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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublikacjaTetraphenylphosphonium 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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Solvent dependency of carbon dioxide Henry's constant in aqueous solutions of choline chloride-ethylene glycol based deep eutectic solvent
PublikacjaThe Henry's constants of carbon dioxide absorbed in aqueous solutions of ethaline (choline chloride-ethylene glycol) were determined for temperatures ranging from 303.15 to 323.15 K based on solubility measurement at CO2 pressure ranging from 0 to 6 bar (0.6 MPa). These studies revealed that the Henry's constant increased with the increase of temperature. Data indicated the highest capacity of CO2 absorption is obtained for ethaline...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublikacjaMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublikacjaHIV‐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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3D X-ray Micro-CT Analysis of Rebar Corrosion in Reinforced Concrete Subjected to a Chloride-Induced Environment
PublikacjaThe paper presents experimental investigations of the concrete cover protective ability to coun-teract rebar corrosion in reinforced concrete cubes. To study and quantify the consequences of corrosion a reinforced concrete sample was subjected to chloride-induced environment in order to get corroded and combined with un-corroded sample. Chloride-accelerated technique can in-duce a high degree of corrosion within at a controlled...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublikacjaIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublikacjaIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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Determination of binder-aggregate adhesion by contact angle measurement
PublikacjaThe key factor in asphalt pavement durability, especially in the presence of water, is adhesion of the bituminous binder to mineral aggregates. There are currently no standard laboratory test procedures that can quickly and accurately measure the strength of the interaction (bond) between the binder and aggregate. In this regard, to evaluate the adhesion force measurements based on the contact angle between the binder and the aggregate...
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Optimization of Chemical Functionalities of Indole-2-carboxamides To Improve Allosteric Parameters for the Cannabinoid Receptor 1 (CB1)
Publikacja5-Chloro-3-ethyl-N-(4-(piperidin-1-yl)phenethyl)-1H-indole-2-carboxamide (1; ORG27569) is a prototypical allosteric modulator for the cannabinoid type 1 receptor (CB1). Here, we reveal key structural requirements of indole-2-carboxamides for allosteric modulation of CB1: a critical chain length at the C3-position, an electron withdrawing group at the C5-position, the length of the linker between the amide bond and the phenyl ring...
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Exploring novel Cd(ii) complexes with 5-methyl-4-imidazolecarboxaldehyde: synthesis, structure, computational insights, and affinity to DNA through switchSense methodology
PublikacjaA series of four Cd(II) complexes with 5-methyl-4-imidazolecarboxaldehyde (L) with different inorganic anions within or outside the coordination sphere of general formula: [CdCl2 L2 ] (1), [CdBr2 L 2] (2), [CdI2L 2] (3), and [CdL4 ](PF6 )2 ·3H2 O (4) was synthesized through one-step and two-step reactions, respectively. All complexes were obtained as colorless crystals without the need for recrystallization and exhibited solubi- lity...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublikacjaIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Treatment of landfill leachate by constructed wetlands: three case studies
PublikacjaThe performance of three CW systems treating landfill leachate, two located in northern Poland (Szadółki near Gdańsk and Gatka near Miastko) and one in southern Sweden (Örebro), is discussed. The CWs differ in size, hydraulic regime, type of hydrophytic plants and type of leachate pre-treatment before discharging to the CW. The CW in Szadółki consists of two parallel beds with sub-surface, horizontal flow of leachate (HSSF) planted...
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Validation of Hydraulic Mechanism during Blowout Trauma of Human Orbit Depending on the Method of Load Application
PublikacjaThe more we know about mechanisms of the human orbital blowout type of trauma, the better we will be able to prevent them in the future. As long as the buckling mechanism’s veracity is not in doubt, the hydraulic mechanism is not based on equally strong premises. To investigate the correctness of the hydraulic mechanism’s theory, two different methods of implementation of the hydraulic load to the finite element method (FEM) model...
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On symmetric extendibility of quantum states and its applications
PublikacjaThis dissertation is focused on analysis of the symmetric extendibility of quantum states and its applications in the quantum information theory, with special attention paid to the area of quantum entanglement distillation, quantum channels theory, quantum security, and monogamy of quantum entanglement in time. We analyze geometry of the set of symmetric extendible states, i.e. such states that possess symmetric extensions and...
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Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei
PublikacjaThe aim of our study was to assess the sequencing of unique nucH gene fragment based on performed bioinformatics analysis as a novel diagnostic method for the identification of difficult to identify staphylococcal human pathogenic strains. Initially, PCR-RFLP-rrn analysis specific to the spacers between 16SrDNA and 23SrDNA followed by HhaI restriction analysis was performed. Further, sequencing of nucH and 16S rDNA genes fragments...
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Low-cost multiband compact branch-line coupler design using response features and automated EM model fidelity adjustment
PublikacjaDesign closure of compact microwave components is a challenging problem because of significant electromagnetic (EM) cross-couplings in densely arranged layouts. A separate issue is a large number of designable parameters resulting from replacement of conventional transmission line sections by compact microstrip resonant cells. This increases complexity of the design optimization problem and requires employment of expensive high-fidelity...
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A comparison of structural and luminescence properties of lead(II) coordination polymers with isomeric thiophenecarboxylate ligands
PublikacjaTwo new lead(II) coordination polymers with isomeric thiophenecarboxylates, namely [Pb(2tpCOO)2]n (1) and [Pb(3tpCOO)2(H2O)]n (2) (2tpCOO− = thiophene-2-carboxylate, 3tpCOO− = thiophene-3-carboxylate), were synthesized and characterized. Single crystal X-ray crystallography revealed a distorted pentagonal pyramidal geometry {PbO6} around Pb in 1 and a distorted dodecahedral geometry {PbO8} in 2. The distortion derived from the...
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Detection of Bioactive Compounds in Organically and Conventionally Grown Asparagus Spears
PublikacjaIn the recent reports, there are contradictory conclusions about the nutritional and health properties of organic and conventionally growing vegetables. We hypothesized that organic cultivation system results in higher quality of asparagus (Asparagus officinalis L.) because of organic manure and effective organisms. Therefore, new analytical methods were applied in order to find the differences in bioactive compounds between the...
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Rapid multi-objective optimization of antennas using nested kriging surrogates and single-fidelity EM simulation models
PublikacjaEver increasing performance requirements make the design of contemporary antenna systems a complex and multi-stage process. One of the challenges, pertinent to the emerging application areas but also some of the recent trends (miniaturization, demands for multi-functionality, etc.), is the necessity of handling several performance figures such as impedance matching, gain, or axial ratio, often over multiple frequency bands. The...
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Design of a Coplanar Waveguide-Fed Wideband Compact-Size Circularly Polarized Antenna and polarization-sense alteration
PublikacjaThis paper presents the design and validation of a geometrically simple circularly polarized(CP) structure featuring flat gain in the sub-6 GHz 5th generation spectrum. The proposed structure is based on coplanar-waveguide-fed, modified wide slot etched in the ground plane. For generating CP waves, the coplanar ground planes are designed with slight asymmetry in both the horizontal and vertical directions. Furthermore, the ground...
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Tolerance-Aware Optimization of Microwave Circuits by Means of Principal Directions and Domain-Restricted Metamodels
PublikacjaPractical microwave design is most often carried out in the nominal sense. Yet, in some cases, performance degradation due to uncertainties may lead to the system failing to meet the prescribed specifications. Reliable uncertainty quantification (UQ) is therefore important yet intricate from numerical standpoint, especially when the circuit at hand is to be evaluated using electromagnetic (EM) simulation tools. Tolerance-aware...
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Physicochemical and Mechanical Performance of Freestanding Boron-Doped Diamond Nanosheets Coated with C:H:N:O Plasma Polymer
PublikacjaThe physicochemical and mechanical properties of thin and freestanding heavy boron-doped diamond (BDD) nanosheets coated with a thin C:H:N:O plasma polymer were studied. First, diamond nanosheets were grown and doped with boron on a Ta substrate using the microwave plasma-enhanced chemical vapor deposition technique (MPECVD). Next, the BDD/Ta samples were covered with nylon 6.6 to improve their stability in harsh environments and...
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Implementation of spatial/polarization diversity for improved-performance circularly polarized multiple-input-multiple-output ultra-wideband antenna
PublikacjaIn this paper, spatial and polarization diversities are simultaneously implemented in an ultra-wideband (UWB) multiple-input-multiple-output (MIMO) antenna to reduce the correlation between the parallel-placed radiators. The keystone of the antenna is systematically modified coplanar ground planes that enable excitation of circular polarization (CP). To realize one sense of circular polarization as well as ultra-wideband operation,...
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Effects of Micro-Arc Oxidation Process Parameters on Characteristics of Calcium-Phosphate Containing Oxide Layers on the Selective Laser Melted Ti13Zr13Nb Alloy
PublikacjaTitania-based films on selective laser melted Ti13Zr13Nb have been formed by micro-arc oxidation (MAO) at different process parameters (voltage, current, processing time) in order to evaluate the impact of MAO process parameters in calcium and phosphate (Ca + P) containing electrolyte on surface characteristic, early-stage bioactivity, nanomechanical properties, and adhesion between the oxide coatings and substrate. The surface...
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On Tradeoffs Between Width- and Fill-like Graph Parameters
PublikacjaIn this work we consider two two-criteria optimization problems: given an input graph, the goal is to find its interval (or chordal) supergraph that minimizes the number of edges and its clique number simultaneously. For the interval supergraph, the problem can be restated as simultaneous minimization of the path width pw(G) and the profile p(G) of the input graph G. We prove that for an arbitrary graph G and an integer t ∈ {1,...
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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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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublikacjaThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Bioaccumulation of Metals in Tissues of Marine Animals, Part I: the Role and Impact of Heavy Metals on Organisms
PublikacjaHeavy metals contribute to the anthropogenic contamination of marine ecosystems. Some of them are essential to the life processes of organisms; others are toxic, even at low concentrations. They penetrate organisms via food, respiratory pathways or the skin. The extent to which metals penetrate organisms is measured by the bioconcentration and bioaccumulation factors and also by their transport between organisms at different trophic...
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Updating a hospital building. A task for innovation design
PublikacjaRefurbishment of a hospital, especially located in a historical building, is a task that goes far beyond a standard framework of architectural practice. A concept of modularity in the architecture of the late nineteenth and early twentieth century was only just to happen, building system installations and technical equipment appeared as the simplest solutions. Inscribing complex functional solutions into such a space is an interesting...
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Low-Cost Yield-Driven Design of Antenna Structures Using Response-Variability Essential Directions and Parameter Space Reduction
PublikacjaQuantifying the effects of fabrication tolerances and uncertainties of other types is fundamental to improve antenna design immunity to limited accuracy of manufacturing procedures and technological spread of material parameters. This is of paramount importance especially for antenna design in the industrial context. Degradation of electrical and field properties due to geometry parameter deviations often manifests itself as, e.g.,...
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Intense and stable room-temperature photoluminescence from nanoporous vanadium oxide formed by in-ambient degradation of VI3 crystals
PublikacjaVanadium oxides have attracted research interest because their optoelectronic properties make them optically active with room-temperature photoluminescence (PL) emission, which, however, is not sufficiently intense for real applications. For this reason, many nanostructured vanadium oxides are currently fabricated through several precursors and different treatments to improve the PL efficiency and enhance the PL intensity. Herein,...
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Heat treatment effect on Eu3+ doped TeO2-BaO-Bi2O3 glass systems with Ag nanoparticles.
PublikacjaGlass systems of 73TeO2-4BaO-3Bi2O3-2Eu2O3-xAg ( in molar ratio where x= 0, 1, 2, 3) compositions have been successfully synthesized. Silver nanoparticles were obtained with the employment of heat treatment (HT) procedure executed at 350 °C. Glass transition temperatures of different compositions have been determined through DSC measurements. XRD measurement results presented characteristic amorphous halo indicating lack of long...
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Artificial Neural Networks as an architectural design tool- generating new detail forms based on the Roman Corinthian order capital
PublikacjaThe following paper presents the results of the research in the field of the machine learning, investigating the scope of application of the artificial neural networks algorithms as a tool in architectural design. The computational experiment was held using the backward propagation of errors method of training the artificial neural network, which was trained based on the geometry of the details of the Roman Corinthian order capital....
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Proximal fibular osteotomy as a treatment for degenerative meniscal extrusion
PublikacjaMeniscal extrusion treatment is a key focus area for research and clinical study of degenerative knee pathology. The contact forces between the meniscus and the bones cause external displacements of the meniscus that are resisted by the circumferential fibres. The main risk factors for the excessive deformation of the meniscus are meniscal root tears, disruption of the circumferential fibres, knee malalignment and high body mass...
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Development and validation of lumbar spine finite element model
PublikacjaThe functional biomechanics of the lumbar spine have been better understood by finite element method (FEM) simulations. However, there are still areas where the behavior of soft tissues can be better modeled or described in a different way. The purpose of this research is to develop and validate a lumbar spine section intended for biomechanical research. A FE model of the 50th percentile adult male (AM) Total Human Model for Safety...
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Photochemical and thermal reaction of intermediates in the phenylnitrene rearangment inside a hemicarcerand
PublikacjaBroadband irradiation (λ > 320 nm) of hemicarceplex H1 between −74 °C and −84 °C, produces encapsulated didehydroazepine (2), triplet phenylnitrene (3PN), 2-azabicyclo[3.2.0]hepta-1,3,6-triene (6), and 4-azaspiro[2.4]hepta-1,4,6-triene (7). The highly strained anti-Bredt imine 6 is formed from 2 via a photochemical four-electron electrocyclization. Under the irradiation conditions, 6 rearranges further to azaspirene 7. In addition,...
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DC and AC Conductivity, Biosolubility and Thermal Properties of Mg-Doped Na2O–CaO–P2O5 Glasses
PublikacjaBioactive glasses have recently been extensively used to replace, regenerate, and repair hard tissues in the human body because of their ability to bond with living tissue. In this work, the effects of replacing Na2O with MgO on the electrical, biosolubility, and thermal properties of the target glass 10Na2O–60P2O5–30CaO (in mol%) were investigated. The electrical properties of the glasses were studied with the impedance spectroscopy...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse 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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The Mechanism of a Retro-Diels–Alder Fragmentation of Luteolin: Theoretical Studies Supported by Electrospray Ionization Tandem Mass Spectrometry Results
PublikacjaThe mechanisms of retro-Diels–Alder fragmentation of luteolin are studied theoretically using the Density Functional Theory method (B3LYP hybrid functional) together with the 6-311++G(d,p) basis set and supported by electrospray ionization tandem mass spectrometry (ESI-MS) results. The reaction paths leading to the formation of 1,3A and 1,3B fragment ions observed as the main spectral features in the ESI-MS spectrum are described...
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The Reactivity of Phosphanylphosphinidene Complexes of Transition Metals Toward Terminal Dihaloalkanes
PublikacjaThe reactivities of phosphanylphosphinidene complexes [(DippN)2W(Cl)(η2-P−PtBu2)]− (1), [(pTol3P)2Pt(η2- P=PtBu2)] (2), and [(dppe)Pt(η2-P=PtBu2)] (3) toward dihaloalkanes and methyl iodide were investigated. The reactions of the anionic tungsten complex (1) with stochiometric Br(CH2)nBr (n = 3, 4, 6) led to the formation of neutral complexes with a tBu2PP(CH2)3Br ligand or neutral dinuclear complexes with unusual tetradentate...
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In-depth characterization of icosahedral ordering in liquid copper
PublikacjaThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublikacjaUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublikacjaFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Thermal Instability of Choline Chloride-Based Deep Eutectic Solvents and Its Influence on Their Toxicity─Important Limitations of DESs as Sustainable Materials
PublikacjaDeep eutectic solvents (DESs) have become a hot topic in many branches of science due to their remarkable properties. They have been studied in a wide variety of applications. In particular, choline chloride (ChCl)-based DESs are one of the most commonly used representatives of these fluids. Nevertheless, in order to apply DESs in some fields, it is essential to guarantee their stability, reusability, and biocompatibility. In this...
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Divulging the anti-acetylcholinesterase activity of Colletotrichum lentis strain KU1 extract as sustainable AChE active site inhibitors
PublikacjaAlzheimer’s disease (AD), also called senile dementia is a neurodegenerative disease seen commonly in the elderly and is characterised by the formation of β-amyloid plaques and neurofbrillary tangles (NFT). Though a complete understanding of the disease is lacking, recent studies showed the role of the enzyme acetylcholinesterase (AChE) in pathogenesis. Finding new lead compounds from natural sources has always been a quest for...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublikacjaIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Deep Eutectic Solvents: Properties and Applications in CO2 Separation
PublikacjaNowadays, many researchers are focused on finding a solution to the problem of global warming. Carbon dioxide is considered to be responsible for the “greenhouse” effect. The largest global emission of industrial CO2 comes from fossil fuel combustion, which makes power plants the perfect point source targets for immediate CO2 emission reductions. A state-of-the-art method for capturing carbon dioxide is chemical absorption using...
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The particle method for simulation of self-organization phenomena
PublikacjaThe aim of the work was to design, implement, and use, in a number of experiments, an abstract software environment (an artificial world)suitable for modelling systems consisting of many moving and interactingobjects distributed in space. The environment, named DigiHive, is directed towards modeling of complex systems manifested by processes of self-organization, self-reproduction and self modifications. The environment is mainly...
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Medium-sized cyclic bis(anisylphosphonothioyl)- disulfanes and their corresponding cyclic sulfane-structures and most characteristic reactions
PublikacjaCyclic 8-, 9-, 10-, and 12-membered bis(anisylphosphonothioyl)disulfanes were synthesized. Next, structurally related 7 to 9-membered cis and trans sulfanes were isolated as a result of sulfur atom extrusion from the parent cyclic disulfanes. The results of the desulfurization of the disulfanes were compared to the results obtained for desulfurization of the respective bis(anisylphosphodithioates). Cyclic disulfanes predominantly...