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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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Combining Computational Fluid Dynamics with a Biokinetic Model for Predicting Ammonia and Phosphate Behavior in Aeration Tanks
PublikacjaThe 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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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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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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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle 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
PublikacjaThe 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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On dynamics of flexible branched shell structures undergoing large overall motion using finite elements
PublikacjaZaprezentowano 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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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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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublikacjaSingle-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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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublikacjaThe 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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Computational Fluid Dynamics Simulation of Gas–Liquid Multiphase Flow in T-junction for CO2 Separation
PublikacjaThe 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
PublikacjaExascale 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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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublikacjaTime-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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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated 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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Adaptive Dynamical Systems Modelling of Transformational Organizational Change: with Focus on Organizational Culture and Organizational Learning
PublikacjaTransformative 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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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn 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
PublikacjaTransformative 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
PublikacjaUnderstanding 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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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublikacjaA 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
PublikacjaThe 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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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublikacjaThe 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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NUMERICAL SIMULATION OF CRATER CREATING PROCESS IN DYNAMIC REPLACEMENT METHOD BY SMOOTH PARTICLE HYDRODYNAMICS
PublikacjaA 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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Robust Parameter Estimation and Output Prediction for Reactive Carrier-Load Nonlinear Dynamic Networks
PublikacjaIn 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
PublikacjaThis 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
PublikacjaDynamic 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
PublikacjaConveyor 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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Numerical Evaluation of Dynamic Response of a Steel Structure Model under Various Seismic Excitations
PublikacjaThe present paper reports the results of the study, which was designed to perform a numerical evaluation of dynamic response of a single-storey steel structure model. The experimental model was previously subjected to a number of different earthquake ground motions during an extensive shaking table investigation. The analyzed structure model was considered as a 1-DOF system with lumped parameters, which were determined by conducting...
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Active dynamic thermography method for TRAM flap blood perfusion mapping in breast reconstruction
PublikacjaThis paper presents the new method of the transverse rectus abdominis musculocutaneous flap blood perfusion mapping based on the active dynamic thermography. The method is aimed at aiding a surgeon during breast reconstruction procedure. A pair of dTnorm and t90_10 parameters were used as parametric image descriptors of the flap blood perfusion. The method was tested on 38 patients that were subjected to breast reconstruction procedure....
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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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Burn depths evaluation based on active dynamic IR thermal imaging - A preliminary study
Publikacja.
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Cable stayed bridge over Vistula river in Plock. Dynamic analysis and site test
PublikacjaBudowę 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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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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Integrated geodetic and hydrographic measurements of the yacht port for nautical charts and dynamic spatial presentation
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Comparative analysis of positioning accuracy of Garmin Forerunner wearable GNSS receivers in dynamic testing
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Dynamic Re-Clustering Leach-Based (Dr-Leach) Protocol for Wireless Sensor Networks
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Earthquake-induced pounding between equal height buildings with substantially different dynamic properties
PublikacjaZderzenia 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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Evaluation of corrosion inhibition of brass -118 in artificial seawater by benzotriazole using dynamic EIS
PublikacjaPrzedstawiono 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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Oiled soil washing in dynamic conditions by micellar surfactants solutions and obtained effluents treatment
PublikacjaZbadano 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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Measurement of dynamic pulsations in bulk solid during silo discharging using ECT method
PublikacjaW 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
PublikacjaW 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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Corrosion resistance evaluation of Al-based alloys by means of dynamic electrochemical impedance spectroscopy
PublikacjaW 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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Microstructural evolution of 6061 aluminium alloy subjected to static and dynamic compression at low temperature
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The dynamic of processes responsible for transformation of nitrogen compounds in hybrid wetlands systems in a temperate climate.
PublikacjaAnalizowano ilościowe i jakościowe przemiany związków azotu po poszczególnych stopniach oczyszczania w hybrydowych systemach hydrofitowych w Wiklinie i Sarbsku.
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Parametric versus nonparametric modelling of dynamic susceptibility contrast enhanced MRI based data
PublikacjaDynamic tracking of a bolus of a paramagnetic agent (dynamic susceptibility contract - DSC) in MRI (magnetic resonance imaging) measurements is successfully used for assessment of the tissue perfusion and the other features and functions of the brain (i.e. cerebral blood flow - CBF, cerebral blood volume - CBV, mean transit time - MTT). The parametric and nonparametric approaches to the identification of MRI models are presented...
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DYNAMIC ANALYSIS OF HISTORIC RAILWAY BRIDGES IN POLAND IN THE CONTEXT OF ADJUSTING THEM TO PENDOLINO TRAINS
PublikacjaThe 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...