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Search results for: ambiguous restraints, coarse-grained models, nmr-assisted protein-structure modeling, unres
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Rapid multi-objective antenna design using point-by-point Pareto set identification and local surrogate models
PublicationAntenna design is inherently a multicriterial problem.Determination of the best possible tradeoffs between conflicting objectives (a so-called Pareto front), such as reflection response, gain, and antenna size, is indispensable from the designer’s point of view, yet challenging when high-fidelity electromagnetic (EM) simulations are utilized for performance evaluation. Here, a novel and computationally...
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The structure of levorin A3, a minor component of levorin complex
PublicationBudowa chemiczna składnika kompleksu leworyn, leworyny A3, została ustalona na podstawie analizy z wykorzystaniem metod spektroskopowych UV, MS i NMR metoksykarbonylometyloamido pochodnej leworyny A3. Widmo UV wskazało obecność chromoforu heptaenowego. Ciężar cząsteczkowy leworyny A3 ustalono jako 1110 j.m. za pomocą spektrometrii masowej z wykorzystaniem techniki FAB, co po uwzględnieniu uwarunkowań biogenetycznych pozwoliło wydedukować...
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The ILs-assisted solvothermal synthesis of TiO2 spheres: the effect of ionic liquids on morphology and photoactivity of TiO2
PublicationEffect of the ionic liquid (IL) structure (chain length in the imidazolium cation) on morphology and photoactivity of TiO2 particles has been systematically investigated. The TiO2 microspheres have been successfully synthesized via facile solvothermal method assisted by ionic liquids, such as 1-butyl-3-methylimidazolium chloride [BMIM][Cl] and 1-decyl-3-methylimidazolium chloride [DMIM][Cl] using tetra-tert-butyl orthotitanate...
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On Accuracy Modeling of Gas Turbine Cycles by the In-house COM-GAS Code
PublicationIn this paper, a comparison of accuracy modeling of gas turbine cycles between the basic (classical) model and the in-house COM-GAS code has been presented. The basic model uses a semi-perfect gas and well known projecting assumption. On the other hand, the computational flow mechanics (CFM) basis on a real gas by using thermodynamic tables. The thermodynamic analysis of thermal cycles, simply gas cycle GT8C and gas turbine cycle...
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Modeling of multi-cavity Fabry-Perot optical fiber sensors
PublicationReflectance characteristics of a two-cavity extrinsic Fabry-Perot optical fiber sensor were investigated using computer modeling. Calculations were performed using a plane wave-based approach, selected for clarity of results. Based on the modeling results, it can be concluded that the two-cavity Fabry-Perot interferometer can be used to measure two different quantities, such as refractive index and temperature, independently. It...
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The Comparison of the Web GIS Applications Relevant for 4D Models Sharing
PublicationThe paper presents results of the project: Cultural Heritage Through Time (CHT 2, http://cht2-project.eu) realized accomplished within the framework of the “Joint Programming Initiative in Cultural Heritage” JPI-CH (http://www.jpi-culturalheritage.eu) by an international consortium: Politecnico di Milano (IT), Newcastle University (UK), Salamanca University (ES), and Stanislaw Staszic Scientific Association SSSA (a non-profit...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublicationIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Electro-chemo-mechanical properties in nanostructured Ca-doped ceria (CDC) by field assisted sintering
PublicationRecent investigations have shown that highly oxygen defective cerium oxides generate non-classical electrostriction that is superior to lead-based ferroelectrics. In this work, we report the effect of field-assisted spark plasma sintering (SPS) on electro-chemo-mechanical properties of calcium doped ceria (CDC). Nanometric powders of Ca.10 nm are rapidly consolidated to form polycrystalline nanostructures with a high degree of...
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To what extent can hyperelastic models make sense the effect of clay surface treatment on the mechanical properties of elastomeric nanocomposites?
PublicationThe poor knowledge about nonlinear mechanical behavior of elastomer nanocomposites arises from the incomplete information on the interface. Application of hyperelastic models provides more insights into the nature and the situation of interaction between the elastomeric matrix and nanofillers. The current work seeks to address the effect of interphase strength on tensile properties of the elastomer nanocomposites under large deformations....
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Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublicationExtracellular vesicles (EVs) were isolated from Pectobacterium zantedeschiae culturing media using direct ultracentrifugation (UC), iodixanol cushion ultracentrifugation (ICUC), and iodixanol density gradient ultracentrifugation (IDGUC) techniques. The isolates were characterized with total protein content assay (bicinchoninic acid assay, BCA), nanoparticles tracking analysis (NTA), and capillary electrophoresis (CE). A satisfactory...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublicationThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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Experimental study on models of cylindrical steel tanks under mining tremors and moderate earthquakes
PublicationThe aim of the study is to show the results of complex shaking table experimental investigation focused on the response of two models of cylindrical steel tanks under mining tremors and moderate earthquakes, including the aspects of diagnosis of structural damage. Firstly, the impact and the sweep-sine tests have been carried out, so as to determine the dynamic properties of models filled with different levels of liquid. Then,...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Modeling and simulation of tool cycle in manufacturing cell
PublicationThe paper addresses issues concerning modeling and analysis of tool flow within a three-machine manufacturing cell used for small batch manufacturing of a definite spectrum of prismatic parts. The approach utilizes a method for job and tool allocation to work centers with limited number of machines and capacity of tool resources, based on the analysis of formalized relations: job - tool sets required. Selected tool flow control...
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Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.
PublicationThe crystal structure of the esterase EstA from the cold-adapted bacteriumPseudoalteromonas sp. 643A was determined in a covalently inhibited form at aresolution of 1.35 A˚. The enzyme has a typical SGNH hydrolase structureconsisting of a single domain containing a five-stranded beta-sheet, with threehelices at the convex side and two helices at the concave side of the sheet, and isornamented with a couple of very short helices...
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Mixture model of NMR - its application to diagnosis and treatment of brain cancer
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Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data
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O-256 Evaluation of the fertility potential of semen using Proton NMR
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Investigation of the Membrane Localization and Interaction of Selected Flavonoids by NMR and FTIR Spectroscopy
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Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
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Badania struktury chemicznej (metodami FTIR i NMR) oraz własności termicznych (metodą DSC) materiałów i ustalenie rodzaju tworzywa sztucznego - Numer umowy: 032257
PublicationPrzeprowadzono badania struktury chemicznej (metodami 1H NMR oraz FTIR) oraz własności termicznych (metodą DSC) materiałów pobranych z dostarczonych obiektów i ustalono typ tworzywa sztucznego z jakiego zostały wykonane dostarczone obiekty.
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A Hyperdense Semantic Domain for Discontinuous Behavior in Physical System Models
PublicationMultiple time models have been proposed for the formalization of hybrid dynamic system behavior. The superdense notion of time is a well-known time model for describing event-based systems where several events can occur simultaneously. Hyperreals provide a domain for defining the semantics of hybrid models that is elegantly aligned with first principles in physics. This paper discusses the value of both time models and shows how...
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Reconstruction of 3D structure of positive corona streamer by local methods
PublicationThe computer algorithms were used for reconstruction of streamer 3D structure. We propose the 3D tree structure model of corona discharge streamer composed with nodes and edges between chosen couples of nodes, which enables easy computation of some important parameters ofstreamers. The 3D model can be derived directly from two projection images by global methods like evolutionary searching or particle simulations. In this paper...
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Finite element models used in diagnostics of transverse cracks in bridge approach pavement
Open Research DataTransverse cracks in the asphalt pavement were observed on bridge structures next to single-module expansion joints with a 5 meter approach slab set at the depth of 1 m. The finite element (FE) models of the approach pavement were created to investigate the reasons of premature cracking and crack initiation mechanism over the back edge of the abutment...
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Training of Deep Learning Models Using Synthetic Datasets
PublicationIn order to solve increasingly complex problems, the complexity of Deep Neural Networks also needs to be constantly increased, and therefore training such networks requires more and more data. Unfortunately, obtaining such massive real world training data to optimize neural networks parameters is a challenging and time-consuming task. To solve this problem, we propose an easy-touse and general approach to training deep learning...
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Analytical modeling of electric drives for vehicle traction control systems
PublicationWheel-torque control bandwidth in vehicle dynamics model is crucial in evaluating optimal tracking ability of tire slip and in analysis of control system stability. Electric drives’ control dynamics are influenced by timing of digital control events, e.g. by sampling instant of motor currents. Reflecting this timing in drive analytical models is therefore important for analysis of vehicle traction systems. The paper considers five...
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Computational Analysis of Transformational Organisational Change with Focus on Organisational Culture and Organisational Learning: An Adaptive Dynamical Systems Modeling Approach
PublicationTransformative Organisational Change becomes more and more significant both practically and academically, especially in the context of organisational culture and learning. However computational modeling and formalization of organisational change and learning processes are still largely unexplored. This chapter aims to provide an adaptive network model of transformative organisational change and translate a selection of organisational...
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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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Injury Prediction Models for Onshore Road Network Development
PublicationIntegrating different modes of transport (road, rail, air and water) is important for port cities. To accommodate this need, new transport hubs must be built such as airports or sea ports. If ports are to grow, they must be accessible, a feature which is best achieved by building new roads, including fast roads. Poland must develop a network of fast roads that will provide good access to ports. What is equally important is to upgrade...
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Uniform sampling in constrained domains for low-cost surrogate modeling of antenna input characteristics
PublicationIn this letter, a design of experiments technique that permits uniform sampling in constrained domains is proposed. The discussed method is applied to generate training data for construction of fast replacement models (surrogates) of antenna input characteristics. The modeling process is design-oriented with the surrogate domain spanned by a set of reference designs optimized with respect to the performance figures and/or operating...
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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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Characterization of Defects Inside the Cable Dielectric With Partial Discharge Modeling
PublicationThe continuous monitoring of power system devices is an important step toward keeping such capital assets safe. Partial discharge (PD)-based measurement tools provide a reliable and accurate condition assessment of power system insulations. It is very common that voids or cavities exist in every solid dielectric insulation medium. In this article, different voids are modeled and analyzed using an advanced finite element (FE)-based...
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Reduced-Cost Microwave Modeling Using Constrained Domains and Dimensionality Reduction
PublicationDevelopment of modern microwave devices largely exploits full-wave electromagnetic (EM) simulations. Yet, simulation-driven design may be problematic due to the incurred CPU expenses. Addressing the high-cost issues stimulated the development of surrogate modeling methods. Among them, data-driven techniques seem to be the most widespread owing to their flexibility and accessibility. Nonetheless, applicability of approximation-based...
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Fast Antenna Optimization Using Gradient Monitoring and Variable-Fidelity EM Models
PublicationAccelerated simulation-driven design optimization of antenna structures is proposed. Variable-fidelity electromagnetic (EM) analysis is used as well as the trust-region framework with limited sensitivity updates. The latter are controlled by monitoring the changes of the antenna response gradients. Our methodology is verified using three compact wideband antennas. Comprehensive benchmarking demonstrates its superiority over both...
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Fast surrogate-assisted simulation-driven design of compact microwave hybrid couplers
PublicationThis work presents a robust methodology for expedited simulation-driven design optimization of compact microwave hybrid couplers. The technique relies on problem decomposition, and a bot-tom–up design strategy, starting from the level of basic building blocks of the coupler, and finishing with a tuning procedure that exploits a fast surrogate model of the entire structure. The latter is constructed by cascading local response surface...
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Sulfate‐reducing bacteria‐assisted hydrogen‐induced stress cracking of 2205 duplex stainless steels
PublicationThe paper presents the results of a laboratory investigation of the microbiologically assisted hydrogen‐induced stress cracking (HISC) of 2,205 duplex stainless steel (DSS). The testing of susceptibility toward HISC was performed with two different methods. Precharged in sulfate‐reducing bacteria (SRB), inoculated medium samples were subjected to slow strain‐rate testing in artificial seawater. In situ constant load tests were...
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Comparative analysis of different numerical models of a steel radial gate
PublicationHydrotechnical structures are important components in water management system and general flooding safety. Their reliability should be ensured since potential damage might lead to catastrophic consequences. Weir gates are considered to be highly vulnerable elements of each hydro power plant, with regard to its dynamic resistance. The aim of the paper is to compare different numerical models and their influence on the results of...
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One-Dimensional Modeling of Flows in Open Channels
PublicationIn this chapter, modeling of the unsteady open channel flow using one-dimensional approach is considered. As this question belongs to the well-known and standard problems of open channel hydraulic engineering, comprehensively presented and described in many books and publications, our attention is focused on some selected aspects only. As far as the numerical solution of the governing equations is considered, one can find out that...
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Local hidden–variable models for entangled quantum states
PublicationWhile entanglement and violation of Bell inequalities were initially thought to be equivalent quantum phenomena, we now have different examples of entangled states whose correlations can be described by local hidden-variable models and, therefore, do not violate any of the Bell inequalities. We provide an up-to-date overview of the existing literature regarding local hidden-variable models for entangled quantum states, in both...
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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublicationZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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Expedited two-objective dimension scaling of compact microwave passives using surrogate models
PublicationGeometry scaling of compact microwave structures is a challenging problem because of complex relationships between the physical dimensions and electrical characteristics, mostly caused by considerable cross-couplings in densely arranged layouts. Here, a procedure for expedited dimension scaling of compact microwave couplers with respect to two independent criteria has been presented. Our approach involves inverse surrogate models...
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Results of implementation of Feed Forward Neural Networks for modeling of heat transfer coefficient during flow condensation for low and high values of saturation temperature
Open Research DataThis database present results of implementation of Feed Forward Neural Networks for modeling of heat transfer coefficient during flow condensation for low and high values of saturation temperature. Databse contain one table and 7 figures.
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Chemical Characteristics and Thermal Oxidative Stability of Novel Cold-Pressed Oil Blends: GC, LF NMR, and DSC Studies
PublicationPlant oils contain a high content of unsaturated fatty acids. Studies of food products have revealed a considerable disproportion in the ratio of ω6 to ω3. This article presents information on the healthful qualities of eight new oil blends that contain a beneficial proportion of ω6 to ω3 fatty acids (5:1), as well as their degradation during heating at 170 and 200 °C. The fatty acid profile was analyzed by gas chromatography (GC),...
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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Indirect adaptive controller based on a self-structuring fuzzy system for nonlinear modeling and control
PublicationIn this paper, a unified nonlinear modeling and control scheme is presented. A self-structuring Takagi-Sugeno (T-S) fuzzymodel is used to approximate the unknown nonlinear plant based on I/O data collected on-line. Both the structure and theparameters of the T-S fuzzy model are updated by an on-line clustering method and a recursive least squares estimation(RLSE) algorithm. The rules of the fuzzy model can be added, replaced or...
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Numerical simulation of asphalt mixtures fracture using continuum models
PublicationThe paper considers numerical models of fracture processes of semi-circular asphalt mixture specimens subjected to three-point bending. Parameter calibration of the asphalt mixture constitutive models requires advanced, complex experimental test procedures. The highly non-homogeneous material is numerically modelled by a quasicontinuum model. The computational parameters are averaged data of the components, i.e. asphalt, aggregate...
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Modeling and optimizing the removal of cadmium by Sinapis alba L. from contaminated soil via Response Surface Methodology and Artificial Neural Networks during assisted phytoremediation with sewage sludge
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Reduced-order models in the finite element analysis
PublicationA novel technique of incorporating macromodels into finite element electromagnetic analysis of waveguide components is presented. Macromodels are generated by using a model order reduction algorithm (ENOR), which results in significant decrease of the number of variables, that describe the computational region. Proposed technique allows for using a few independent macromodels as well as to duplicating one macromodel in many subregions...
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