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Search results for: NEURONAL DYNAMICS
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Dynamic characteristics of the proton exchange membrane fuel cell module
PublicationThe paper describes a fuel cell based system and its performance. The system is based on two fuel cell units, DC/DC converter, DC/AC inverter, microprocessor control unit, load unit, bottled hydrogen supply system and a set of measurement instruments. In the study presented in the paper a dynamic response of the proton exchange membrane (PEM) fuel cell system to unit step change load as well as to periodical load changing cycles...
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Timber frame houses resistant to dynamic loads - seismic analysis
PublicationThe aim of the article is to present results of seismic analysis results of two real-sized timber frame buildings subjected to seismic excitations. The first model was insulated with mineral wool, the second one with polyurethane foam. Technology and specifications involved in both models construction is based on the previously conducted experimental research on timber frame houses, including wall panels tests, wall numerical models...
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Dynamic analysis of the railway bridge span under moving loads
PublicationThe first part of this paper provides a review of the state of knowledge of the dynamic behaviour of railway bridges under moving loads. Particular attention is paid to developments in modelling railway bridge loading and dynamic vehicle-span (structure) interaction. The most important aspects determining the advancements in this area of knowledge are identified. The contemporary techniques for defining bridge span finite element...
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Analysis of data fusion algorithms for the vessel with the dynamic positioning system
PublicationThe dynamic positioning (DP) system on the vessel is operated to control the position and heading of the vessel with the use of propellers and thrusters installed on the board. On DP vessels redundant measurement systems of position, heading and the magnitude and direction of environmental forces are required for safety at sea. In this case, a fusion of data is needed from individual measurement devices. The article proposes a...
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On time-dependent nonlinear dynamic response of micro-elastic solids
PublicationA new approach to the mechanical response of micro-mechanic problems is presented using the modified couple stress theory. This model captured micro-turns due to micro-particles' rotations which could be essential for microstructural materials and/or at small scales. In a micro media based on the small rotations, sub-particles can also turn except the whole domain rotation. However, this framework is competent for a static medium....
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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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DYNAMIC POSITIONING CAPABILITY ASSESSMENT BASED ON OPTIMAL THRUST ALLOCATION
PublicationThe article presents an efficient method of optimal thrust allocation over the actuators in a dynamically positioned ship, according to the DNV-ST-0111 standard, Level 1. The optimisation task is approximated to a convex problem with linear constraints and mathematically formulated as quadratic programming. The case study is being used to illustrate the use of the proposed approach in assessing the DP capability of a rescue ship....
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Computational modelling of concrete behavior under static and dynamic conditions
PublicationW artykule zaproponowano wyniki obliczeń MES dla betonu podczas dynamicznego obciążenia. Przyjęto model sprężysto-plastyczno-lepki z nielokalnym osłabieniem. Obliczenia MES dla elementów betonowych pod obciążeniem dynamicznym o różnej prędkości obciążenia porównano bezpośrednio z doświadczeniami.
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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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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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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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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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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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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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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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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 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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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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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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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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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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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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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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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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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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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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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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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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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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Spike patterns and chaos in a map-based neuron model
PublicationThe work studies the well-known map-based model of neuronal dynamics introduced in 2007 by Courbage, Nekorkin and Vdovin, important due to various medical applications. We also review and extend some of the existing results concerning β-transformations and (expanding) Lorenz mappings. Then we apply them for deducing important properties of spike-trains generated by the CNV model and explain their implications for neuron behaviour....
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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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Topological-numerical analysis of a two-dimensional discrete neuron model
PublicationWe conduct computer-assisted analysis of a two-dimensional model of a neuron introduced by Chialvo in 1995 [Chaos, Solitons Fractals 5, 461–479]. We apply the method of rigorous analysis of global dynamics based on a set-oriented topological approach, introduced by Arai et al. in 2009 [SIAM J. Appl. Dyn. Syst. 8, 757–789] and improved and expanded afterward. Additionally, we introduce a new algorithm to analyze the return times...
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Connection matrix theory for discrete dynamical systems
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Connection matrix theory for discrete dynamical systems
PublicationIn [C] and [F1] the connection matrix theory for Morse decomposition is developedin the case of continuous dynamical systems. Our purpose is to study the case of discrete timedynamical systems.
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Dynamika piły tarczowej i wrzeciona przecinarki
PublicationOpisano metodykę określania właściwości dynamicznych układu wrzecionowego pilarki tarczowej w sposób eksperymentalny. Opisana metoda pozwala wykazać, że w określonych przypadkach o zachowaniu piły decydującą rolę może odgrywać wrzeciono pilarki i sposób jego napędu.
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Metody sprzęgania modeli dynamiki rurociągów przemysłowych
PublicationArtykuł opisuje dwie metody sprzęgania modeli dynamiki rurociągów przesyłowych. Stanowią one niezbędny element przy budowie efektywnych systemów symulacji rozległych i złożonych instalacji rurociągów stosowanych w przemyśle. Pierwsza z proponowanych metod (globalna metoda sprzęgania - GMS) wykorzystuje 'globalne' (w skali modelu) zależności (oraz fizyczne przybliżone zależności) pomiędzy ciśnieniem i przepływem masowym medium w...
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Zatrudnienie i bezrobocie a dynamika wzrostu gospodarczego
PublicationW pierwszej części artykułu przedstawiono koncepcję teoretyczną opisującaą związki pomiędzy dynamiką wzrostu produktu krajowego a stopą wzrostu zatrudnienia i stopą bezrobocia w warunkach zmian nakładów kapitałowych i postępu technicznego. W następnej kolejności przedstawiono model teoretyczny opisujący te związki i sformułowano założenia leżące u jego podstaw. W końcowej części artykułu, na podstawie informacji kwartalnych z lat...
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Dynamical properties of ordered Fe–Pt alloys
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Laboratorium Dynamiki i Automatyzacji Maszyn Technologicznych
PublicationW dokumencie zawarto opis profilu działalności Laboratorium Dynamiki i Automatyzacji Maszyn Technologicznych utworzonego w ramach Katedry Technologii Maszyn i Automatyzacji Produkcji. Na dołączonych ilustracjach przedstawiono najważniejsze stanowiska badawczo- dydaktyczne oraz kilka przykładowych wyników testów zautomatyzowanych napędów.
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Problem opisu dynamiki recyrkulacji w reaktorach.
PublicationOmówiono aktualne problemy związane z kwestią recyrkulacji w obiektach oczyszczalni ścieków. Wskazano na znaczny wzrost stosowanych stopni recyrkulacji w ostatnim czasie i przeanalizowano jego przypuszczalne przyczyny oraz konsekwencje. Omówiono wyniki badań przeprowadzonych w laboratoryjnym modelu osadnika.
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Badania dynamiki wybranych morskich obiektów pływających
PublicationPraca zawiera - w ujęciu skróconym materiał z zakresu ogólnych badań dynamiki morskich obiektów pływających - w ujęciu rozszerzonym i pogłębionym - materiał z badań dynamiki morskich obiektów pływających, należących do klasy pływakowych obiektów segmentowych. Dla obiektów segmentowych reprezentujących katamarany i trimarany załączone są wyniki obliczeń i badań modelowych.
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Wybrane elementy nieliniowej dynamiki struktur kratowych
PublicationW pracy jest dyskutowany problem nieliniowej dynamiki struktur kratowych. Zastosowano stacjonarny opis Lagrange'a (ang. Total Lagrange), pokazano silne i słabe sformułowanie dla pręta kratowego, jego aplikację do MES. W zakresie całkowania równań ruchu przedstawiono metodę Newmarka i metodę-a dla problemów liniowych i nieliniowych. Załączony przykład numeryczny ilustruje cechy przedstawionych metod.
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Neural Modelling of Steam Turbine Control Stage
PublicationThe paper describes possibility of steam turbine control stage neural model creation. It is of great importance because wider application of green energy causes severe conditions for control of energy generation systems operation Results of chosen steam turbine of 200 MW power measurements are applied as an example showing way of neural model creation. They serve as training and testing data of such neural model. Relatively simple...
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Neural Architecture Search for Skin Lesion Classification
PublicationDeep neural networks have achieved great success in many domains. However, successful deployment of such systems is determined by proper manual selection of the neural architecture. This is a tedious and time-consuming process that requires expert knowledge. Different tasks need very different architectures to obtain satisfactory results. The group of methods called the neural architecture search (NAS) helps to find effective architecture...
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Concept of Neural Model of the Sea Bottom Surface
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Artificial Neural Network for Multiprocessor Tasks Scheduling
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