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Search results for: xrd molecular structures
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Developing Polycentricity to Shape Resilient Metropolitan Structures: The Case of the Gdansk–Gdynia–Sopot Metropolitan Area
PublicationMaking the metropolitan area resilient, in many cases, calls for amending its spatial structures. This may take various forms, including both reshaping the metropolitan core and redeveloping the entire regional network of cities and centres, making them part of a coherent structure. The latter strategy is associated with reinforcing secondary urban centres as well as shaping new connections between them. In this case, the term...
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On Fast Multi-objective Optimization of Antenna Structures Using Pareto Front Triangulation and Inverse Surrogates
PublicationDesign of contemporary antenna systems is a challenging endeavor, where conceptual developments and initial parametric studies, interleaved with topology evolution, are followed by a meticulous adjustment of the structure dimensions. The latter is necessary to boost the antenna performance as much as possible, and often requires handling several and often conflicting objectives, pertinent to both electrical and field properties...
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Design-oriented modeling of antenna structures by means of two-level kriging with explicit dimensionality reduction
PublicationThe employment of full-wave electromagnetic (EM) analysis is a practical necessity in the design of contemporary antenna structures. This is because simpler models are generally not available or of limited accuracy. At the same time, EM-based design is computationally expensive. Consequently, the ways of accelerating tasks such as parametric optimization or uncertainty quantification have to be sought. A possible workaround that...
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On Nature-Inspired Design Optimization of Antenna Structures Using Variable-Resolution EM Models
PublicationNumerical 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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A Novel Trust-Region-Based Algorithm with Flexible Jacobian Updates for Expedited Optimization of High-Frequency Structures
PublicationSimulation-driven design closure is mandatory in the design of contemporary high-frequency components. It aims at improving the selected performance figures through adjustment of the structure’s geometry (and/or material) parameters. The computational cost of this process when employing numerical optimization is often prohibitively high, which is a strong motivation for the development of more efficient methods. This is especially...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations
PublicationThe reaction of silicon disulfide with alkylphenols leads to tetraphenoxysilane, cyclodisilthiane and silanethiol. The products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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The application of environmental issues in designing urban structures – a framework for comprehensive local planning policies
PublicationThe implementation of environmental issues in planning and designing urban structures is becoming a novel approach and a common practice consistent with the paradigm of sustainable development. Maintaining environmental quality in urban areas, managing natural resources and understanding the complexity of urban systems is becoming increasingly challenging. Therefore, it is important to develop strategies for the integration of...
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RF Input-Quasi-Reflectionless Dispersive-Delay Structures Based on Complementary-Diplexer Circuits
PublicationA class of RF dispersive-delay structures (DDSs) with input-quasi-reflectionless behavior is reported. It is based on the exploitation of complementary-diplexer circuit networks, in which the out-of-band RF-input-power echoes reflected by the main bandpass-filter-(BPF)-type channel are dissipated by the resistively-terminated auxiliary bandstop-filter-(BSF)-type channel. Specifically, it is shown that the influence of the absorptive...
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The new diphosphanylphosphido complexes of tungsten(VI) and molybdenum(VI). Their synthesis, structures and properties
PublicationWe report on the reactivity of R2P–P(Li)–PR’2 (R = tBu, iPr, R’ = NEt2, iPr) towards diimido complexes [(dippN)2MCl2·dme] (M = Mo, W and dipp = 2,6-iPr2C6H3). A series of new complexes with diphosphanylphosphido ligands R2P–P–PR’2 were isolated. The solid-state structures of [(dippN)2M(Cl)(1,2-η-iPr2P–P– PiPr2)] (2Mo and 2W) and [(dippN)2M(Cl){1,2-η-tBu2P–P–P(NEt2)2}] (3Mo and 3W) were established by single-crystal X-ray diffraction...
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Accelerated Parameter Tuning of Antenna Structures by Means of Response Features and Principal Directions
PublicationPopularity of numerical optimization has been steadily on the rise in the design of modern antenna systems. Resorting to mathematically rigorous parameter tuning methods is a matter of practical necessity as interactive techniques (e.g., parameter sweeping) are no longer adequate when handling several performance figures over multi-dimensional parameter spaces. The most common design scenarios involve local tuning since decent...
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Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF
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Fast EM-driven size reduction of antenna structures by means of adjoint sensitivities and trust regions
PublicationIn this letter, a simple yet robust and computationally efficient optimization technique for explicit size reduction of antenna structures is presented. Our approach directly handles the antenna size as the main design objective, while ensuring satisfactory electrical performance by means of suitably defined penalty functions. For the sake of accuracy, the antenna structure is evaluated using high-fidelity EM simulation. In order...
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Relationship between vortex structures and shear localization in 3D granular specimens based on combined DEM and Helmholtz-Hodge decomposition.
PublicationRelationship between vortex structures and shear localization in 3D granular specimens based on combined DEM and Helmholtz-Hodge decomposition. Granular Matter, doi:10.1007/s10035-018-0815-0, 2018.
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Plasma Treatment as an Unconventional Molecular Magnet Engineering Method
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Molecular diagnosis in type I epithelial ovarian cancer
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Role of electronic correlations in the transport characteristics of molecular junctions
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An efficient molecular docking using conformational space annealing
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Lipid-protein interactions in membranes: a molecular modelling study
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Molecular factors involved in the development of diabetic foot syndrome.
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Shape resonance of the ethylene anion stabilized in a molecular trap
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
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Solar light driven degradation of norfloxacin using as-synthesized Bi 3+ and Fe 2+ co-doped ZnO with the addition of HSO 5 – : Toxicities and degradation pathways investigation
PublicationIn this study, solar light responsive Bi3+ and Fe2+ doped ZnO were synthesized and used for photocatalytic degradation of norfloxacin (NOR), an emerging water pollutant. Analysis with Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), selected area electron...
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Hydrothermal synthesis of vanadium ammonium compounds – the crucial role of the pressure
PublicationDue to the structural diversity and chemical activity, vanadium oxides and their derivatives are continuingly in the great interest of scientist. In a large family of vanadium compounds, one of the most interesting are ammonium vanadates (with the general formula (NH4)xVyOz). They have received much attention because of their promising application as cathode material in mono- and multivalent-ion batteries [1]. Hydrothermal synthesis...
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From structure to luminescence investigation of oxyfluoride transparent glasses and glass-ceramics doped with Eu3+/Dy3+ ions
PublicationGlasses and glass-ceramics with nominal composition 73 TeO2– 4BaO– 3Bi2O3–18SrF2-2RE2O3 (where RE = Eu, Dy) have been synthesized by conventional melt-quenching technique and subsequent heat treatment at 370 °C for 24 h in air atmosphere. Various Eu3+ to Dy3+ molar ratio have been applied to investigate luminescence properties in both glass and glass-ceramic matrices. Especially, white light emission through simultaneous excitation...
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Insight into (Electro)magnetic Interactions within Facet-Engineered BaFe12O19/TiO2 Magnetic Photocatalysts
PublicationA series of facet-engineered TiO2/BaFe12O19 composites were synthesized through hydrothermal growth of both phases and subsequent deposition of the different, faceted TiO2 nanoparticles onto BaFe12O19 microplates. The well-defined geometry of the composite and uniaxial magnetic anisotropy of the ferrite allowed alternate interfaces between both phases and fixed the orientation between the TiO2 crystal structure and the remanent...
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Mono- and bimetallic (Pt/Cu) titanium(IV) oxide core–shell photocatalysts with UV/Vis light activity and magnetic separability
PublicationTitanium(IV) oxide is one of the most widely investigated photocatalysts. However, separation of nano-sized particulate titania might result in profitless technologies for commercial applications. Additionally, bare titania is almost inactive under the Vis range of solar spectrum due to its wide bandgap. Therefore, the present study aims to prepare novel coreinterlayer- shell TiO2 magnetic photocatalysts modified with metal nanoparticles...
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Design and Preparation of Magnetically-Oriented Poly(styr-co-MMA)-3MPS Capped Fe(ZnO) Hybrid Microspheres for Ion Exchange Removal of Toxic Pollutants from Wastewater
PublicationIn this work, polymeric microspheres derived from polystyrene-co-methyl methacrylate embedded with magnetic ZnO nanoparticles (poly(styrene-co-MMA)-3MPS-Fe (ZnO)) were synthesized using the suspension polymerization method. The surfaces of polymeric Fe(ZnO) microspheres were improved by functionalization with amino and sulphonate groups. The physicochemical analysis indicated a large number of positively charged (anion exchange)...
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Enhancement of photocatalytic-based processes by mono- and bimetallic (CuPd) rutile loaded nanoparticles for antibiotic resistance genes and facultative pathogenic bacteria removal
PublicationThe aim of the study was the strong reduction of facultative pathogenic bacteria (FPB), and clinically relevant antibiotic resistance genes (ARGs) from secondary effluent. To evaluate the ARGs removal efficiency comparative study of individual unit processes and combined AOPs has been performed. The present work investigated: i) removal of selected ARGs, namely blaTEM, ermB, qnrS, tetM, five FPB as well as 16S rDNA and the integrase...
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Virulence, antifungal susceptibility and molecular mechanisms of echinocandin resistance among Candida isolates recovered from clinical specimens
PublicationFungi of the genus Candida belong to the natural microflora of healthy individuals. However, they can also be a cause of opportunistic infections especially among patients with an impaired immune system. The first line therapy of Candida infections is based on triazoles. However, in recent years there an increase of azole resistant Candida spp., in particular C. glabrata and C. krusei, has been observed. For this reason, echinocandin...
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Study of the Effectiveness of Model Order Reduction Algorithms in the Finite Element Method Analysis of Multi-port Microwave Structures
PublicationThe purpose of this paper is to investigate the effectiveness of model order reduction algorithms in finite element method analysis of multi-port microwave structures. Consideration is given to state of the art algorithms, i.e. compact reduced-basis method (CRBM), second-order Arnoldi method for passive-order reduction (SAPOR), reduced-basis methods (RBM) and subspace-splitting moment-matching MOR (SSMM-MOR)
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On Accelerated Metaheuristic-Based Electromagnetic-Driven Design Optimization of Antenna Structures Using Response Features
PublicationDevelopment of present-day antenna systems is an intricate and multi-step process requiring, among others, meticulous tuning of designable (mainly geometry) parameters. Concerning the latter, the most reliable approach is rigorous numerical optimization, which tends to be re-source-intensive in terms of computing due to involving full-wave electromagnetic (EM) simu-lations. The cost-related issues are particularly pronounced whenever...
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Destruction of shell structures under the dynamic load on the human skull trauma basis
PublicationThe main aim of this work is to investigate patterns of potential orbital bone fractures due to mechanical injuries. The solution of the main problem is followed by analysis of several testing examples having straight correlation with civil engineering structures, in which materials of wide range of stiffness are applied. To solve the main problem, the three-dimensional finite element method (FEM) model of the orbital region has...
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Functional Bi2O3/Gd2O3 Silica-Coated Structures for Improvement of Early Age and Radiation Shielding Performance of Cement Pastes
PublicationThis study presents a new approach towards the production of sol-gel silica-coated Bi2O3/Gd2O3 cement additives towards the improvement of early mechanical performance and radiation attenuation. Two types of silica coatings, which varied in synthesis method and morphology, were used to coat Bi2O3/Gd2O3 structures and evaluated...
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Low-cost EM-Simulation-based Multi-objective Design Optimization of Miniaturized Microwave Structures
PublicationIn this work, a simple yet reliable technique for fast multi-objective design optimization of miniaturized microwave structures is discussed. The proposed methodology is based on point-by-point identification of a Pareto-optimal set of designs representing the best possible trade-offs between conflicting objectives such as electrical performance parameters as well as the size of the structure of interest. For the sake of computational...
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Molecular basis of the low activity of antitumor anthracenediones, mitoxantrone and ametantrone, in oxygen radical generation catalyzed by NADH dehydrogenase. Enzymatic and molecular modelling studies
PublicationSyntetyczne antracenodionowe leki przeciwnowotworowe, w przeciwieństwie do antybiotyków antracyklinowych, charakteryzują się słabym wytwarzaniem wolnych rodników w układach z dehydrogenazą NADH. Wyniki prezentowane w artykule wskazują, że ani potencjał redukcyjny, ani konformacja łańcuchów bocznych, ani energie orbitali granicznych (LUMO i HOMO) nie determinują zdolności antracenedionów do stymulacji wytwarzania reaktywnych form...
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Towards More Realistic Probabilistic Models for Data Structures: The External Path Length in Tries under the Markov Model
PublicationTries are among the most versatile and widely used data structures on words. They are pertinent to the (internal) structure of (stored) words and several splitting procedures used in diverse contexts ranging from document taxonomy to IP addresses lookup, from data compression (i.e., Lempel- Ziv'77 scheme) to dynamic hashing, from partial-match queries to speech recognition, from leader election algorithms to distributed hashing...
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Syntheses, Structures and Reactivity of Terminal Phosphido Complexes of Iron(II) Supported by a β-Diketiminato Ligand
PublicationWe report the synthesis of the first series of terminal phosphido iron complexes supported by a β‐diketiminato ligand (Dippnacnac) and their catalytic activity in dehydrocoupling of secondary phosphines. Anionic and neutral mono‐ or diphosphido complexes were obtained from the reaction of [(Dippnacnac)FeCl2Li(dme)2] with the R2PLi (R = iPr, tBu, Cy, Ph) phosphides by tuning the stoichiometric ratio, polarity of the solvent, and...
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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An MOR Algorithm Based on the Immittance Zero and Pole Eigenvectors for Fast FEM Simulations of Two-Port Microwave Structures
PublicationThe aim of this article is to present a novel model-order reduction (MOR) algorithm for fast finite-element frequency-domain simulations of microwave two-port structures. The projection basis used to construct the reduced-order model (ROM) comprises two sets: singular vectors and regular vectors. The first set is composed of the eigenvectors associated with the poles of the finite-element method (FEM) state-space system, while...
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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Development of novel optoelectronic sensory structures utilising colour centres in nanodiamonds and their interactions with analytes
PublicationThe goal of this dissertation was to develop and assess surface modifications of fluorescent nanodiamonds (NDs) for optical sensing. Three modification routes were tested, each aimed at a different application. Modification with poly-L-lysine (pLys) was verified for optical sensing of pH via an interrelationship between electrically negative (NV¯) and neutral (NV0) nitrogen-vacancy centres. Immobilisation of Ochratoxin A (OTA),...
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Normalized Partial Scattering Cross Section for Performance Evaluation of Low-Observability Scattering Structures
PublicationThe development of diffusion metasurfaces created new opportunities to elevate the stealthiness of combat aircraft. Despite the potential significance of metasurfaces, their rigorous design methodologies are still lacking, especially in the context of meticulous control over the scattering of electromagnetic (EM) waves through geometry parameter tuning. Another practical issue is insufficiency of the existing performance metrics,...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...