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Search results for: DYNAMIKA ZATRUDNIENIA
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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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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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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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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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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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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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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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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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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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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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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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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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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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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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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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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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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the 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 are not very different from bulk water. The local...
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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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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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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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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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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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Parametric versus nonparametric modelling of dynamic susceptibility contrast enhanced MRI based data
PublicationDynamic 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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Application of quartz crystal microbalance and dynamic impedance spectroscopy to the study of copper corrosion inhibitors
PublicationThe study investigates the application of Dynamic Electrochemical Impedance Spectroscopy (DEIS) and Electrochemical Quartz Crystal Microbalance (EQCM) techniques to examine the corrosion inhibition of copper by Benzotriazole and Sodium Folate in a 0.1 M NaCl solution. DEIS, an advanced version of Electrochemical Impedance Spectroscopy (EIS), allows for real-time monitoring of non-stationary electrochemical systems,...
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Modeling of wood frame structures with different insulation materials under damaging dynamic loading
PublicationWood frame buildings are very popular in regions that are exposed to different dynamic excitations, such as damaging earthquakes. Their seismic resistance is really important in order to prevent structural damages and human losses. This paper presents the results of advanced numerical investigation carried out using the FEM. Based on the models of wall panels, the numerical model of real structure of the wood frame building has...
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Dynamic analysis of temporary steel grandstand subjected to human-induced excitations due to jumping
PublicationSteel grandstands are structures that are frequently used during sport games and many other non-sporting events, such as festivals, music concerts, or even politicians rallies, with participation of a large number of attendees. Unfortunately, the presence of unexpected excessive dynamic loads due to unpredictable behaviour of spectators (e.g. synchronized harmonic jumping or swaying) may lead to...
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Approximation of Fractional Order Dynamic Systems Using Elman, GRU and LSTM Neural Networks
PublicationIn the paper, authors explore the possibility of using the recurrent neural networks (RNN) - Elman, GRU and LSTM - for an approximation of the solution of the fractional-orders differential equations. The RNN network parameters are estimated via optimisation with the second order L-BFGS algorithm. It is done based on data from four systems: simple first and second fractional order LTI systems, a system of fractional-order point...
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STUDY OF ARRAY OF MEMS INERTIAL MEASUREMENT UNITS UNDER QUASI-STATIONARY AND DYNAMIC CONDITIONS
PublicationA measurement system includes all components in a chain of hardware and software that leads from a measured variable to processed data. In that context, the type and quality of the sensors or measuring devices are critical to any measurement system. MEMS/IMU sensors lag behind leading technologies in this respect, but the MEMS/IMU performance rapidly changes while is relatively inexpensive. For this reason, the paper proposes...
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Implementation of high-precision computation capabilities into the open-source dynamic simulation framework YADE
PublicationThis paper deals with the implementation of arbitrary precision calculations into the open-source discrete element framework YADE published under the GPL-2+ free software license. This new capability paves the way for the simulation framework to be used in many new fields such as quantum mechanics. The implementation details and associated gains in the accuracy of the results are discussed. Besides the "standard" double (64 bits)...
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Ship weather routing optimization with dynamic constraints based on reliable synchronous roll prediction
PublicationShip routing process taking into account weather conditions is a constrained multi-objective optimization problem and it should consider various optimization criteria and constraints. Formulation of a stability-related, dynamic route optimization constraint is presented in this paper. One of the key objectives of a cross ocean sailing is finding a compromise between ship safety and economics of operation. This compromise should...
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Dynamic impedance measurements of the Direct Methanol Fuel Cell cathode at various operating temperatures
PublicationThis article discusses the application of impedance analysis for diagnosing the cathode of a direct methanol fuel cell at various operating temperatures. The Dynamic Electrochemical Impedance Spectroscopy technique coupled with a linear current scan was applied for this purpose. This technique allowed the observation of changes in the cathode's properties in the fuel cell operating under real working conditions. An equivalent model...
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Microstructural evolution of 6061 aluminium alloy subjected to static and dynamic compression at low temperature
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The Application of Dynamic Electrochemical Impedance Spectroscopy (DEIS) Technique in Corrosion and Corrosion Inhibition Studies
Publicationorrosion studies have attracted considerable interest in the areas of materials chemistry and industrial chemistry, as it affects the direct and indirect costs of industry, leading to huge economic setbacks due to the need for repair, maintenance, and even shutdowns due corrosion damage. This new volume is a comprehensive resource that presents new and up-to-date, theoretical, and experimental corrosion inhibition studies.
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Merton-type default risk and financial performance: the dynamic panel moderation of firm size
PublicationPurpose – The main purpose of this study is to evaluate the probability of default and examine the relationship between default risk and financial performance, with dynamic panel moderation of firm size. Design/methodology/approach – This study utilizes a total of 1,500 firm-year observations from 2013 to 2018 using dynamic panel data approach of generalized method of moments to test the relationship between default risk and financial...
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Dynamic fracture of brittle shells in a space-time adaptive isogeometric phase field framework
PublicationPhase field models for fracture prediction gained popularity as the formulation does not require the specification of ad-hoc criteria and no discontinuities are inserted in the body. This work focuses on dynamic crack evolution of brittle shell structures considering large deformations. The energy contributions from in-plane and out-of-plane deformations are separately split into tensile and compressive components and the resulting...
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Dynamic Re-Clustering Leach-Based (Dr-Leach) Protocol for Wireless Sensor Networks
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Effect of pavement roughness and vehicle dynamic loads on decrease of fatigue life of flexible pavements
PublicationDue to the fact that pavement surfaces are not ideally even, dynamic loads of vehicle axles deviate from static loads. Higher dynamic loads contribute to faster pavement distress. The distribution of dynamic loads is similar to normal distribution and can be described by static load and factors DI (dynamic impact) and DLC (dynamic load coefficient). With the deterioration of pavement condition its evenness decreases as well and...
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Simplified approach to assess the dynamic response of a container ship subjected to bow slamming load
PublicationSimplified approach to assess the dynamic response of a container ship subjected to the bow slamming load, resulting in a transient vibratory response, typically called a 'whip-ping', is presented. The accurate numerical modelling is very complex and involves cou-pling of the hydrodynamic and structural solution at every time step, leading to huge com-putational and workload cost. Thus, the one-way coupling methodology is adopted,...
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Numerical investigation on dynamic response of a steel lattice tower under various seismic events
PublicationThe present paper presents the results of the numerical study designed to investigate the soil-structure flexibility effects on modal parameters (i.e. fundamental frequencies) and time-history analysis response (represented by the top relative displacements) of a 46.8 m high steel lattice tower subjected to a number of ground motions including also one mining tremor. In addition to the fixed-base condition, three different soil...
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Comparison of properties of the new electro-mechanical model and circumferential model of the inductive-dynamic drive
PublicationThe article presents a new electromechanical model of inductive-dynamic drive. The model is implemented in two environments: Maxwell for analyzing electrodynamic phenomena including moving of the disc and Ansys which allows for stress analysis on the basis of the volume forces imported from Maxwell. Additionally, a model validation by comparing with the existing circumferential model was carried out.
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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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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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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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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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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...