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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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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Structural Insights into σ1 Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Molecular Dynamics study of short and medium range order in modified BGO glasses.
PublicationArtykuł przedstawia wyniki symulacji dynamiczno-molekularnychniemodyfikowanych i modyfikowanych szkieł BGO o różnych stechiometriach. Otrzymane wyniki dokładnie przedyskutowano pod kątem blisko- i średnio-zasięgowego uporządkowania atomów i porównano z innymi dostępnymi danymi literaturowymi.
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Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels
PublicationBadania polegały na przeprowadzeniu porównawczej dynamiki molekularnej dla dwóch typów kanałów amfoterycyny B. Obie symulacje różniły się rodzajem sterolu (cholesterol lub ergosterol). Na podstawie wyników przeprowadzonych prac ustalono jakie elementy strukturalne badanych kanałów mogą być odpowiedzialne za selektywne działanie amfoterycyny B.
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JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL
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X-ray diffraction spectra of nitrogen-doped carbon in hybrid materials containing praseodymium oxide
Open Research DataX-ray powder diffraction patterns of samples were carried out by Philips X’Pert diffractometer, which was radiated by graphite monochromatized Cu Kα (l equal 1.540598). The operating voltage was maintained at 40 kV, the current was maintained at 30 mA and analyzed in the range from 20° to 90°. The data presented confirmed the presence of the PrBSCF...
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Differential cross sections for elastic electron scattering in argon over the angular range 130-180 st.
PublicationPomiary różniczkowych przekrojów czynnych na rozpraszanie sprężyste na atomach argonu w zakresie kątów 130-180 st. dla elektronów o energiach 5, 7.5 i 10 eV. W pomiarach wykorzystano technikę lokalnego pola magnetycznego.
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Electromagnetic plane wave scattering from a cylindrical object with an arbitrary cross section using a hybrid technique
PublicationA hybrid technique combining finite-element and mode-matching methods for the analysis of scattering problems in open and closed areas is presented. The main idea of the analysis is based on the utilization of the finite-element method to calculate the post impedance matrix and combine it with external excitation. The discrete analysis, which is the most time- and memory-consuming, is limited here only to the close proximity of...
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Rotating Magnetic Field-Assisted Reactor Enhances Mechanisms of Phage Adsorption on Bacterial Cell Surface
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Rapid ion-exchange matrix removal for a decrease of detection limits in the analysis of salt-rich reservoir waters for fluorobenzoic acids by liquid chromatography coupled with tandem mass spectrometry
PublicationA matrix removal procedure with ion-exchange resin prior to analysis for 18 fluorinated benzoic acids (FBAs) tracers in saline (>25% salt) reservoir water was optimized. The elimination of >98% of salt and the simultaneous matrix sample cleanup allowed the direct analysis using the supernatant by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). This resulted in a gain in detection limits for most of the tracers...
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Ecotoxicity and chemical sediment data classification by the useof self-organising maps
PublicationArtykuł dotyczy przedstawiania nowej interpretacji szacowania jakości osadów. To oryginalne podejście bada powiązania między parametrami ekotoksyczności (ostrej i chronicznej) i składnikami chemicznymi (zanieczyszczenia takie jak polichlorowane bifenyle, pestycydy, wielopierścieniowe węglowodory aromatyczne, metale ciężkie) próbek osadów Jeziora Turawskiego (Polska) poprzez zastosowanie samoorganizujących się map (SOM) wobec badanego...
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Molecular modeling of amphotericin B - ergosterol primary complex in water II
PublicationPrezentowane badania dotyczą oddziaływania antybiotyku polienowego anfoterycyny B (AmB) i ergosterolu (ERG) (typowego sterolu błonowego komórek grzybowych) na poziomie molekularnym. W odróżnieniu od badanego poprzednio kompleksu binarnego analizowany obecnie kompleks AnB/ERG/AmB charakteryzuje się zdecydowanie wiekszą stabilnością i wzglednie sztywną, sandwiczową geometrią. Za trwałość i geometrie kompleksu odpowiedzialne są oddziaływania...
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Technology of an adhesive silicone film as drug carrier in transdermal therapy I. Analytical methods used for characterization and design of the universal elastomer layers
PublicationSilicone polymers possess unique properties, which make them suitable for many different applications, for example in the pharmaceutical and medical industry. To create an adhesive silicone film, the appropriate silicone components have to be chosen first. From these components two layers were made: an adhesive elastomer applied on the skin, and a non-adhesive elastomer on the other side of the film. The aim of this study was...
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X-ray diffraction patterns of BaCe0.6Zr0.2Y0.1M0.1O3-δ (M = Fe, Pr, Tb)
Open Research DataThe dataset consists of three raw X-ray diffraction (XRD) files collected using a Phillips X’Pert Pro diffractometer (CuKα radiation (𝜆 = 1.541 Å), under 40 kV and 30 mA). The diffraction patterns of BaCe0.6Zr0.2Y0.1Fe0.1O3-δ (BCZYFe), BaCe0.6Zr0.2Y0.1Pr0.1O3-δ (BCZYPr), and BaCe0.6Zr0.2Y0.1Tb0.1O3-δ (BCZYTb) were collected at room temperature. Collected...
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Incensfuran: isolation, X-ray crystal structure and absolute configuration by means of chiroptical studies in solution and solid state
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Crystallization and preliminary X-ray analysis of the isomerase domain of glucosamine-6-phosphate synthase from Candida albicans
PublicationSyntaza 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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A three-dimensional meso-scale approach with cohesive elements to concrete fracture based on X-ray μCT images.
PublicationArtykuł omawia wyniki numeryczne dotyczące pękania betonu uzyskane stosując trójwymiarowy model mezoskopowy z elementami kohezyjnymi. Obliczenia trójwymiarowe zostały wykonane dla zginanej belki betonowej. Beton został opisany jako model 3-fazowy. Mikrostruktura betonu odpowiadała zdjęciom tomograficznym. Wyniki numeryczne zostały porównane z wynikami doświadczalnymi. Uzyskano b. dobra zgodność między wynikami numerycznymi i doświadczalnymi.
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Small signal admittance spectroscopy applied for extraction of charge carrier mobility in thin organic layers
PublicationPraca przedstawia nowy sposób wyznaczania ruchliwości nośników ładunku w cienkich warstwach organicznych w oparciu o pomiary widm małosygnałowej admitancji.
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Floodplain inundation Mapping using SAR Scattering Coefficient Thresholding and Observed Discharge Data
PublicationInundation area time series are important for wetlands monitoring and hydrological model validation. This study is conducted in Biebrza floodplain, which is a natural wetland with complex inundation generation processes. In order to map 2014-2018 series of inundation in the floodplain we test our automatic thresholding method on Sentinel 1 data. The threshold value is optimized using correlation of the inundation area with observed...
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Application of time-series-cross-section data in case of sale forecasting in an enterprise
PublicationW artykule wskazano możliwości wykorzystania danych przestrzenno-czasowych do prognozowania sprzedaży w przedsiębiorstwie. Przedstawiono różne podejścia do prognozowania ekonometrycznego przy użyciu tego typu danych. Wyznaczono krótkookresowe prognozy sprzedaży benzyny bezołowiowej Pb95 w przekroju województw oraz dokonano oceny ich jakości przy użyciu mierników ex-post. Dwie najdokładniejsze metody prognozowania wykorzystano do...
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Absolute configurations of C34 and C35 of antibiotic niphimycin A
PublicationThe relative configurations of four stereogenic centers of the C33-C42 fragment of niphimycin A were assigned as 2S*, 3R*, 4S* and 6S*, based upon (1)H NMR analysis with double-quantum filtered COSY and nuclear Overhauser spectroscopy experiments. These data were then correlated with absolute configurations at C36 and C38 of niphimycin A, which were declared previously as 36S and 38S [3]. This allowed for the assignment of the...
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Absolute configurations of C34 and C35 of antibiotic niphimycin A
PublicationThe relative configurations of four stereogenic centers of the C33-C42 fragment of niphimycin A were assigned as 2S*, 3R*, 4S* and 6S*, based upon 1H NMR analysis with double-quantum filtered COSY and nuclear Overhauser spectroscopy experiments. These data were then correlated with absolute configurations at C36 and C38 of niphimycin A, which were declared previously as 36S and 38S [3]. This allowed for the assignment of the absolute...
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JOURNAL OF PHYSICAL AND CHEMICAL REFERENCE DATA
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Comparison of hydrophilic interaction and reversed phase liquid chromatography coupled with tandem mass spectrometry for the determination of eight artificial sweeteners and common steviol glycosides in popular beverages
PublicationHydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry (MS/MS) was used to separate artificial and natural sweeteners approved for use in European Union (EU). Among three tested HILIC columns (BlueOrchid PAL-HILIC, Ascentis Express Si and Acclaim™ Trinity™ P2) the last one was selected for the development of HILIC method due to the best results obtained with it. Early eluting and coeluting compounds...
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Toward Mechanosynthesis of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics Comparison of Conditions for the STM Tip Driven Mechanosynthesis on Hydrogenated Si(111), Si(110) and Si(100) Surfaces.
Publicationmożliwość prototypowania przejściowych generacji nano-urządzeń otrzymanych drogą pozycjonowanej mechanosyntezy za pomocą stm wyposażonego w ostrze typu swcnt są analizowane metodą kwantowo-chemicznej dynamiki molekularnej. proponowana strategia syntezy polega na insercji atomów si oraz cząsteczek sih2 we wiązania si-h na uwodornionej powierzchni si(111), si(110) oraz si(100) kryształu krzemu. rezultaty modelowania sugerują, że...
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Molecular picture of hydroxide anion hydration in aqueoussolutions studied by FT-IR ATR spectroscopy
PublicationHydratacja anionu hydroksylowego w wodnych roztworach wodorotlenków metali alkalicznych (LiOH, NaOH, KOH) została zbadana metodą spektroskopii oscylacyjnej FT-IR całkowitego wewnętrznego odbicia (ATR). Widma oscylacyjne wody dostarczają cennych informacji na temat stanu strukturalnego cząsteczek wody w sferach hydratacyjnych, wynikających ze sprzężeń oscylatorów w układzie. Wykazano, że drganie normalne rozciągające cząsteczki...
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Magnetic hydrophobic deep eutectic solvents for orbital shaker-assisted dispersive liquid-liquid microextraction (MAGDES-OS-DLLME) - determination of nickel and copper in food and water samples by FAAS
PublicationIn this work, a cheap and widely applicable dispersive liquid-liquid microextraction (DLLME) method was developed for the extraction of Ni(II) and Cu(II) from water and food samples and analysis using flame atomic absorption spectrometry. DLLME was assisted by orbital shaker, while ferrofluid as an extractant was based on deep eutectic solvent (DES). This ferrofluid was made of hydrophobic DES (hDES), composed of lauric acid and...
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Electrochemical Impedance Spectroscopy data of PDA-modified TiO2 nanotubes
Open Research DataThis dataset contains Electrochemical Impedance Spectroscopy data of the samples from TiO2 nanotubes modified with polydopamine. The studies were presented as a part of the research on "Band Gap Engineering toward Semimetallic Character of Quinone-Rich Polydopamine" (DOI: 10.1021/acs.jpcc.2c08804).
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Elastic electron scattering and vibrational excitation of isoxazole molecules in the energy range from 2 to 20 eV
PublicationDifferential cross sections for elastic electron scattering and the excitation of the C-H vibrational modes of isoxazole molecules were measured in the energy range from 2 to 20 eV and over the scattering angle range from 10◦ to 180◦. The cross sections at the scattering angles of and above 90◦ were accessible with the use of a magnetic angle changer. The differential cross sections were integrated to yield integral and momentum...
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The role of hydrogen bonding on tuning hard-soft segments in bio-based thermoplastic poly(ether-urethane)s
PublicationThis work describes the preparation of bio-based thermoplastic poly(ether-urethane)s (TPU) via a prepolymer method and investigates the effect of varying the interphase hydrogen-bonding (H-bonding) on physicochemical, thermal and mechanical properties. This was achieved by varying the glycol type and molar ratio of [NCO]/[OH] groups used during the prepolymer chain extending step. The TPUs’ chemical structure was analyzed by Fourier...
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Two-step Conversion of Crude Glycerol Generated by Biodiesel Production into Biopolyols: Synthesis, Structural and Physical Chemical Characterization
PublicationIn this work biopolyols were synthesized via two-step process from crude glycerol and castor oil. For better evaluation of analyzed process, the impact of its time and temperature on the structure and properties of biopolyols was determined. Obtained results fully justified conducting of synthesis in two steps. Prepared materials were characterized by hydroxyl value and water content comparable to polyols industrially applied in...
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Hanna Obracht-Prondzyńska dr inż. arch.
PeopleHanna Obracht-Prondzyńska, PhD MArch, Eng. Assistant Professor at the University of Gdańsk, Department of Spatial Management, academic teacher of urban design and spatial data analyses. Architect and urban planner experienced in data driven urban design and planning. She defended her PhD with distinction in engineering and technical sciences in the discipline of architecture and urban planning in 2020 at the Faculty of Architecture...
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The structure of vanadate glass-ceramics containing BaTiO3 measured with X-ray diffraction method
Open Research DataThe structure of vanadate glass-ceramics doped with BaTiO3 was measured by XRD. Samples of the composition of x[BaO,TiO2]–(80 − x)V2O5–20Bi2O3 where x = 5, 10 and 15 in mol% were prepared by a conventional melt quenching technique. The melting was performed in alumina crucibles at the temperature of 1273 K–1373 K. The melts were poured on a preheated...
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Orientational Order and Dynamics of Nematic Multipodes Based on Carbosilazane Cores Using Optical and Dielectric Spectroscopy
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Study of Direct Methanol Fuel Cell Process Dynamics Using Dynamic Electrochemical Impedance Spectroscopy
PublicationA new technique, which was developed to characterize the direct methanol fuel cell under work conditions, has been presented in this paper. The impedance measurements were made using dynamic electrochemical impedance spectroscopy research technique in the galvanostatic mode, using multiple sinusoidal excitation. Obtained results show, that together with an increase of the temperature and working load, the global impedance...
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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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Modeling saturation of main magnetic circuit of cage induction motors in presence of eccentricity
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Designing Atomic Resonance Conditions for $^{93m}$Mo Isomer Depletion Via Nuclear Excitation by Electron Capture in a Beam-based Scenario for Selected Targets
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Triticale extrudates – Changes of macrostructure, mechanical properties and molecular water dynamics during hydration
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MEL zeolite nanosheet membranes for water purification: insights from molecular dynamics simulations
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Combining tight-binding and molecular dynamics methods to model the behaviour of metals in the plastic regime
PublicationOpisujemy zastosowanie metody dwuskalowej (kwantowo-klasycznej) w zastosowaniu do metali. Region energetycznie najważniejszy jest traktowany kwantowo, podczas gdy reszta układu jest traktowana klasycznie. Wprowadzamy własną implementację metody oraz przedstawiamy uzyskane wyniki dla metali.
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublicationWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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JOURNAL OF MAGNETIC RESONANCE
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Numerical modeling of cross-flow heat exchanger for air-conditioning purposes in preliminary study.
PublicationPraca przedstawia wyniki obliczeń numerycznych krzyżowego płytowo-rurowego wymiennika ciepła przeznaczonego do celów klimatyzacyjnych w początkowym etapie jego projektowania.
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Differential cross sections for low-energy elastic electron scattering from tetrahydrofuran in the angular range 20°-180°
PublicationWartości absolutne różniczkowych przekrojów czynnych na rozproszenie sprężyste elektronów o energii 6-20eV na cząsteczce tetrahydrofuranu w zakresie kątów 20°-180°. W pomiarach wykorzystano technikę lokalnego pola magnetycznego. Wyznaczono także całkowity przekrój czynny na rozproszenie sprężyste oraz przekrój czynny na przekazanie pędu poprzez scałkowanie zmierzonych różniczkowych przekrojów czynnych dla wybranych energii.
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Observation of the de Vries behavior in SmA* phase of a liquid crystal using polarised Raman scattering and infrared spectroscopy
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