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Wyniki wyszukiwania dla: MOLECULAR DOCKING SIMULATIONS
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Molywood: streamlining the design and rendering of molecular movies
PublikacjaMotivation 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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Numerical simulations of a triaxial test in granular bodies using discrete particle simulations with contact moments
PublikacjaW artykule przedstawiono wyniki symulacji badania trójosiowego dla materiałów granulowanych. Obliczenia wykonano przy zastosowaniu metody DEM. Pokazano wpływ momentów kontaktowych na wytrzymałość próbki. Zbadano wpływ parametrów mikroskopowych.
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Fatty acids as molecular carriers in cleavable antifungal conjugates
PublikacjaConjugates 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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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Dane BadawczeThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublikacjaTelomerase 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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Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublikacjaThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
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CCDC151 Mutations Cause Primary Ciliary Dyskinesia by Disruption of the Outer Dynein Arm Docking Complex Formation
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Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates
PublikacjaInefficient 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
PublikacjaCurrently, 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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Molecular Biology of Meniscal Healing: A Narrative Review
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Simulations of wave propagation and attenuation in fields of colliding ice floes
Dane BadawczeThis dataset contains results of numerical smulations of sea ice-wave interactions, corresponding to laboratory experiments conducted at the Large Ice Model Basin (LIMB) at the Hamburg Ship Model Basin (HSVA) as part of the LS-WICE ("Loads on Structure and Waves in Ice"; https://zenodo.org/record/1067170#.XrLt_dhpxhE) project. THe simulations were conducted...
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Non-uniqueness of fracture parameter choice in simulations of concrete cracking at mesoscale level
PublikacjaIn the paper a non-uniqueness of fracture parameter choice in simulations of cracking process in plain concrete specimens at mesoscale level under monotonic static loading is analysed. The Finite Element Method is used, where cracks are defined in a discrete way using interface cohesive elements with nonlinear material law including softening. The concrete mesostructure (such as: cement matrix, air voids, aggregates, and Interfacial...
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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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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublikacjaWe 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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Fast Multi-Objective Antenna Design Through Variable-Fidelity EM Simulations
PublikacjaA technique for fast multi-objective antenna optimization is introduced. A kriging interpolation surrogate constructed from sampled coarse-mesh EM simulations is utilized by multi-objective evolutionary algorithm (MOEA) to obtain the initial Pareto front approximation. The surrogate is defined in a subset of the original design space, determined by means of independently optimized individual objectives. Response correction techniques...
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Modelling and simulations in time-fractional electrodynamics based on control engineering methods
PublikacjaIn this paper, control engineering methods are presented with regard to modelling and simulations of signal propagation in time-fractional (TF) electrodynamics. That is, signal propagation is simulated in electromagnetic media described by Maxwell’s equations with fractional-order constitutive relations in the time domain. We demonstrate that such equations in TF electrodynamics can be considered as a continuous-time system of...
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Paweł Możejko dr hab.
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Application of advanced CFD simulations in seakeeping analysis of ships (case study)
PublikacjaThe novel design process of many types of ships needs estimation of seakeeping properties. Especially ships like Offshore Supply Vessels, Wind Farm Support Vessels, Research Vessels, ferries, military vessels, rescue vessels require extended analysis of ship behavior on rough sea. The main reason for improving ships operability in different sea conditions is need of rising efficiency of propulsion system, reducing hull added resistance,...
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Measurements and Simulations of Engineered Ultrasound Loudspeakers
PublikacjaSimulation and measurement results of the sound emitted from an ultrasound custom-made system with high spatial directivity are presented. The proposed system is using modulated ultrasound waves which demodulate in nonlinear medium resulting in audible sound. The system is aimed at enhancing the users’ personal audio space, therefore the measurements are performed using the Head and Torso Simulator which provides realistic reproduction...
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Simulations CAE of wood pellet machine
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FE simulations of a soil structure interface.
PublikacjaPrzedstawiono warunki brzegowe do opisu szorstkości ściany konstrukcji w kontakcie z gruntem. Wykonano doświadczenia i symulacje MES na bazie mikropolarnego prawa hipoplastycznego.
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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
PublikacjaThis 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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Improvement of ships seakeeping performance by application of the Full-scale CFD simulations – case study
PublikacjaThe ship’s fuel economy is increasingly important. The paper presents the effect of redesigning a case study ship for increasing seakeeping performance. Selected wave parameters reflects very difficult operational con-ditions existing on the North Sea and the Baltic Sea. The analyzed variants of a case study ship represent the latest developments of modern hull forms. The concepts similar to V-shaped bulbous bow, X-bow, X-aft,...
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Numerical Simulations and Tracer Studies as a Tool to Support Water Circulation Modeling in Breeding Reservoirs
PublikacjaThe article presents a proposal of a method for computer-aided design and analysis of breeding reservoirs in zoos and aquariums. The method applied involves the use of computer simulations of water circulation in breeding pools. A mathematical model of a pool was developed, and a tracer study was carried out. A simplified model of two-dimensional flow in the form of a biharmonic equation for the stream function (converted into...
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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublikacjaIn the paper experimental tests and numerical simulations of a full cross-section segment of ultimately designed foot-and cycle-bridge are presented. The experimental tests were conducted on element with length reduced to 3 m and unchanged (target) cross-section dimensions. The external skin of structure is GFRP laminate while internal core is PET foam. Several quasi-static tests were performed using hydraulic cylinder to generate...
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublikacjaMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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International Journal of Gaming and Computer-Mediated Simulations
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FDTD Simulations on Disjoint Domains with the Use of Discrete Green's Function Diakoptics
PublikacjaA discrete Green's function (DGF) approach to couple disjoint domains in the finite-difference time-domain (FDTD) grid is developed. In this method, total-field/scattered-field (TFSF) FDTD domains are associated with simulated objects whereas the interaction between them is modeled with the use of the DGF propagator. Hence, source and scatterer are simulated in separate domains and updating of vacuum cells, being of little interest,...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublikacjaThe 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
PublikacjaOver 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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SIMULATIONS OF FRACTURE IN CONCRETE BEAMS UNDER BENDING USING A CONTINUUM AND DISCRETE APPROACH
PublikacjaThe paper describes two-dimensional meso-scale results of fracture in notched concrete beams under bending. Concrete was modelled as a random heterogeneous 4-phase material composed of aggregate particles, cement matrix, interfacial transitional zones and air voids. Within continuum mechanics, the simulations were carried out with the finite element method based on a isotropic damage constitutive model enhanced by a characteristic...
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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublikacjaThis paper aimed at developing a new method of estimating the impact speed of a passenger car at the moment of a crash into a W-beam road safety barrier. The determination of such a speed based on the accident outcomes is demanding, because often there is no access to full accident data. However, accurate determination of the impact speed is one of the key elements in the reconstruction of road accidents. A machine learning algorithm...
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Static Load Test on Instrumented Pile – Field Data and Numerical Simulations
PublikacjaFor some time (since 8-10 years in Poland) a special static load tests on instrumented piles are carried out. Such studies are usually of a scientific nature and provide detailed quantitative data on the load transfer into the ground and characteristics of particular soil layers interaction with a pile shaft and pile base. Deep knowledge about the pile-subsoil interaction can be applied for a various design purposes, e.g. numerical...
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Machine Learning Algorithm-Based Tool and Digital Framework for Substituting Daylight Simulations In Early- Stage Architectural Design Evaluation
PublikacjaThe aim of this paper is to examine the new method of obtaining the simulation-based results using backpropagation of errors artificial neural networks. The primary motivation to conduct the research was to determine an alternative, more efficient and less timeconsuming method which would serve to achieve the results of daylight simulations. Three daylight metrics: Daylight Factor, Daylight Autonomy and Daylight Glare Probability have...
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Convergence of Monte Carlo algorithm for solving integral equations in light scattering simulations
PublikacjaThe light scattering process can be modeled mathematically using the Fredholm integral equation. This equation is usually solved after its discretization and transformation into the system of algebraic equations. Volume integral equations can be also solved without discretization using the Monte Carlo (MC) algorithm, but its application to the light scattering simulations has not been sufficiently studied. Here we present implementation...
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Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations
PublikacjaIn this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas–liquid...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublikacjaC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Molecular Oncology
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MOLECULAR PHARMACOLOGY
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Finite element method simulations of various cases of crash tests with N2/W4/A steel road barrier
PublikacjaThe subject of this study is performance of N2/W4/A steel road safety barrier investigated in numerical simulations. System was checked under several types of initial conditions, which were assumed basing on the TB11 and TB32 normative crash tests. The main goal of present study is to investigate the relationship between initial conditions (angle and velocity) of the impact and the severity indices (associated to the vehicle occupant) during...
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublikacjaAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Molecular Umbrellas Modulate the Selective Toxicity of Polyene Macrolide Antifungals
PublikacjaAntifungal 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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Real-Time PCR: molecular technique of many applications
PublikacjaReal-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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Broadening the scope of measurement and analysis of vibrations of an organ pipe employing intensity probe, simulations, and highspeed camera
PublikacjaThis paper shows an integrated approach to measure, analyze, and model phenomena occurring in an organ pipe driven by pressurized air. The aim of this paper is two-fold, i.e., to measure the pressure signal and the intensity field around the mouth by means of an intensity probe and to visualize and observe the motion of the air jet, which represents the excitation mechanism of the system. This is realized through two techniques,...
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Ocean mixed layer dynamics: high-resolution simulations of wind, wave and convective effects
Dane BadawczeThis dataset contains results of high-resolution numerical simulations of the ocean mixed layer (OML) forced by wind, waves and cooling from the atmosphere, i.e., under strongly turbulent, convective conditions. The goal is to provide detailed, three-dimensional information about OML circulation, turbulent kinetic energy, and temperature and salinity...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublikacjaThree 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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Monte Carlo simulations of the fracture resistance degradation of asphalt concrete subjected to environmental factors
PublikacjaThe paper presents the results of laboratory tests of SCB (semi-circular beam) samples of asphalt concrete, subjected to the destructive effect of water and frost as well as the aging processes. The determined values of material parameters show significant dispersions, which makes the design of mixtures difficult. Statistical analysis of the test results supplemented by computer simulations made with the use of the proprietary...
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Expedited Trust-Region-Based Design Closure of Antennas by Variable-Resolution EM Simulations
PublikacjaThe observed growth in the complexity of modern antenna topologies fostered a widespread employment of numerical optimization methods as the primary tools for final adjustment of the system parameters. This is mainly caused by insufficiency of traditional design closure approaches, largely based on parameter sweeping. Reliable evaluation of complex antenna structures requires full-wave electromagnetic (EM) analysis. Yet, EM-driven...
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Capillary Electrophoresis in Determination of Low Molecular Mass Organic Acids
PublikacjaThis 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...