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Search results for: microbial molecular biology
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Cognitive neuroscience: Theta network oscillations coordinate development of episodic memory
PublicationOur ability to remember life events matures through childhood and adolescence. A new study has revealed how theta oscillations between two anatomical brain regions supporting memory and executive functions are synchronized and develop across age through functional and structural connectivity.
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The relationship between standard reduction potentials of catechins and biological activities involved in redox control
PublicationRedox homeostasis involves factors that ensure proper function of cells. The excess reactive oxygen species (ROS) leads to oxidative stress and increased risk of oxidative damage to cellular components. In contrast, upon reductive stress, insufficient ROS abundance may result in faulty cell signalling. It may be expected that dietary antioxidants, depending on their standard reduction potentials (E°), will affect both scenarios....
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Direct brain stimulation modulates encoding states and memory performance in humans
PublicationPeople often forget information because they fail to effectively encode it. Here, we test the hypothesis that targeted electrical stimulation can modulate neural encoding states and subsequent memory outcomes. Using recordings from neurosurgical epilepsy patients with intracranially implanted electrodes, we trained multivariate classifiers to discriminate spectral activity during learning that predicted remembering from forgetting,...
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Spectroscopic and photophysical properties of ZNTPP in a room temperature ionic liquid
PublicationThe steady-state absorption and emission spectra and the time-resolved Soret- and Q-band excited fluorescence profiles of the model metalloporphyrin, ZnTPP, have been measured in a highly purified sample of the common room temperature ionic liquid, [bmim][PF(6)]. S(2)-S(0) emission resulting from Soret-band excitation behaves in a manner completely consistent with that of molecular solvents of the same polarizability. The ionic...
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Dynamic mechanical properties and flexing fatigue resistance of tire sidewall rubber as function of waste tire rubber reclaiming degree
PublicationA stepwise downsizing method of gel particles in reclaimed rubber to a micro-nano scale and its excellent dynamic performance in tire sidewall were introduced by this work. The results showed that the size of gel particles decreased from several micrometers to micro-nanometers with the increase of reclaiming degree, accompanied by reduced molecular weight and widened molecular weight distribution of sol fraction. The addition of...
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Polymer Modified Bitumen
PublicationIn this paper we present the benefits of using polymers as an asphalt modifiers, especially the low molecular weight reactive compounds, which are capable of forming an polymer network with bitumen "in situ" in the process of its modification.
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Big Data i 5V – nowe wyzwania w świecie danych (Big Data and 5V – New Challenges in the World of Data)
PublicationRodzaje danych, składające się na zbiory typu Big Data, to m.in. dane generowane przez użytkowników portali internetowych, dane opisujące transakcje dokonywane poprzez Internet, dane naukowe (biologiczne, astronomiczne, pomiary fizyczne itp.), dane generowane przez roboty w wyniku automatycznego przeszukiwania przez nie Internetu (Web mining, Web crawling), dane grafowe obrazujące powiązania pomiędzy stronami WWW itd. Zazwyczaj,...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Ultrasound assisted extraction
PublicationThe use of green and sustainable extraction techniques is very popular topic in the multidisciplinary area of chemistry, biology and technology. There is no doubt that extraction constitutes a very important step of analytical procedures of separation, detection, identification and determination of wide spectrum analytes from samples characterized by complex and very often nonhomogeneous composition of matrix. Traditional techniques...
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Predicting Value of Binding Constants of Organic Ligands to Beta-Cyclodextrin: Application of MARSplines and Descriptors Encoded in SMILES String
PublicationThe quantitative structure–activity relationship (QSPR) model was formulated to quantify values of the binding constant (lnK) of a series of ligands to beta–cyclodextrin (β-CD). For this purpose, the multivariate adaptive regression splines (MARSplines) methodology was adopted with molecular descriptors derived from the simplified molecular input line entry specification (SMILES) strings. This approach allows discovery of regression...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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An optimal designed experiment for the alkaline hydrolysis of feather keratin
PublicationFeathers, burdensome waste from the poultry industry, can be a cheap source of keratin, a protein with excellent physico- chemical, biological, and mechanical properties. Acid and alkaline hydrolyses are usually adopted for isolation of keratin from its natural resources. This study aimed at assessing the statistically significant effect of input variables in the alkaline hydrolysis of keratin from chicken feathers on the process...
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Homoisocitrate dehydrogenase from Candida albicans: properties, inhibition, and targeting by an antifungal pro-drug
PublicationThe LYS12 gene from Candida albicans, coding for homoisocitrate dehydrogenase was cloned and expressed as a His-tagged protein in Escherichia coli. The purified gene product catalyzes the Mg2+- and K+-dependent oxidative decarboxylation of homoisocitrate to alpha-ketoadipate. The recombinant enzyme demonstrates strict specificity for homoisocitrate. SDS-PAGE of CaHIcDH revealed its molecular mass of 42.6±1 kDa, while in size-exclusion...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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abiotic degradation of chlorinated ethanes and ethenes in water
PublicationIntroduction Chlorinated ethanes and ethenes are among themost frequently detected organic pollutants of water. Theirphysicochemical properties are such that they can contaminateaquifers for decades. In favourable conditions, they canundergo degradation. In anaerobic conditions, chlorinatedsolvents can undergo reductive dechlorination.Degradation pathways Abiotic dechlorination is usuallyslower than microbial but abiotic dechlorination...
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The occurrence and role of Nitrospira in nitrogen removal systems
PublicationApplication of the modern microbial techniques changed the paradigm about the microorganisms performing nitrification. Numerous investigations recognized representatives of the genus Nitrospira as a key and predominant nitrite-oxidizing bacteria in biological nutrient removal systems, especially under low dissolved oxygen and substrate conditions. The recent discovery of Nitrospira capable of performing complete ammonia oxidation...
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The Occurrence and Role of Tetrasphaera in Enhanced Biological Phosphorus Removal Systems
PublicationThe application of enhanced biological phosphorus removal (EBPR) in wastewater treatment plants (WWTPs) has commonly been utilized worldwide. However, the optimum efficiency has not been realized over the past decades, prompting many studies and publications. The limitations, especially comprehension of the abundance and actual potential of polyphosphate-accumulating organisms (PAOs), are not fully understood. Recently identified...
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Synthetic Principles Determining Local Organization of Copolyesters Prepared from Lactones and Macrolactones
PublicationA highly effective and facile technique for catalytic ring-opening copolymerization (cROP) of lactones viz. ε- caprolactone and ε-decalactone with ω-pentadecalactone is being described. The reactions were mediated by Zn- and Cabased tridentate Schiff base complexes and benzyl alcohol as initiator. The catalysts were successfully employed for the preparation of numerous block and random copolymers. To unravel the composition of...
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Understanding the formation of metastable furan dication in collisions with ions
PublicationThis work relies on complementary theoretical and experimental studies of the processes induced by ion-furan collisions. Results of the Molecular Dynamics simulations and exploration of the energy profiles combined with coincidence mass spectrometry provide complete picture of the fragmentation of furan dication.
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Vibrational Sum-Frequency Generation Activity of a 2,4-Dinitrophenyl Phospholipid Hybrid Bilayer: Retrieving Orientational Parameters from a DFT Analysis of Experimental Data
PublicationThe vibrational nonlinear activity of films of 2,4-dinitrophenyl phospholipid (DNP) at the solid interface is measured by sum-frequency generation spectroscopy (SFG). Hybrid bilayers are formed by a LangmuirSchaefer approach in which the lipid layer is physisorbed on top of a self-assembled monolayer of dodecanethiol on Pt with the polar heads pointing out from the surface. The SFG response is investigated in two vibrational frequency...
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Linear and branched polyester resins based on dimethyl-2,5-furandicarboxylate for coating applications
PublicationIn this study, novel bio-based hydroxyl-functional (co)polyesters from dimethyl-2, 5-furandicarboxylate (DMF), 2,3-butanediol, and a variety of comonomers viz. glycerol, pentaerythritol or trimethylolpropane are prepared using a solvent-free, bulk polycondensation technique. Extensive molecular and thermal characterization was performed to elucidate the properties of these materials. The materials showed suitable properties for solvent-borne...
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Modern trends in solid phase extraction: New sorbent media
PublicationBased on the recently published literature, this review provides an update of the most important features and application of formats and devices employed in solid phase extraction (SPE). Special attention was paid on new trapping media proposed in SPE prior the chromatography analysis, based on the use of nanostructured materials, including carbon nanomaterials, electrospun nanofibers, dendrimes and magnetic nanoparticles, molecular...
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Computational modeling of molecularly imprinted polymers as a green approach to the development of novel analytical sorbents
PublicationThe development of novel molecularly imprinted polymers (MIP) sorbents for specific chemical compounds require a lot of tedious and time-consuming laboratory work. Significant quantities of solvents and reagents are consumed in the course of the verification of appropriate configurations of polymerization reagents. Implementation of molecular modeling in the MIP sorbent development process appears to provide a solution to this...
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Collagen and hyaluronic acid hydrogel in water-in-oil microemulsion delivery systems
PublicationThe efficacy of microemul-sion in dermal and transdermal delivery of active ingredients. Here, we assessed the water-in-oilmicroemulsion capacity to incorporate two natural polymers, i.e. collagen and hyaluronic acid withlow and high molecular weight. Systems were extensively characterized in terms of conductivity, phaseinversion studies, droplet diameter, polydispersity index and rheological properties. The results of thisresearch...
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Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules
PublicationThe ability to selectively control chemical reactions related to biology, combustion, and catalysis has recently attracted much attention. In particular, the hydrogen atom relocation may be used to manipulate bond-breaking and new bond-forming processes and may hold promise for far-reaching applications. Thus, the hydrogen atom migration preceding fragmentation of the gas-phase pyridine molecules by the H+, H2+, He+, He2+, and...
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Proton affinity and proton transfer energy for selected organic molecules
PublicationThe Hartree-Fock method in 6-311G** molecular orbitals basis set has been applied to calculations of proton affinities and proton transfer reaction energies for water, methanol, acetaldehyde, ethanol, acetone, acetic acid, methyl acetate and ethyl acetate.
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Niebezpieczeństwo ukryte w żywności-aminy biogenne. Cz. II. Metody oznaczania i wyzwania.
PublicationZe względu na aktywność biologiczną amin biogennych ich oznaczanie zarówno jakościowe, jak i ilościowe w żywności ma istotne znaczenie w celu zapewnienia ochrony zdrowia i życia ludzkiego. Obecnie do monitoringu amin biogennych w żywności najczęściej wykorzystuje się: wysokosprawną chromatografię cieczową (HPLC), chromatografię cienkowarstwową (TLC) oraz absorpcyjną spektrofotometrię cząsteczkową. Są to jednak techniki czasochłonne,...
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Hyperbaric Storage at Subzero Temperature – the Effect on the Shelf-Life and Selected Quality Characteristics of Raw Pork Sausages
PublicationThe aim of this study was to determine the microbiological stability and changes occurring in selected physicochemical properties of raw pork sausages during hyperbaric storage at subzero temperature (HS-ST). It was shown that storage at moderate pressures (up to 111 MPa) led to a reduction in microbial populations. After 21 days of storage under these conditions, no microorganisms were detected in the samples. Additionally, the...
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Rapid Evaluation of Poultry Meat Shelf Life Using PTR-MS
PublicationThe use of proton transfer reaction mass spectrometry (PTR-MS) for freshness classification of chicken and turkey meat samples was investigated. A number of volatile organic compounds (VOCs) were selected based on the correlation (> 95%) of their concentration during storage at 4 °C over a period of 5 days with the results of the microbial analysis. In order to verify if the selected compounds are not sample-specific, a number...
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Electron-impact ionization of fluoromethanes – Review of experiments and binary-encounter models
PublicationExperiments and recommended data on electron-impact ionization of methane and fluoromethanes (CH3F, CH2F2, CHF3, CF4) are reviewed and compared with binary-encounter models (Gryzinski’s, ´ Deutsch and Märk’s, and Kim and Rudd’s). A good agreement between recent experiments and the two latter classical-like models is shown. Kim and Rudd’s model (calculated presently in the restricted HartreeFock 6-31**G orbital basis) predicts well...
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Searching for Solvents with an Increased Carbon Dioxide Solubility Using Multivariate Statistics
PublicationIonic liquids (ILs) are used in various fields of chemistry. One of them is CO2 capture, a process that is quite well described. The solubility of CO2 in ILs can be used as a model to investigate gas absorption processes. The aim is to find the relationships between the solubility of CO2 and other variables—physicochemical properties and parameters related to greenness. In this study, 12 variables are used to describe a dataset...
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Isocyanate-Free Polyurethanes
PublicationIsocyanate-free polyurethanes (also called non-isocyanate polyurethanes, or NIPUs) are alternatives to the conventional (commercially used) polyurethanes synthesized using di- or polyisocyanates, polyols, and chain extenders with low molecular weight. The major routes of NIPUs’ synthesis involve polyaddition of cyclic carbonates and di- or polyamines, polycondensation of carbamates, and diols. The most important intermediates are...
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Chiral Pyrazolo[4,3-e][1,2,4]triazine Sulfonamides—Their Biological Activity, Lipophilicity, Protein Affinity, and Metabolic Transformations
PublicationReferring to our previous laboratory results related to the tyrosinase and urease inhibition by pyrazolo[4,3-e][1,2,4]triazine sulfonamides, we examined here in silico the mechanism of action at the molecular level of the investigated pyrazolotriazine sulfonamides by the molecular docking method. The studied compounds being evaluated for their cytotoxic effect against cancer cell lines (MCF-7, K-562) and for recombinant Abl and...
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Calculation of Vibrational Resonance Raman Spectra of Molecules Using Quantum Chemistry Methods
PublicationThe understanding and interpretation of experimental resonance Raman (RR) spectra can strongly benefit from theoretical simulations. These can be achieved by combining quantum chemistry (QC) methods to calculate the electronic and vibrational molecular properties, together with appropriate models and approximations to compute the Raman intensities. This chapter presents the main and most commonly employed approaches to calculate...
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Cognitive motivations and foundations for building intelligent decision-making systems
PublicationConcepts based on psychology fit well with current research trends related to robotics and artificial intelligence. Biology-inspired cognitive architectures are extremely useful in building agents and robots, and this is one of the most important challenges of modern science. Therefore, the widely viewed and far-reaching goal of systems research and engineering is virtual agents and autonomous robots that mimic human behavior in...
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Technologia biomems - przegląd zastosowań
PublicationThe paper reviews the issues related to technology, MEMS (Micro-Electro Systems-Mechanical) in the context of applications in biotechnology and biomedical systems. Systems of this type, with applications in biology and medicine, have the name of our common BioMEMS systems. This pertains to a wide range of technology BioMEMS. The aim of this study is to determine future medical MEMS microphones with particular emphasis on their...
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ANALYZING TITLES OF ECONOMY NEWS TO UNDERSTAND IMPACT OF COVID-19 ON ECONOMICAL SITUATION
PublicationCovid-19 affected the whole world in a short time, causing serious panic and uncertainty in society. Because it was an unprecedented disease, the medical community has worked hard to find out how to deal with it, and it continues to do so. The rapid spread of the disease, the shortage of hospital capacity and the increase in deaths drove the whole world to a closure, so to speak. In this time period, life in the world came to a...
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Selection of an artificial pre-training neural network for the classification of inland vessels based on their images
PublicationArtificial neural networks (ANN) are the most commonly used algorithms for image classification problems. An image classifier takes an image or video as input and classifies it into one of the possible categories that it was trained to identify. They are applied in various areas such as security, defense, healthcare, biology, forensics, communication, etc. There is no need to create one’s own ANN because there are several pre-trained...
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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublicationThe design of a database for positron interactions with biomolecular systems is outlined. The database contains only scattering cross sections, which are derived from theory. The data model is defined in a very flexible way, which facilitates the usage of weakly bound clusters of molecules and molecular systems with many tautomeric forms.
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Low energy differential elastic electron scattering from trichloromethane
PublicationExperimental differential cross sections for low energy electron scattering from trichloromethane is measured utilizing a crossed electron-molecular beam experiment via the relative flow method, for the incident electron energies in the range of E = 0.5 eV-30 eV and the scattering angles in the range of θ = 10◦ − 130◦ .
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Reactions of cobalt(ii) chloride and cobalt(ii) acetate with hemisalen-type ligands: ligand transformation, oxidation of cobalt and complex formation. Preliminary study on the cytotoxicity of Co(ii) and Co(iii) hemisalen complexes
PublicationSeveral molecular cobalt(II) complexes, one Co(II) coordination polymer, and one ionic cobalt(III) complex with imine hemisalen ligands were synthesized. The hemisalen ligands were synthesized from o-vanillin (oVP) and diverse aminopyridines (compounds HL1–HL4) or aminophenol (compound HL5). It was observed that cobalt(II) chloride in dry acetonitrile catalyzes a transformation of HL1 and HL3 instead of complex formation. The conversion...
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The role of bile salts in digestion
PublicationBile salts (BS) are bio-surfactants present in the gastrointestinal tract (GIT) that play a crucial role in the digestion and absorption of nutrients. The importance of BS for controlled release and transport of lipid soluble nutrients and drugs has recently stimulated scientific interest in these physiological compounds. BS are so-called facial amphiphiles showing a molecular structure that is very distinct from classical surfactants....
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Coordination complexes of Mn(II), Co(II), Ni(II), Zn(II) and Cd(II) with histaminol – Crystal structures and formation constants in aqueous solution
PublicationStability constants were determined for a series of coordination complexes of Mn(II), Co(II), Ni(II), Zn(II) and Cd(II) with histaminol in aqueous solution. The tendency of histaminol to form chelate complexes has been confirmed by the isolation of several complex species in the monocrystalline form and determination of their molecular structures.
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Electron impact iozization of CCl4 and SF6 embedded in superfluid helium droplets
PublicationElectron impact ionization of helium nano-droplets containing several 104 He atoms and doped with CCl4 or SF6 molecules is studied with high-mass resolution. The mass spectra show significant clustering of CCl4 molecules, less so for SF6 under our experimental conditions. Positive ion efficiency curves as a function of electron energy indicate complete immersion of the molecules inside the helium droplets in both cases. For CCl4...
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Synthetic strategies in construction of organic macromolecular carrier–drug conjugates
PublicationMany metabolic inhibitors, considered potential antimicrobial or anticancer drug candidates, exhibit verylimited ability to cross the biological membranes of target cells. The restricted cellular penetration ofthose molecules is often due to their highhydrophilicity. One of the possible solutions to this problem is aconjugation of an inhibitor with a molecular organic nanocarrier. The conjugate thus formed should beable to penetrate...
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Progress in non-isocyanate polyurethanes synthesized from cyclic carbonate intermediates and di- or polyamines in the context of structure–properties relationship and from an environmental point of view
PublicationCommercially, polyurethanes are produced by the reaction of diisocyanates, polyols (polyester or polyether) and low molecular weight chain extender. Toxicity, moisture sensitivity and phosgene-based synthesis of diisocyanates resulted in investigations focused on obtaining the non-isocyanate polyurethanes (NIPUs). This work presents the review of synthesis and structure–properties relationship of non-isocyanate polyurethanes obtained...
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Structure-rheology relationship of fully bio-based linear polyester polyols for polyurethanes - Synthesis and investigation
PublicationThe synthesis of polyols from renewable substances as an alternative for petrochemical-based polyols play important matter in the polyurethane industry. In this work, the fully bio-based linear polyester polyols with different catalyst amounts were synthesized via two-step polycondensation method. The effect of various catalyst content on the structure and rheological behavior were established. Fourier Transform Infrared Spectroscopy,...