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Search results for: MOLECULAR MOTORS
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Molecular mechanism(s) of regulation(s) of c-MET/HGF signaling in head and neck cancer
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling
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Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse 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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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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Selective adsorption of BTEX on calixarene-based molecular coordination network determined by 13C NMR spectroscopy
PublicationBenzene, toluene, ethylbenzene, and xylenes (BTEX), a class of volatile organic compounds, are harmful pollutants but also very important precursors in organic industrial chemistry. Among different approaches used for the BTEX treatment, the adsorption technology has been recognized as an efficient approach because it allows to recover and reuse both adsorbent and adsorbate. However, the selective adsorption of the components is...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublicationChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publicationnthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another...
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Virtual screening for small molecular non-covalent binders of the SARS-CoV-2 main protease
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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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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular 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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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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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublicationTime dependent density functional theory calculations are applied on a series of molecular photocatalysts of the type [(tbbpy)2M1(tpphz)M2X2]2+ (M1 = Ru, Os; M2 = Pd, Pt; X = Cl, I) in order to provide information concerning the photochemistry occurring upon excitation of the compounds in the visible region. To this aim, the energies, oscillator strengths and orbital characters of the singlet and triplet excited states are investigated....
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Chromatic monitoring technique for thickness measurementof thin transparent films.IV Workshopon Atomic and Molecular Physics.
PublicationW pracy opisano nową technikę monitorowania grubości cienkich warstw podczas procesu ich syntezy. Jest to optyczna metoda oparta na zdegenerowanej analizie widmowej tzw. modulacji chromatycznej. Umożliwia ona precyzyjny ciągły pomiar zmian grubości wzrastających warstw stosowanych w optyce.
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Influence of molecular organization of photo-active azo-phanes on thereactivity in monolayers at the air-water interface.
PublicationStwierdzono, że molekularna organizacja monowarstw na granicy powietrze-woda, otrzymanych z amfifilowego azofanu z nierozgałęzionym podstawnikiem n-dodecylowym różni się od tej uzyskanej dla analogu z objętościowym podstawnikiem ''tert''-oktylowym pod względem powierzchni zajmowanej przez cząsteczkę. Kompleksowanie jonów sodu z subfazy wodnej, jak wywnioskowano z pomiaru potencjału powierzchniowego, jest ułatwione w przypadku azofanu...
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Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublicationW 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
PublicationPraca 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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A cumulative probability function of instantaneous flicker sensation values measured in the industrial power system supplying the rolling mill motors
Open Research DataThe dataset presents a cumulative probability function CPF of the instantaneous flicker sensation level measured on the bus bars of the main switchgear of the industrial power network for the supply of rolling mills. The data were obtained during an experiment whose purpose was to determine a level of short-term and long-term flicker caused by voltage...
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The Adaptive Backstepping Control of Permanent Magnet Synchronous Motor Supplied by Current Source Inverter
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Computational investigations of acoustic radiation from end shields of small-power electric motor
PublicationW artykule omówiono rozwój metod modelowania własności akustycznych maszyn elektrycznych. Wskazano na pomijalny dotąd, znaczący udział drgań tarcz łożyskowych w emitowaniu hałasu przez silniki małej mocy. Na podstawie równania falowego potencjału prędkości wyprowadzono analityczne formuły do obliczeń akustycznych w polu bliskim tarczy łożyskowej. Zamieszczono uzyskane z serii obliczeń dla pracującego silnika, rozkłady ciśnienia...
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Novel adaptive flux observer for wide speed range sensorless control of induction motor
PublicationA new adaptive flux observer of induction motor is presented in the paper. The Lyapunov theory is utilized for derivation of the adaptation law of rotor flux angular speed, which acts as unknown parameter in an augmented induction motor model. In the field weakening region, where stray fluxes are comparable with rotor flux magnitude, the air-gap flux stabilization is proposed. An air-gap flux multiscalar model is derived for stator...
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Comparison of two methods for parameters selection of the proportional observer of induction motor state variables
PublicationArtykuł opisuje problemy odtwarzania prędkości obrotowej wału maszyny indukcyjnej przy wykorzystaniu estymatorów MRAS. Porównano dwie metody doboru wzmocnień obserwatora, analityczną i bazującą na algorytmach genetycznych
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Control Systems of an Induction and Synchronous Motor Supplied by Current Source Converter Working as Generator
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The Methodology for Determining the Theoretical Based on the Characteristics of Effective Absorbency Versus Pressure Drop in the Motor
PublicationThis article describes a method for determining the theoretical and actual working volume of a hydraulic motor. It has been shown that the actual working volume of the motor is the sum of the theoretical working volume and the additional volume that depends on the pressure drop in the working chambers of the motor. It was also shown that the volumetric losses in the hydraulic motor are not only a function of the pressure drop in...
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Nonlinear control of five phase induction motor with synchronized third harmonic flux injection
PublicationThe paper deals with the novel control system for five phase induction motor (IM) that enables the injection of the rotor flux 3rd harmonic component. Two multiscalar models are transformed from the 1-1 and 2-2 vector models developed in the 1st and 3rd harmonic planes. Based on the obtained multiscalar models the synthesis of dual multiscalar control is established. The obtained two multiscalar control systems can independently...
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The effect of the motor filters on earth fault current waveform in circuits with variable speed drives
PublicationIn circuits with variable speed drives distorted earth fault current flows. Earth fault current distortion influences the threshold of ventricular fibrillation. This paper presents earth fault current distortion in circuits with variable speed drives when motor filter is used. Two types of motor filter are analyzed. For every type of filter the effect of earth fault current distortion on ventricular fibrillation is evaluated.
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The effect of the motor filters on earth fault current waveform in circuits with variable speed drives
PublicationIn circuits with variable speed drives distorted earth fault current flows. Earth fault current distortion influences the threshold of ventricular fibrillation. This paper presents earth fault current distortion in circuits with variable speed drives when motor filter is used. Two types of motor filter are analyzed. For every type of filter the effect of earth fault current distortion on ventricular fibrillation is evaluated.
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Assembling and testing of quasi-static hybrid piezoelectric motor based on electroactive lubrication principle
PublicationThe presented paper concerns a novel concept of hybrid piezoelectric motor based on electroactive lubrication principle. Its structure is combined of quasi-static and resonance piezoelectric actuators, synchronizing their work to generate the rotary movement. The hybrid motor topology is compared to the existing piezoelectric motors, regarding its field of applications in embedded systems with very high security requirements. The...
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Losses and power balance in hydraulic satellite motor supplied with oil and HFA-E emulsion
PublicationMineral oil and HFA-E emulsion are liquids which differ in viscosity, density and lubricant properties. Therefore, supplying hydraulic satellite motor with these liquids, differences between quantity of hydraulic, volumetric and mechanical losses are observed. These losses influence efficiency of conversion of hydraulic energy into mechanical energy and thereby power balance of motor. The research of satellite motor has been conducted...
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Theoretical and mathematical models of the torque of mechanical losses in a hydraulic rotational motor for hydrostatic drive
PublicationW pracy przedstawiono modele teoretyczne i matematyczne momentu strat mechanicznych występujących w silniku hydraulicznym obrotowym o stałej teoretycznej chłonności qMt silnika na obrót wału (o stałej teoretycznej objętości roboczej VMt silnika) i o zmiennej chłonności qMgv = bM qMt na obrót wału (o zmiennej geometrycznej objętości roboczej VMgv silnika). Modele mają służyć badaniom laboratoryjnym i symulacyjnym strat energetycznych...
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Review of Linear Electric Motor Hammers—An Energy-Saving and Eco-Friendly Solution in Industry
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Model-Free Controller Tuning Based on DFT Processing: Application to Induction Motor Drives
PublicationIn this paper, we present a new approach based on discrete Fourier transform (DFT) analysis for controller tuning of the closed-loop system with unknown plant. The DFT analysis is used to process the closed-loop measurements collected online to derive the frequency response of an initial closed-loop system that does not provide a good performance. Based on the closed-loop frequency response data, we propose two methods for tuning PID...
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Sensorless Field Oriented Control of Five Phase Induction Motor with Third Harmonic Injection
PublicationIn this paper, a sensorless field oriented control system of five-phase induction machine with the 3rd harmonic rotor flux is presented. Two vector models, α1-β1 and α3-β3, were transformed into d1-q1, d3-q3 models oriented in rotating frames, which correspond to the 1st and 3rd harmonic plane respectively. The authors proposed the linearization of the model in d-q coordinate frames by introducing a new variable “x” which is proportional...
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Targeting mTORs by omega-3 fatty acids: A possible novel therapeutic strategy for neurodegeneration?
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The Influence of Water and Mineral Oil on Mechanical Losses in a Hydraulic Motor for Offshore and Marine Applications
PublicationIn this paper, mechanical losses in a hydraulic motor supplied with water and mineral oil (two liquids having significantly different viscosity and lubricating properties) are described and compared. The experimental tests were onducted using a special design (prototype) of a hydraulic satellite motor. The design of the satellite motor is presented. This motor was developed to supply both with water and mineral oil and features...
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Weather Hazard Avoidance in Modeling Safety of Motor-Driven Ship for Multicriteria Weather Routing
PublicationWeather routing methods find the most suitable ocean?s route for a vessel, taking into account changeable weather conditions and navigational constraints. In the multicriteria approach based on the evolutionary SPEA algorithm one is able to consider a few constrained criteria simultaneously. The approach applied for a ship with hybrid propulsions has already been presented by one of the authors on previous TransNav?2009. This time...
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Energy Loss Coefficients ki in a Displacement Pump and Hydraulic Motor used in Hydrostatic Drives
PublicationThe article aims at defining and analysing the energy loss coefficients in design solutions of rotating displacement machines, with a piston machine as an example. The energy losses observed in these machines include mechanical loss, volumetric loss, and pressure loss. The scale and relations between these losses in different machines depend on machine design and manufacturing quality, and on operating parameters. The operating...
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The influence of the motor filtrers on harmonic current emmision in the pro-ective connection of drive systems.
PublicationThis paper contains detailed analysis of currents in protective wire in engine supplied from frequency converter without any external filters added. It was found that the peak value of current in protective conductor of engine was about 1500 mA at frequencies 5 Hz 50 Hz. In the continuation of research the dU/dt type motor filter and the sinusoidal filter were tested. It was found that the current in protective wire decreased...
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CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
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Advances In Atomic Molecular and Optical Physics
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International Journal of Molecular and Cellular Medicine
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Statistical Applications in Genetics and Molecular Biology
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International Journal of Molecular Epidemiology and Genetics
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Hormone Molecular Biology and Clinical Investigation
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