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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Induced-fit binding of laccase to gold and carbon electrodes for the biological fuel cell applications
PublikacjaAnalogues of laccase natural substrates (syringic, veratric, ferulic, vanillic, isovanillic, 3,5-dimethoxybenzoic aldehydes) were employed to bind and orient laccase molecules in a way which facilitates adsorption of the catalyst molecules and their electrical connection with the conductive support. Laccase was bound efficiently to these substrates both on gold and carbon electrodes forming, respectively, 2D and 3D films sensitive...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Preparation of DNA films for studies under vacuum conditions
PublikacjaExperiments were carried out to determine the optimum conditions required for the preparation of uniform films of supercoiled plasmid DNA to be used in irradiation experiments under high vacuum conditions. Investigations reveal that significant damage to the DNA molecules occurs due to the evacuation process when films were formed from DNA samples in ultra high purity water only. A variety of bases were tested for their possible...
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Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: The example of dibenzazepine derivatives
PublikacjaIt is widely believed that the hydrophobic effect governs the binding of guest molecules to cyclodextrins (CDs). However, it is also known that high hydrophobicity of guest molecules does not always translate to the formation of stable inclusion complexes with CDs. Indeed, a plethora of other factors can play a role in the efficiency of guest–CD interactions, rendering structure-based prediction of the complexation efficiency with...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublikacjaThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Self-assembly of secondary aryl amides in cocrystals with perfluoroaryl coformers: structural analysis and synthon preferences
PublikacjaCooperation of aryl⋯perfluoroaryl stacking interactions and hydrogen bonds was utilized in the construction of six novel cocrystals of aromatic cis-amides with pentafluorobenzoic acid (pfba) and pentafluorophenol (pfp). They were obtained by crystallization from solution and structurally characterized. In four instances, the components form heterotetrameric motifs, in which amide:amide homodimer interacts symmetrically on two sides...
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Investigation of interaction between xanthene dye rhodamine B and metagenomic-derivated methylthioadenosine phosphorylase RSFP
PublikacjaIn the previous study we found that the expression of the metagenomic - derived methylthioadenosine phosphorylase gene (rsfp) in E. coli cells and the presence of rhodamine B in the growth medium were crucial for the pink fluorescence of one E. coli colony from Antarctic soil metagenomic library (Cieśliński et al., 2009). In this study, rsfp gene expression was induced by an arabinose promoter in an LMG194 E. coli strain and the...
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The Quality of the Outflow from Conventional WWTPs and Treatment Wetlands
PublikacjaUntil recently the humic substances were considered to have no negative impact on human health. Therefore elimination of these substances from potable water was only performed due to aesthetic reasons. In the recent years, however, it was found out that humic substances may cause unacceptable smell of water or cumulate toxic substances by complexing metal ions and adsorption of persistent organic pollutants such as pesticides,...
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Dissociation of 2-oxopropanoic acid by low energy electrons
PublikacjaElectron attachment to molecular target can lead to a variety of negative fragment ions. We experimentally probe the main dissociative electron attachment (DEA) channels in 2-oxopropanoic acid (CH3 - CO - COOH) - an important trace component in the Earth's atmosphere. In our studies we utilise nearly mono-energetic electrons at electron energies from 0 eV up to 15 eV.
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The nonlinear effects of sound in a liquid with relaxation losses
PublikacjaThe nonlinear effects of sound in electrolyte with a chemical reaction are examined. The dynamic equations that govern non-wave modes in the field of intense sound are derived, and acoustic forces of vortex, entropy, and relaxation modes are determined in the cases of low-frequency sound and high-frequency sound. The difference in the nonlinear effects of sound in electrolyte and in a gas with excited vibrational degrees of molecules,...
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Nano-structured Pt embedded in the acidic salts of heteropolymolybdate matrices: MS XAFS study
PublikacjaMultiple-scattering extended X-ray absorption fine structure (MS EXAFS) study combined with TEM and XRD analysis of a novel Pt-based catalyst operating at low temperature fuel cells (FCs) is presented. Innovation in the case of the considered catalyst resides in the use of a porous inorganic matrix of acidic heteropolymolybdate salts as a catalyst support. Obtained results show the relation between the matrix composition and the...
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A Goal-Oriented Error Estimator for Reduced Basis Method Modeling of Microwave Devices
PublikacjaThis letter proposes a novel a-posteriori error estimator suitable for the reduced order modeling of microwave circuits. Unlike the existing error estimators based on impedance function residuals, the new one exploits the residual error associated with the computation of the scattering matrix. The estimator can be effectively used in the Reduced Basis Method (RBM) to automatically generate reduced-order models. The results of numerical...
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Numerical Characterization of Thresholds for the Focusing 1d Nonlinear Schrödinger Equation
PublikacjaThe focusing nonlinear Schrödinger equation arises in various physical phenomena and it is therefore of interest to determine mathematical conditions on the initial data that guarantee whether the corresponding solution will blow up in finite time or exist globally in time. We focus on solutions to the mass‐supercritical nonlinear Schrödinger equation (1) in 1D case. In particular, we investigate numerical thresholds between blow...
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Analysis of Corrugated Coaxial Line with the Use of Body of Revolution and Finite Element Method
PublikacjaA combination of the body-of-revolution and finite element methods is utilized to the analysis of coaxial lines with corrugated rod and wall. Both periodic and non-periodic structures can be investigated. As the structure is axially symmetrical the two dimensional scalar-vector finite element method can be used, which allows for the investigation of complex geometries and is computationally efficient. A generalized impedance matrix...
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Effects of Ca2+, Mg2+, Na+, and K+ substitutions on the microstructure and electrical properties of GdCoO3 ceramics
PublikacjaGdCoO3-δ, Gd0.975Na0.025CoO3-δ, Gd0.98K0.02CoO3-δ, Gd0.98Ca0.02CoO3-δ, and GdCo0.99Mg0.01O3-δ ceramics were prepared via a solid-state reaction route. Among the dopants studied, substitution with Ca2+ slightly enhanced the densfication of GdCoO3 ceramics. All the lattice parameters of the doped ceramics were larger than those of pure GdCoO3-δ ceramic (a = 5.223 Å, b = 5.389 Å and c = 7.451 Å), and their cell volumes increased by...
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The influence of ammonia and selcted amines on the characteristics of calcium carbonate precipitated from calcium chloride solutions via carbonation
PublikacjaThe precipitation of calcium carbonate was carried out by passing a gasous mixture of carbon dioxide and air into a calcium chloride solution. The selected compounds enhancing carbon dioxide absorption were used as additives which promote the formation of carbonate ions in the solution. The additives were ammonia, monoethanolamine, triethylamine and triethanolamine. The resulting calcium carbonate particles varied in polymorphic...
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Intramolecular interactions in crystals of tris(2,6-diisopropylphenoxy)silanethiol and its sodium salts
PublikacjaHydrolytically stable tris(2,6-diisopropylphenoxy)silanethiol has been obtained and reacted with sodium. Solid state interactions within and between the molecules of tris(2,6-diisopropylphenoxy)silanethiol including S-H---π-interactions between the S-H unit and the π-system of the arene have been analyzed. The interactions are documented by X-ray diffraction and FT-IR spectroscopy.
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O 1s excitation and ionization processes in the CO2 molecule studied via detection of low-energy fluorescence emission
PublikacjaOxygen 1s excitation and ionization processes in the CO2 molecule have been studied with dispersed and non-dispersed fluorescence spectroscopy as well as with the vacuum ultraviolet (VUV) photon-photoion coincidence technique. The intensity of the neutral O emission line at 845 nm shows particular sensitivity to core-to-Rydberg excitations and core-valence double excitations, while shape resonances are suppressed. In contrast,...
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Effect of Semiconductor Element Substitution on the Electric Properties of Barium Titanate Ceramics
PublikacjaThe investigated ceramics were prepared by a solid-state reaction from simple oxides and carbonates with the use of a mixed oxide method (MOM). The morphology of BaTi0.96Si0.04O3 (BTSi04) ceramics was characterised by means of a scanning electron microscopy (SEM). It was found that Si+4 ion substitution supported the grain growth process in BT-based ceramics. The EDS results confirmed the high purity and expected quantitative composition...
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Copper(II) complexes with substituted imidazole and chlorido ligands: X-ray, UV-Vis, magnetic and EPR studies and chemotherapeutic potential
PublikacjaCrystal structures, UV-Vis and EPR spectra and magnetic properties of four copper(II) complexes with chloride anions and 4-methylimidazole, 2-ethylimidazole, 2-isopropylimidazole or 2-ethyl-4-methylimidazole are described. In the solid state three of the complexes are mononuclear and one complex with 2-ethylimidazole is binuclear with bridging chlorido ions. UV-Vis spectra of the methanolic solutions of the complexes show LMCT...
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The Issue of Shading Photovoltaic Installation Caused by Dust Accumulation on the Glass Surface
PublikacjaThe issue of accumulation of dust and other pollutants on the surface of photovoltaic modules was thoroughly analysed over the years. One of the first surveys in this field of knowledge linked pollutant accumulation on the module surface with transmittance loss of its glass covering, which leads to lessened amount of solar radiation reaching solar cells. First stage of this accumulation process is linear transparency loss, and second...
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Membrane technologies assisting plant-based and agro-food by-products processing: A comprehensive review
PublikacjaBackground Nowadays, membrane-based technologies (e.g. microfiltration, ultrafiltration, nanofiltration, membrane distillation, and pervaporation) have demonstrated to meet the requirements to be involved in different food and bioproduct processes. Scope and approach Several applications have been developed, including either separation, recovery or concentration of bioactive molecules from agro-food products and by-products,...
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Gas selectivity enhancement by sampling-and-hold method in resistive gas sensors
PublikacjaCommercial resistive gas sensors exhibit various sensitivity to numerous gases when working at different elevated temperatures. That effect is due to a change in velocity of adsorption and desorption processes which can be modulated by temperature. Thus, to reach better selectivity of gas detection, we propose to apply a known method (called the sampling-and-hold method) of cooling down the gas sensor in the presence of the investigated...
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Design of Microwave Lossy Filter Based on Substrate Integrated Waveguide (SIW)
PublikacjaIn this letter, we propose a lossy three-pole Chebyshev filter centered at 5.15 GHz, based on the substrate integrated waveguide (SIW) with scattering characteristics shifted down by 5.68 dB. The filter is composed of three directly coupled SIW cavities with three lossy couplings between nonadjacent resonators. These additional couplings are realized using mixed coupled slot and microstrip lines connected with metal electrode leadless...
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Raman spectroscopic investigation of blood and related materials
PublikacjaThis paper reports preliminary studies on use of Raman spectroscopy for investigation of blood. High quality blood spectra were recorded in-vitro with excitation wavelengths of 830 nm. Because of complex composition of the blood as well as by light attenuation and scattering in the tissues, spectra set up from wide, low-intensive Raman bands and intensive optical background. To get information about origin of bands in Raman spectra...
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Porous Phantoms Mimicking Tissues – Investigation of Optical Parameter Stability Over Time
PublikacjaIn terms of optical parameters, optical phantoms can now replace live tissues and be used to validate optical measurement methods. Therefore, whether these parameters would be maintained after storage for 6 months was examined. The absorption and scattering coefficients were obtained from the measured transmittance and reflectance measurements taken 6 months apart and then compared. All of the measurements were conducted using...
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Efficient Finite Element Analysis of Axially Symmetrical Waveguides and Waveguide Discontinuities
PublikacjaA combination of the body-of-revolution and finite element methods is adopted for full-wave analysis of waveguides and waveguide discontinuities involving angular field variation. Such an approach is highly efficient and much more flexible than analytical techniques. The method is performed in two different cases: utilizing a generalized impedance matrix to determine the scattering parameters of a single waveguide section and utilizing...
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[N,N'-Bis(2,6-diisopropylphenyl)pentane-2,4-diamine(1-)-2[kappa]2N,N']-[mu]2-chlorido-1:2[kappa]2Cl:Cl-chlorido-2[kappa]Cl-bis(1,2-dimethoxyethane-1[kappa]2O,O')iron(II)lithium
PublikacjaIn the title compound, [FeLi(C29H41N2)Cl2(C4H10O2)2], theFeII atom is coordinated by two N and two Cl atoms,generating a distorted FeN2Cl2 tetrahedral geometry. Additionally,one of the chloride atoms bridges to a lithium ion,which is solvated by two dimethoxyethane molecules and iscoordinated in a distorted trigonal-bipyramidal environment.The central Fe, Cl (*2) and Li atoms are coplanar with amaximum deviation of 0.034 A ° .
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Effect of Cyclodextrins on Coupling of o-Ethoxybenzenediazonium Salt with Pyrrole, Imidazole and 2-Methylimidazole
PublikacjaThe effect of b-cyclodextrin on o-ethoxybenzenediazonium salt coupling with pyrrole, imidazole and 2-methylimidazole has been studied. The differences in the reaction course, the overall yield and products distribution have been analyzed. Experiments without cyclodextrins and selected reactions with a- and c-cyclodextrins have been performed for comparison. The results are discussed in terms of co-conformation of azole molecules...
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Optical Coherence Tomography for nanoparticles quantitative characterization
PublikacjaThe unique features of nanocomposite materials depend on the type and size of nanoparticles, as well as their placement in the composite matrices. Therefore the nanocomposites manufacturing process requires inline control over certain parameters of nanoparticles such as dispersion and concentration. Keeping track of nanoparticles parameters inside a matrix is currently a difficult task due to lack of a fast, reliable and cost effective...
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Optical properties of the chemotherapy drugs used in the central nervous system lymphoma therapy: monitoring drug delivery
PublikacjaOur aim is to optically monitor the delivery of the chemotherapy drugs for brain tumours, particularly used in the central nervous system (CNS) lymphoma therapy. In vivo monitoring would help to optimize the treatment and avoiding unnecessary medications. Moreover, it would be beneficial to be able to measure which of the multi-regimen drugs actually do penetrate and how well into the brain tissue. There exist several potential...
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Inverse Nonlinear Eigenvalue Problem Framework for the Synthesis of Coupled-Resonator Filters With Nonresonant Nodes and Arbitrary Frequency-Variant Reactive Couplings
PublikacjaA novel, general circuit-level description of coupledresonator microwave filters is introduced in this article. Unlike well-established coupling-matrix models based on frequency-invariant couplings or linear frequency-variant couplings (LFVCs), a model with arbitrary reactive frequencyvariant coupling (AFVC) networks is proposed. The engineered formulation is more general than prior-art ones—with the only restriction that the coupling...
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Supervised-learning-based development of multi-bit RCS-reduced coding metasurfaces
PublikacjaCoding metasurfaces have been introduced as efficient tools allowing meticulous control over the electromagnetic (EM) scattering. One of their relevant application areas is radar cross section (RCS) reduction, which principally relies on the diffusion of impinging EM waves. Despite its significance, careful control of the scattering properties poses a serious challenge at the level of practical realization. This article is concerned...
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Standard and modified falling mass impact tests on preplaced aggregatefibrous concrete and slurry infiltrated fibrous concrete
PublikacjaAlthough several studies have been conducted to evaluate the impact response of concrete using theAmerican Concrete Institute (ACI) 544-2R falling mass impact test, the variations in test results are themain drawback of this testing method. This study aims to reduce the variations in experimental impacttest results by introducing two simple test setup modifications; (1) using coarse or fine aggregate bed-ding as an alternative...
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Charge density wave and crystalline electric field effects in TmNiC2
PublikacjaSingle crystals of TmNiC2 were grown by the optical floating-zone technique and were investigated by x-ray diffraction (XRD), thermal expansion, electrical resistivity, specific heat, and magnetic susceptibility measurements. Single-crystal XRD reveals the formation of a commensurate charge density wave (CDW) characterized by a CDW modulation vector q2c = (0.5, 0.5, 0.5), which is accompanied by a symmetry change from the orthorhombic...
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Lipopolysaccharides: regulated biosynthesis and structural diversity
PublikacjaThe cell envelope of Gram-negative bacteria contains two distinct membranes, an inner (IM) and an outer (OM) membrane, separated by the periplasm, a hydrophilic compartment that includes a thin layer of peptidoglycan. The most distinguishing feature of such bacteria is the presence of an asymmetric OM with phospholipids located in the inner leaflet and lipopolysaccharides (LPSs) facing the outer leaflet. The maintenance of this...
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ThreSpect – A Program for the Determination of the Appearance Energies of Neutral and Ionized Species
PublikacjaCollisions of photons and charged particles with molecules lead to their excitation, ionization, and dissociation into neutral and ionized fragments. Accurately determining thresholds of the formation of particular products plays a vital role in analyzing processes occurring during these interactions. Therefore, we present a computer program, “ThreSpect,” that allows calculating threshold energies of various species generated in...
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Structural, magnetic and spectral properties of tetrahedral cobalt(II) silanethiolates: a variety of structures and manifestation of field-induced slow magnetic relaxation
PublikacjaBlue crystals of five heteroleptic cobalt(II) silanethiolates 1–5 have been obtained by the reaction of [Co{SSi (tBuO)3}2(NH3)]2 with aminopyridines and aminomethylpyridines at an appropriate molar ratio and their structural, spectral, thermal and magnetic properties have been established and described. All complexes 1–5 contain Co(II) ions in a tetrahedral CoN2S2 environment formed by (tBuO)3SiS− residues and pyridines and present...
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Treatment of bitumen post oxidative effluents by sulfate radicals based advanced oxidation processes (S-AOPs) under alkaline pH conditions
PublikacjaSulfate radicals based Advanced Oxidation Processes (S-AOPs), namely Persulfate and peroxymonosulfate, were used for the treatment of post oxidative effluents from a production of petroleum bitumens under alkaline pH. Studies on the identification and monitoring of the volatile organic compounds (VOCs) along with COD, BOD and sulfide ions reduction were performed. Persulfate with a ratio between the oxygen from the oxidant and...
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Synthesis and physical properties of the 10.6 K ferromagnet NdIr3
PublikacjaThe magnetic, transport, and thermodynamic properties of NdIr3 are reported. Its PuNi3-type crystal structure (space group R−3m), with lattice parameters a= 5.3262(1)Å and c=26.2218(3)Å, was confirmed by powder x-ray diffraction. Our measurements indicate that NdIr3 exhibits a previously unreported paramagnetic to ferromagnetic phase transition below TC=10.6 K(determined by using the Arrott plot). The magnetic susceptibility obeys...
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Synthesis, Structure, and Spectroscopic Properties of Calcium Thiophenecarboxylate Polymers. Structural Comparison with Analogous Lead Complexes
PublikacjaThree novel calcium coordination polymers [Ca(2tpCOO)2(2mpa)(H2O)]n (1), [Ca(3tpCOO)2(2mpa)(H2O)]n (2), and {[Ca(3tpacCOO)2(H2O)2]⋅⋅⋅H2O}n (3) (2tpCOO− or 3tpCOO− – thiophene-2- or thiophene-3-carboxylate, 3tpacCOO− – thiophene-3-acetate, 2mpa – 2-methylpropanal), were synthesised using a self-assembly method. The obtained polymers were characterised using SC-XRD, FTIR, UV-Vis DRS, thermogravimetric and luminescence analyses. The...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublikacjaAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Energy conversion in systems-contained laser irradiated metallic nanoparticles - comparison of results from analytical solutions and numerical methods
PublikacjaThis work introduces the theoretical method of metallic nanoparticles’ (NPs’) heat and mass transfer where the particles are coated on a surface (base), together with considering the case wherein nanoparticles move freely in a pipe. In order to simulate the heat transfer, energy and radiative transfer equations are adjusted to the considered issue. NPs’ properties are determined following the nanofluidic theories, whereas absorption...
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Functionalization of Parylene During Its Chemical Vapor Deposition
PublikacjaTwo possible mechanisms for the reaction of four halogenated (metha)acrylate-based molecules with Parylene [poly (paraxylylene)] during its chemical vapor deposition were proposed. The chemical reactivity of acrylate double bond with the paraxylylene biradical was calculated for all four (metha)acrylate-based molecules. These calculations allowed the evaluation of the energetically favorable mechanism and indeed a direct correlation...
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Preparation and characterization of asphaltene based adsorbents for gas-solid adsorption systems
PublikacjaThe dissertation presents results of the experimental research on asphaltene-based adsorbents (support coated with asphaltene layer) for gas-solid adsorption systems, with special reference to volatile organic compounds (VOCs) removal from gas streams. Analysis of gas adsorption properties revealed that asphaltenes isolated from oxidized bitumen have strong affinity toward VOCs. Interactions with target gas molecules, and selectivity...
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Aryl and N-arylamide carbon nanotubes for electrical coupling of laccase to electrodes in biofuel cells and biobatteries
PublikacjaSingle walled carbon nanotubes (SWCNTs) were equipped with aryl residues by chemical reactions. These insoluble materials were used to substitute classical soluble mediators, which help to transfer electrical charge between the conducting electrode and the redox active center of enzyme molecules. The effect of different aryl residues on the efficiency of the catalytic reduction of dioxygen in the presence of laccase was systematically...
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Numerical simulation of cold flow and combustion in a swirl stabilized combustor
PublikacjaA numerical simulation model was developed to investigate the cold flow and combustion using Ansys FLUENT 2021R1. The governing equations were solved using the pressure-based method, and pressure–velocity coupling was performed using the SIMPLE method. To model the turbulent process, the RSM model was used. Non-premixed model is chosen to solve the chemical kinetics between fuel and oxigen. Radiation heat transfer was calculated...
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Poly(hydroxybutyrate-co-hydroxyvalerate) as a biodegradable binder in a negative electrode material for lithium-ion batteries
PublikacjaIn this work, graphite-based negative electrode for lithium-ion battery consisting a novel and biodegradable binder poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) is compared with standard graphite electrode with polyvinylidene fluoride (PVDF) as a binder. The rate and cycling performance of lithium ion insertion/extraction of electrodes with PHBV in a half-cell configuration are evaluated. Moreover, on the basis of the electrochemical...