aggregate structure on fracture process in concrete using 2D lattice model
PublikacjaArtykuł przedstawia symulacje rys w betonie przy zastosowaniu nowego modelu siatkowego. Zbadano wpływ rozkładu i wielkości kruszywa oraz wpływ strefy kontaktu na nośność i propagacje rys. Obliczenia były dwuwymiarowe.
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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublikacjaExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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Mass spectrometry based identification of geometric isomers during metabolic stability study of a new cytotoxic sulfonamide derivatives supported by quantitative structure-retention relationships
PublikacjaA set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships...
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Shallow Water Equations as a Mathematical Model of Whitewater Course Hydrodynamics
PublikacjaPredicting the positions of local hydraulic phenomena, as well as accurately esti-mating the depth and velocity of the water flow are necessary to correctly config-ure a whitewater canoeing course. Currently, a laboratory and full 3D CFD model-ing are typically used in the design process to meet these needs. The article points to another possibility which can be useful at the preliminary stage of the design. The authors show that...
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Biotransformation of Modified Benzylisoquinoline Alkaloids: Boldine and Berberine and In Silico Molecular Docking Studies of Metabolites on Telomerase and Human Protein Tyrosine Phosphatase 1B
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Toolchain Modeling: Comprehensive Engineering Plans for Industry 4.0
PublikacjaThe fourth industrial revolution (Industry 4.0) elevates the complexity and autonomy of industrial systems and engineering environments to levels not seen before. The novel challenges involve not only the software running on the partaking autonomous devices, but also architectural considerations and the technological infrastructure around the entire engineering process. In this paper, complementing the trends in industrial systems...
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Structure and computationally-efficient simulation-driven design of compact UWB monopole antenna
PublikacjaIn this letter, a structure of a small ultra-wideband (UWB) monopole antenna, its design optimization procedure as well as experimental validation are presented. According to our approach, antenna compactness is achieved by means of a meander line for current path enlargement as well as the two parameterized slits providing additional degrees of freedom that help to ensure good impedance matching. For the sake of reliability, the...
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Energy Consumption Modeling in SPMD and DAC Applications
PublikacjaIn this chapter, we show a study of energy consumption during execution of SPMD and DAC application – the same applications which time of execution we modeled in the previous two chapters. We measured an average power usage at a single node of the GALERA+ cluster during application execution and then we modeled the total energy consumption by the application. Next we simulated the applications using MERPSYS and we compared the...
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Proteolysis of whey protein isolates in nanoemulsion systems: impact of nanoemulsification and additional synthetic emulsifiers
PublikacjaNanoemulsions are currently of interest in the functional food sector because their small droplet size (100–500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic...
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A Triplet-learnt Coarse-to-Fine Reranking for Vehicle Re-identification
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Reliable computationally-efficient behavioral modeling of microwave passives using deep learning surrogates in confined domains
PublikacjaThe importance of surrogate modeling techniques has been steadily growing over the recent years in high-frequency electronics, including microwave engineering. Fast metamodels are employed to speedup design processes, especially those conducted at the level of full-wave electromagnetic (EM) simulations. The surrogates enable massive system evaluations at nearly EM accuracy and negligible costs, which is invaluable in parameter...
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An interactive system for remote modeling and design validation of hybrid photovoltaic systems
PublikacjaIn the paper a multi-functional demonstrator of the interactive system designed to modeling, monitoring and validation of hybrid photovoltaic systems assisted by fuel cells and thermoelectric generators is presented. The purpose of this paper is to report the system solution expressed in the form of a block diagram. Technical parameters of demonstrator components such as: silicon photovoltaic modules, fuel cells, thermoelectric...
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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublikacjaSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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Grand Challenges on the Theory of Modeling and Simulation
PublikacjaModeling & Simulation (M&S) is used in many different fields and has made many significant contributions. As a field in its own right, there have been many advances in methodologies and technologies. In 2002 a workshop was held in Dagstuhl, Germany, to reflect on the grand challenges facing M&S. Ten years on, a series of M& S Grand Challenge activities are marking a decade of progress and are providing an opportunity to reflect...
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Expedited Acquisition of Database Designs for Reduced-Cost Performance-Driven Modeling and Rapid Dimension Scaling of Antenna Structures
PublikacjaFast replacement models have been playing an increasing role in high-frequency electronics, including the design of antenna structures. Their role is to improve computational efficiency of the procedures that normally entail large numbers of expensive full-wave electromagnetic (EM) simulations, e.g., parametric optimization or uncertainty quantification. Recently introduced performance-driven modeling methods, such as the nested...
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Modeling lubricant flow between thrust-bearing pads
PublikacjaInlet temperature is one of the main inputs in all models for the analysis of fluid film bearing performance. At the same time, inlettemperature distribution and also oil velocity distribution at the inlet are the result of flow phenomena in the gap between the bearingpads. These phenomena are complex and in many cases further affected by any special arrangements of forced oil supply to the gapbetween pads. The reason for such...
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Synergic Effect of Selected Ingredients and Calcium Chloride on the Technological, Molecular and Microbial Usefulness of Eggshells and Their Impact on Sensory Properties in a Food Model System
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublikacjaAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublikacjaThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Objectivity in the non-Markovian spin-boson model
PublikacjaObjectivity constitutes one of the main features of the macroscopic classical world. An important aspect of the quantum-to-classical transition issue is to explain how such a property arises from the microscopic quantum theory. Recently, within the framework of open quantum systems, there has been proposed such a mechanism in terms of the so-called spectrum broadcast structures. These are multipartite quantum states of the system...
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Multi-Fidelity Local Surrogate Model for Computationally Efficient Microwave Component Design Optimization
PublikacjaIn order to minimize the number of evaluations of high-fidelity (“fine”) model in the optimization process, to increase the optimization speed, and to improve optimal solution accuracy, a robust and computational-efficient multi-fidelity local surrogate-model optimization method is proposed. Based on the principle of response surface approximation, the proposed method exploits the multi-fidelity coarse models and polynomial interpolation...
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Experimental investigations and simulations of the microturbine unit with permanent magnet generator
PublikacjaIn dispersed power generation, low power devices are used for local combined generating of heat end electric power. There are developing concepts of micropower plants with electric generators driven by steam or gas microturbines. The paper presents the results of an experimental investigations of the microturbine set consists of the turbine with partial admission, permanent magnet generator and three phase AC-to-DC rectifier. The...
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Molecular picture of hydroxide anion hydration in aqueoussolutions studied by FT-IR ATR spectroscopy
PublikacjaHydratacja anionu hydroksylowego w wodnych roztworach wodorotlenków metali alkalicznych (LiOH, NaOH, KOH) została zbadana metodą spektroskopii oscylacyjnej FT-IR całkowitego wewnętrznego odbicia (ATR). Widma oscylacyjne wody dostarczają cennych informacji na temat stanu strukturalnego cząsteczek wody w sferach hydratacyjnych, wynikających ze sprzężeń oscylatorów w układzie. Wykazano, że drganie normalne rozciągające cząsteczki...
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How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure–Property Relationship Modeling of Nanofluids
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Structure–activity relationships study on biological activity of peptides as dipeptidyl peptidase IV inhibitors by chemometric modeling
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Thin-walled frames and grids - statics and dynamics
PublikacjaFrames and grids assembled with thin-walled beams of open cross-section are widely applied in various civil engineering and vehicle or machine structures. Static and dynamic analysis of theses structures may be carried out by means of different models, startingfrom the classical models made of beam elements undergoing the Kirchhoff assumptions to the FE discretization of whole frame into plane elements. The former model is very...
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Alternative Modeling of Volunteer Based Systems
PublikacjaThe canonical approach to model a flow of a voluntary based computing, as presented in Chapter 7 may tax the capacity of the simulator, especially when a more complex model of Voluntary Computing, proposed in [1], is used which would imply that, for typical heterogeneous groups of volunteers, several thousands of threads would have to be run inside the simulator, to mimic closely the behaviour of every volunteer. This chapter presents...