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Search results for: Molecular dynamics simulations
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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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Surrogate modeling of impedance matching transformers by means of variable‐fidelity electromagnetic simulations and nested cokriging
PublicationAccurate performance evaluation of microwave components can be carried out using full‐wave electromagnetic (EM) simulation tools, routinely employed for circuit verification but also in the design process itself. Unfortunately, the computational cost of EM‐driven design may be high. This is especially pertinent to tasks entailing considerable number of simulations (eg, parametric optimization, statistical analysis). A possible...
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Towards improved energy efficiency of future smart ships by application of advanced CFD simulations – case study
PublicationThe international trade plays crucial role in today’s globally developed world’s economy. Many people are unaware of the unimaginable volume of cargo being transported every year by oceans and seas. For most of the time invisible from land the shipping industry preserves its strong position of the most cost-efficient and environmental friendly mean of transport. However during last years the shipping industry is under great pressure...
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Expedited Gradient-Based Design Closure of Antennas Using Variable-Resolution Simulations and Sparse Sensitivity Updates
PublicationNumerical optimization has been playing an increasingly important role in the design of contemporary antenna systems. Due to the shortage of design-ready theoretical models, optimization is mainly based on electromagnetic (EM) analysis, which tends to be costly. Numerous techniques have evolved to abate this cost, including surrogate-assisted frameworks for global optimization, or sparse sensitivity updates for speeding up local...
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublicationIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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Rapid Yield Optimization of Miniaturized Microwave Passives by Response Features and Variable-Fidelity EM Simulations
PublicationThe operation of high-frequency devices, including microwave passive components, can be impaired by fabrication tolerances but also incomplete knowledge concerning operating conditions (temperature, input power levels) and material parameters (e.g., substrate permittivity). Although the accuracy of manufacturing processes is always limited, the effects of parameter deviations can be accounted for in advance at the design phase...
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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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Comparative 3D DEM simulations of sand–structure interfaces with similarly shaped clumps versus spheres with contact moments.
PublicationThree-dimensional simulations of a monotonic quasi-static interface behaviour between initially dense cohesionless sand and a rigid wall of different roughness during tests in a parallelly guided direct shear test under constant normal stress are presented. Numerical modelling was carried out by the discrete element method (DEM) using clumps in the form of convex non-symmetric irregularly shaped grains. The clumps had an aspect...
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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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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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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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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Mathematical Modeling of Ice Dynamics as a Decision Support Tool in River Engineering
PublicationThe prediction of winter flooding is a complicated task since it is affected by many meteorological and hydraulic factors. Typically, information on river ice conditions is based on historical observations, which are usually incomplete. Recently, data have been supplemented by information extracted from satellite images. All the above mentioned factors provide a good background of the characteristics of ice processes, but are not...
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Mitigation effect of face shield to reduce SARS-CoV-2 airborne transmission risk: Preliminary simulations based on computed tomography
PublicationWe aimed to develop a model to quantitatively assess the potential effectiveness of face shield (visor) in reducing airborne transmission risk of the novel coronavirus SARS-CoV-2 during the current COVID-19 pandemic using the computational fluid dynamics (CFD) method. The studies with and without face shield in both an infected and healthy person have been considered in indoor environment simulation. In addition to the influence...
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Mitigation effect of face shield to reduce SARS-CoV-2 airborne transmission risk: Preliminary simulations based on computed tomography
PublicationWe aimed to develop a model to quantitatively assess the potential effectiveness of face shield (visor) in reducing airborne transmission risk of the novel coronavirus SARS-CoV-2 during the current COVID-19 pandemic using the computational fluid dynamics (CFD) method. The studies with and without face shield in both an infected and healthy person have been considered in indoor environment simulation. In addition to the influence...
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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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New Peptide Based Fluconazole Conjugates with Expanded Molecular Targets
PublicationInfections of Candida spp. etiology are frequently treated with azole drugs. Among azoles, the most widely used in the clinical scenario remains fluconazole (FLC). Promising results in treatment of dangerous, systemic Candida infections demonstrate the advantages of combined therapies carried out with combinations of at least two different antifungal agents. Here, we report five conjugates composed of covalently linked FLC and...
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublicationThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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Three dimensional simulations of FRC beams and panels with explicit definition of fibres-concrete interaction
PublicationHigh performance concrete (HPC) is a quite novel material which has been rapidly developed in the last few decades. It exhibits superior mechanical properties and durability comparing to normal concrete. HPC can achieve also superior tensile performance if strong fibres (steel or carbon) are implemented in the matrix. Thus, there exist the unabated interest in studying how the addition of different types of fibres modifies 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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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Wireless Network Selection: A Population Dynamics Approach
PublicationW artykule rozpatruje się środowisko wireless multihoming, gdzie terminal bezprzewodowy może w każdej chwili połączyć się z jedną z wielu dostępnych sieci bezprzewodowych. Zwrócono uwagę na rolę informacji zwrotnej z sieci powiadamiającej terminal o bieżącym stanie sieci. Zaproponowano trzy dynamiczne modele wyboru sieci, różniące się dostępem terminala do informacji zwrotnej dotyczących sieci, z którą nie jest aktualnie połączony.
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Dynamics of Railway Vehicles Movement on Transition Curves
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Method for assessing the dynamics and efficiency of diving fins
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Dynamics of changes in Poland in the light of the Industry 4.0
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Stochastic approach to the dynamics of marine floating object
PublicationAnalizowany jest ruch jednostki pływającej z uwzględnieniem w równaniach stochastycznych nieliniowości, występującej w wymuszeniach zewnętrznych działających na obiekt. Stochastyczne równania różniczkowe są zapisane dla sprzężonych ruchów symetrycznych.
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Combinatorial-topological framework for the analysis of global dynamics
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Quantitative hyperbolicity estimates in one-dimensional dynamics
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Dynamics study on single and multiple β-sheets
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Dynamics of the total system of the circular sawing machine
PublicationW pracy przedstwaiono przyczyny i efekty zmiany położenia ostrzy piły tarczowej. Opisana metoda pomiaru zachowania dynamicznego piły pozwala uzytkownikowi okreslic przyczyny drgań. Ponadto, może wskazać drogi efektywnej ich minimalizacji.
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Stochastic approach to the dynamics of a linear floating object
PublicationArtykuł stanowi prezentację metody różniczkowych równań stochastycznych w zastosowaniu do analizy dynamiki obiektów pływających. Analizowany jest ruch jednostki pływającej jako obiektu liniowego z uwzględnieniem w równaniach stochastycznych nieliniowości, występującej w wymuszeniach zewnętrznych działających na obiekt. Stochastyczne równania różniczkowe są zapisane dla sprzężonych ruchów symetrycznych.
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User authentication based on keystroke dynamics analysis
PublicationW pracy przedstawiono kilka metod, które można wykorzystać do uwierzytelniania użytkowników na podstawie rytmu pisania na klawiaturze. Dwie z opisanych metod wykorzystują miarę odległości zdefiniowaną do porównywania wpisywanych tekstów, natomiast trzecia analizuje parametry rozkładów cech wydobytych z wpisywanych tekstów. Algorytmy te zostały przetestowane na dwóch zbiorach danych. Ponadto oceniona została efektywność metody powstałej...
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Circular saw blade dynamics - the measurement method
PublicationW pracy przedstawiono przyczyny i efekty zmiany położenia ostrzy piły tarczowej w układzie przecinania. Przedstawiony sposób pomiaru dynamiki piły tarczowej umożliwia określenie przyczyn drgań, co stanowi podstawę skutecznej ich minimalizacji.
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Dynamics of the circular sawing machine spindle system
PublicationW pracy przedstawiono wyniki badań wpływu prędkości obrotowej na dynamikę układu wrzecionowego pilarki tarczowej. Czynnikami badanymi były bicie osiowe i promieniowe wrzeciona, które mierzono za pomocą czujników wiroprądowych na kierunku działania przekładni pasowej, a także na kierunku do niego prostopadłym. Przeprowadzone badania eksperymentalne wykazały, że wartość prędkości obrotowej wrzeciona oraz sposób przekazywania mocy...
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Lattice dynamics of the rare-earth element samarium
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First-principles calculations of the lattice dynamics of CuInSe2
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Lattice Dynamics and Structural Phase Transitions in Eu2O3
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Dynamics and stability of icosahedral Fe–Pt nanoparticles
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Billiard in a rotating half-plane: modeling and dynamics
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Thin-walled frames and grids - statics and dynamics
PublicationFrames and grids assembled with thin-walled beams of open cross-section are widely applied in various civil engineering and vehicle or machine structures. Static and dynamic analysis of theses structures may be carried out by means of different models, startingfrom the classical models made of beam elements undergoing the Kirchhoff assumptions to the FE discretization of whole frame into plane elements. The former model is very...
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Influence of IED Explosion on Lateral Dynamics of a Vehicle
PublicationThe paper describes field test results of heavy vehicle tire blow-outs. Both civilian and military vehicles are subjected to sudden loss of inflation pressure in one or more wheels, often accompanied by serious tire damage. Selected results related to the lateral dynamic of vehicle during and just after explosive tire destruction are reported
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Gas bubble dynamics - experiment and fractal analysis.
PublicationPrzedstawiono nieliniowe aspekty generowania pęcherzyków gazowych z dysz szklanych umieszczonych pod powierzchnią cieczy. W badaniach eksperymentalnych zastosowano układ laser diodowy- fotodetektor oraz hydrofon. Sygnały z fotodetektora i hydrofonu były wzmacniane, rejestrowane za pomocą karty dźwiękowej, a następnie poddane analzie fraktalnej. W wyniku obliczeń ustalono mapy występowania chaosu w funkcji strumienia objętości gazu.
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Statistical and fractal analysis of human heart dynamics.
PublicationPrzedstawiono sposób obliczania podstawowych i bardziej zaawansowanych (dyskrepancja) wielkości statystycznych do analizy dynamiki ludzkiego serca. Oprócz analizy statystycznej pokazano elementy analizy fraktalnej (wykresy Poincare). Przedstawiona analiza umożliwia wykrywanie patologicznych sytuacji i jest pomocna lekarzom w diagnostyce.
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Novel strategies to enhance hydrodynamic cavitation in a circular venturi using RANS numerical simulations
PublicationHydrodynamic cavitation is a popular advanced oxidation technique and it has received wide range of applications from waste water treatment to the nanoparticles synthesis in recent years. The enhancement of the intensity of the hydrodynamic cavitation is always been an emerging field of research. Within this framework, we have proposed and investigated three distinct strategies to enhance the intensity of cavitation in a circular...
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A concept of heterogeneous numerical model of concrete for GPR simulations
PublicationThe Ground Penetrating Radar (GPR) method, which is increasingly being used in the non-destructive diagnostics of reinforced concrete structures, often needs more accurate interpretation tools for analysis of experimental data. Recently, there has been growing interest in developing of various numerical models for exhaustive understanding of GPR data. This paper presents the concept of a heterogeneous numerical model of concrete,...