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Wyniki wyszukiwania dla: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Molecular geometry of phenylboronic acid
Dane BadawczeData presents molecular geometry of the ground singlet state of phenylboronic acid. The geometry was obtained via DFT calculations using Becke–Lee–Yang–Parr density functional (B3LYP) with the balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublikacjaDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Dynamics of Ice Jam Formation and Release
PublikacjaThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
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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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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublikacjaMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Modelling gene expression of a self-regulating protein
PublikacjaWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation
PublikacjaIntroduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession...
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Perceptual and Motor Effects of Muscle Co-activation in a Force Production Task
PublikacjaWe tested several predictions of the theory of motor control with spatial referent coordinates related to effects of muscle coactivation on force production and perception. In particular, we predicted that subjects would produce unintentional force increase by finger flexors and be unaware of this force increase. Healthy subjects performed steady force production task in isometric conditions with visual feedback on the force level....
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Structure and properties comparison of poly(ether-urethane)s based on nonpetrochemical and petrochemical polyols obtained by solvent free two-step method
PublikacjaThe application of thermoplastic polyurethanes (TPU) is becoming more and more extensive, and the decreasing of used petrochemical monomers and reduction of energy for the polymerization and processing processes is getting increasingly important. In this paper, we confirmed the positive influence of high bio-based monomers contents (by replacing petrochemical polyol and glycol by bio-based counterparts) on processing and properties...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Some Aspects of Shear Behavior of Soft Soil–Concrete Interfaces and Its Consequences in Pile Shaft Friction Modeling
PublikacjaThis paper examines the stiffness degradation and interface failure load on soft soil–concrete interface. The friction behavior and its variability is investigated. The direct shear tests under constant normal load were used to establish parameters to hyperbolic interface model which provided a good approximation of the data from instrumented piles. Four instrumented piles were used to obtain reference soil–concrete interface behavior....
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Modeling of a rock fall using the discrete element method and study of the seismic signal
PublikacjaW artykule przedstawiono opis fal sejsmicznych, zastosowanie dyskretnej metody elementów do opisu obrywu skalnego, opis programów obliczeniowych oraz obliczenia numeryczne wg. podanych programów obliczeniowych.
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Approaches to experiment based friction modeling: polynomial approximation versus ann approximation
PublikacjaBadano warunki (poziom wymuszeń), przy których następowało wzbudzenie drgań mechanicznych przy tarciu ślizgowym konforemnego skojarzenia próbek wykonanych z Al2O3 (płaskie czoło tulei obracającej się względem swojej osi - powierzchnia płaska). Uzyskane dane eksperymentalne wykorzystano następnie do zbudowania modeli - stosując aproksymację wielomianami albo sztuczną siecią neuronową (ANN).
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Modeling saturation of main magnetic circuit of cage induction motors in presence of eccentricity
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Wybrane problemy modelowania obiektów technicznych : Chosen problems in the modeling of technical objects
PublikacjaBudowa modeli obiektów technicznych połączona z identyfikacją przyjętych wstępnie parametrów oraz diagnostyką weryfikacyjną porównującą obiekt z modelem w celu sprawdzenia rzeczywistych przedziałów wartości istotnych właściwości obiektu, jest cyklicznym procesem udoskonalającym zarówno model, jak również kolejne wersje obiektu rzeczywistego. Wirtualne programy w pamięciach komputerowych pozwalają projektantom na sprawdzenie swojego...
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<title>Modeling of noncontact temperature measurement system using multiwavelength pyrometry</title>
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Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in Tissues
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Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry
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Modeling of TiO2-Based Electron-Selective Contacts for Crystalline Silicon Solar Cells
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Assessment of the Reliability of Wind Farm Device on the Basis of Modeling Its Operation Process
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3D Modeling of Discontinuity in the Spatial Distribution of Apartment Prices Using Voronoi Diagrams
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Experimental Study and Finite Element Modeling of Reinforced Concrete Column Having an Opening
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<title>Cavity control system essential modeling for the TESLA linear accelerator</title>
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TESLA cavity modeling and digital implementation in FPGA technology for control system development
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Modeling the risk of ship grounding—a literature review from a risk management perspective
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New method of fractional order integrator analog modeling for orders 0.5 and 0.25
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Coal-derived conductive pavement for winter de-icing: prototype, modeling, and simulation
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Time Domain Modeling of Propeller Forces due to Ventilation in Static and Dynamic Conditions
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Activity evaluation of some psychoactive drugs with the application of QSAR/QSPR modeling methods
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Three-dimensional CFD modeling of thermal behavior of a disc brake and pad for an automobile
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Modeling of selected transducer designs for optical pressure sensors using polarization interferometry
PublikacjaW artykule przedstawiono wyniki modelowania metodą Elementów Skończonych wybranych konstrukcji membran do zastosowań w interferometrycznych czujnikach ciśnienia. Omówiono zależność prametrów membran od kształtu membrany, jej wymiarów i zastosowanego materiału. Zakres odkształcen badanych membran jest niezbyt duży, co może pogarszać dokładność pomiaru czujników ciśnienia, w których będą one stosowane Omówiono kierunki dalszych...
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Attempt to modeling with FEM of the impact of initial oval shape of tube into creep process.
PublikacjaOpisano zasady modelowania metodą elementów skończonych zjawiska pełzania dla elementów typu rura oraz pokazano wynik próby modelowania za pomocą MES wpływu początkowej owalności rury na proces pełzania.
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Impact of trajectory simplification methods on modeling carbon dioxide emissions from ships
PublikacjaModels of ship fuel consumption and emissions play an essential role in estimating global shipping’s greenhouse gas emissions. They are also widely used for verification of reported CO2 emissions for systems like EU MRV (Monitoring, Reporting and Verification) or IMO DCS (Data Collection System). Such models achieve high accuracy using historical spatiotemporal information about each ship from AIS data. However, this approach requires substantial...
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Transformation of Energy Markets: Description, Modeling of Functioning Mechanisms and Determining Development Trends
PublikacjaOne of the key contemporary economic and social issues today is the global energy transition. Energy transition processes are having a significant impact on the development of world economies, increasing their TFP and leading to an increase in their level of innovation through the transfer of myriad new technologies. These processes also contribute to an increase in foreign direct investment and, consequently, an increase in the...
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Modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models
PublikacjaThe present study deals with assessment of ecotoxicological parameters of 9 drugs (diclofenac (sodium salt), oxytetracycline hydrochloride, fluoxetine hydrochloride, chloramphenicol, ketoprofen, progesterone, estrone, androstenedione and gemfibrozil), present in the environmental compartments at specific concentration levels, and theirmutual combinations by couples against Microtox® and XenoScreen YES/YAS® bioassays. As the quantitative...
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RENOVATION OF ARCHIVE AUDIO RECORDINGS USING SPARSE AUTOREGRESSIVE MODELING AND BIDIRECTIONAL PROCESSING
PublikacjaThe paper presents a new approach to elimination of broadband noise and impulsive disturbances from archive audio recordings. The proposed adaptive Kalman-like algorithm, based on a sparse autoregressive model of the audio signal, simultaneously detects noise pulses, interpolates the irrevocably distorted samples and performs signal smoothing. It is shown that bidirectional (forward-backward) processing of the archive signal improves...
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Modeling the effect of parasitic capacitances on the dead-time distortion in multilevel NPC inverters
PublikacjaA simple model is derived and verified for evaluating the effect of parasitic capacitances on the dead-time related voltage distortion in multilevel NPC voltage source inverters. The model permits well-defined and precise compensation of dead-time distortion, exhibiting meaningful improvement on compensation methods neglecting the effects of parasitic capacitances. A simple formula is given for evaluating the capacitances as serial/parallel...
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Modeling of a rock fall using the discrete element method and study of the seismic signal
PublikacjaMechanizm dużego spadającego bloku skalnego lub lawiny pozostaje nadal słabo rozpoznany zarówno w zakresie pęknięć jak i procesów propagacji. Jedynie ilościowe dane, które aktualnie są mierzone i uchwytne podczas spadania skały, zarejestrowane są jako sejsmiczne sygnały przez szereg sejsmografów. Właściwości sygnału (amplituda, trwanie, częstotliwość) są wyraźnie powiązane z cechami spadania (masa, wysokość spadania, odległość...
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Modeling of hazards, consequences and risk for safety assessment of ships in damaged conditions in operation
PublikacjaPraca dotyczy problematyki związanej z modelowaniem zagrożeń, konsekwencji i ryzyka, w metodzie oceny bezpieczeństwa statków w stanie uszkodzonym. Metoda oparta jest na podejściu zorientowanym na ocenę zachowania się statku i ocenę ryzyka wypadku. Kolejne moduły metody dotyczą identyfikacji zagrożeń i scenariuszy wypadków oraz oceny i kontroli ryzyka. Ocenę ryzyka można przeprowadzić przy zastosowaniu elementów metodyki Przypadku...
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Evaluation of Multimedia Stream Processing Modeling Language from the Perspective of Cognitive Dimensions
PublikacjaW referacie zawarto opis zastosowania wymiarów poznawczych do oceny języka modelowania przetwarzania strumieni multimedialnych, nazwanego MSP-ML, w trakcie tworzenia tego języka. Poszczególne części referatu prezentują kontekst i motywacje oceny MSP-ML, metodę oceny, rezultaty oceny oraz porównanie rezultatów oceny z wynikami otrzymanymi za pomocą innych metod oceny języków modelowania wizualnego.
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Modeling of Composite Shells in 6-Parameter Nonlinear Theory with Drilling Degree of Freedom
PublikacjaWithin the framework of a 6-parameter nonlinear shell theory, with strain measures of Cosserat type, constitutive relations are proposed for thin elastic composite shells. The material law is expressed in terms of five engineering constants of classical anisotropic continuum plus an additional parameter accounting for drilling stiffness. The theory allows for unlimited displacements and rotations. A number of examples are presented...
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KOLMOGOROV EQUATION SOLUTION: MULTIPLE SCATTERING EXPANSION AND PHOTON STATISTICS EVOLUTION MODELING
PublikacjaWe consider a formulation of the Cauchy problem for the Kolmogorov equation which corresponds to a localized source of particles to be scattered by a medium with a given scattering amplitude density. The multiple scattering amplitudes are introduced and the corresponding series solution of the equation is constructed. We investigate the integral representation for the first series terms, its estimations and values of the photon...
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Modeling of subarachnoid space width change caused by blood circulation in brain vessels
PublikacjaThe subarachnoid space is an anatomic space, lying in the central nervous system, between the arachnoid membrane and the pia mater. It is filled with cerebrospinal fluid, which protects and nourishes the brain. The pathological disorder of the subarachnoid space (i.e. increase or decrease of its width) a ects the nervous system. Therefore, it is important to diagnose the width changes of the subarachnoid space. One way to support...
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Modeling of Transient Photocurrent in Organic Semiconductors Incorporating the Annihilation of Excitons on Charge Carriers
PublikacjaThe role of the annihilation of excitons on charge carriers has been theoretically investigated in organic semiconductors. We have developed the numerical drift-diffusion model by incorporation terms which describe the annihilation process. The transient photocurrent has been calculated for different injection barrier heights, exciton mobilities, and annihilation rate constants. We have demonstrated that the annihilation has a...
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Modeling of bearing capacity of footings on sand within stochastic micro-polar hypoplasticity.
PublikacjaAnalizowano numerycznie efekt wstępnego rozkładu wskaźnika porowatości na wytrzymałość i strefy ścinania w problemach fundamentów na piasku w skali modelowej. Obliczenia wykonano przy zastosowaniu stochastycznej metody elementów skończonych i mikropolarnego modelu hipoplastycznego. Wskaźnik porowatości miał formę skorelowanych pól stochastycznych. Dodatkowo obliczono efekt skali dla 3 różnych szerokości fundamentów.
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Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublikacjaW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublikacjaPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Ljung-Box test values of selected companies of the Warsaw Stock Exchange
Dane BadawczeThe following dataset includes the Warsaw Stock Exchange market analysis using the Ljung-Box test. Partial autocorrelations up to the 5th order were analyzed, because it will allow to observe the relationship within one week of stock exchange quotations. In the case of the WIG index, the 1st and 2nd order correlation turned out to be statistically significant....