Filtry
wszystkich: 97
Wyniki wyszukiwania dla: MOLECULAR MODELS
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublikacjaOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublikacjaIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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Fractional Calculus Evaluation of Hyaluronic Acid Crosslinking in a Nanoscopic Part of Articular Cartilage Model System
PublikacjaThis work presents a study of the mechanism of physical crosslinking of hyaluronic acid in the presence of common phospholipids in synovial joint organ systems. Molecular dynamic simulations have been executed to understand the formation of hyaluronan networks at various phospholipid concentrations. The results of the simulations suggest that the mechanisms exhibit subdiffusion characteristics. Transportation quantities derive...
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Paweł Możejko dr hab.
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Calculation of Vibrational Resonance Raman Spectra of Molecules Using Quantum Chemistry Methods
PublikacjaThe 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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Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublikacjaA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
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Application 2D Descriptors and Artificial Neural Networks for Beta-Glucosidase Inhibitors Screening
PublikacjaBeta-glucosidase inhibitors play important medical and biological roles. In this study, simple two-variable artificial neural network (ANN) classification models were developed for beta-glucosidase inhibitors screening. All bioassay data were obtained from the ChEMBL database. The classifiers were generated using 2D molecular descriptors and the data miner tool available in the STATISTICA package (STATISTICA Automated Neural...
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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
PublikacjaAmphotericin 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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Vibrational Sum-Frequency Generation Activity of a 2,4-Dinitrophenyl Phospholipid Hybrid Bilayer: Retrieving Orientational Parameters from a DFT Analysis of Experimental Data
PublikacjaThe 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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Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublikacjaOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
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Low energy differential elastic electron scattering from acetonitrile (CH3CN)
PublikacjaMeasurements of elastic differential cross sections for electron scattering from acetonitrile (CH3CN) have been performed utilizing a crossed electron-molecular beam experiment and with the relative flow method, for the incident electron energy range of 0.7 eV–30 eV and the scattering angle range of 10◦–130◦. These differential cross sections have been used to calculate the elastic integral and momentum- transfer cross sections,...
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Models in the Research Process of Psoriasis
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Average Size of a Suffix Tree for Markov Sources
PublikacjaWe study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size of such a suffix tree is asymptotically equivalent to the average size of a trie built over n independentsequences from the same Markovian source. This equivalenceis only known for memoryless...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Problems with modelling the strength properties of sailing vessels rigging ropes
PublikacjaThis article presents the basic parameters of soft ropes: natural fibre ropes, soft wire ropes and synthetic fibre ropes used for running rigging. There are only several materials still used for the production of natural fibre ropes, including cotton, jute, hemp, sisal and manila hemp. The most commonly used soft wire ropes are twisted pair ropes; for smaller diameters there is a 6x19M - FC rope and for larger diameters – 6x37M...
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Negative Poisson’s ratio from pentagons: A new auxetic structure combining three different auxetic mechanisms
PublikacjaA novel class of two-dimensional auxetic structures based on the pentagon motif is proposed. Their mechanical properties are investigated by combining molecular mechanics simulations with a simple three-parameter mechanical model which assumes perfectly elastic behavior. It is predicted that the proposed structures – termed as double re-entrant honeycomb – may possess unique mechanical characteristics, which include complete and...
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Integrating Statistical and Machine‐Learning Approach for Meta‐Analysis of Bisphenol A‐Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
PublikacjaBisphenols are important environmental pollutants that are extensively studied due to different detrimental effects, while the molecular mechanisms behind these effects are less well understood. Like other environmental pollutants, bisphenols are being tested in various experimental models, creating large expression datasets found in open access storage. The meta‐analysis of such datasets is, however, very complicated for various...
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Transplantable Melanomas in Hamsters and Gerbils as Models for Human Melanoma. Sensitization in Melanoma Radiotherapy—From Animal Models to Clinical Trials
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Nonconventional 1,8-Diazafluoren-9-One Aggregates for Green Light Enhancement in Hybrid Biocompatible Media
PublikacjaOrganic aggregates currently play a prominent role, mainly for their unique optoelectronic properties in the aggregated state. Such properties can be related to the aggregates’ structure and the molecular packing mode. In the literature, we have well-established models of H and J aggregates defined based on the molecular exciton model. However, unconventional aggregates, the most unrecognized forms, have been generating interest...