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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublikacjaPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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TIME-DOMAIN NUMERICAL EVALUATION OF SHIP RESISTANCE AND MOTION IN REGULAR WAVES BY USING THE CFD URANS METHOD
PublikacjaTaking into account the International Maritime Organization's (IMO) strategy to radically reduce the...
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Determining the optimal course alteration maneouvre in a multi-target encounter situation for a given ship domain model
PublikacjaW artykulee przedstawiono nową deterministyczną metodę wyznaczania niezbędnego manewru kursem dla sytuacji spotkania z wieloma obiektami obcymi i dla dowolnej zadanej domeny. Jej prostota i niska złożoność obliczeniowa czynią ją dobrą alternatywą dla obecnie stosowanych metod. Główny algorytm został przedstawiony wprost, tak aby mógł być bezpośrednio zastosowany w pokładowych systemach antykolizyjnych lub w systemach VTS.
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Combined analysis of whole human blood parameters by Raman spectroscopy and spectral-domain low-coherence interferometry
PublikacjaIn this article the simultaneous investigation of blood parameters by complementary optical methods, Raman spectroscopy and spectral-domain low-coherence interferometry, is presented. Thus, the mutual relationship between chemical and physical properties may be investigated, because low-coherence interferometry measures optical properties of the investigated object, while Raman spectroscopy gives information about its molecular...
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A Framework of A Ship Domain-Based Near-Miss Detection Method Using Mamdani Neuro-Fuzzy Classification
PublikacjaSafety analysis of navigation over a given area may cover application of various risk measures for ship collisions. One of them is percentage of the so called near- miss situations (potential collision situations). In this article a method of automatic detection of such situations based on the data from Automatic Identification System (AIS), is proposed. The method utilizes input parameters such as: collision risk measure based...
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Low-Cost Modeling of Microwave Components by Means of Two-Stage Inverse/Forward Surrogates and Domain Confinement
PublikacjaFull-wave electromagnetic (EM) analysis is one of the most important tools in the design of modern microwave components and systems. EM simulation permits reliable evaluation of circuits at the presence of cross-coupling effects or substrate anisotropy, as well as for accounting for interactions with the immediate environment. However, repetitive analyses required by EM-driven procedures, such as parametric optimization or statistical...
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Photoplethysmographic Time-Domain Heart Rate Measurement Algorithm for Resource-Constrained Wearable Devices and its Implementation
PublikacjaThis paper presents an algorithm for the measurement of the human heart rate, using photoplethysmography (PPG), i.e., the detection of the light at the skin surface. The signal from the PPG sensor is processed in time-domain; the peaks in the preprocessed and conditioned PPG waveform are detected by using a peak detection algorithm to find the heart rate in real time. Apart from the PPG sensor, the accelerometer is also used to...
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Reduced-Cost Microwave Modeling Using Constrained Domains and Dimensionality Reduction
PublikacjaDevelopment 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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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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Improved Uniform Sampling in Constrained Domains for Data-Driven Modelling of Antennas
PublikacjaData-driven surrogate modelling of antenna structures is an attractive way of accelerating the design process, in particular, parametric optimization. In practice, construction of surrogates is hindered by curse of dimensionality as well as wide ranges of geometry parameters that need to be covered in order to make the model useful. These difficulties can be alleviated by constrained performance-driven modelling with the surrogate...
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Performance-Driven Inverse/Forward Modeling of Antennas in Variable-Thickness Domains
PublikacjaDesign of contemporary antenna systems is a challenging endeavor. The difficulties are partially rooted in stringent specifications imposed on both electrical and field characteristics, demands concerning various functionalities, but also constraints imposed upon the physical size of the radiators. Furthermore, conducting the design process at the level of full-wave electromagnetic (EM) simulations, otherwise dictated by reliability,...
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Application of a hybrid finite difference-mode matching method to the analysis of circular cavities loaded with cylindrical metallic objects
PublikacjaW artykule przedstawiono badania rezonatorów cylindrycznych zawierających obiekty cylindryczne o dowolnym przekroju poprzecznym z wykorzystaniem metody hybrydowej stanowiącej połączenie metody różnic skończonych z metodą dopasowania rodzajów. W ramach badań określono częstotliwości rezonansowe dla wybranych struktur rezonatorów. Wyniki numeryczne zostały zweryfikowane eksperymentalnie.
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Analysis of scattering from arbitrary configuration of cylindrical objects using hybrid finite-difference mode-matching method
PublikacjaW artykule przedstawiono nową metodę hybrydową stanowiącą połączenie metody różnic skończonych z metodą dopasowania rodzajów, pozwalającą na analizę obiektów cylindrycznych o dowolnym przekroju poprzecznym. W prezentowanej metodzie poszczególne obiekty reprezentowane są poprzez wielorodzajową macierz impednacyjną zdefiniowaną na powierzchni bocznej zastępczego cylindra zawierającego badany obiekt. Celem określenia parametrów rozproszenia...
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Analysis of waveguide junctions containing axially-symetrical posts using hybrid finite-difference mode-matching technique
PublikacjaArtykuł opisuję hybrydową metodę analizy złącz falowodowych zawierających osiowo-symetryczne obiekty rozpraszające. Metoda jest oparta na metodzie dopasowania rodzajów oraz metodzie różnic skończonych w dziedzinie częstotliwości.
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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
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The existence and stability of the anions matching the formula (M=Li, Na, K, Be, Mg, Ca, B, Al, Ga)
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The Effectiveness of Catching Cutworm (Lepidoptera: Noctuidae: Noctuinae) (= Agrotinae) in Pheromone Traps and Light Traps, for Short-Term Forecasting
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Hybrid finite-difference/mode-matching method for analysis of scattering from arbitrary configuration of rotationally-symmetrical posts
PublikacjaW artykule przedstawiona została metoda hybrydowa pozwalająca na analizę zjawiska rozpraszania od dowolnej konfiguracji obiektów o osiowej symetrii. Proponowana metoda oparta jest na reprezentacji obiektu lub dowolnej konfiguracji obiektów poprzez zastępczy obiekt kulisty ze znanymi warunkami brzegowymi. W analizie pojedynczego obiektu wykorzystana została metoda hybrydowa stanowiąca połączenie metody różnic skończonych z metodą...
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Multi-objective optimization of compact UWB impedance matching transformers using Pareto front exploration and adjoint sensitivities
PublikacjaIn this paper, a technique for fast multi-objective optimization of impedance matching transformers has been presented. In our approach, a set of alternative designs that represent the best possible trade-offs between conflicting objectives (here, the maximum reflection level within a frequency band of interest and the circuit size) is identified by directly exploring the Pareto front. More specifically, the subsequent Pareto-optimal...
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An Analysis of Cylindrical Posts of Arbitrary Convex Cross Sections Located in Waveguide Junctions with the Use of Field Matching Method
PublikacjaA problem of electromagnetic wave scattering from cylindrical posts of arbitrary cross section located in waveguide junction is presented. The method of analysis is based on the direct field matching technique. Multimode scattering matrices of every section of waveguide junction are calculated and cascading procedure is utilized to investigate the whole structure. The results are verified by comparing them with those obtained from...
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Efficient Gradient-Based Algorithm with Numerical Derivatives for Expedited Optimization of Multi-Parameter Miniaturized Impedance Matching Transformers
PublikacjaFull-wave electromagnetic (EM) simulation tools have become ubiquitous in the design of microwave components. In some cases, e.g., miniaturized microstrip components, EM analysis is mandatory due to considera¬ble cross-coupling effects that cannot be accounted for otherwise (e.g., by means of equivalent circuits). These effects are particularly pronounced in the structures in¬volving slow-wave compact cells and their numerical...
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A Subspace-Splitting Moment-Matching Model-Order Reduction Technique for Fast Wideband FEM Simulations of Microwave Structures
PublikacjaThis article describes a novel model-order reduction (MOR) approach for efficient wide frequency band finite-element method (FEM) simulations of microwave components. It relies on the splitting of the system transfer function into two components: a singular one that accounts for the in-band system poles and a regular part that has no in-band poles. In order to perform this splitting during the reduction process, the projection...
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LSA Is not Dead: Improving Results of Domain-Specific Information Retrieval System Using Stack Overflow Questions Tags
PublikacjaThe paper presents the approach to using tags from Stack Overflow questions as a data source in the process of building domain-specific unsupervised term embeddings. Using a huge dataset of Stack Overflow posts, our solution employs the LSA algorithm to learn latent representations of information technology terms. The paper also presents the Teamy.ai system, currently developed by Scalac company, which serves as a platform that...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublikacjaHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Crystallization and preliminary X-ray analysis of the isomerase domain of glucosamine-6-phosphate synthase from Candida albicans
PublikacjaSyntaza glukozamino-6-fosforanu (EC 2.6.1.16) katalizuje pierwszy, praktycznie nieodwracalny etap w szlaku biosyntezy heksozoamin, którego produktem końcowym jest UDP-GlcNAc, kluczowy substrat dla tworzenia ściany komórkowej drobnoustrojów. Otrzymano kryształy domeny izomerazowej syntazy GlcN-6-P z Candida albicans, składającej się z reszt 346-712 (42 kDa). Analiza rentgenograficzna kryształu wykazała, że należy on do grupy przestrzennej...
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Analysis of impact of lossy audio compression on the robustness of watermark embedded in the DWT domain for non-blind copyright protection
PublikacjaA methodology of non-blind watermarking of the audio content is proposed. The outline of audio copyright problem and motivation for practical applications are discussed. The algorithmic theory pertaining watermarking techniques is briefly introduced. The system architecture together with employed workflows for embedding and extracting the watermarks are described. The implemented approach is described and obtained results are reported....
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Multivalent Display of SARS-CoV-2 Spike (RBD Domain) of COVID-19 to Nanomaterial, Protein Ferritin Nanocages
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Influence of the Square Wave Voltage on Dynamical Properties of a Flat Voltammetric Electrode in the Time Domain by the Electrochemical Reversible Reaction
PublikacjaIn this article there is a presentation of the analysis of the polarizing voltage shape influencing dynamic properties of voltammetric electrodes when on their surface reversible reaction takes place in the time domain. The electrode polarization with linearly increasing voltage and with a square component, was analyzed. The analysis that were conducted showed that the voltammetric electrode behaves like a first order transducer....
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Analytical Expression for the Time-Domain Green's Function of a Discrete Plane Wave Propagating in the 3-D FDTD Grid
PublikacjaIn this paper, a closed-form expression for the time-domain dyadic Green’s function of a discrete plane wave (DPW) propagating in a 3-D finite-difference time-domain (FDTD) grid is derived. In order to verify our findings, the time-domain implementation of the DPW-injection technique is developed with the use of the derived expression for 3-D total-field/scattered-field (TFSF) FDTD simulations. This implementation requires computations...
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High frequency dynamics of an isotropic Timoshenko periodic beam by the use of the Time-domain Spectral Finite Element Method
PublikacjaIn this work results of numerical simulations and experimental measurements related to the high frequency dynamics of an aluminium Timoshenko periodic beam are presented. It was assumed by the authors that the source of beam structural periodicity comes from periodical alterations to its geometry due to the presence of appropriately arranged drill-holes. As a consequence of these alterations dynamic characteristics of the beam...
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Fast multi-objective design optimization of microwave and antenna structures using data-driven surrogates and domain segmentation
PublikacjaPurpose Strategies and algorithms for expedited design optimization of microwave and antenna structures in multi-objective setup are investigated. Design/methodology/approach Formulation of the multi-objective design problem oriented towards execution of the population-based metaheuristic algorithm within the segmented search space is investigated. Described algorithmic framework exploit variable fidelity modeling, physics- and...
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Low-cost data-driven modelling of microwave components using domain confinement and PCA-based dimensionality reduction
PublikacjaFast data-driven surrogate models can be employed as replacements of computationally demanding full-wave electromagnetic simulations to facilitate the microwave design procedures. Unfortunately, practical application of surrogate modelling is often hindered by the curse of dimensionality and/or considerable nonlinearity of the component characteristics. This paper proposes a simple yet reliable approach to cost-efficient modelling...
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Analytical Expression for the Time-Domain Discrete Green's Function of a Plane Wave Propagating in the 2-D FDTD Grid
PublikacjaIn this letter, a new closed-form expression for the time-domain discrete Green's function (DGF) of a plane wave propagating in the 2-D finite-difference time-domain (FDTD) grid is derived. For the sake of its verification, the time-domain implementation of the analytic field propagator (AFP) technique was developed for the plane wave injection in 2-D total-field/scattered-field (TFSF) FDTD simulations. Such an implementation of...
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Volterra series usefulness in modelling of the time-domain cross-talk phenomena in coupled microstrip lines with nonlinear termination
PublikacjaW pracy przedyskutowano możliwość wykorzystania szeregów Volterry do analizy zjawiska przesłuchu w sprzężonych liniach mikropaskowych z nieliniowym obciążeniem. Apracowano algorytm metody, zaś uzyskane wyniki numeryczne zweryfikowano poprzez porównania z wynikami badań eksperymentalnych linii obciążonych w torze transmisyjnym diodą Schottky'ego.
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Electrodes array for contactless ECG measurement of a bathing person - a sensitivity analysis
PublikacjaAn applicability of a remote (contactless) electrocardiogram (ECG) measurements in a bathtub is presented in the paper. Possibility of ECG measurements in shallowly filled tube with a water was examined. A bathing person was, both, sitting and lying during experiments performed. The problem became non-trivial when the bathing person was moving in reference to a fixed set of electrodes and located at the longer walls of the bathtub....
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A Taxonomy of Model-Based Testing for Embedded Systems from Multiple Industry Domains
PublikacjaThis chapter provides a taxonomy of Model-Based Testing (MBT) based on the approaches that are presented throughout this book as well as in the related literature. The techniques for testing are categorized using a number of dimensions to familiarize the reader with the terminology used throughout the chapters that follow. In this chapter, after a brief introduction, a general definition of MBT and related work on available MBT...
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Expedited Variable-Resolution Surrogate Modeling of Miniaturized Microwave Passives in Confined Domains
PublikacjaDesign of miniaturized microwave components is largely based on computational models, primarily, full-wave electromagnetic (EM) simulations. EM analysis is capable of giving an accurate account for cross-coupling effects, substrate and radiation losses, or interactions with environmental components (e.g., connectors). Unfortunately, direct execution of EM-based design tasks such as parametric optimization or uncertainty quantification,...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublikacjaThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Derivation of Executable Test Models From Embedded System Models using Model Driven Architecture Artefacts - Automotive Domain
PublikacjaThe approach towards system engineering compliant to Model-Driven Architecture (MDA) implies an increased need for research on the automation of the model-based test generation. This applies especially to embedded real-time system development where safety critical requirements must be met by a system. The following paper presents a methodology to derive basic Simulink test models from Simulink system models so as to execute them...
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Time-domain measurement methods for R, L and C sensors based on aversatile direct sensor-to-microcontroller interface circuit
PublikacjatIn the paper new time-domain measurement methods for determining values of resistive (R), inductive(L) and capacitive (C) sensors based on a versatile direct sensor-to-microcontroller interface for microcon-trollers with internal analog-to-digital converters (ADCs) and analog comparators (ACs) are presented.The interface circuit consists of a reference resistor Rrworking as a voltage divider, a given R, L or C sensorand a microcontroller...
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Multi-objective design optimization of antennas for reflection, size, and gain variability using kriging surrogates and generalized domain segmentation
PublikacjaCost-efficient multi-objective design optimization of antennas is presented. The framework exploits auxiliary data-driven surrogates, a multi-objective evolutionary algorithm for initial Pareto front identification, response correction techniques for design refinement, as well as generalized domain segmentation. The purpose of this last mechanism is to reduce the volume of the design space region that needs to be sampled in order...
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Variable‐fidelity modeling of antenna input characteristics using domain confinement and two‐stage Gaussian process regression surrogates
PublikacjaThe major bottleneck of electromagnetic (EM)-driven antenna design is the high CPU cost of massive simulations required by parametric optimization, uncertainty quantification, or robust design procedures. Fast surrogate models may be employed to mitigate this issue to a certain extent. Unfortunately, the curse of dimensionality is a serious limiting factor, hindering the construction of conventional data-driven models valid over...
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Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in theClostridium thermocellumcellulosome
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3-D finite-difference time-domain modelling of ground penetrating radar for identification of rebars in complex reinforced concrete structures
PublikacjaThis paper presents numerical and experimental investigations to identify reinforcing bars using the ground penetrating radar (GPR) method. A novel element of the paper is the inspection of different arrangements of reinforcement bars. Two particular problems, i.e. detection of few adjacent transverse bars and detection of a longitudinal bar located over or under transverse reinforcement, have been raised. An attention was also...
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Low-Cost and Highly-Accurate Behavioral Modeling of Antenna Structures by Means of Knowledge-Based Domain-Constrained Deep Learning Surrogates
PublikacjaThe awareness and practical benefits of behavioral modeling methods have been steadily growing in the antenna engineering community over the last decade or so. Undoubtedly, the most important advantage thereof is a possibility of a dramatic reduction of computational expenses associated with computer-aided design procedures, especially those relying on full-wave electromagnetic (EM) simulations. In particular, the employment of...
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Cost-Efficient Surrogate Modeling of High-Frequency Structures Using Nested Kriging with Automated Adjustment of Model Domain Lateral Dimensions
PublikacjaSurrogate models are becoming popular tools of choice in mitigating issues related to the excessive cost of electromagnetic (EM)-driven design of high-frequency structures. Among available techniques, approximation modeling is by far the most popular due to its versatility. In particular, the surrogates are exclusively based on the sampled simulation data with no need to involve engineering insight or problem-specific knowledge....
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Uniform sampling in constrained domains for low-cost surrogate modeling of antenna input characteristics
PublikacjaIn 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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Transport properties of microemulsions with ionic liquid apolar domains as a function of ionic liquid content
PublikacjaThe specific conductivity, dynamic viscosity and apparent diffusion coefficient of each of four aqueous ionic liquid microemulsions (IL-MEs) were measured as a function of ionic liquid (IL) content. The investigated systems were composed of water, hydrophobic ILs (1-butyl-3-methylimidazolium hexafluorophosphate or bis(trifluoromethanesulphonyl)imide) and the nonionic surfactant Triton X-100 or its mixture with cosurfactant (butanol)....
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Expedited Yield-Driven Design of High-Frequency Structures by Kriging Surrogates in Confined Domains
PublikacjaUncertainty quantification is an important aspect of engineering design, also pertaining to the development and performance evaluation of high-frequency structures systems. Manufacturing tolerances as well as other types of uncertainties, related to material parameters (e.g., substrate permittivity) or operating conditions (e.g., bending) may affect the characteristics of antennas or microwave devices. For example, in the case...