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Wyniki wyszukiwania dla: AMBIGUOUS RESTRAINTS, COARSE-GRAINED MODELS, NMR-ASSISTED PROTEIN-STRUCTURE MODELING, UNRES
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublikacjaFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Application of Bayesian Multilevel Modeling in the Quantitative Structure–Retention Relationship Studies of Heterogeneous Compounds
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Chiral analysis of chloro intermediates of methylamphetamine by one-dimensional and multidementional NMR and GC/MS
PublikacjaImpurity profiling and classification of abused drugs using chiral analytical techniques is of particular interest and importance because of the additional information obtained fromthis approach. When these methods are applied to the synthesis of illicitly used substances, they can supply valuable information about the conditions/chemicals used in the synthesis. We have applied GC and NMR methods to the study of intermediates found...
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Reliable low-cost surrogate modeling and design optimisation of antennas using implicit space mapping with substrate segmentation
PublikacjaAbstract: In this work, a reliable methodology for fast simulation-driven design optimisation of antenna structures is proposed. The authors’ approach exploits implicit space mapping (ISM) technology. To adopt it for handling antenna structures, they introduce substrate segmentation with separate dielectric permittivity value assigned for each segment as ISM preassigned parameters. At the same time, the coarse model for space mapping...
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Naturally-derived hydrogels for 3D pancreatic tumor models: A short review
PublikacjaStatistics suggest a high proportion of mortality rate by pancreatic cancer, which is a solid tumor characterized by high heterogeneity and the presence of a complex extracellular matrix. The very low effectiveness of pancreatic cancer treatment roots in the high metastatic potential and drug resistance of this tumor. Therefore, the quest for efficient cellular models enabling precise mimicking in vivo conditions, and anticancer...
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Language Models in Speech Recognition
PublikacjaThis chapter describes language models used in speech recognition, It starts by indicating the role and the place of language models in speech recognition. Mesures used to compare language models follow. An overview of n-gram, syntactic, semantic, and neural models is given. It is accompanied by a list of popular software.
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Triangulation-based Constrained Surrogate Modeling of Antennas
PublikacjaDesign of contemporary antenna structures is heavily based on full-wave electromagnetic (EM) simulation tools. They provide accuracy but are CPU-intensive. Reduction of EM-driven design procedure cost can be achieved by using fast replacement models (surrogates). Unfortunately, standard modeling techniques are unable to ensure sufficient predictive power for real-world antenna structures (multiple parameters, wide parameter ranges,...
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublikacjaTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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Bridging the gap between business process models and use-case models
PublikacjaToday's software development methodologies are equipped with a plethora of methods and techniques for business process engineering and Requirements Engineering. However, heavy investments in IT have not brought forth expected results. What seems to be lacking is a systematic approach that consolidates both disciplines to gain a synergistic effect. To address this challenge we extend Use-Case Driven Approach (UCDA) by binding use...
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Performance-Based Nested Surrogate Modeling of Antenna Input Characteristics
PublikacjaUtilization of electromagnetic (EM) simulation tools is mandatory in the design of contemporary antenna structures. At the same time, conducting designs procedures that require multiple evaluations of the antenna at hand, such as parametric optimization or yield-driven design, is hindered by a high cost of accurate EM analysis. To certain extent, this issue can be addressed by utilization of fast replacement models (also referred...
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Crystal structure and electronic structure of CePt2In7
PublikacjaWe report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt–In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of...
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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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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublikacjaIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Comparison of technology adoption models
PublikacjaThere are several technology adoption models, that try to explain, how and why the technologies are adopted and used. Among those, that are widely used to explain, how the older adults accept technologies, there are some general models and models specific to the group of older users. Among the general ones I would recommend paying attention to the following models: Technology Acceptance Model (TAM) proposed by Davis...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: their in silico assessment as potential ligands for N-protein of SARS-CoV-2
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Zastosowanie metod NMR i DSC do badania mieszanek zawierających olej palmowy
PublikacjaW pracy badano olej palmowy oraz mieszanki oleju palmowego z uwodornionym lub ciekłym olejem rzepakowym o różnym składzie procentowym. W metodach NMR i DSC stosowano podobne sposoby termostatowania tzn. próbki przed analizą były termostatowane przez 1 godz. w temp 0oC (podobnie jak tłuszcz uwodorniony w normie ISO) lub przez 16 godz. w temp. 10oC (podobnie jak olej palmowy w normie ISO). Dodatkowo metodą DSC analizowano wszystkie...
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On Nature-Inspired Design Optimization of Antenna Structures Using Variable-Resolution EM Models
PublikacjaNumerical optimization has been ubiquitous in antenna design for over a decade or so. It is indispensable in handling of multiple geometry/material parameters, performance goals, and constraints. It is also challenging as it incurs significant CPU expenses, especially when the underlying computational model involves full-wave electromagnetic (EM) analysis. In most practical cases, the latter is imperative to ensure evaluation reliability....
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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublikacjaDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublikacjaAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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AFM-assisted investigation of conformal coatings in electronics
PublikacjaPurpose – This paper aims to presents a new method of investigation of local properties of conformal coatings utilized in microelectronics. Design/methodology/approach – It is based on atomic force microscopy (AFM) technique supplemented with the ability of local electrical measurements, which apart from topography acquisition allows recording of local impedance spectra, impedance imaging and dc current mapping. Potentialities...
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CAUSALITY IN MODELS OF THERMAL PROCESSES IN SHIP ENGINE ROOMS WITH THE USE OF BOND GRAPH (BG) METHOD
PublikacjaWith a single approach to modeling elements of different physical nature, the method of Bond Graph (BG) is particularly well suited for modeling energy systems consisting of mechanical, thermal, electrical and hydraulic elements that operate in the power system engine room. The paper refers to the earlier presented new concept of thermal process modeling using the BG method. The authors own suggestions for determining causality...
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The structure of nystatin A2
PublikacjaBudowa chemiczna składnika kompleksu nystatyn (nystatyny A2) została ustalona na podstawie analizy estru metylowego N-acetylonystatyny A2 przy pomocy metod spektroskopowych UV, MS i NMR. Widmo UV wskazało obecność w badanym związku chromoforu tetraenowego. Ciężar cząsteczkowy ustalono jako 909 j.m. na postawie analizy MS z wykorzystaniem techniki FAB, co pozwoliło wydedukować skład elementarny nystatyny A2 jako C47H75NO16. Analizy...
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Modeling of truss with cold-formed section and positive eccentricity in the node
PublikacjaThis work is dedicated to establishing the load carrying capacity of tensed and compressed truss’ nodes made of cold-formed open cross sections. The occurrence of bending in the truss’ nodes is the result of a specific production technology for system lattice girders assumed by the designer and the producer. The aim of this research is to present the methodology of conduct for creation of computational models that best depict the...
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EBE: elastic blob ensemble for coarse human tracking
PublikacjaProponujemy nowy probabilistyczny algorytm śledzenia oparty na elastycznym zespole kropelkowym (EBE), który ma zastosowanie przy śledzeniu obiektów elastycznych. Wynikiem jest wskazówka nt. zgrubnego ruchu w postaci lokalizacji i orientacji obiektu wraz z lokalizacją kropelki. Głównym założeniem jest to, że orientacja całego obiektu nie zmienia się znacznie między sąsiednimi klatkami. Dyskretna przestrzeń rozwiązań jest tworzona...
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Design-Oriented Constrained Modeling of Antenna Structures
PublikacjaFast surrogate models are crucially important to reduce the cost of design process of antenna structures. Due to curse of dimensionality, standard (data-driven) modeling methods exhibit serious limitations concerning the number of independent geometry parameters that can be handled but also (and even more importantly) their parameter ranges. In this work, a design-oriented modeling framework is proposed in which the surrogate is...
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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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Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations
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Multibody models for gait analysis
PublikacjaThe aim of this study was to create multibody biomechanical models to analyze a normal gait of the human. Proposed models can be used to identify joint moments of the lower limbs during normal gait in the single and double support phases. Applying Newton-Euler formulation, following planar models were developed: 1) a mathematical 6DOF model describing a gait in the sagittal plane of the body for single support phase and double...
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Response Feature Technology for High-Frequency Electronics. Optimization, Modeling, and Design Automation
PublikacjaThis book discusses response feature technology and its applications to modeling, optimization, and computer-aided design of high-frequency structures including antenna and microwave components. By exploring the specific structure of the system outputs, feature-based approaches facilitate simulation-driven design procedures, both in terms of improving their computational efficiency and reliability. These benefits are associated...
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Experimental and Numerical Analysis of Air Trapping in a Porous Medium with Coarse Textured Inclusions
PublikacjaThe paper presents a 2D upward infiltration experiment performed on a model porous medium consisting of fine sand background with two inclusions made of coarser sands. The purpose of the experiment was to investigate the effects of structural air trapping, which occurs during infiltration as a result of heterogeneous material structure. The experiment shows that a significant amount of air becomes trapped in each of the inclusions. Numerical...
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Open Data Capability Architecture - An Interpretive Structural Modeling Approach
PublikacjaDespite of increasing availability of open data as a vital organizational resource, large numbers of startups and organizations fail when it comes to utilizing open data effectively. This shortcoming is attributable to the poor understanding of what types of capabilities are required to successfully conduct data related activities. At the same time, research on open data capabilities and how they relate to one another remains sparse....
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublikacjaFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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Accelerated multi-objective design optimization of antennas by surrogate modeling and domain segmentation
PublikacjaMulti-objective optimization yields indispensable information about the best possible design trade-offs of an antenna structure, yet it is challenging if full-wave electromagnetic (EM) analysis is utilized for performance evaluation. The latter is a necessity for majority of contemporary antennas as it is the only way of achieving acceptable modeling accuracy. In this paper, a procedure for accelerated multi-objective design of...
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Improvement of Task Management with Process Models in Small and Medium Software Companies
PublikacjaSmall and medium software companies exhibit many special features that give reason for a dedicated approach to process improvement. They often cannot afford implementing maturity models or quality standards both in terms of time and money. Instead, they expect simpler solutions that can allow to run projects in more systematic and repeatable way, increase quality and knowledge management. In this paper, we present a method focused...
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Application of human bile salts for in vitro digestion models
PublikacjaIn this study, experimental in vitro models simulating the environment of the human gastrointestinal tract were used to assess the impact of physiological surfactants, such as bile salts, on the kinetics of digestion. Bile salts are biosurfactants synthesised in the liver and secreted together with bile into the small intestine. There are many reports on the role of bile salts in lipolysis, but the knowledge of their influence...
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Smart Modeling of Maritime Vessels
PublikacjaCurrently, the market offers many visualization tools available to graphic designers, engineers, managers and academics working on maritime environments. The practice of visualization involves making and manipulating images that convey novel phenomena and ideas. Visual communication, together with virtual reality environments, is an emerging and rapidly evolving discipline. It brings great advantage over written word or voice alone,...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Antenna Modeling Using Variable-Fidelity EM Simulations and Constrained Co-Kriging
PublikacjaUtilization of fast surrogate models has become a viable alternative to direct handling of fullwave electromagnetic (EM) simulations in EM-driven design. Their purpose is to alleviate the difficulties related to high computational cost of multiple simulations required by the common numerical procedures such as parametric optimization or uncertainty quantification. Yet, conventional data-driven (or approximation) modeling techniques...
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Computer-assisted assessment of learning outcomes in the laboratory of metrology
PublikacjaIn the paper, didactic experience with broad and rapid continuous assessment of students’ knowledge, skills and competencies in the Laboratory of Metrology, which is an example of utilisation of assessment for learning, is presented. A learning management system was designed for manage, tracking, reporting of learning program and assessing learning outcomes. It has ability to provide with immediate feedback, which is used by the...
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The synthesis and structure of a potential immunosuppressant: N-mycophenoyl malonic acid dimethyl ester
PublikacjaThe synthesis of a potential immunosuppressant, i.e. dimethyl ester of N-mycophenoyl malonic acid was optimized in the reaction of mycophenolic acid (MPA) with amino malonic dimethyl ester in the presence of propanephosphonic anhydride (T3P) as a coupling reagent. The structural properties of the obtained MPA derivative were investigated by NMR, MS and single crystal X-ray diffraction methods. Theoretical considerations of conformational...
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Two-Stage Variable-Fidelity Modeling of Antennas with Domain Confinement
PublikacjaSurrogate modeling has become the method of choice in solving an increasing number of antenna design tasks, especially those involving expensive full-wave electromagnetic (EM) simulations. Notwithstanding, the curse of dimensionality considerably affects conventional metamodeling methods, and their capability to efficiently handle nonlinear antenna characteristics over broad ranges of the system parameters is limited. Performance-driven...
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Developments in ultrasound-assisted microextraction techniques for isolation and preconcentration of organic analytes from aqueous samples
PublikacjaThe great potential of ultrasonic assistance in sample preparation, especially extraction, is being recognized. In this review, we discuss the applications of ultrasonic radiation in assisting microextraction. Topics covered include ultrasound-assisted emulsification microextraction, ultrasound-assisted-emulsification-dispersive liquid-liquid microextraction, and ultrasound-assisted hollow-fiber liquid-phase microextraction with...
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Low-Cost Behavioral Modeling of Antennas by Dimensionality Reduction and Domain Confinement
PublikacjaBehavioral modeling has been rising in importance in modern antenna design. It is primarily employed to diminish the computational cost of procedures involving massive full-wave electromagnetic (EM) simulations. Cheaper alternative offer surrogate models, yet, setting up data-driven surrogates is impeded by, among others, the curse of dimensionality. This article introduces a novel approach to reduced-cost surrogate modeling of...
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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Substituent effects on ^15N NMR chemical shifts in selected N-alkylthiohydroxamic acids. A comparative study
PublikacjaNa podstawie widm 15N NMR przeanalizowano wpływy podstawników wybranych kwasów tiohydroksamowych na przesunięcia chemiczne N-15. Analiza porównawcza z przesunięciami chemicznymi strukturalnie podobnych amidów, tioamidów i kwasów hydroksamowych pozwoliła na stwierdzenie, że nie zatłoczenie steryczne a grupa N-OH jest odpowiedzialna za osłabienie efektów odsłaniających zarówno podstawników bezpośrednio związanych z atomem azotu jak...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublikacjaThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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Rapid design optimization of antennas using variable-fidelity EM models and adjoint sensitivities
PublikacjaPurpose – Development of techniques for expedited design optimization of complex and numerically expensive electromagnetic (EM) simulation models of antenna structures validated both numerically and experimentally. The paper aims to discuss these issues. Design/methodology/approach – The optimization task is performed using a technique that combines gradient search with adjoint sensitivities, trust region framework, as well as...
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Physical models in the education of architectural history
PublikacjaIn this article, the authors present the long tradition and common use of physical models in the process of teaching the history of architecture in higher education institutions. The research described in the article is focused on the use of physical models and mock-ups as stimulants during architectural history classes to support lectures and increase the learning capabilities of students. The authors also cover the general use...