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Search results for: DYNAMIC%20SIMULATION
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Simulation model for evaluation of QOS dynamic routing
PublicationCurrent informational networks use a large variety of technologies to support data exchange. Most of them are focused on IP protocol and include mechanisms which by definition should supply demanded QoS. One of those mechanisms is efficient path calculation - routing. Traffic offered to the network can change very rapidly in short term. Routing should support such traffic changes and all the time calculate valid paths in terms...
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Tracing of dynamic objects in distributed interactive simulation systems
PublicationDistributed interactive simulation systems require integration of several areas of computer science and applied mathematics to enable each individual simulation object to visualize effectively dynamic states of other objects. Objects are unpredictable,i.e., controlled by their local operators, and are remote, i.e., must rely on some transmission media to visualize dynamic scene from their local perspectives. The paper...
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Molecular dynamics simulation of polymerization of p-xylylene
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DYNAMIC SYSTEMS AND APPLICATIONS
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Experimental study and numerical simulation of the dynamic penetration into dry clay
PublicationTests of dry clay were carried out in a uniaxial stress state using the experimental setup which implements the split Hopkinson pressure bar method. Based on the results of these experiments, the compressive strength of clay was determined as an important element of S.S. Grigoryan’s model of the soil medium. In addition, the parameters of this model are determined from the results of experiments using the modified Kolsky method...
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Detection of stress corrosion cracking dynamics by dynamic electrochemical impedance spectroscopy
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublicationThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Detection of stress corrosion cracking dynamics by dynamic electrochemical impedance spectroscopy.
PublicationKlasyczne badania korozji naprężeniowej nie dają precyzyjnych informacji o dynamice takiego procesu korozyjnego. Nowa technika dynamicznej elektrochemicznej spektroskopii impedanyjnej, która została opracowana w Katedrze Elektrochemii, Korozji i Inżynierii Materiałowej stwarza takie możliwości. Fakt ten związany z zastosowaną metodologią analizy umożliwiającą selektywną analizą czasowo-częstotliwościową danych pomiarowych.Praca...
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Dynamics of Opposing Polymer Brushes: A Computer Simulation Study
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Nonlinear modeling of traction transformer with coiled iron core for dynamic simulation
PublicationW referacie przedstawiono wyprowadzenie zastępczego modelu obwodowego transformatora trakcyjnego o rdzeniu zwijanym do analiz zachowania sie transformatora w układzie napedowym jednostki trakcyjnej. Model zakłada nieliniowa charakterystyke magnesowania B-H i anizotropowe właściwosci magnetyczne i elektryczne zwijanego rdzenia. Wyprowadzenie modelu oparto na metodzie energetycznej Lagrange'a. Uzwojenia zostały zamodelowanie jako...
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Kinetics of spinodal decomposition in the Ising model with dynamic lattice liquid (DLL) dynamics
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Molecular-dynamics simulation of clustering processes in sea-ice floes
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Simulation of the Dynamics of Renewable Energy Sources with Energy Storage Systems
PublicationThe intermittency of renewable energy sources (RES) constitutes a challenge for effective power system control. Fossil-fuel-based units offering ancillary power services to meet the short-term power imbalance are a financial and environmental burden for the society. Energy storage systems (ESS) can be the solution in view of the electricity market development and growing environmental concern. The major questions are, in what circumstances...
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Early stage of critical clusters growth in phenomenological and Molecular Dynamic simulation models
PublicationW artykule opisano wzrost klastrów krytycznych w ramach klasycznego podejścia fenomenologicznego oraz dynamiczno-molekularnego (MD). Została wyprowadzona nowa formuła opisujaca liczbę klastrów krytycznych. Sformułowano równania opisujace wczesne etapy wzrostu kropli o rozmiarach krytycznych. Opisano wyniki symulacji dynamiczno-molekularnych powstawania klastrów w jednorodnej parze przesyconej oraz podano czasowe zmiany rozkładu...
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Simulation Results of Dynamic Capacity Reallocation in Hierarchical Cell Structure of UMTS Network
PublicationIn the paper simulation results of dynamic capacity reallocation between different layers of hierarchical cell structure of UMTS network has been described. This approach for load management seems to be useful for improving the resource utilization perfmorance.
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Dynamic simulation as a tool for evaluation of the nitrogen removal capabilities at the "Gdańsk-Wschód" WWTP
PublicationCelem badań było przedstawienie możliwości zastosowania złożonego modelu biokinetycznych ASM2d do symulacji procesu usuwania azotu w oczyszczalni ścieków ''Wschód'' w Gdańsku. Szybkość procesów nitryfikacji i denitryfikacji została wyznaczona w warunkach laboratoryjnych za pomocą tzw. testów zlewkowych. Wyniki tych badań zostały wykorzystane do kalibracji modelu, w trakcie której zmieniano wartości tylko 5 parametrów kinetycznych....
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Early stage of critical clusters growth in phenomenological and Molecular Dynamic simulation models.
PublicationOpisano proces kondensacji pary wodnej w ujĘciu fenomenologicznymi dynamiczno-molekularnym. Wczesne fazy wzrostu klastra opisano w ramach klasycznej teorii Hertza-Knudsena. Obszernie przedstawiono wyniki symulacji dynamiczno-molekularnych zjawiska kondensacji pary wodnej z jednorodnej fazy gazowej (przebieg powstawania małych klastrów H2O i szybkość wzrostu klastrów ponadkrytycznych).
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Non-linearity of multibody dynamic equations with respect to Lagrange multipliers: application to railway dynamics
PublicationPraca koncentruje się na dynamice układów wieloczłonowych z zamkniętymi łańcuchami członów. Głównym punktem zainteresowania jest modelowanie układów z występującymi nieliniowymi zależnościami opisującymi wpływ siły mnożników Lagrange'a na dynamikę układu (nieliniowe modele siły tarcia.). Aby zbudować model dynamiki układu zawierającego zamknięte łańcuchy członów, wspomniane łańcuchy są "rozcinane" i budowana jest struktura drzewa...
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
PublicationPraca poświęcona jest badaniom struktury blisko i średniozasięgowej częściowo zredukowanego szkła ołowiowo-krzemianowego o stechiometrii 1Pb1PbO1SiO2 uzyskanego na drodze symulacji dynamiczno-molekularnych. Otrzymane rezultaty porównamy z danymi otrzymanymi dla szkła niemodyfikowanego (2PbO1SiO2) i całkowicie zredukowanego (2Pb1SiO2).
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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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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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Study of Direct Methanol Fuel Cell Process Dynamics Using Dynamic Electrochemical Impedance Spectroscopy
PublicationA new technique, which was developed to characterize the direct methanol fuel cell under work conditions, has been presented in this paper. The impedance measurements were made using dynamic electrochemical impedance spectroscopy research technique in the galvanostatic mode, using multiple sinusoidal excitation. Obtained results show, that together with an increase of the temperature and working load, the global impedance...
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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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Spectroscopic, molecular docking and molecular dynamic simulation studies on the complexes of β-lactoglobulin, safranal and oleuropein
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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2D numerical simulation of tear film dynamics: Effects of shear-thinning properties
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublicationGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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New possibilities of the passive layer cracking dynamics detection using a new Dynamic Electrochemical Impedance Spectroscopy.
PublicationNowa metoda Dynamicznej Elektrochemicznej Spektroskopii Impedancyjnej opracowana w Katedrze Elektrochemii, Korozji i Inżynierii Materiałowej Politechniki Gdańskiej daje możliwości określania charakterystyki impedancyjnej w dziedzinie czasu podczas procesu pękania ochronnej warstwy pasywnej. Fakt ten jest związany z procedurą analizującą wspomnianej techniki, która umożliwia selektywną analizę czasowo-częstotliwościową uzyskanych...
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Study on population dynamics for triple-linked food chain using a simulation-based approach
PublicationThe procedures based on simulation have become a feasible testing method that does not require investing valuable resources to create a concrete prototype, especially with the increasing computational power of computers. Thus, design changes can be adopted and design errors can be fixed before it is too late. Simulation turns to be a cheap, safe and often more acceptable from an ethical perspective. In our work we summarize the...
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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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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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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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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Computational fluid dynamics simulation of heat transfer from densely packed gold nanoparticles to isotropic media
PublicationThis work aims to determine and compare heat generation and propagation of densely packed gold nanoparticles (Au NPs) induced by a resonant laser beam (532 nm) according to the Mie theory. The heat flux propagation is transferred into the materials, which here are: silica glass; soda-lime-silica glass; borosilicate glass; polymethyl methacrylate (PMMA); polycarbonate (PC); and polydimetylosiloxane (PDMS). This analysis aims to...
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Simulation of the number of storm overflows considering changes in precipitation dynamics and the urbanisation of the catchment area: a probabilistic approach
PublicationThis paper presents a probabilistic methodology that allows the study of the interactions between changes in rainfall dynamics and impervious areas in urban catchment on a long- and short-term basis. The proposed probabilistic model predict future storm overflows while taking into account the dynamics of changes in impervious areas and rainfall. In this model, a logistic regression method was used to simulate overflow resulting...
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A Dynamic Forecast Demand Scenario Analysis to Design an Automated Parcel Lockers Network in Pamplona (Spain) Using a Simulation-Optimization Model
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JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
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Journal of Simulation
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SIMULATION & GAMING
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Simulation in Healthcare
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Dynamic Games and Applications
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Dynamic coloring of graphs
PublicationDynamics is an inherent feature of many real life systems so it is natural to define and investigate the properties of models that reflect their dynamic nature. Dynamic graph colorings can be naturally applied in system modeling, e.g. for scheduling threads of parallel programs, time sharing in wireless networks, session scheduling in high-speed LAN's, channel assignment in WDM optical networks as well as traffic scheduling. In...
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The consequences of dynamic BPM
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MACHINE DYNAMICS PROBLEMS
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Cultural Dynamics
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Structural Dynamics
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