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Search results for: PROTEINS, DATA-ASSISTED MODELING, CONFORMATIONAL ENSEMBLES, NUCLEAR MAGNETIC RESONANCE, SMALL-ANGLE X-RAY SCATTERING, CHEMICAL CROSS-LINKING COUPLED WITH MASS SPECTROSCOPY, MOLECULAR DYNAMICS, COARSE GRAINING
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Carbon nanowalls: A new versatile graphene based interface for laser desorption/ionization-mass spectrometry detection of small compounds in real samples.
PublicationCarbon nanowalls, vertically aligned graphene nanosheets, attract attention owing to their tunable band-gap, high conductivity, high mechanical robustness, high optical absorbance and other remarkable properties. In this paper, we report for the first time, the use of hydrophobic boron-doped carbon nanowalls (CNWs) for laser desorption/ionization of small compounds and their subsequent detection by mass spectrometry (LDI-MS). The...
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Billiard in a rotating half-plane: modeling and dynamics
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Reliable data-driven modeling of high-frequency structures by means of nested kriging with enhanced design of experiments
PublicationData-driven (or approximation) surrogate models have been gaining popularity in many areas of engineering and science, including high-frequency electronics. They are attractive as a way of alleviating the difficulties pertinent to high computational cost of evaluating full-wave electromagnetic (EM) simulation models of microwave, antenna, and integrated photonic components and devices. Carrying out design tasks that involve massive...
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Cross sections for electron scattering from furan molecules; measurements and calculations
PublicationZmierzono i policzono przekroje czynne (TCS) na rozproszenie elektronów na drobinach furanu (C4H4O). Całkowite przekroje czynne zmierzono metodą transmisyjną w zakresie energii 0.6 - 400 eV. Sprężysty i jonizacyjny przekrój czyny obliczono dla energii zderzenia do 4 keV; powyżej 70 eV suma obu przekrojów pozostaje w dobrej zgodności z mierzonymi wartościami TCS.
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Electron-scattering total cross sections for triatomic molecules: NO2 and H2O
PublicationZmierzono całkowite przekroje czynne na rozpraszanie elektronów na drobinach NO2 i H2O, odpowiednio w zakresie energii od 3 do 370 eV oraz 0,5 do 370 eV. Dla średniej energii zderzenia obliczono ponadto przekroje na rozproszenie sprężyste i jonizację.
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Electron scattering from hexafluoroacetone molecules: cross section measurements and calculations
PublicationZmierzono absolutne całkowite przekroje czynne na zderzenie elektronów z drobinami hexafluoroacetonu (HFA). Pomiary przeprowadzono dla energii zderzenia od 1 do 400 eV. Zależność energetyczna przekroju czynnego wykazała obecność struktur związanych z procesami o charakterze rezonansowym. Wykonano obliczenia sprężystego i jonizacyjnego przekroju czynnego dla drobin HFA i acetonu. Suma obliczonych przekrojów wykazuje dużą zgodność...
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Isomer effects on the total cross section for electron scattering from C4F6molecules.
PublicationZmierzono całkowity przekrój czynny (TCS) na rozpraszanie elektronów na drobinach 1,3-C4F6. Pomiary przeprowadzono w zakresie energii elektronu od 0,6do 370 eV. Wyniki porównano z TCS otrzymanym poprzednio dla 2-C4F6. Stwierdzono wpływ różnic strukturalnych na otrzymane energetyczne zależności TCS (tzw. efekt izomeryczny).
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Cross section calculations for electron scattering from DNA and RNA bases.
PublicationPoliczono różniczkowy i scałkowany przekrój czynny na rozproszenie sprężyste elektronów (w przybliżeniu atomów niezależnych) na uracylu, cytozynie, guaninie, adeninie i tyminie w zakresie energii od 50-4000 eV. W przybliżeniu modelu BEB policzono również przekroje czynne na jonizację tych molekuł.
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Cross sections for electron scattering from selected components of DNA and RNA
PublicationWykorzystując metodę atomów niezależnych obliczono różniczkowe i całkowite przekroje czynne na sprężyste rozproszenie elektronów na wybranych drobinach, będących analogami składników DNA i RNA. Przekroje te obliczono w zakresie energii zderzenia od 50eV do 200 eV dla następujących drobin: C4H8O, C4H8O2, C5H10O2 oraz H3PO4. Przy użyciu metody BEB (binary-ecounter Bethe method) dla powyższych związków obliczono również przekroje...
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Data set generation at novel test-rig for validation of numerical models for modeling granular flows
PublicationSignificant effort has been exerted on developing fast and reliable numerical models for modeling particulate flow; this is challenging owing to the complexity of such flows. To achieve this, reliable and high-quality experimental data are required for model development and validation. This study presents the design of a novel test-rig that allows the visualization and measurement of particle flow patterns during the collision...
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Estimation of optical parameters of highly scattering materials by time-of-flight spectroscopy.
PublicationPrzedstawiono metody wyznaczania podstawowych parametrów materiałów silnie rozpraszających światło na podstawie pomierzonego rozkładu czasu przelotu krótkich impulsów laserowych. W algorytmie wykorzystano metodę Monte Carlo i metodę dyfuzji do opisu propagacji światła. Oszacowano dokładność oszacowywania tych parametrów.
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Influence of magnetic interaction on lattice dynamics of FeBO 3
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Mechanical and fracture properties of concrete reinforced with recycled and industrial steel fibers using Digital Image Correlation technique and X-ray micro computed tomography
PublicationPaper presents investigation of fracture phenomenon in plain concrete and in concrete reinforced with both recycled steel fibers (RSF) and industrial steel fibers (ISF). The wedge splitting test (WST), which enables stable crack propagation for quasi-brittle materials, was carried out on 75 75 75 mm cube samples. Initially, fracture process zone development was investigated only on the surface of samples using Digital Image Correlation...
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Structure of Kα1,2 - and Kβ1,3 -emission x-ray spectra for Se, Y, and Zr
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Precise x-ray energies of gadolinium determined by a combined experimental and theoretical approach
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Two-photon double ionization of atoms in attosecond x-ray radiation fields
PublicationWe consider two-photon double ionization of helium with 100, 200, and 400 eV excess energy for the two ejected electrons, corresponding to photon energies of 89.5, 139.5, and 239.5 eV, respectively. We focus on the case of ultrashort pulses (two oscillations of the field) and develop an approach to calculate the two-photon transition matrix elements within the lowest order of the time-dependent perturbation theory. One of the...
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Use of X-Ray Computed Tomography for Ice Detection Applied to Organ Cryopreservation
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Ovarian tissue cryopreservation by stepped vitrification and monitored by X-ray computed tomography
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X-ray and NMR structural studies of the series of porphyrazines with peripheral pyrrolyl groups
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BIOLOGICAL AGE ASSESSMENT ALGORITHMS BASED ON X-RAY IMAGES OF BONE TISSUE
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Creating private and public value in data-related management projects: a cross-border case study from Switzerland and Italy
PublicationThe literature in the field of smart cities shows a continuous emphasis and interest in the topic of big data due to the extensive use of Information and Communication Technologies by public and private institutions within each city. There is undoubtedly value in big data: in data lie insights on the city, its stakeholders, citizens, products, and services. Challenges, though, lie in data’s variety, volume, and velocity, but also...
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Magnetic resonance imaging of radiation dose distributions using a polymer-gel dosimeter
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Image Quality Assessment Tool for Conventional and Dynamic Magnetic Resonance Imaging Acquisitions
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T1 RELAXATION TIME CALLIBRATION IN MAGNETIC RESONANCE IMAGING USING NANODIAMOND PHANTOMS
PublicationMRI is increasingly used in radiation treatment planning because of the excellent soft tissue contrast in the obtained images. It allows more precise definition of the boundaries between healthy tissues and those affected by cancerous lesions. To obtain good image quality, the difference in signal between two types of tissue must be significant despite the noise so it must be properly calibrated. This calibration includes...
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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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Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies.
PublicationAmfoterycyna B jest antybiotykiem z grupy polienów makrolidowych. Stosowany jest on w leczeniu układowych infekcji grzybowych. Wiadomo że związek ten oddziałuje ze składnikami błon lipidowych i tworzy kanały. W przedstawianej pracy prezentowane są wyniki symulacji przeprowadzonej dynamiką molekularną układu składającego się z 200 cząsteczek lipidów DMPC i jednej cząsteczki amfoterycyny ułożonej na powierzchni błony. Z przeprowadzonej...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...
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Conformational Preferences of Proline Derivatives Incorporated into Vasopressin Analogues: NMR and Molecular Modelling Studies
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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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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Spectroscopy and Dynamics of Cryptolepine in the Nanocavity of Cucurbit[7]uril and DNA
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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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Mechanical and radiation shielding properties of concrete reinforced with boron--basalt fibers using Digital Image Correlation and X--ray micro--computed tomography
PublicationThe paper presents experimental investigations of the radiation shielding, mechanical and fracture properties of concrete reinforced with 5 kg/m3 of novel basalt fibers infused with boron oxide (BBF). However, further studies concerning other dosages i.e. 1 kg/m3, 10 kg/m3, 15 kg/m3 and 20 kg/m3 are currently carried out. Experiments with neutron source revealed that addition of BBF as a dispersed concrete reinforcement could improve...
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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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Resonance conditions for Mo93m isomer depletion via nuclear excitation by electron capture in a beam-based scenario
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The X-ray crystallographic structures, spectral and magnetic properties of nickel(II), copper(II) and cobalt(II) complexes with tetra(3-iso-propylpyrazol-1-yl)borate
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FT-Raman Spectroscopy as a Tool to Study the Secondary Structures of Wheat Gliadin Proteins
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Mobile Gas Chromatographs Coupled with Mass and Ion Mobility Spectrometers and their Applications
PublicationThe articles describes the developments un combining of mass and ion mobility spectrometers (MS, IMS0 with miniature gas chromatographs (GC). The examples of applications of miniaturised GC-MS and GC-IMS devices are presented.
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
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Scattering in a section of ferrite coupled microstrip lines: theory and application in nonreciprocal devices
PublicationPrzeprowadzono analizę pełnofalową sekcji sprzężonych ferrytowych linii mikropaskowych wykorzystującą w rozwinięciu pola em fale prowadzone w izotropowych złączach wejściowych sekcji oraz jej fajl ferrytowych. W wyniku określono macierz S sekcji. Przeprowadzono modelowanie własności rozproszenia układu oraz symulację parametrów transmisyjnych układów niewzajemnych projektowanych z wykorzystaniem proponowanego układu ferrytowego.
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The image of the City on social media: A comparative study using “Big Data” and “Small Data” methods in the Tri-City Region in Poland
Publication“The Image of the City” by Kevin Lynch is a landmark planning theory of lasting influence; its scientific rigor and relevance in the digital age were in dispute. The rise of social media and other digital technologies offers new opportunities to study the perception of urban environments. Questions remain as to whether social media analytics can provide a reliable measure of perceived city images? If yes, what implication does...
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A hierarchical porous composite magnetic sorbent of reduced graphene oxide embedded in polyvinyl alcohol cryogel for solvent‐assisted‐solid phase extraction of polycyclic aromatic hydrocarbons
PublicationA hierarchical porouscomposite magnetic sorbent was fabricated and applied tothe dispersive solvent-assisted solid-phase extraction of five polycyclic aromatichydrocarbons. A sorbent was first prepared by incorporating graphene oxide,calcium carbonate, and magnetite nanoparticles into a polyvinyl alcohol cryo-gel. The graphene oxide was converted to reduced graphene oxide using ascorbicacid and a hierarchical porous structure was...
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Shape resonance of H[sub 2][sup −] anion stabilized in a molecular trap
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Synthesis and characterization of novel renewable polyesters based on 2,5-furandicarboxylic acid and 2,3-butanediol
PublicationNovel polyesters from 2,5-furandicarboxylic acid or 2,5-dimethyl-furandicarboxylate and 2,3-butanediol have been synthesized via bulk polycondensation catalyzed by titanium (IV) n-butoxide, tin (IV) ethylhexanoate, or zirconium (IV) butoxide. The polymers were analyzed by size exclusion chromatography, nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy (FTIR), matrix-assisted laser ionization-desorption...
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Characterization of GM3 Gangliosides in Human Milk throughout Lactation: Insights from the Analysis with the Use of Reversed-Phase Liquid Chromatography Coupled to Quadrupole Time-Of-Flight Mass Spectrometry
PublicationGangliosides are complex lipids found in human milk that play important structural and biological functions. In this study, we utilized reversed-phase liquid chromatography coupled to quadrupole time-of-flight mass spectrometry to evaluate the molecular distribution of GM3 in human milk samples collected at distinct lactation stages, ranging from colostrum to advanced lactation samples. Throughout lactation, GM3 d40:1 emerged as...