Search results for: NON-EQUILIBRIUM MOLECULAR DYNAMICS
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π-Conjugated Donor-acceptor Polyelectrolytes: Toward Artificial Photosynthesis
PublicationGreat advances have been made in the development of conjugated polyelectrolytes (CPEs), which provide tunable properties including water solubility and processability, main-chain exciton and charge transport, variable energy light absorption and fluorescence, non-covalent interactions, and formation of tertiary structures via self-assembly.[1] These characteristics allow CPEs to be considered for use in various optoelectronic applications,...
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Latest Insights on Novel Deep Eutectic Solvents (DES) for Sustainable Extraction of Phenolic Compounds from Natural Sources
PublicationPhenolic compounds have long been of great importance in the pharmaceutical, food, and cosmetic industries. Unfortunately, conventional extraction procedures have a high cost and are time consuming, and the solvents used can represent a safety risk for operators, consumers, and the environment. Deep eutectic solvents (DESs) are green alternatives for extraction processes, given their low or non-toxicity, biodegradability, and reusability....
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Robust asymptotic super twisting sliding mode observer for non-linear uncertain biochemical systems
PublicationThe problem of state estimation (reconstruction of the state vector) for a given class of biochemical systems under uncertain system dynamics has been addressed in this paper. In detail, the bioreactor at a water resource recovery facility represents the considered biochemical systems. The biochemical processes taking place in the bioreactor have been modelled using an activated sludge model. Based on this model, an appropriate...
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral 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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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Thermophysical study of the binary mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide – Experimental and theoretical approach
PublicationDensities at (293.15, 298.15, 303.15 and 308.15) K, and viscosities and ultrasonic velocities at 298.15 K of binary liquid mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide have been measured over the entire range of composition at p = 0.1 MPa. From the experimental data, values of excess molar volume, excess isentropic compressibility, viscosity deviation and excess Gibbs energy...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Dynamical description of quantum computing: generic nonlocality of quantumnoise
PublicationWe develop a dynamical non-Markovian description of quantum computing in the weak-coupling limit, in the lowest-order approximation. We show that the long-range memory of the quantum reservoir (such as the 1/t4 one exhibited by electromagnetic vacuum) produces a strong interrelation between the structure of noise and the quantum algorithm, implying nonlocal attacks of noise. This shows that the implicit assumption of quantum error...
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Spontaneous electron emission vs dissociation in internally hot silver dimer anions
PublicationReferring to a recent experiment, we theoretically study the process of a two-channel decay of the diatomic silver anion (Ag2-), namely the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag. The ground state potential energy curves of the silver molecules of diatomic neutral and negative ion were calculated using proper pseudo-potentials and atomic basis sets. We also estimated the non-adiabatic...
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Footbridges. Dynamic Design – Selected Problems
PublicationModern footbridges create challenge in esthetic and structural design. Breaking the proven canons is a recipe for architectural success. However esthetic form has to be also a functional pedestrian bridge. Therefore a good FEM modeling is a key element in engineering part of design. The paper presents selected problems related to the modeling of the dynamic construction of footbridges. Several basic dynamic problems concerning...
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublicationThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublicationThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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A non-adiabatic wavepacket dynamical study of the low energy chargetransfer process in the S3+ + H collision
PublicationThe collisional system S3+ + H?S2+ + H+ has been studied using a time-dependent wavepacket methodologyin two-dimensions. Using available potential energy surfaces and coupling matrix elementsobtained from multireference ab initio calculations, five non-adiabatically coupled electronic states of1P symmetry have been included in the dynamical simulations. The collision has been studied in thelow energy regime of 1-10 eV. The wavepacket...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation
PublicationThe 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Bio‑derived polyurethanes obtained by non‑isocyanate route using polyol‑based bis(cyclic carbonate)s—studies on thermal decomposition behavior
PublicationNon-isocyanate polyurethanes (NIPUs) constitute one of the most prospective groups of eco-friendly materials based on their phosgene-free synthesis pathway. Moreover, one of the steps of their obtaining includes the use of carbon dioxide (CO 2 ), which allows for the promotion of the development of carbon dioxide capture and storage technologies. In this work, non- isocyanate polyurethanes were obtained via three-step synthesis...
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Seashore sediment and water chemistry at the Admiralty Bay (King George Island, Maritime Antarctica) – geochemical analysis and correlations between the concentrations of chemical species
PublicationThis study covers water and sediment chemical characteristics by the western shore of Admiralty Bay (King George Island, Antarctica) in 2016. Chemical processes between sediment and water have been described based on the determination of ions, metals, non-metals, and TOC concentrations. Rock weathering is an important source of Fe, Ni, Co, Al in the seashore area. The PCA shows the impact of acidification in the release metals...
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One-dimensional chaos in a system with dry friction: analytical approach
PublicationWe introduce a new analytical method, which allows to find chaotic regimes in non-smooth dynamical systems. A simple mechanical system consisting of a mass and a dry friction element is considered. The corresponding mathematical model is being studied. We show that the considered dynamical system is a skew product over a piecewise smooth mapping of a segment (the so-called base map). For this base map we demonstrate existence of...
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Influence and development of new kinematic systems in flat surface lapping
PublicationThe face grinding and lapping technology is widely used in the field of the precise and ultraprecise manufacturing. It has become an indispensable technology in the manufacture of many parts. An absence of material restrictions allows machining both metal and non-metallic materials, including technical ceramics [1]. Nowadays there are mainly two kinematic systems in lapping machines [2]. The machining plane-parallel surfaces is...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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Deep eutectic solvents – Ideal solution for clean air or hidden danger?
PublicationThe industrial sector is one of the fastest-growing sources of greenhouse gases, due to its excessive energy consumption to meet the rapidly growing demand for energy-intensive products. The use of deep eutectic solvents (DESs) has been studied extensively in order to cope with these harmful gases, but their usage can be an issue in respect to ecological reasons. Do deep eutectic solvents harm the atmosphere? Yes, these solvents...
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Experimental and theoretical solubility advantage screening of bi-component solid curcumin formulations
PublicationA comprehensive experimental and theoretical screening was performed for identification of curcumin solubilizers. Experimental data led to formulation of a non-linear QSPR model correlating molecular descriptors with measured solubilities. The majority of synthesized binary systems exhibited a moderate enhancement of curcumin solubility, which was found to be the highest in the case of curcumin cocrystallized with pyrogallol. New...
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Perspectives on the replacement of harmful organic solvents in analytical methodologies: a framework toward the implementation of a generation of eco-friendly alternatives
PublicationVolatile organic solvents derived from non-renewable fossil feedstocks are commonplace in analytical laboratories. In spite of their convenient performance in countless unit operations, their environmental, health and safety issues represent a major area of concern. The progressive replacement of organic solvents obtained from fossil resources by eco-friendly alternatives would involve remarkable advances within the framework of...
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Synteza, struktura chemiczna i właściwości bezizocyjanianowych poliuretanów otrzymywanych z wykorzystaniem CO2 oraz surowców pochodzenia naturalnego.
PublicationZ uwagi na wciąż rosnącą świadomość proekologiczną, politykę zrównoważonego rozwoju, a także nurt zielonej chemii wiodącym trendem w przemyśle tworzyw sztucznych jest poszukiwanie alternatywnych metod otrzymywania materiałów polimerowych. Komercyjnie poliuretany otrzymywane są w wyniku reakcji poliaddycji di- lub poliizocyjanianów z poliolami i małocząsteczkowymi przedłużaczami łańcucha. Z uwagi na niekorzystne właściwości diizocyjanianów,...
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublicationSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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Golden artefacts, resin figurines, body adhesives and tomb sediments from the pre-Columbian burial site El Caño (Gran Coclé, Panamá): tracing organic contents using molecular archaeometry
PublicationThis research aimed to determine the origin of organic residues from funerary contexts in the El Ca~no settlement (Gran Cocl�e area, Panam�a, Central America) by means of multiple molecular probing techniques (GC-MS of organic solvent extracts and pyrolysis-GC-MS, THM-GC-MS and FTIR of solid samples). The samples include particles of precious resin figurines, fillings of golden objects, tomb sediments, plant exudates from extant...
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POLAND’S ENERGY DEPENDENCE AT THE TURN OF THE 21ST CENTURY
PublicationThe following article is an attempt to assess Poland's energy independence in the years 1993-2020. The main aim of the paper is to present Poland's dependence on raw materials from foreign partners - in the field of imports of electricity, natural gas, crude oil, non-renewable energy resources, i.e., hard coal and lignite, and the country's dynamics in the amount of imports. In addition, the aim of the work is to answer research...
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Laser-Induced Graphitization of Polydopamine on Titania Nanotubes
PublicationSince the discovery of laser-induced graphite/graphene, there has been a notable surge of scientific interest in advancing diverse methodologies for their synthesis and applications. This study focuses on the utilization of a pulsed Nd:YAG laser to achieve graphitization of polydopamine (PDA) deposited on the surface of titania nanotubes. The partial graphitization is corroborated through Raman and XPS spectroscopies and supported...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublicationTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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Phylogenetic trees of genus Oncidium Sw. based on analysis of DNA sequences
Open Research DataGenus Oncidium Sw. is widely regarded as a polyphiletic, and the taxonomic boundaries between him and such genera as Odontoglossum Kunth. or Miltonia Lindley remain blurred. The goal of the study was to determine the phylogenetic relationships within the genus Oncidium s.lato based on the DNA sequences analysis. The correlation between molecular data...
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Computational analysis of power-law fluids for convective heat transfer in permeable enclosures using Darcy effects
PublicationNatural convection is a complex environmental phenomenon that typically occurs in engineering settings in porous structures. Shear thinning or shear thickening fuids are characteristics of power-law fuids, which are non-Newtonian in nature and fnd wide-ranging uses in various industrial processes. Non-Newtonian fuid fow in porous media is a difcult problem with important consequences for energy systems and heat transfer. In this...
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Hyperelastic Microcantilever AFM: Efficient Detection Mechanism Based on Principal Parametric Resonance
PublicationThe impetus of writing this paper is to propose an efficient detection mechanism to scan the surface profile of a micro-sample using cantilever-based atomic force microscopy (AFM), operating in non-contact mode. In order to implement this scheme, the principal parametric resonance characteristics of the resonator are employed, benefiting from the bifurcation-based sensing mechanism. It is assumed that the microcantilever is made...
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Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin.
PublicationEnterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). Acquisition of resistance determinants not only seriously limits available therapeutic options but also increases available gene pool for other species. It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred...
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Optoelectronic system for monitoring of thin diamond layers growth
PublicationDevelopment of the optoelectronic system for monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during mu PA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The multi-point Optical Emission Spectroscopy (OES) and Raman spectroscopy were employed as non-invasive optoelectronic tools. Dissociation of H-2 molecules, excitation and ionization of hydrogen...
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Genetic and Epigenetic Aspects of Atopic Dermatitis
PublicationAtopic dermatitis is a heterogeneous disease, in which the pathogenesis is associated with mutations in genes encoding epidermal structural proteins, barrier enzymes, and their inhibitors; the role of genes regulating innate and adaptive immune responses and environmental factors inducing the disease is also noted. Recent studies point to the key role of epigenetic changes in the development of the disease. Epigenetic modifications...
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Wiktoria Wojnicz dr hab. inż.
PeopleDSc in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2019 PhD in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2009 (with distinction) List of papers (2009 - ) Wojnicz W., Wittbrodt E., Analysis of muscles' behaviour. Part I. The computational model of muscle. Acta of Bioengineering and Biomechanics, Vol. 11, No.4, 2009, p. 15-21 Wojnicz W., Wittbrodt E., Analysis of...
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Non-Isocyanate-Based Waterborne Polyurethanes
PublicationNon-isocyanate polyurethanes (NIPUs) are a greener alternative for the conventional polyurethanes synthesized using toxic and moisture-sensitive di- or polyisocyanates. The most often described method of NIPU synthesis involves the reaction of five-membered cyclic carbonates with amines, and resulting polymers containing primary and secondary hydroxyl groups (so they are also known as polyhydroxyurethanes), which can be further...
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Synthesis, Chemical Characterization and Multiscale Biological Evaluation of a dimericcRGD Peptide for Targeted Imaging of αVβ3 Integrin Activity
PublicationCyclic peptides containing the Arg-Gly-Asp (RGD) sequence have been shown to specifically bind the angiogenesis biomarker α V β3 integrin. We report the synthesis, chemical characterization, and biological evaluation of two novel dimeric cyclic RGD-based molecular probes for the targeted imaging of α V β3 activity (a radiolabeled version, 64Cu-NOTA-PEG4-cRGD2, for PET imaging, and a fluorescent version, FITC-PEG4-cRGD2, for in...
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Computational fluid dynamics simulation of heat transfer from densely packed gold nanoparticles to isotropic media
PublicationThis work aims to determine and compare heat generation and propagation of densely packed gold nanoparticles (Au NPs) induced by a resonant laser beam (532 nm) according to the Mie theory. The heat flux propagation is transferred into the materials, which here are: silica glass; soda-lime-silica glass; borosilicate glass; polymethyl methacrylate (PMMA); polycarbonate (PC); and polydimetylosiloxane (PDMS). This analysis aims to...
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Smart acoustic band structures
PublicationSmart acoustic band structures exhibit very interesting and non-standard physical properties due to the periodic nature of their certain characteristic on different scale levels. They manifest mostly in their frequency spectra as socalled frequency band-gaps or stop-bands, what has a great impact on the behaviour of these structures in relation to the propagation of vibro-acoustic signals that can be transmitted through the structures...
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Impact of thermal backfill parameters on current-carrying capacity of power cables installed in the ground
PublicationProper design of power installations with the participation of power cables buried in homogeneous and thermally well-conductive ground does not constitute a major problem. The situation changes when the ground is non-homogeneous and thermally low-conductive. In such a situation, a thermal backfill near the cables is commonly used. The optimization of thermal backfill parameters to achieve the highest possible current-carrying capacity...
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Theoretical examination of the fracture behavior of BC3 polycrystalline nanosheets: Effect of crack size and temperature
Publication2D carbon graphene nanostructures are elements of advanced materials and systems. This theoretical survey provides explanation to the mechanical and fracture behavior of mono- and polycrystalline BC3 nanosheets (denoted as MC- and PCBC3NS, respectively) as a function of temperature and the type of crack defects. The mechanical performance of PCBC3NS at elevated temperatures was monitored varying the number of grain boundaries (the...