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Search results for: atomic and molecular physics
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A Wideband Channel Model for Body Area Networks in Circular Metallic Indoor Environments
PublicationIn this paper, the wideband characterization of the propagation channel in circular metallic indoor environments is addressed, regarding Body Area Networks and 5G small cells, an analytical model for the dependence of the mean delay and the average delay spread on the circle radius, the working frequency and the distance between the transmitter and the receiver being proposed. The derivation of the model is initially done analytically,...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublicationThe design of a database for positron interactions with biomolecular systems is outlined. The database contains only scattering cross sections, which are derived from theory. The data model is defined in a very flexible way, which facilitates the usage of weakly bound clusters of molecules and molecular systems with many tautomeric forms.
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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Reactions of cobalt(ii) chloride and cobalt(ii) acetate with hemisalen-type ligands: ligand transformation, oxidation of cobalt and complex formation. Preliminary study on the cytotoxicity of Co(ii) and Co(iii) hemisalen complexes
PublicationSeveral molecular cobalt(II) complexes, one Co(II) coordination polymer, and one ionic cobalt(III) complex with imine hemisalen ligands were synthesized. The hemisalen ligands were synthesized from o-vanillin (oVP) and diverse aminopyridines (compounds HL1–HL4) or aminophenol (compound HL5). It was observed that cobalt(II) chloride in dry acetonitrile catalyzes a transformation of HL1 and HL3 instead of complex formation. The conversion...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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The role of bile salts in digestion
PublicationBile salts (BS) are bio-surfactants present in the gastrointestinal tract (GIT) that play a crucial role in the digestion and absorption of nutrients. The importance of BS for controlled release and transport of lipid soluble nutrients and drugs has recently stimulated scientific interest in these physiological compounds. BS are so-called facial amphiphiles showing a molecular structure that is very distinct from classical surfactants....
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Effects of solution composition and electrophoretic deposition voltage on various properties of nanohydroxyapatite coatings on the Ti13Zr13Nb alloy
PublicationThe purpose of the research was to establish the influence of the solution composition and the electrophoretic deposition voltage on the coating homogeneity and thickness, nanohardness, adhesion, corrosion resistance and wettability. The Ti13Zr13Nb alloy was coated by the electrophoretic technique with hydroxyapatite in a solution containing 0.1, 0.2 or 0.5 g nanoHAp in 100 mL of suspension and at voltage 15, 30 or 50 V. The scanning...
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Second-order Stark effect and polarizability of a relativistic two-dimensional hydrogenlike atom in the ground state
PublicationThe second-order Stark effect for a planar Dirac one-electron atom in the ground state is analyzed within the framework of the Rayleigh-Schrödinger perturbation theory, with the use of the Sturmian series expansion of the generalized Dirac-Coulomb Green's function. A closed-form analytical expression for the static dipole polarizability of that system is found. The formula involves the generalized hypergeometric function ${}_{3}F_{2}$...
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Structure and optical parameters of Eu doped tellurium oxide thin films prepared by reactive magnetron sputtering method
PublicationIn this work the structural properties and photoluminescence of tellurium dioxide thin films doped by europium were described. Thin films were deposited by magnetron sputtering method and simultaneously heated at 200 °C. Presence of Eu ions and their valence states was confirmed by X-ray photoemission spectroscopy measurements. The structure of the films as well as the influence of europium dopant on crystalline structure of the...
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Coordination complexes of Mn(II), Co(II), Ni(II), Zn(II) and Cd(II) with histaminol – Crystal structures and formation constants in aqueous solution
PublicationStability constants were determined for a series of coordination complexes of Mn(II), Co(II), Ni(II), Zn(II) and Cd(II) with histaminol in aqueous solution. The tendency of histaminol to form chelate complexes has been confirmed by the isolation of several complex species in the monocrystalline form and determination of their molecular structures.
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Synthetic strategies in construction of organic macromolecular carrier–drug conjugates
PublicationMany metabolic inhibitors, considered potential antimicrobial or anticancer drug candidates, exhibit verylimited ability to cross the biological membranes of target cells. The restricted cellular penetration ofthose molecules is often due to their highhydrophilicity. One of the possible solutions to this problem is aconjugation of an inhibitor with a molecular organic nanocarrier. The conjugate thus formed should beable to penetrate...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Structure-rheology relationship of fully bio-based linear polyester polyols for polyurethanes - Synthesis and investigation
PublicationThe synthesis of polyols from renewable substances as an alternative for petrochemical-based polyols play important matter in the polyurethane industry. In this work, the fully bio-based linear polyester polyols with different catalyst amounts were synthesized via two-step polycondensation method. The effect of various catalyst content on the structure and rheological behavior were established. Fourier Transform Infrared Spectroscopy,...
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Evaluation of Three Peptide Immobilization Techniques on a QCM Surface Related to Acetaldehyde Responses in the Gas Phase
PublicationThe quartz-crystal microbalance is a sensitive and universal tool for measuring concentrations of various gases in the air. Biochemical functionalization of the QCM electrode allows a label-free detection of specific molecular interactions with high sensitivity and specificity. In addition, it enables a real-time determination of its kinetic rates and affinity constants. This makes QCM a versatile bioanalytical screening tool for...
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Progress in non-isocyanate polyurethanes synthesized from cyclic carbonate intermediates and di- or polyamines in the context of structure–properties relationship and from an environmental point of view
PublicationCommercially, polyurethanes are produced by the reaction of diisocyanates, polyols (polyester or polyether) and low molecular weight chain extender. Toxicity, moisture sensitivity and phosgene-based synthesis of diisocyanates resulted in investigations focused on obtaining the non-isocyanate polyurethanes (NIPUs). This work presents the review of synthesis and structure–properties relationship of non-isocyanate polyurethanes obtained...
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Optical photoluminescent, and electroluminescent properties of organic solids
PublicationThis chapter discusses optical, photoluminescence and electroluminescence properties of organic materials. First, the spectral features of individual molecules and molecular solid states are analysed. Next, the excitonic processes in organic materials are discussed. The chapter reviews experimental methods leading to the determination of basic excitonic parameters. Finally, the electroluminescence phenomena in organic materials...
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Rzeczywistość rozszerzona – potencjał w kształceniu (przyszłych) pomorskich inżynierów
PublicationEdukacja młodzieży w zakresie nauk eksperymentalnych – takich jak chemia i fizyka – stanowi obecnie w obliczu ograniczeń zaplecza dydaktycznego w szkołach ogromne wyzwanie. Placówki edukacyjne nie posiadają często odpowiednich laboratoriów, lecz dysponują pracowniami komputerowymi. W ramach Projektu EDUAR, współfinansowanego przez NCBiR, przeprowadzono badania w 20 szkołach – po 10 z obszarów wiejskich i miejskich, podczas których...
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Electronic structure of intertwined kagome, honeycomb, and triangular sublattices of the intermetallics MCo2Al9 ( M = Sr, Ba)
PublicationIntermetallics are an important playground to stabilize a large variety of physical phenomena, arising from their complex crystal structure. The ease of their chemical tunabilty makes them suitable platforms to realize targeted electronic properties starting from the symmetries hidden in their unit cell. Here, we investigate the family of the recently discovered intermetallics MCo2Al9 (M=Sr, Ba) and we unveil their electronic structure....
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Ab initio and density functional theory calculations of proton affinities for volatile organic compounds
PublicationThe Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets and the density function theory-B3LYP have been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for volatile organic compounds. Calculated values of proton affinities are compared with experimental data.
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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Nitrogen-Doped Diamond Film for Optical Investigation of Hemoglobin Concentration
PublicationIn this work we present the fabrication and characterization of a diamond film which can be utilized in the construction of optical sensors for the investigation of biological samples. We produced a nitrogen-doped diamond (NDD) film using a microwave plasma enhanced chemical vapor deposition (MWPECVD) system. The NDD film was investigated with the use of scanning electron microscopy (SEM), atomic force microscopy (AFM) and Raman...
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New plasmonic platform for enhanced luminescence of Valrubicin
PublicationLuminescence enhanced by new structure of plasmonic platform with aluminum oxide (Al2O3) buffer layer deposited on gold nanostructures is investigated. Regularly distributed gold nanostructures of average dimension of 50 nm formed the active part of plasmonic platforms. They were manufactured on Corning 1737 glass substrate by melting of gold thin film. The nanostructures were coated by dielectric Al2O3 thin film with thickness...
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Synthesis, structure and properties of novel poly(hydroxyurethane)s obtained by non-isocyanate route
PublicationNon-isocyanate polyurethanes (NIPUs) can be synthesized by polyaddition of five-membered bis(cyclic carbonate)s and primary diamines. NIPUs are an alternative for the commonly used (in the form of foams, elastomers, coatings or fibers) in the industry polyurethanes obtained using toxic and moisture sensitive diisocyanates, polyols and low-molecular weight chain extenders. The main aim of this work was to synthesize non-isocyanate...
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In-Reactor Polypropylene Functionalization─The Influence of Catalyst Structures and Reaction Conditions on the Catalytic Performance
PublicationTo unravel the relationship between silylene-bridged metallocene catalyst structures and polymerization conditions and their effect on the performance in in-reactor functionalization of polypropylene, the behaviors of rac-Me2Si(2-Me-4-Ph-Ind)2ZrCl2/MMAO, rac-Me2Si(Ind)2ZrCl2, rac-Me2Si(2-Me-4-Ph-Ind)2HfCl2, and rac-Me2Si(Ind)2HfCl2 in propylene/aluminum alkyl-passivated 10-undecen-1-ol copolymerization were compared. Kinetic analysis...
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Nonconventional 1,8-Diazafluoren-9-One Aggregates for Green Light Enhancement in Hybrid Biocompatible Media
PublicationOrganic aggregates currently play a prominent role, mainly for their unique optoelectronic properties in the aggregated state. Such properties can be related to the aggregates’ structure and the molecular packing mode. In the literature, we have well-established models of H and J aggregates defined based on the molecular exciton model. However, unconventional aggregates, the most unrecognized forms, have been generating interest...
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Structure versus hydrolytic and thermal stability of bio-based thermoplastic polyurethane elastomers composed of hard and soft building blocks with high content of green carbon
PublicationNowadays, sustainability plays a key role in the design and synthesis of new materials. One of the methods for the preparation of green materials is incorporation into their structure the monomers with a high content of green carbon. Therefore, the aim of this work was to investigate the influence of the type and molecular mass of two bio-based polyester polyols and bio-glycol on the properties of aliphatic partially bio-based...
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Fibrillar aggregates in powdered milk
PublicationThis research paper addresses the hypothesis that powdered milk may contain amyloid fibrils. Amyloids are fibrillar aggregates of proteins. Up to this time, research on the presence of amyloids in food products are scarce. To check the hypothesis we performed thioflavin T fluorescence assay, X-ray powder diffraction, atomic force microscopy and fluorescence microscopy imaging. Our preliminary results show that commercially available...
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Optimization of the femtosecond laser impulse for excitation and the Spin-Orbit mediated dissociation in the NaRb Dimer
PublicationWe study the dynamics of multiple coupled states under the influence of an arbitrary time-dependent external field to investigate the femtosecond laser-driven excitation and the spin-orbit mediated dissociation in the NaRb dimer. In this process, the dimer is excited from the ground triplet state 1^3Sigma+ to the 1^3Pi state using the femtosecond laser impulse and the spin-orbit coupling between the 1^3Pi and 2^1Sigma+ states results...
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Nonlinear and linear impedance of bismuth vanadate ceramics and its relation to structural properties
PublicationThe nonlinear and linear electrical properties, topography, and microstructure of bismuth-vanadate ceramics, were studied. The structurewas observed with the use of X-ray diffraction (XRD), scanning electronmicroscopy (SEM), atomic force microscopy (AFM) and confocal microscopy methods. The obtained results showed that ceramic is porous. Two phase transitionswere determinedwith the use of DSC measurements. The linear and nonlinear ac...
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Evaluation of adhesive forces and the specific surface energy of zirconia stabilized by yttria with alumina additions ceramic by AFM method
PublicationThe adhesive forces and the specific surface energy of ceramic material surfaces are very important for further tribological and biomedical applications of ceramics. Partially stabilized zirconia (zirconium oxide) is popular for manufacturing various medical products. ZrO2 stabilized by Y2O3 with additions of 5 wt% alumina was produced by slip casting method with a subsequent sintering. Structure and chemical composition of ceramic...
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Application of titanium dioxide thin films in fiber optic sensors
PublicationThe advance in the nanotechnology and fabrication of micro- and nanostructures has significant impact on development of new optical sensors. Presented study focuses on the applications of the titanium dioxide (TiO2) thin films in fiber optic sensors. The concept of a sensing fiber optic interferometer integrating TiO2 thin film is presented. The cavity of this interferometer is delimited by a 80 nm film fabricated on the end-face...
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Yields and Time-of-Flight Spectra of Neutral High-Rydberg Fragments at the K Edges of the CO2 Molecule
PublicationWe have studied the production of neutral fragments in high-Rydberg (HR) states at the C 1s and O 1s edges of the CO2 molecule by performing two kinds of experiments. First, the yields of neutral HR fragments were measured indirectly by ionizing such fragments in a static electric field and by collecting resulting singly charged positive ions as a function of the photon energy. Such measurements reveal not only excitations below...
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Influence of electropolymerization conditions on the morphological and electrical properties of PEDOT film
PublicationIn this work the effects of electropolymerization conditions on the morphological properties and conductivity of poly(3,4-ethylenedioxythiophene) (PEDOT) film have been studied. PEDOT films were electrochemically synthesized in a one step process from acetonitrile solution containing 3,4-ethylenedioxythiophene (EDOT) and lithium perchlorate. Based on atomic force microscopy, scanning electron microscopy, cyclic voltammetry and...
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ZnO ALD-Coated Microsphere-Based Sensors for Temperature Measurements
PublicationIn this paper, the application of a microsphere-based fiber-optic sensor with a 200 nm zinc oxide (ZnO) coating, deposited by the Atomic Layer Deposition (ALD) method, for temperature measurements between 100 and 300°C, is presented. The main advantage of integrating a fiber-optic microsphere with a sensing device is the possibility of monitoring the integrity of the sensor head in real-time, which allows for higher accuracy during...
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Properties of Barium Cerate-Zirconate Thin Films
PublicationIn this work, we review several experimental results showing the electrical properties of barium cerate-zirconate thin films and discuss them in view of the possible influence of various factors on their properties. Most of the presented Ba(Ce, Zr, Y)O3 thin films were formed by the pulsed laser deposition (PLD) technique, however thin films prepared using other methods, like RF magnetron sputtering, electron-beam deposition, powder...
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Integration of Fluorescent, NV-Rich Nanodiamond Particles with AFM Cantilevers by Focused Ion Beam for Hybrid Optical and Micromechanical Devices
PublicationIn this paper, a novel fabrication technology of atomic force microscopy (AFM) probes integrating cantilever tips with an NV-rich diamond particle is presented. Nanomanipulation techniques combined with the focused electron beam-induced deposition (FEBID) procedure were applied to position the NV-rich diamond particle on an AFM cantilever tip. Ultrasonic treatment of nanodiamond suspension was applied to reduce the size of diamond...
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Microsphere structure application for supercapacitor in situ temperature monitoring
PublicationConstant, real-time temperature monitoring of the supercapacitors for efficient energy usage is in high demand and seems to be crucial for further development of those elements. A fiber-optic sensor can be an effective optoelectronic device dedicated for in-situ temperature monitoring of supercapacitors. In this work, the application of the fiber-optic microstrucutre with thin zinc oxide (ZnO) coating fabricated in the atomic layer...
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Non-destructive Testing of Wooden Elements
PublicationExamining the condition of wooden elements is crucial from the perspective of proper structure performance. If the deterioration in the internal wood condition, which displays no symptoms visible from the outside, is detected, the further spread of the deterioration can be prevented. Test results often point to the necessity of conducting repairs and, renovations, replacing the structure of wooden beams, or even substituting a...
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Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment)
PublicationThe molecular-typing strategy, ERIC-PCR was used in an attempt to determine the genomic relationship of 28 P. aeruginosa strains isolated from faeces of healthy bovine, bovine mastitis and from faeces of hospital patients as well as from environment. ERIC-PCR fingerprinting revealed large molecular differentiation within this group of isolates. Twenty two out of 28 strains tested generated unique patterns of DNA bands and only...
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The influence of polypropylene-block/graft-polycaprolactone copolymers on melt rheology, morphology, and dielectric properties of polypropylene/polycarbonate blends
PublicationThe paper discusses the relationship between rheology and morphology of immiscible polypropylene (matrix))/polycarbonate (dispersed phase) blends compatibilized with novel polypropylene-polycaprolactone block and graft copolymers. Transmission electron microscopy (TEM) experiments revealed uniform droplet morphologies and a reduction of the average size of the dispersed phase upon addition of the compatibilizer. The results suggested...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublicationWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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Development of Safirinium dyes for new applications: fluorescent staining of bacteria, human kidney cells, and the horny layer of the epidermis
PublicationLow-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...