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Search results for: MOLECULAR DYNAMICS SIMULATION
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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublicationAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
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Simulation of signal acquisition from a rotary flowmeter
Open Research DataThe dataset contains results of simulation measuring the flow of homogeneous substances by rotational flow meter: a moment of impulse at the output of flow meter, time between successive pulses, number of pulses counted from standard generator and relative error of measurement.
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Mechanical simulation of artificial gravity in torus-shaped and cylindrical spacecraft
PublicationLarge deformations and stress analyses in two types of space structures that are intended for people to live in space have been studied in this research. The structure under analysis is assumed to rotate around the central axis to create artificial gravitational acceleration equal to the gravity on the Earth's surface. The analysis is fully dynamic, which is formulated based on the energy method by using the first-order shear deformation...
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Numerical simulation of natural convection of Glycol-Al2O3 nanofluids from a horizontal cylinder
PublicationThis paper deals with natural convection around a circular cylinder with constant heat flux in a cavity using computational fluid dynamics. As fluids ethylene glycol and a mixture of ethylene glycol with Al2O3 nanoparticles (mass concentrations of nanoparticles: 0.1% and 1%) are chosen. Rayleigh number ranges from 3104 to 3105. The nanofluids are modeled with single-phase approach. For the investigated range of nanoparticle concentration, the...
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Cost-efficient simulation-driven design of compact impedance matching transformers
PublicationIn this paper, an algorithmic framework for cost-efficient design optimization of miniaturized impedance matching transformers has been presented. Our approach exploits a bottom-up design that involves translating the overall design specifications for the circuit at hand to its elementary building blocks (here, compact microstrip resonant cells, CMRCs), as well as fast surrogate-assisted optimization of the cells followed by simulation-based...
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Modular high precision high current source for special applications — Simulation and verification
PublicationThis paper presents selected issues concerning realization of high precision high current source for special applications, where high demands of output parameters of such device are required. A new 80 kW prototype of modular high precision high current source is presented, where output current accuracy reaches 5x10-5. This paper presents also results of operation of the simulation model and of the prototype converter. In order...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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The dynamics of the total output of the Japanese fisheries sector: An analysis using input-output approach
PublicationThe purpose of this study is to investigate the dynamics of the total output of the fisheries industry when the changes of the final demand occur. This study focuses on the case of Japan. This study employs a demand-pull Input-Output (IO) quantity model, one of the calculation instruments in the IO analysis, as an analysis tool. Two conditions are included in calculation and analysis parts, namely (1) “whole sector change”, and...
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Performance and Emission Modelling and Simulation of Marine Diesel Engines using Publicly Available Engine Data
PublicationTo analyse the behaviour of marine diesel engines in unsteady states for different purposes, for example to determine the fuel consumption or emissions level, to adjust the control strategy, to manage the maintenance, etc., a goal-based mathematical model that can be easily implemented for simulation is necessary. Such a model usually requires a wide range of operating data, measured on a test stand. This is a time-consuming process...
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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublicationThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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Modeling and Simulation for Exploring Power/Time Trade-off of Parallel Deep Neural Network Training
PublicationIn the paper we tackle bi-objective execution time and power consumption optimization problem concerning execution of parallel applications. We propose using a discrete-event simulation environment for exploring this power/time trade-off in the form of a Pareto front. The solution is verified by a case study based on a real deep neural network training application for automatic speech recognition. A simulation lasting over 2 hours...
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation
PublicationA wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various low and high frequencies are spatiotemporally coordinated across the human brain during memory processing is inconclusive. They can either be coordinated together across a wide range of the frequency spectrum or induced in specific bands. We used a large dataset of human intracranial electroencephalography...
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Low-Cost EM-Simulation-Driven Multi-Objective Optimization of Antennas
PublicationA surrogate-based method for efficient multi-objective antenna optimization is presented. Our technique exploits response surface approximation (RSA) model constructed from sampled low-fidelity antenna model (here, obtained through coarse-discretization EM simulation). The RSA model enables fast determination of the best available trade-offs between conflicting design goals. A low-cost RSA model construction is possible through...
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Entropic Measures of Complexity of Short-Term Dynamics of Nocturnal Heartbeats in an Aging Population
PublicationTwo entropy-based approaches are investigated to study patterns describing differences in time intervals between consecutive heartbeats. The first method explores matrices arising from networks of transitions constructed following events represented by a time series. The second method considers distributions of ordinal patterns of length three, whereby patterns with repeated values are counted as different patterns. Both methods provide...
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Fast Simulation-Driven Design of a Planar UWB Dipole Antenna with an Integrated Balun
PublicationThe paper presents a design of an ultra-wideband (UWB) antenna with an integrated balun. A fully planar balun interfacing the microstrip input of the structure to the coplanar stripline (CPS) input of the dipole antenna is introduced. The electromagnetic (EM) model of the structure includes the dipole, the balun, and the microstrip input to account for interactions over the UWB band. The EM model is adjusted for low reflection...
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Molecular Metabolism
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Molecular Autism
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Molecular Cytogenetics
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Molecular Brain
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Molecular Astrophysics
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Molecular Syndromology
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MOLECULAR CARCINOGENESIS
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Molecular Pain
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MOLECULAR BIOLOGY
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MOLECULAR ENDOCRINOLOGY
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MOLECULAR PSYCHIATRY
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MOLECULAR INTERVENTIONS
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Molecular Imaging
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Molecular Neurodegeneration
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MOLECULAR BREEDING
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Molecular Biomedicine
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Molecular Plant
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MOLECULAR CELL
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MOLECULAR THERAPY
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MOLECULAR VISION
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Simulation of the Remanence Influence on the Transient States of the Single-Phase Transformer Including Feedback Preisach Model
PublicationThis paper presents the results of the experimental and simulation investigation concerning the influence of remanence in the core of a single-phase transformer at the no-load transient state. Experimental studies consisted of the discharge of the capacitor through the primary winding at several different values of the residual magnetic flux. The paper presents a model of the transformer test system, taking into account the magnetic...
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Trust Dynamics Analysis of CTR Scheme Subversion under Virtual Anonymity and Trust-Unaware Partner Selection
PublicationWe propose a framework to study Markovian trust value dynamics in a centralized Computational Trust and Reputation (CTR) scheme under trust-unaware partner selection using a mean-value approximation. Analytically founded answers are sought to questions like: Can dishonest agents subvert the CTR scheme (i.e., acquire higher trust values than honest agents)? Is indirect reciprocity incentivized? Is there a qualitative impact of a...
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Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
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Unusual dynamics and nonlinear thermal self-focusing of initially focused magnetoacoustic beams in a plasma
PublicationUnusual thermal self-focusing of two-dimensional beams in plasma which axis is parallel to the equilibrium straight magnetic field is considered. The equi- librium parameters of plasma determine scenario of a beam divergence (usual or unusual) which is stronger as compared with a flow without magnetic field. Nonlinear thermal self-action of a magnetosonic beam behaves differently in the ordinary and unusual cases. Damping of wave...
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Virtual instruments for stroboscopic effects simulation
PublicationPrzedstawiono korzyści wynikające z wykorzystania edukacyjnych przyrządów wirtualnych w nauczaniu metrologii. Jako przykład pokazano przyrządy wirtualne umożliwiające zasymulowanie efektu stroboskopowego, m.in. do analizy działania częstościomierza rezonansowego.
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Image simulation and annotation for color blinded
PublicationW pracy przedstawiono metody symulacji obrazów widzianych przez osoby ze ślepota barw. Ukazano również metody tworzenia obrazów ukazujących różnicę w percepcji kolorów pomiędzy normalnym obserwatorem a osobą ze ślepotą barw. W artykule opisano również metodę interaktywnego opisu koloru wskazywanego piksela obrazu. W rezultacie użytkownik ze ślepota barw może uzyskać informacje opisowe o występujących w obrazie kolorach.
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Numerical simulation of hardening of concrete plate
PublicationThe paper presents a theoretical formulation of concrete curing in order to predict temperature evolution and strength development. The model of heat flow is based on a well-known Fourier equation. The numerical solution is implemented by means of the Finite Difference Method. In order to verify the model, the in situ temperature measurements at the top plate of a road bridge were carried out. A high agreement between numerical...
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Simulation and measurements for the substance identification by AFM
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Artificjal environment for simulation of emergent behaviour
PublicationPrzedstawiono opracowane środowisko dla modelowania zjawisk, w których współdziałanie wielu prostych jednostek prowadzi do powstawania złozonych struktur. Sposób oddziaływania jednostki zawarty jest w jej strukturze, która interpretowana jest poprzez specjalnie zdefiniowany język podobny do Prologu.
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Systems modeling and simulation for environmental management.
PublicationW pracy omówiono podstawy systemowego modelowania i symulacji w szerokim zakresie zagadnień związanych z zarządzaniem przepływami informacji w środowisko naturalnym.
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Analysis and simulation of the reliable multicast protocol.
PublicationArtykuł przedstawia badania dotyczące protokołu grupowego porządkowania wiadomości-RMP. Opisana została podstawowa idea algorytmów działania protokołu oraz jego najważniejsze własności. Ponadto został on zimplementowany jako część symulatora protokołów komunikacji grupowej. Wyniki badań i dogłębna analiza mechanizmów działania protokołu pozwoliła na wprowadzenie szeregu modyfikacji w stosunku do oryginalnej specyfikacji,...
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Simulation and identification of damage in bar structures.
PublicationPraca zawiera opis i testy 3 procedur badawczych dotyczących lokalizacjizniszczeń w konstrukcjach. Procedury bazują na danych modalnych jakie obiektgeneruje podczas swoich drgań tzn. częstościach własnych i postaciach drgań Badane są zmiany podatności układu, zmiany krzywizn postaci drgań i wrażli-wość częstości na założone zniszczenia. Odpowiednie procedury wiążące się ztymi trzema metodami są przestestowane na przykładzie wspornika...
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PROPELLER INVESTIGATIONS BY MEANS OF NUMERICAL SIMULATION
PublicationThe analyses of hydroacoustics are of high interest at the moment due to strong impact of hydroacoustic phenomena on marine environment; the noises, generated e.g. by marine traffic, may be harmful for sea life. The analyses presented here are focused on one of main sources of noises generated by ships, i.e. cavitating propeller. The goal of the work is the assessment of the cavitation phenomenon, carried out with the standard...