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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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Reply to Comment on ‘Nanodiamond incorporated human liver mimicking phantoms: prospective calibration medium of magnetic resonance imaging’
PublicationDependence of the spin–lattice (T1) relaxation times on the nanodiamond concentration in human liver phantoms is discussed. Factors affecting stability and and reproducibility of these phantoms are presented. The need for comparative measurements on multiple MRI scanners for better understanding of potential variations in the obtained imaging data is emphasised.
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Modeling of soft N, M and L X-ray lines from tungsten relevant to plasma parameters in the WEST tokamak
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublicationThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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Selection of material for X-ray tomography analysis and DEM simulations: comparison between granular materials of biological and non-biological origins
PublicationPhysical properties and X-ray tomography images of five different granular materials: glass bead, glass grit, short grain white rice, sorghum and clay granules (Seramis) are investigated to select the most promising materials for numerical simulations and time-lapse X-ray tomography imaging. The examined materials represent granular materials of non-biological origin (glass bead, glass grit and Seramis) and granular plant materials...
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A study of the structure of mixed micellar solutions based on heptaethylene glycol monotetradecyl ether and sodium (lithium) dodecyl sulfate by the small-angle neutron scattering method
PublicationZbadano micelizację w układach mieszanych bazujących na nowym surfaktancie niejonowym, heptaoksyetylenowanym alkoholu tetradecylowym (C14E7) i surfaktantach anionowych, dodecylosiarczanie sodu, decylosiarcznie sodu oraz dodecylosiarcznie litu za pomocą metody niskokątowego rozproszenia neutronów.Przedstawione zostały wstępne wyniki zachowania wodnych roztworów C14E7 (o dwóch stężeniach 0,17 i 0,50%) przy niewielkim udziale trzech...
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Post-Chromatographic Derivatization Coupled with Mass Spectrometry as a Method of Profiling and Identification of Antioxidants; Ligustrum vulgare Phytocomplex as an Example
PublicationHigh-performance liquid chromatography (HPLC) and high-performance thin-layer chromatography (HPTLC) coupled with radical scavenging assays, such as 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) can be both used for the detection of the antioxidants in plant extracts. In this study, the ethanolic (70% v/v) extracts from different morphological parts of Ligustrum vulgare collected...
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Contact angle of the ferronanofluid and influence of the magnetic field on the drying droplet
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SDN testbed for validation of cross-layer data-centric security policies
PublicationSoftware-defined networks offer a promising framework for the implementation of cross-layer data-centric security policies in military systems. An important aspect of the design process for such advanced security solutions is the thorough experimental assessment and validation of proposed technical concepts prior to their deployment in operational military systems. In this paper, we describe an OpenFlow-based testbed, which was...
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Inner-shell fragmentation of molecules into neutral fragments in high-Rydberg states induced by soft X-ray excitation with pulsed-field ionization
PublicationIn the present communication, we will show the results of measurements probing the production of neutral high-Rydberg fragments at the K edges of the molecules containing oxygen and nitrogen atoms. The experiments were performed at the Gas Phase beamline of the Elettra synchrotron radiation laboratory (Trieste, Italy), exploiting a combined soft X-ray excitation with pulsed-field ionization and ion time-of-flight (TOF) spectrometry...
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Variable-temperature X-ray diffraction study of structural parameters of NH---S hydrogen bonds in triethylammonium and pyridinium silanethiolates
PublicationHydrogen bonds in triethylammonium and pyridinium silanethiolate salts have been characterized by X-ray, FT–IR and NMR spectroscopies. DFT calculations reveal strongly asymmetric double-well minima at the potential energy curves of the studied compounds
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Building Information Modeling in Small and Middle Sized Buildings – Case Study
PublicationBuilding Information Modeling (BIM) is a technology designed to improve and integrate all engineering aspects in the construction design process. Tools that incorporate the idea of BIM are becoming more advanced and also more popular. Available software solutions have already reached an assumable high level of development, but still are not as widespread and used on nearly as many construction projects as could be expected. Therefore...
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Application of data driven methods in diagnostic of selected process faults of nuclear power plant steam turbine
PublicationArticle presents a comparison of process anomaly detection in nuclear power plant steam turbine using combination of data driven methods. Three types of faults are considered: water hammering, fouling and thermocouple fault. As a virtual plant a nonlinear, dynamic, mathe- matical steam turbine model is used. Two approaches for fault detection using one class and two class classiers are tested and compared.
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Use of X-ray radiography in the diagnosis of bonded anchors
PublicationKotwy wklejane należą do najbardziej popularnych metod montażu elementów konstrukcyjnych. Promieniowanie rentgenowskie częściowo umożliwia diagnostykę zespolenia lepiszcza z podłożem. W pracy przedstawiono wyniki analizy wpływu parametrów technicznych aparatów rentgenowskich na sposób i dokładność wykonania zdjęć diagnostycznych osadzenia kotew stalowych przy zastosowaniu lepiszcza syntetycznego
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X-ray photoelectron spectroscopy, Raman and photoluminescence studies on formation of defects in Cu:ZnO thin films and its role in nonlinear optical features
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Determination of hormones in water samples using liquid chromatography coupled with tandem mass spectrometry
PublicationOver the past few years, many synthetic (ethinylestradiol) and natural (estradiol,estriol, estrone) compounds present in the environment have been affecting the hormonalbalance of humans and animals. Steroid hormones are very often used for medical purposesand have high estrogenic activity what makes them endocrine disrupters. Most hormonalcompounds are released into the water as a result of their incomplete removal in wastewatertreatment...
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The influence of of cross-linking process on the physicochemical properties of new copolyesters containing xylitol
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Immobilization of thermostable beta glucosidase from Sulfolobus shibatae by cross-linking with transglutaminase
PublicationOpracowano metodę immobilizacji termostabilnej beta-glukozydazy przez katalizowane transglutaminazą sieciowanie na nośniku krzemionkowym. Aktywność uzyskanego preparatu wynosi 3883 U/g nośnika. Największą wydajność unieruchamiania uzyskano w temperaturze 50C, przy pH 5,0. Immobilizacja prawie nie zmieniała optymalnego pH działania enzymu, który uzyskiwał największą aktywność w temperaturze 98C. Badania w reaktorze kolumnowym wykazały...
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Molecular basis of TRF proteins and their interactions with peptides
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ANYTIME POLYNOMIAL HEURISTIC ALGORITHM FOR PARTITIONING GROUPS OF DATA WITH PRESERVING CLASS PROPORTIONS FOR CROSS-VALIDATION
PublicationThe article describes a problem of splitting data for k-fold cross-validation, where class proportions must be preserved, with additional constraint that data is divided into groups that cannot be split into different cross-validation sets. This problem often occurs in e.g. medical data processing, where data samples from one patient must be included in the same cross-validation set. As this problem is NP-complete, a heuristic...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Online Volatile Compound Emissions Analysis Using a Microchamber/Thermal Extractor Coupled to Proton Transfer Reaction-Mass Spectrometry
PublicationIndoor air is a complex and dynamic mixture comprising manifold volatile organic compounds (VOCs) that may cause physiological and/or psychological discomfort, depending on the nature of exposure. This technical note presents a novel approach to analyze VOC emissions by coupling a microchamber/thermal extractor (μ-CTE) system to a proton transfer reaction-mass spectrometer (PTR-MS). This configuration provides an alternative to...
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3D X-ray Micro-CT Analysis of Rebar Corrosion in Reinforced Concrete Subjected to a Chloride-Induced Environment
PublicationThe paper presents experimental investigations of the concrete cover protective ability to coun-teract rebar corrosion in reinforced concrete cubes. To study and quantify the consequences of corrosion a reinforced concrete sample was subjected to chloride-induced environment in order to get corroded and combined with un-corroded sample. Chloride-accelerated technique can in-duce a high degree of corrosion within at a controlled...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Rapid determination of multiple aminoglycoside antibiotics in veterinary formulations by ion-pair chromatography coupled with evaporative light scattering detection
PublicationA fast and simple method for simultaneous determination of eight aminoglycoside antibiotics using ion-pairing liquid chromatography (IPLC) coupled with evaporative light scattering detection (ELSD) has been developed and validated. Separation of amikacin, apramycin, gentamicin (as a sum of gentamicin C1, C2 and C1A), kanamycin A, neomycin B, paromomycin, streptomycin and tobramycin was achieved using C18 column with H2O and MeOH/acetone,...
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The preparation and evaluation of core-shell magnetic dummy-template molecularly imprinted polymers for preliminary recognition of the low-mass polybrominated diphenyl ethers from aqueous solutions
PublicationThe design, preparation process, binding abilities, morphological characteristic and prospective field of application of dummy-template magnetic molecularly imprinted polymer (DMMIP) for preliminary recognition of the selected low-mass polybrominated diphenyl ethers (PBDE-47 and PBDE-99) from aquatic environment were investigated. The surface of iron oxide (Fe3O4) nanopowder (50-100 nm particles size) was modified with tetraethoxysilane...
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Shape resonance of the ethylene anion stabilized in a molecular trap
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Measurements of inelastic electron scattering from molecular oxygen at high scattering angles
PublicationBadano procesy wzbudzenia oscylacyjnego poziomów v = 1-9 stanu podstawowego X3 sigma g oraz v=0 stanu wzbudzonego a1 delta g cząsteczki tlenu dla energii 10eV w przedziale kąta rozproszenia od 90 do 180 st. Dla pomiaru v=1 stanu X3 sigma g wyznaczono różniczkowy przekrój czynny na wzbudzenie. W pomiarach wykorzystano podwójny hemisferyczny spektrometr elektrostatyczny wykorzystujący nowozaprojektowane źródło lokalnego pola magnetycznego.
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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CALIBRATION OF LOW ENERGY X-RAY EXPERIMENTAL SETUP WITH STRONGLY FILTERED BEAM USING DATA FROM A SEMICONDUCTOR AND A THERMOLUMINESCENT DETECTORS
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Nonlinear planar modeling of massive taut strings travelled by a force-driven point-mass
PublicationThe planar response of horizontal massive taut strings, travelled by a heavy point-mass, either driven by an assigned force, or moving with an assigned law, is studied. A kinematically exact model is derived for the free boundary problem via a variational approach, accounting for the singularity in the slope of the deflected string. Reactive forces exchanged between the point-mass and the string are taken into account via Lagrange...
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Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies
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Ab initio and nuclear inelastic scattering studies of Fe3Si/GaAs heterostructures
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Soft X-ray Induced Production of Neutral Fragments in High-Rydberg States at the O 1s Ionization Threshold of the Water Molecule
PublicationDissociation of water molecules after soft X-ray absorption can yield neutral fragments in high-Rydberg (HR) states. We have studied the production of such fragments by field ionization and ion time-of-flight (TOF) spectrometry. Neutral HR fragments are created at all resonances below the O 1s ionization potential (IP) and particularly within 1 eV above the O 1s IP. The latter effect is due to the recapture of the O 1s photoelectrons...
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Buried Object Characterization Using Ground Penetrating Radar Assisted by Data-Driven Surrogate-Models
PublicationThis work addresses artificial-intelligence-based buried object characterization using 3-D full-wave electromagnetic simulations of a ground penetrating radar (GPR). The task is to characterize cylindrical shape, perfectly electric conductor (PEC) object buried in various dispersive soil media, and in different positions. The main contributions of this work are (i) development of a fast and accurate data driven surrogate modeling...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublicationFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Modeling and optimization of chemical-treated torrefaction of wheat straw to improve energy density by response surface methodology
PublicationToday, torrefaction is important technique for extending the potential of biomass for improvement of energy density. The independent variables investigated for torrefaction study were temperature, retention time, acid concentration, and particle size. The experiment was designed by central composite design (CCD) method using design expert (version 11). The three dependent variables were higher heating value (HHV), energy enhancement...
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Chemical and biological characterization of Ocimum basilicum L. phenolic extract and essential oil derived through ultrasound and microwave-assisted extraction techniques
PublicationPlant-derived bioactive molecules are increasingly utilized in food processing as natural additives, driven by a growing interest in healthier lifestyles. This trend has spurred industries to reformulate products to meet the demands of health-conscious consumers. This study investigates the phenolic extract and essential oil of O. basilicum L. obtained via ultrasound-assisted extraction and microwave-assisted extraction, respectively. Characterization...
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Low-Cost Data-Driven Surrogate Modeling of Antenna Structures by Constrained Sampling
PublicationFull-wave electromagnetic (EM) analysis has become one of the major design tools for contemporary antenna structures. Although reliable, it is computationally expensive which makes automated simulation-driven antenna design (e.g., parametric optimization) difficult. This difficulty can be alleviated by utilization of fast and accurate replacement models (surrogates). Unfortunately, conventional data-driven modeling of antennas...
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Open Data Capability Architecture - An Interpretive Structural Modeling Approach
PublicationDespite 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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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublicationInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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Response of thermoluminescence dosemeters statically exposed to X-ray radiation
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High-pressure X-ray Diffraction Study of SrSi2O2N2:Eu2+
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Cross-linking of polymer films using phenol-formaldehyde resins with different functional groups
PublicationWell-know phenol-formaldehyde resins are used in the production of press-materials, glues, protective coating, mastics. They take a special place among known oligomers because the products based on them are characterized by a low cost and a series of positive properties. Aim of the work: to show the possibility to create polymeric films based on epoxy resins and modified phenol-formaldehyde resins, which contain unsaturated double...
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublicationGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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Coupled cluster and DFT calculations of 14N nuclear quadrupole coupling constants
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