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Search results for: NISKOWYMAROWA DYNAMIKA
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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A non-adiabatic wavepacket dynamical study of the low energy chargetransfer process in the S3+ + H collision
PublicationThe collisional system S3+ + H?S2+ + H+ has been studied using a time-dependent wavepacket methodologyin two-dimensions. Using available potential energy surfaces and coupling matrix elementsobtained from multireference ab initio calculations, five non-adiabatically coupled electronic states of1P symmetry have been included in the dynamical simulations. The collision has been studied in thelow energy regime of 1-10 eV. The wavepacket...
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Combining Computational Fluid Dynamics with a Biokinetic Model for Predicting Ammonia and Phosphate Behavior in Aeration Tanks
PublicationThe aim of this study was to use computational fluid dynamics for predicting the behavior of reactive pollutants (ammonia and phosphate) in the aerobic zone of the bioreactor located at the Wschod wastewater treatment plant in Gdansk, Poland. The one-dimensional advection-dispersion equation was combined with simple biokinetic models incorporating the Monod-type expressions as source terms for the two pollutants. The problem was...
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Aerodynamic shape optimization by variable-fidelity computational fluid dynamics models: a review of recent progress
PublicationA brief review of some recent variable-fidelity aerodynamic shape optimization methods is presented.We discuss three techniques that—by exploiting information embedded in low-fidelity computationalfluid dynamics (CFD) models—are able to yield a satisfactory design at a low computational cost, usu-ally corresponding to a few evaluations of the original, high-fidelity CFD model to be optimized. Thespecific techniques considered here...
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Orientational Order and Dynamics of Nematic Multipodes Based on Carbosilazane Cores Using Optical and Dielectric Spectroscopy
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Firing map for periodically and almost-periodically driven integrate-and-fire models: a dynamical systems approach
PublicationWe consider the Leaky Integrate-and-Fire and Perfect Integrator models of neuron’s dynamics with the input function being periodic and almost-periodic (in the sense of Stepanov). In particular we analyze properties and dynamics of the so-called firing map, which iterations give timings of consecutive spikes of a neuron. In case of a periodic input function we provide a detailed description of the sequence of interspike-intervals,...
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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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On dynamics of flexible branched shell structures undergoing large overall motion using finite elements
PublicationZaprezentowano autorski algorytm do analizy dynamicznej powłok sprężystych oparty na niejawnym schemacie Newmarka. Rozważania dotyczą całkowania po czasie dynamicznych równań ruchu sformułowanych w ramach nieliniowej sześcioparametrowej teorii powłok. Opracowanie zawiera pewne elementy analizy statycznej, poprzedzającej badania dynamiczne. Przykłady numeryczne prezentują zastosowanie algorytmu stanowią podstawową część pracy.
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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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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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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Adaptive Dynamical Systems Modelling of Transformational Organizational Change: with Focus on Organizational Culture and Organizational Learning
PublicationTransformative Organizational Change becomes more and more significant both practically and academically, especially in the context of organizational culture and learning. However computational modeling and a formalization of organizational change and learning processes are still largely unexplored. This paper aims to provide an adaptive network model of transformative organizational change and translate a selection of organizational...
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Adaptive Dynamical Systems Modelling of Transformational Organizational Change with Focus on Organizational Culture and Organizational Learning
PublicationTransformative Organizational Change becomes more and more significant both practically and academically, especially in the context of organizational culture and learning. However computational modeling and a formalization of organizational change and learning processes are still largely unexplored. This paper aims to provide an adaptive network model of transformative organizational change and translate a selection of organizational...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublicationTime-dependent density functional theory calcula- tions combinedwith the Marcus theory of electron transfer (ET) were app lied on the molecular photocatalys t [(tbbpy) 2 Ru(tpph z)PdC l 2 ] 2 + in order to elucidate thelight-in- duced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational resultsshow that after the initial excitation, metal (Ru) to ligand (tpphz)chargetransfer...
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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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Computational Fluid Dynamics Simulation of Gas–Liquid Multiphase Flow in T-junction for CO2 Separation
PublicationThe article presents the results of a computational fluid dynamics (CFD) analysis of gas-liquid multiphase flow. The simulation was conducted using CFD code and the Euler–Euler approach. The presented study relates to the non–reactive, steady-state, turbulent flow of water and carbon dioxide mixture in a 3D pipe. Separation phenomenon between phases is observed. The solution was obtained using a mixture model. Different values...
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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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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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On quantum cryptography with bipartite bound entangled states
PublicationOstatnio pokazano bezpośrednie zastosowanie splątania związanego w kryptografii kwantowej. W niniejszym artykule dokonano przeglądu niektórych najnowszych osiągnięć dotyczących tego zagadnienia. W szczególności przypomniano istotne pojęcia i definicje. Ponadto podano nową konstrukcję stanów o splątaniu związanym, posiadających bezpieczne korelacje, dostarczając w ten sposób niskowymiarowe (6x6) stany o splątaniu związanym z niezerowym...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Burn depths evaluation based on active dynamic IR thermal imaging - A preliminary study
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Corrosion resistance evaluation of Al-based alloys by means of dynamic electrochemical impedance spectroscopy
PublicationW pracy przedstawiono wyniki badań stopów aluminium wykonane za pomocą dynamicznej elektrochemicznej spektroskopii. Na podstawie uzyskanych widm impedancyjnych zostały pokazane zmiany parametrów elektrycznego schematu zastępczego z potencjałem. Stwierdzono, że dodatek magnezu do badanego stopu obniża właściwości przeciwkorozyjne stopu.
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Robust Parameter Estimation and Output Prediction for Reactive Carrier-Load Nonlinear Dynamic Networks
PublicationIn this paper an extension of on-line model simplification technique for a class of networked systems, namely reactive carrier-load nonlinear dynamic networked system (RCLNDNS), kept within point-parametric model (PPM) framework is addressed. The PPM is utilised to acquire a piece wise constant time-varying parameter linear structure for the RCLNDNS suitable for the on-line one step ahead prediction that may be applied to monitoring...
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Creating dynamic maps of noise threat using pl-grid infrastructure; materiały konferencyjne
PublicationThis paper presents functionality and operation results of the system for creating dynamic maps of noise thread with the use of the PL-Grid infrastructure integrated with distributed sensors network for measuring, modeling and rendering noise level distribution. The work presented provides a demonstration of the services being prepared within the PLGrid Plus project. Specific computational environments, so called domain grids,...
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DYNAMIC MECHANICAL BEHAVIOUR OF GFRP COMPOSITES WITH SiO2 NANO PARTICLES REINFORCED EPOXY MATRIX
PublicationDynamic mechanic (DMA) tests were performed to compare the mechanical behaviour of glass fibre reinforced epoxy laminate composites with SiO2 nanoparticle reinforced matrix. The selection of the most promising nanoparticle concentrations was considered in terms of elastic modulus and glass transition temperature. The reference specimens (0% nanoparticles) did not contain diluent accordingly the results do not allow the exact comparison...
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Dynamic mass measurement in checkweighers using a discrete time-variant low-pass filter
PublicationConveyor belt type checkweighers are complex mechanical systems consisting of a weighing sensor (strain gauge load cell, electrodynamically compensated load cell), packages (of different shapes, made of different materials) and a transport system (motors, gears, rollers). Disturbances generated by the vibrating parts of such a system are reflected in the signal power spectra in a form of strong spectral peaks, located usually in...
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DYNAMIC ANALYSIS OF HISTORIC RAILWAY BRIDGES IN POLAND IN THE CONTEXT OF ADJUSTING THEM TO PENDOLINO TRAINS
PublicationThe article presents the dynamic analysis of the historic railway bridge in Tczew as an example of the usefulness of such type of bridge for high-speed trains. The model of the bridge and the simulation of rolling stock passage was performed in SOFISTIK program. The scope of work includes experimental studies, the solution of the problem concerning the correct solution features dynamic model takes into account the dependencies...
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Corrosion resistance evaluation of Al‐based alloys by means of dynamic electrochemical impedance spectroscopy
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Evaluation of corrosion inhibition of brass-118 in artificial seawater by benzotriazole using Dynamic EIS
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Evaluation of corrosion inhibition of brass -118 in artificial seawater by benzotriazole using dynamic EIS
PublicationPrzedstawiono wyniki korozji mosiądzu 118 w sztucznej wodzie morskiej oraz efekt inhibicyjny benzotriazolu (BTA) przy użyciu nowoczesnej dynamicznej elektrochemicznej spektroskopii impedancyjnej (DEIS). metoda ta pozwala śledzić dynamikę procesu korozyjnego i efektu inhibicyjnego poprzez ocenę parametrów elektrycznych obwodu zastępczego. Chwilowe widma impedancyjne rejestrowane przez 10h wykazują iż ekspozycja przez okres kilku...
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Measurement of dynamic pulsations in bulk solid during silo discharging using ECT method
PublicationW pracy przedstawiono wyniki pomiarów pulsacji materiału sypkiego pomieroznych z zastosowaniem metody pomiarowej ECT. Analizę dynamicznych zmian koncetracji przperowadzono dla podstawowych(surowych) danych pomiarowych oraz danych zrekonstruowanych
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Investigation effect of benzotriazole on the corrosion of brass-MM55 alloy in artificial seawater by dynamic EIS
PublicationW pracy przedstawiono wyniki badań impedancyjnych otrzymanych podczas ekspozycji stopu MM55 w środowisku sztucznej wody morskiej. Wykazano ścisłą korelację charakterystyk impedancyjnych ze stężeniem benzotriazolu. Przedstawiono czasową ewolucję ochronnego efektu inhibicyjnego.
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Dynamic Re-Clustering Leach-Based (Dr-Leach) Protocol for Wireless Sensor Networks
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Cable stayed bridge over Vistula river in Plock. Dynamic analysis and site test
PublicationBudowę mostu przez rzekę Wisłę w Płocku ukończono w 2006 roku. Główne przęsło o długości 375 m zaprojektowano jako stalową konstrukcję podwieszoną. W celu weryfikacji konstrukcji zbudowano przestrzenny model MES. Badano zachowanie się konstrukcji mostu pod wpływem statycznego i dynamicznego obciążenia. W dalszym etapie przeprowadzono badania in - situ weryfikujące analizy numeryczne oraz założenia projektowe. Na bazie modelu MES...
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NUMERICAL SIMULATION OF CRATER CREATING PROCESS IN DYNAMIC REPLACEMENT METHOD BY SMOOTH PARTICLE HYDRODYNAMICS
PublicationA theoretical base of SPH method, including the governing equations, discussion of importance of the smoothing function length, contact formulation, boundary treatment and finally utilization in hydrocode simulations are presented. An application of SPH to a real case of large penetrations (crater creating) into the soil caused by falling mass in Dynamic Replacement Method is discussed. An influence of particles spacing on method...
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Microstructural evolution of 6061 aluminium alloy subjected to static and dynamic compression at low temperature
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Multicoil dynamic wireless power transfer topology with shared primary side compensation system
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Digital processing of pulse signal from light-to-frequency converter under dynamic condition
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Oiled soil washing in dynamic conditions by micellar surfactants solutions and obtained effluents treatment
PublicationZbadano możliwość zastosowania micelarnych roztworów biosurfaktantu (JBR 425), surfaktantów syntetycznych (Rokanolu NL5, NL6, NL8) i ich mieszanin (Rokanol NL6 : JBR 425) do wymywania oleju syntetycznego z gruntu w procesie mycia gleby w warunkach dynamicznych. Micelarne roztwory Rokanolu NL6 oraz NL8 wykazały nieznacznie wyższą efektywność wymywania oleju z gruntu w porównaniu z efektywnością usuwania oleju przy pomocy roztworów...
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Earthquake-induced pounding between equal height buildings with substantially different dynamic properties
PublicationZderzenia pomiędzy konstrukcjami budowlanymi podczas trzęsień ziemi mogą prowadzić do znacznych uszkodzeń czy nawet całkowitego zniszczenia. Celem niniejszego artykuły jest analiza zderzeń pomiędzy budynkami o jednakowej wysokości i różnych parametrach dynamicznych. W artykule przedstawiono wyniki badań numerycznych przeprowadzonych na nieliniowych modelach dyskretnych o skupionych masach z wykorzystaniem nieliniowego modelu lepkosprężystego...
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Identification analysis of dynamic changes in the composition of biogas and their impact on the operation of internal combustion engines
PublicationW pracy zamieszczono wyniki badań składu biogazu pozyskiwanego na komunalnym wysypisku śmieci. Pozyskiwany biogaz jest wykorzystywany do zasilania biogazowych zespołów prądotwórczych wyposażonych w silniki o zapłonie iskrowym dostosowanych do zasilania tym paliwem. Pozyskiwany biogaz powstaje w sposób naturalny w procesie beztlenowej fermentacji zachodzącej przez ok. 20 lat, w organicznej części pryzmy odpadów składowanych na wysypisku...
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The dynamic performance analysis of the Micro-turbine's rotor supparted on slide and roling element bearings
PublicationThis article presents the results of investigations of dynamic characteristics of a small-dimension rotor with slide and rolling element bearings. The object of investigations was the rotor-bearing system designed for the ORC based low-power steam micro-turbine. The investigations were performed using MESWIR series programs, as well as commercial FEA software ABAQUS and MADYN 2000. The results of modal analysis of the micro-rotor...