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Search results for: QM/MM FREE ENERGY SIMULATIONS
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Curved Surface Minijet Impingement Phenomena Analysed with ζ-f Turbulence Model
PublicationThe jet impingement phenomenon plays an important role among the heat transfer intensification methods. Very often its application and analyses refer to simple flat surfaces, while there is a lack of information in the literature for cases addressing curved surfaces. In the present work, the single jet impingement on the non-flat (concave and convex) surface is studied for a wide range of geometries, which originate from the mini-jet...
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DMSO hydration redefined: Unraveling the hydrophobic hydration of solutes with a mixed hydrophilic–hydrophobic characteristic
PublicationHydrophobic hydration of solutes with a mixed hydrophilic--hydrophobic characteristics is still poorly understood. This is because both experimental and theoretical methods find it difficult to see the ice-like water structure around the nonpolar solute groups, unlike hydrogen bonds with the hydrophilic groups. In order to unravel this problem, we have investigated DMSO hydration by means of infrared spectroscopy and theoretical...
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Rheological, Mechanical, Microstructural and Radiation Shielding Properties of Cement Pastes Containing Magnetite (Fe3O4) Nanoparticles
PublicationThis work examines the influence of iron oxide nanoparticles (Fe3O4 NPs) on neutron and gamma-ray radiation shielding characteristics of Portland cement paste. Experimental evaluations were supplemented with theoretical studies using NXCom program. Portland cement pastes with 5, 10, 15, 20, and 30 wt% of nanomagnetite cement replacement were produced. Moreover, rheological, early strength development, compressive strength, and...
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Expermental investigation on adsorption of methylene blue dye from waste water using corncob cellulose-based hydrogel
PublicationHydrogel from corncob cellulose was synthesized in this investigation. The synthesized Hydrogel was characterized by SEM, XRD, and FTIR instruments. As the results indicate the synthesized hydrogel has required and important features, these suggest the suitability of hydrogel for the adsorption of methylene blue dye (MBD). Three important process variables (dosage, contact time, and initial concentration) with three levels were...
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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Phospholipid-functionalized gold electrode for cellular membrane interface studies - interactions between DMPC bilayer and human cystatin C
PublicationThis work describes the electrochemical studies on the interactions between V57G mutant of human cystatin C (hCC V57G) and membrane bilayer immobilized on the surface of a gold electrode. The electrode was modified with 6-mercaptohexan-1-ol (MCH) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). DMPC was used as a membrane mimetic for monitoring electrochemical changes resulting from the interactions between the functionalized...
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Studies on Silver Ions Releasing Processes and Mechanical Properties of Surface-Modified Titanium Alloy Implants
PublicationDispersed silver nanoparticles (AgNPs) on the surface of titanium alloy (Ti6Al4V) and titanium alloy modified by titania nanotube layer (Ti6Al4V/TNT) substrates were produced by the chemical vapor deposition method (CVD) using a novel precursor of the formula [Ag5(O2CC2F5)5(H2O)3]. The structure and volatile properties of this compound were determined using single crystal X-ray diffractometry, variable temperature IR spectrophotometry...
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Synergistic effects of hybrid advanced oxidation processes (AOPs) based on hydrodynamic cavitation phenomenon – A review
PublicationHigh-performance water treatment systems based on cavitational processes have received an increasing interest of scientific community in the past few decades. Numerous studies indicated the advantageous application of hydrodynamic cavitation as an alternative, reagent-free treatment method of various pollutants in water. Both approaches were proved as an effective method to achieve mineralization of many organic contaminants as...
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Rapid design optimization of antennas using variable-fidelity EM models and adjoint sensitivities
PublicationPurpose – Development of techniques for expedited design optimization of complex and numerically expensive electromagnetic (EM) simulation models of antenna structures validated both numerically and experimentally. The paper aims to discuss these issues. Design/methodology/approach – The optimization task is performed using a technique that combines gradient search with adjoint sensitivities, trust region framework, as well as...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Thermally activated natural chalcopyrite for Fenton-like degradation of Rhodamine B: Catalyst characterization, performance evaluation, and catalytic mechanism
PublicationIn this work, catalytic activity of natural chalcopyrite (CuFeS2) was improved by thermal activation. The modified chalcopyrite was used as efficient catalyst for degradation of organic dye Rhodamine B (RhB) through advanced oxidation process (AOP). Effects of catalyst dosage, H2O2 concentration, reaction temperature, solution pH, anions, and natural organic matter on the degradation efficiency of RhB were investigated. This study...
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Experimental investigation of thermal energy storage in shell-and-multi-tube unit with nano-enhanced phase change material
PublicationThis paper deals with thermal energy storage with use of nanoparticle enhanced phase change material in shell-and-multitube unit. The experiments are conducted under atmospheric pressure. Paraffin wax and two different fatty acids are used as base phase change material. Graphite and multi-walled carbon nanotubes serve as nanoparticles. Graphite nanoparticles are tested at the concentrations of 0.1%, 1% and 5% by weight, while multi-walled...
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Facilitated water transport in composite reduced graphene oxide pervaporation membranes for ethanol upgrading
PublicationHigh purity ethanol is one of the most sought-after renewable energy sources. However, standard production methods yield ethanol of insufficient quality. Membrane processes such as pervaporation are recognized as a viable method for upgrading ethanol. Their performance and selectivity depend solely on membrane employed. Hydrophilic polyvinyl alcohol (PVA) membranes are used industrially for this purpose, but there is a trade-off...
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Advancing electrochemical impedance analysis through innovations in the distribution of relaxation times method
PublicationElectrochemical impedance spectroscopy (EIS) is widely used in electrochemistry, energy sciences, biology, and beyond. Analyzing EIS data is crucial, but it often poses challenges because of the numerous possible equivalent circuit models, the need for accurate analytical models, the difficulties of nonlinear regression, and the necessity of managing large datasets within a unified framework. To overcome these challenges, non-parametric...
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Intramolecular Proton Transfer in the Radical Anion of Cytidine Monophosphate Sheds Light on the Sensitivities of Dry vs Wet DNA to Electron Attachment-Induced Damage
PublicationSingle-strand breaks (SSBs) induced via electron attachment were previously observed in dry DNA under ultrahigh vacuum (UHV), while hydrated electrons were found not able to induce this DNA damage in an aqueous solution. To explain these findings, crossed electron-molecular beam (CEMB) and anion photoelectron spectroscopy (aPES) experiments coupled to density functional theory (DFT) modeling were used to demonstrate the fundamental...
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Polyurethane/Silane-Functionalized ZrO2 Nanocomposite Powder Coatings: Thermal Degradation Kinetics
PublicationA polyurethane (PU)-based powder coating reinforced with vinyltrimethoxysilane (VTMS)-functionalized ZrO2 nanoparticles (V-ZrO2) for thermal stability was developed. Chemical structure, microstructure and thermal degradation kinetics of the prepared coatings were investigated. The peak of aliphatic C–H vibrating bond in the Fourier transform infrared (FTIR) spectrum of V-ZrO2 was a signature of VTMS attachment. Scanning electron...
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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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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 neighbouring 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 it equals to approximately 0.28 nm....
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Earthquake-induced pounding between equal height multi-storey buildings considering soil-structure interaction
PublicationThe present paper investigates the coupled effect of the supporting soil flexibility and pounding between neighbouring, insufficiently separated equal height buildings under earthquake excitation. Two adjacent three-storey structures, modelled as inelastic lumped mass systems with different structural characteristics, have been considered in the study. The models have been excited using a suit of ground motions with different peak...
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Multi-objective optimization of water quality, pumps operation, and storage sizing of water distribution systems
PublicationA multi-objective methodology utilizing the Strength Pareto Evolutionary Algorithm (SPEA2) linked to EPANET for trading-off pumping costs, water quality, and tanks sizing of water distribution systems is developed and demonstrated. The model integrates variable speed pumps for modeling the pumps operation, two water quality objectives (one based on chlorine disinfectant concentrations and one on water age), and tanks sizing cost...
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Nonlinear Control of a Doubly Fed Generator Supplied by a Current Source Inverter
PublicationNowadays, wind turbines based on a doubly fed induction generator (DFIG) are a commonly used solution in the wind industry. The standard converter topology used in these systems is the voltage source inverter (VSI). The use of reverse-blocking insulated gate bipolar transistor (RB-IGBT) in the current source inverter topology (CSI), which is an alternative topology, opens new possibilities of control methods. This paper presents...
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Triplet–Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC
PublicationTriplet−triplet annihilation upconversion (TTA-UC) implemented in nanoparticle assemblies is of emerging interest in biomedical applications, including in drug delivery and imaging. As it is a bimolecular process, ensuring sufficient mobility of the sensitizer and annihilator to facilitate effective collision in the nanoparticle is key. Liposomes can provide the benefits of two-dimensional confinement and condensed concentration...
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DoA Estimation Using Reconfigurable Antennas in Millimiter-Wave Frequency 5G Systems
PublicationTo achieve low latency and high throughputs, future 5G systems will have to utilize complex antenna systems able to provide beamforming and direction-of-arrival (DoA) estimation capabilities. Most of the concepts available in the literature rely on analog or digital beamforming, which is well developed and can be used both at a base station and in a user terminal. However, in applications, in which...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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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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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Adaptive Algorithm of a Tap-Changer Controller of the Power Transformer Supplying the Radial Network Reducing the Risk of Voltage Collapse
Publicationhe development of renewable energy, including wind farms, photovoltaic farms as well as prosumer installations, and the development of electromobility pose new challenges for network operators. The results of these changes are, among others, the change of network load profiles and load flows determining greater volatility of voltages. Most of the proposed solutions do not assume a change of the transformer regulator algorithm....
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A new construction of shell-and-tube heat exchanger with impinging jets and minichannels technologies for heat recovery from gases – experimental analysis
PublicationA dynamic development of technologies allowing waste heat utilization is observed in a correspondence with a pro-ecological approach of the zero waste idea. Such approach becomes the most demanding in the area of low-temperature was heat sources, especially gaseous media. Till now, they were usually not utilized due to unfavorable thermal conditions and high costs. Therefore, the zero waste approach directs research on techniques...
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Investigating Layered Topological Magnetic Materials as Efficient Electrocatalysts for the Hydrogen Evolution Reaction under High Current Densities
PublicationDespite considerable progress, high-performing durable catalysts operating under large current densities (i.e., >1000 mA/cm2) are still lacking. To discover platinum group metal-free (PGMfree) electrocatalysts for sustainable energy, our research involves investigating layered topological magnetic materials (semiconducting ferromagnets) as highly efficient electrocatalysts for the hydrogen evolution reaction under high current...
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A Comprehensive Survey on Antennas On-Chip Based on Metamaterial, Metasurface, and Substrate Integrated Waveguide Principles for Millimeter-Waves and Terahertz Integrated Circuits and Systems
PublicationAntennas on-chip are a particular type of radiating elements valued for their small footprint. They are most commonly integrated in circuit boards to electromagnetically interface free space, which is necessary for wireless communications. Antennas on-chip radiate and receive electromagnetic (EM) energy as any conventional antennas, but what distinguishes them is their miniaturized size. This means they can be integrated inside...
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Systemic analysis of a manufacturing process based on a small scale bakery
PublicationThe main aim of the article is to present two new innovative concepts of reliability of a functioning manufacturing system in the process of making bread in small-scale bakeries. Reliability is understood as one of the representations of an operator acting on specifc streams in time to - t. One of these represents the global reliability of a system as a function of parallel action of all the streams of the system in time to to...
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RANS-based design optimization of dual-rotor wind turbines
PublicationPurpose An improvement in the energy efficiency of wind turbines can be achieved using dual rotors. Because of complex flow physics, the design of dual-rotor wind turbines (DRWTs) requires repetitive evaluations of computationally expensive partial differential equation (PDE) simulation models. Approaches for solving design optimization of DRWTs constrained by PDE simulations are investigated. The purpose of this study is to determine...
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Preliminary Results from the Removal of Phosphorus Compounds with Selected Sorption Material
PublicationDue to the resources of phosphorous are limited and are exhausted in the next 30 years the management of the resources is become current issue. Most of the phosphorus compounds is lost forever, because it is discharged with sewage into surface waters, causing eutrophication and in this way causing a further problem and challenge. On the other hand, there is a considerable need for phosphorus compounds, primarily in bioavailable...
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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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Experimental validation of the rolling resistance measurement method including updated draft standard
PublicationThe main objective of ROSANNE is the harmonisation and standardisation of the measurement of skid resistance, noise emission and rolling resistance of road pavements. Regarding rolling resistance characterisation, a draft for standardization of a harmonized procedure for classification of road surfaces across Europe has been prepared within WP3 (deliverable 3.5). The procedure deals with the direct measurement on real roads of...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublicationIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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A novel cold-active beta-D-galactosidase from the Paracoccus sp. 32d - gene cloning, purification and characterization
PublicationBeta-D-galactosidase (EC 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Cold-active beta-D-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (I) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (II) convert lactose to glucose and galactose which...
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Rare earth ions doped K 2 Ta 2 O 6 photocatalysts with enhanced UV–vis light activity
PublicationNew rare earth-doped K2Ta2O6 photocatalysts were successfully synthesized by hydrothermal method. The effect of dopant type (Y,Yb,Ho,Pr,Er) and amount of rare earth precursor (2,4,8 and 10 mol%) on the physicochemical and photocatalytic properties of RE-K2Ta2O6 have been investigated. All as-prepared materials were characterized by UV–vis diffuse reflectance spectroscopy, Brunauer-Emmett-Teller specific surface area measurement,...
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Development of Biocompatible Fe3O4@SiO2 Nanoparticles as Subcellular Delivery Platform for Glucosamine-6-phosphate Synthase Inhibitors
PublicationNumerous inhibitors of glucoseamine-6-phophate synthase (GlcN-6-P), the enzyme responsible from catalysis of the first step of metabolic pathway leading to metabolism 5’-diphospho-N-acetyl-D- glucosamine, were reported as effective agents for inhibiting the growth of various fungal pathogens. Among the reported inhibitors,...