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Search results for: ION MOLECULAR RECOGNITION
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Automatic recognition of males and females among web browser users based on behavioural patterns of peripherals usage
PublicationPurpose The purpose of this paper is to answer the question whether it is possible to recognise the gender of a web browser user on the basis of keystroke dynamics and mouse movements. Design/methodology/approach An experiment was organised in order to track mouse and keyboard usage using a special web browser plug-in. After collecting the data, a number of parameters describing the users’ keystrokes, mouse movements and clicks...
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Fatty acids as molecular carriers in cleavable antifungal conjugates
PublicationConjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker, demonstrate good in vitro activity against human pathogenic yeasts of Candida spp. The minimal inhibitory concentrations (MIC) values for the most active conjugates containing caprylic...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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The influence of nanostructures size on V2O5 electrochemical properties as cathode materials for lithium ion battery
PublicationIn this paper, V2O5 nanostructures with a size depending on the annealing temperature are successfully synthesized by a sol-gel method. The crystal structure and morphology of samples are characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), selected area electron diffraction (SEAD) and scanning electron microscopy (SEM), respectively. Electrochemical testing such...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Exploring ion-ion preferences through structure-property correlations: amino acid-derived, bis(guanidinium) disiloxane salts
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Sulfonamides with hydroxyphenyl moiety: Synthesis, structure, physicochemical properties, and ability to form complexes with Rh(III) ion
PublicationSulfonamides are the first successfully synthesized antimicrobial drugs. The mechanism of sulfonamides’ antimicrobial action involves competitive inhibition of folic acid synthesis and prevention of the growth and reproduction of bacteria. Even though they have been applied in therapy for more than 75 years, sulfonamides are still the drugs of choice for the treatment of various diseases. The aim of this work was to synthesize...
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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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The Influence of Selecting Regions from Endoscopic Video Frames on The Efficiency of Large Bowel Disease Recognition Algorithms
PublicationThe article presents our research in the field of the automatic diagnosis of large intestine diseases on endoscopic video. It focuses on the methods of selecting regions of interest from endoscopic video frames for further analysis by specialized disease recognition algorithms. Four methods of selecting regions of interest have been discussed: a. trivial, b. with the deletion of characteristic, endoscope specific additions to the...
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Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates
PublicationInefficient transportation of polar metabolic inhibitors through cell membranes of eukaryotic and prokaryotic cells precludes their direct use as drug candidates in chemotherapy. One of the possible solutions to this problem is application of the ‘Trojan horse’ strategy, i.e. conjugation of an active substance with a molecular carrier of organic or inorganic nature, facilitating membrane penetration. In this work, the synthetic...
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Bio‐polyols synthesized by liquefaction of cellulose: Influence of liquefaction solvent molecular weight
PublicationCurrently, the plastics industry including polyurethanes is based on the use of petrochemicals. For this reason, scientists are looking for new types of renewable resources for the substitution of petrochemical substances. This work aims to evaluate the effect of polyethylene glycols (PEG) with different molecular mass impact on properties of bio-based polyols synthesized via biomass liquefaction of cellulose. To date, research...
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Examining Feature Vector for Phoneme Recognition / Analiza parametrów w kontekście automatycznej klasyfikacji fonemów
PublicationThe aim of this paper is to analyze usability of descriptors coming from music information retrieval to the phoneme analysis. The case study presented consists in several steps. First, a short overview of parameters utilized in speech analysis is given. Then, a set of time and frequency domain-based parameters is selected and discussed in the context of stop consonant acoustical characteristics. A toolbox created for this purpose...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Molecular Biology of Meniscal Healing: A Narrative Review
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Dipodal Tetraamide Derivatives of 1,10-Diaza-18-Crown-6 and Alkylmalonic Acids—Synthesis and Use as Ionophores in Ion Selective Membrane Electrodes
PublicationNovel dipodal derivatives of an 18-membered diaza-crown ether with two diamide chains featuring methylmalonic or butylmalonic acid residues were obtained and tested as ionophores in ion-selective plasticized membrane electrodes. The objective of the study was to identify measurement conditions which ensure the most favorable performance for magnesium ion-selective electrodes. The relationship between the molar lipophilic anion...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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Hard carbon derived from rice husk as low cost negative electrodes in Na-ion batteries
PublicationHere, we report the synthesis of hard carbon materials (RH) made from natural rice husk through a single pyrolysis process and their application as an anode in sodium-ion batteries. The studies show that the electrochemical properties of RHs are affected by the treatment temperatures, which determine the materials morphology, in particular, their degree of graphitization and extent of continuous channels (nanovoids). The latter...
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Solid-Contact Ion-Selective Electrodes with Highly SelectiveThioamide Derivatives of p-tert-Butylcalix[4]arene for theDetermination of Lead(II) in Environmental Samples
PublicationThioamide derivatives of p-tert-butylcalix[4]arene were used as ionophores in the development of solid-contact ion-selective electrodes based on conducting polymer poly(3,4-ethylenedioxythiophene)/polystyrene sulfonate (PEDOT/PSS) which was synthesized by electrodeposition on the glassy carbon electrodes. The typical ion-selective membranes with optionally two different plasticizers [bis(2-ethylhexyl)sebacate (DOS) and 2-nitrophenyl...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Determination of toxic gases based on the responses of a single electrocatalytic sensor and pattern recognition techniques
PublicationA response from an electrocatalytic gas sensor contains fingerprint information about the type of gas and its concentration. As a result, a single gas sensor can be used for the determination of different gases. However, information about the type of gas and its concentration is hidden in the unique shape of the current–voltage response and it is quite difficult to explore. One of the ways to get precise information about the measured...
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1D convolutional context-aware architectures for acoustic sensing and recognition of passing vehicle type
PublicationA network architecture that may be employed to sensing and recognition of a type of vehicle on the basis of audio recordings made in the proximity of a road is proposed in the paper. The analyzed road traffic consists of both passenger cars and heavier vehicles. Excerpts from recordings that do not contain vehicles passing sounds are also taken into account and marked as ones containing silence....
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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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Determination of thiocyanate (biomarkers of ETS) and other inorganic ions in human nasal discharge samples using ion chromatography
PublicationEnvironmental tobacco smoke (ETS) is a mixture of air and tobacco smoke containing more than 4000 chemical substances. In view of the health risks of many of these substances, studies are needed to determine biomarkers of exposure to ETS constituents in people who actively or passively are exposed to the toxic compounds. The methodologies for determining most biomarkers from saliva, urine and blood samples are known, but methods...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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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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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Vowel recognition based on acoustic and visual features
PublicationW artykule zaprezentowano metodę, która może ułatwić naukę mowy dla osób z wadami słuchu. Opracowany system rozpoznawania samogłosek wykorzystuje łączną analizę parametrów akustycznych i wizualnych sygnału mowy. Parametry akustyczne bazują na współczynnikach mel-cepstralnych. Do wyznaczenia parametrów wizualnych z kształtu i ruchu ust zastosowano Active Shape Models. Jako klasyfikator użyto sztuczną sieć neuronową. Działanie systemu...
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Recognition, understanding and aestheticization of freehand drawing flowcharts
PublicationIn this paper a concept of FCA, a system for recognizing, understanding and aestheticization of freehand drawing flow charts is described. The system is based on a proposed by the author FlowGram graph grammar describing flow charts drawing. An open format FlowChartML for flow charts description is also proposed. The aestheticization criterion is formulated that allows for automatic beautification of flow charts. First experiments...
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Acylic congener of cucurbituril: synthesis and recognition properties.
PublicationZaprezentowano syntezę analogów acyklicznych cucurbiturilu oraz ich zdolności do kompleksowania wybranych 16 amin, dioli, kwasów dikarboksylowych, pochodnych guanidyny oraz pirydyny. Obserwowane tworzenie kompleksów przebiegało około 180 razy słabiej niż dla cucurbiturilu. Wyniki te świadczą o potencjalnych możliwościach zbliżonych do analogów cyklicznych pod względem tworzenia kompleksów i rozpoznawania wyżej wymienionych...
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Multimodal Audio-Visual Recognition of Traffic Events
PublicationPrzedstawiono demonstrator systemu wykrywania niebezpiecznych zdarzeń w ruchu drogowym oparty na jednoczesnej analizie danych wizyjnych i akustycznych. System jest częścią systemu automatycznego nadzoru bezpieczeństwa. Wykorzystuje on kamery i mikrofony jako źródła danych. Przedstawiono wykorzystane algorytmy - algorytmy rozpoznawania zdarzeń dźwiękowych oraz analizy obrazu. Zaprezentowano wyniki działania algorytmów na przykładzie...
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Speech recognition system for hearing impaired people.
PublicationPraca przedstawia wyniki badań z zakresu rozpoznawania mowy. Tworzony system wykorzystujący dane wizualne i akustyczne będzie ułatwiał trening poprawnego mówienia dla osób po operacji transplantacji ślimaka i innych osób wykazujących poważne uszkodzenia słuchu. Active Shape models zostały wykorzystane do wyznaczania parametrów wizualnych na podstawie analizy kształtu i ruchu ust w nagraniach wideo. Parametry akustyczne bazują na...
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Gazetteer compression technique based on substructure recognition
PublicationAutomaty skończone są najlepszą formą reprezentacji słowników do przetwarzania języka naturalnego. Przedstawiamy nową technikę kompresji, która jest szczególnie użyteczna w stosunku do pewnego rodzaju słowników. Zastępujemy wielokrotnie występujące podstruktury ich niepowtarzalnymi reprezentantami. Do ich znalezienia traktujemy wektor przejść jako tekst i stosujemy technikę kompresji tekstu w stylu Ziv-Lempel, która znajduje powtórzenia...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Chitosan-Based Membranes as Gentamicin Carriers for Biomedical Applications — Influence of Chitosan Molecular Weight
PublicationOver the past decade, much attention has been paid to chitosan as a potential drug carrier because of its non-toxicity, biocompatibility, biodegradability and antibacterial properties. The effect of various chitosan characteristics on its ability to carry different antibiotics is discussed in the literature. In this work, we evaluated the influence of the different molecular weights of this polymer on its potential as an antibacterial...
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Molecular Umbrellas Modulate the Selective Toxicity of Polyene Macrolide Antifungals
PublicationAntifungal polyene macrolide antibiotics Amphotericin B (AmB) and Nystatin (NYS) were conjugated through the ω-amino acid linkers with diwalled “molecular umbrellas” composed of spermidine-linked deoxycholic or cholic acids. The presence of “umbrella” substituents modulated biological properties of the antibiotics, especially their selective toxicity. Some of the AmB-umbrella conjugates demonstrated antifungal in vitro activity...
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Automatic Watercraft Recognition and Identification on Water Areas Covered by Video Monitoring as Extension for Sea and River Traffic Supervision Systems
PublicationThe article presents the watercraft recognition and identification system as an extension for the presently used visual water area monitoring systems, such as VTS (Vessel Traffic Service) or RIS (River Information Service). The watercraft identification systems (AIS - Automatic Identification Systems) which are presently used in both sea and inland navigation require purchase and installation of relatively expensive transceivers...
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Real-Time PCR: molecular technique of many applications
PublicationReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...
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Luminescence recognition material as an INHIBIT logic gate in presence of Pb2+ and Cu2+ ions in aqueous solutions
PublicationA recognition material consisting of silica xerogel with amino-modified surface selectively recognizes Pb2+ and Cu2+ (but only in presence of Pb2+ ions) in aqueous solutions of other metal ions. The analytical action of the material is based on a significant change in luminescence emission spectra of the material after chemisorption of Pb2+ ions. In the presence of Pb2+ in octahedral coordination environment, a new broad and strong...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublicationThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...
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Equilibration Time of Solid Contact Ion-Selective Electrodes
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Efficient reagent immobilization procedure for ion-sensitive optomembranes
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Ionophores in polymeric membranes for selective ion recognition:impedance studies
PublicationW pracy badano dwa typy elektrod: membranowe elektrody jonoselektywne (ISE) oraz elektrody nowego typu all-solid-state (AAS). Elektrody AAS zawierają przewodzącą warstwę polimerową na węglu szklistym lub platynie, na który nałożona jest membrana zawierająca jonofor. Do badań użyto dwa jonofory: p-tert-butylokaliks[4]aren-korona-4 (L1) selektywnie kompleksująca jony Na+ oraz kaliks[4]aren-korona-6 (L2) selektywnie kompleksująca...
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Capillary Electrophoresis in Determination of Low Molecular Mass Organic Acids
PublicationThis paper presents overviews the capabilities of capillary electrophoretic techniques to determine low molecular mass organic acids in a variety of aqueous, gas and solid samples. It mainly focuses on short - chain carboxylic acids containing one or more carboxylic groups and possibly some other functional groups (hydroxyl, keto-, amino- etc.). Finally the procedures applied to the determine the acids in different matrices are...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...