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Search results for: MOLECULAR DYNAMICS SIMULATION
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MOLECULAR PHARMACEUTICS
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Bias-Dependent Dynamics of Degradation and Recovery in Perovskite Solar Cells
PublicationDegradation of perovskite solar cells (PSCs) is often found to be partially or fully reversible when the cells are allowed to recover in the dark. Unlike the dynamics of degradation, knowledge about the dynamics of PSC cell recovery is very limited. Here, we demonstrate that the PSC recovery strongly depends on the electrical bias conditions during the light-induced degradation and that it can be manipulated by applying an external...
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Towards detecting programmers’ stress on the basis of keystroke dynamics
PublicationThe article describes the idea of detecting stress among programmers on the basis of keystroke dynamics. An experiment with a group of students of artificial intelligence classes was performed. Two samples of keystroke data were recorded for each case, the first while programming without stress, the second under time pressure. A number of timing and frequency parameters were calculated for each sample. Then statistical analysis...
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Dynamics of Field Line Mappings in Magnetic Flux Tubes
PublicationWe study the topological constraints on the dynamics of magnetic field lines in flux tubes. Our approach is based on the application of the topological invariant: fixed point index. We consider periodic flux tubes and find various restrictions on the field lines that come from the sequence of fixed point indices of iterations. We also analyze the case of a tube with a cylindrical obstacle, deducing some special dynamical properties...
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Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
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Keystroke Dynamics Patterns While Writing Positive and Negative Opinions
PublicationThis paper deals with analysis of behavioural patterns in human–computer interaction. In the study, keystroke dynamics were analysed while participants were writing positive and negative opinions. A semi-experiment with 50 participants was performed. The participants were asked to recall the most negative and positive learning experiences (subject and teacher) and write an opinion about it. Keystroke dynamics were captured and...
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Simulation investigation of perovskite-based solar cells
PublicationThree models of thin-layer lead-halide perovskite solar cells with different electron-transport layers (TiO2,SnO2,ZnO) were investigatedby the simulation method. The perovskite layer thickness was optimized for all the systems. The analysis of the standard photovoltaic cell performanceparameters at various operating temperatures was performed. The best performance was achieved for the system with theSnO2conductive layer.
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Simulation of Parallel Applications on Large-scale Distributed Systems
PublicationThis chapter has a form of a review article in the field of simulating High-Performance Computing systems. We justify the need for a new versatile simulator considering heterogeneity, energy efficiency and reliability of HPC systems. We sketch the problems that need to be solved by such simulator and rationalize using discrete-event simulation for this purpose. Based on a review of existing discrete-event HPC simulation solutions...
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Prediction of coking dynamics for wet coal charge
PublicationA one-dimensional transient mathematical model describing thermal and flow phenomena during coal coking in an oven chamber was studied in the paper. It also accounts for heat conduction in the ceramic oven wall when assuming a constant temperature at the heating channel side. The model was solved numerically using partly implicit methods for gas flow and heat transfer problems. The histories of temperature, gas evolution and internal...
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Electromagnetic Simulation with 3D FEM for Design Automation in 5G Era
PublicationElectromagnetic simulation and electronic design automation (EDA) play an important role in the design of 5G antennas and radio chips. The simulation challenges include electromagnetic effects and long simulation time and this paper focuses on simulation software based on finite-element method (FEM). The state-of-the-art EDA software using novel computational techniques based on FEM can not only accelerate numerical analysis, but...
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The Dynamics of Trade Relations between Ukraine and Romania: Modelling and Forecasting
PublicationThe article examines the monthly dynamics of exports, imports and balance of trade between Ukraine and Romania in the period from 2005 to 2021. Time series from 2015 to 2021 were used for modelling and forecasting (since the date the European Union–Ukraine Association Agreement took effect). Adequate models of the dynamics series of the Box-Jenkins methodology were built: additive models with seasonal component ARIMA (Autoregressive...
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Clinical Simulation in Nursing
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Multi-agent large-scale parallel crowd simulation
PublicationThis paper presents design, implementation and performance results of a new modular, parallel, agent-based and large scale crowd simulation environment. A parallel application, implemented with C and MPI, was implemented and run in this parallel environment for simulation and visualization of an evacuation scenario at Gdansk University of Technology, Poland and further in the area of districts of Gdansk. The application uses a...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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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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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Molecular properties with dual basis set methods
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Experimentation, material modelling and simulation of bonded joints with a flexible adhesive
PublicationThe paper deals with material parameters identification of a flexible adhesive and the numerical simulation of its behaviour in a single lap bonded joint. The material modelling was based on the simple shear and tensile-shear laboratory tests of the bonded joints made of thin aluminium and polyurethane plates with the flexible adhesive Terostat MS 9360 manufactured by Henkel AG & Co. The adhesive was considered as a hyperelastic...
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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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Model-based testing for execution algorithms in the simulation of cyber-physical systems
PublicationThe understanding of simulation semantics of a hybrid system is a challenge for computational engineers as it requires expertise in computer science, engineering, numerical methods, and mathematics at once. The testing methods for the execution of a simulation are being researched but not yet applied on the industrial level. Consequently, the semantics of the simulation becomes a critical artifact in the system development process....
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Analysis of dynamics of a map-based neuron model via Lorenz maps
PublicationModeling nerve cells can facilitate formulating hypotheses about their real behavior and improve understanding of their functioning. In this paper, we study a discrete neuron model introduced by Courbage et al. [Chaos 17, 043109 (2007)], where the originally piecewise linear function defining voltage dynamics is replaced by a cubic polynomial, with an additional parameter responsible for varying the slope. Showing that on a large...
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Numerical solution of threshold problems in epidemics and population dynamics
PublicationA new algorithm is proposed for the numerical solution of threshold problems in epidemics and population dynamics. These problems are modeled by the delay-differential equations, where the delay function is unknown and has to be determined from the threshold conditions. The new algorithm is based on embedded pair of continuous Runge–Kutta method of order p = 4 and discrete Runge–Kutta method of order q = 3 which is used for the...
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Intelligent monitoring the vertical dynamics of wheeled inspection vehicles
PublicationThe problem of intelligent monitoring of the vertical dynamics of wheeled inspection vehicles is addressed. With the independent MacPherson suspension system installed, the basic analysis focuses on the evaluation of the parameters of the so-called quarter car model. To identify a physically motivated continuous description, in practice, dedicated integral-horizontal filters are used. The obtained discrete model, which retains...
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Electrochemical simulation of enzymatic transformations studied for the selected antitumor acridine derivatives
PublicationThe elucidation of the metabolic pathways and the biotransformation mechanisms of potential drugs is a crucial point in drug development. It allows to know the activation routes of the new biologically active compounds, especially in respect to their possible toxicity. Generally, in vivo or in vitro experiments with liver microsomes or hepatocytes are performed. However, these testing schemes are tedious, time consuming and of...
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublicationThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Usefulness of Keystroke Dynamics Features in User Authentication and Emotion Recognition
PublicationThe study presented in the article focuses on keystroke dynamics analysis applied to recognize emotional states and to authenticate users. An overview of some studies and applications in these areas is presented. Then, an experiment is described, i.e. the way of collecting data, extracting features, training classifiers and finding out the most appropriate feature subsets. The results show that it is difficult to indicate a universal...
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Sylwester Kaczmarek dr hab. inż.
PeopleSylwester Kaczmarek received his M.Sc in electronics engineering, Ph.D. and D.Sc. in switching and teletraffic science from the Gdansk University of Technology, Gdansk, Poland, in 1972, 1981 and 1994, respectively. His research interests include: IP QoS and GMPLS and SDN networks, switching, QoS routing, teletraffic, multimedia services and quality of services. Currently, his research is focused on developing and applicability...
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Optimization of hydrodynamic vortex separator for removal of sand particles from storm water by computational fluid dynamics
PublicationStorm water treatment has been gradually acknowledged for the removal of pollutants from urban areas using the hydro cyclone separation technique. The separation efficiency of the hydrodynamic vortex separator (HDVS) is a complex phenomenon. With the aim enhance the separation potency of HDVS for storm runoff to get rid of sand particles, the HDVS with different structural configurations was studied by computational fluid dynamics....
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Directed electromagnetic pulse dynamics: projecting operators method
PublicationIn this article, we consider a one-dimensional model of electromagnetic pulse propagation in isotropic media, takinginto account a nonlinearity of the third order. We introduce a method for Maxwell's equation transformation on thebasis of a complete set of projecting operators. The operators correspond to wave dispersion branches including thedirection of propagation. As the simplest result of applying the method, we derive a system...
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Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation
PublicationIntroduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession...
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Management Simulation Game - LATO 2022/2023 - DZIENNE
e-Learning Courses -
Management Simulation Game wykład 2021/2022 STAC
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Management Simulation Game LATO 2022/2023 ZAOCZNE
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Management Simulation Game wykład 2021/2022 ns
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The dynamics of the total output of the fishery sector: The case of Indonesia
PublicationThe purpose of this study is to analyze the dynamics of the total output of the Indonesian fishery industry when the changes of the final demand occur. This study employs a demand-pull Input-Output (IO) quantity model, one of the calculation tools in the IO analysis, as an analysis instrument. Two conditions are noticed in calculation and analysis parts, namely (1) “whole sector change”, and (2) “pure change”. An initial period...
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Simulation model of IMS/NGN call processing performance
PublicationIn current telecommunications it is assumed that demands of the information society for quickly delivered services will be satisfied by the Next Generation Network (NGN) architecture, which includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS), proper design and dimensioning of NGN is absolutely necessary, for which appropriate models have to be proposed. As the NGN architecture is very complicated,...
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BACTERIAL INACTIVATION VIA LASER-DRIVEN GOLD NANOPARTICLE HEATING: SIMULATION AND ANALYSIS
PublicationThis study utilizes CFD technique to simulate the inactivation of E. coli bacteria within a microfluidic chamber, employing gold nanoparticles irradiated by a laser beam. Employing a single-phase model, the presence of bacteria is considered by treating thermal properties in the governing equations as effective, combining those of water and bacteria using established correlations from scientific literature. The conversion of light...
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Simulation-Driven Design of Microstrip Antenna Subarrays
PublicationA methodology for computationally efficient simulation-driven design of microstrip antenna subarrays is presented. Our approach takes into account the effect of the feed (e.g., a corporate network) on the subarray side lobe level and allows adjusting both radiation and reflection responses of the structure under design within a single automated process. This process is realized as surrogate-based optimization that produces designs...
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Dynamics of Chains as a Tool to Study Thermomechanical Properties of Proteins.
PublicationPolymer dynamics can be formulated on different levels of detail. One approach eliminates microscopic degrees of freedom and a polymer molecule is represented by a simplified structure—a chain. In the simplest case monomers of ideal chain have fixed length, and their orientation is independent of the orientations and positions of neighbouring monomers. This is reason that two monomers can co-exist at the same place. Ideal chain...
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Structural Change and Economic Dynamics
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Modeling and simulation of tool cycle in manufacturing cell
PublicationThe paper addresses issues concerning modeling and analysis of tool flow within a three-machine manufacturing cell used for small batch manufacturing of a definite spectrum of prismatic parts. The approach utilizes a method for job and tool allocation to work centers with limited number of machines and capacity of tool resources, based on the analysis of formalized relations: job - tool sets required. Selected tool flow control...
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Modelling, Simulation and Optimization of the Wavemaker in a Towing Tank
PublicationThe paper analyses the problem of experimental identification (frequency response), modelling and optimization of the towing tank wavemaker in the Scilab/Xcos environment. The experimental identification of the objects (the towing tank wavemaker placed in the hydrodynamic laboratory of the CTO S.A. Ship Design and Research Centre (CTO)) and the implementation of the models in the simulation environment, enable to perform: 1. tuning...
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Transmission Protocol Simulation Framework For The Resource-Constrained Wireless Sensor Network
PublicationIn this paper a prototype framework for simulation of wireless sensor network and its protocols are presented. The framework simulates operation of a sensor network with data transmission, which enables simultaneous development of the sensor network software, its hardware and the protocols for wireless data transmission. An advantage of using the framework is converging simulation with the real software. Instead of creating...
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Modelowanie i symulacja CFD (Computional Fluid Dynamics)
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Finite Resolution Dynamics
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Molecular structures of two E-azobenzocrown ethers
PublicationRentgenowska analiza strukturalna monokryształów posłużyła do scharakteryzowania struktury izomerów E dwóch azobenzokoron: 13- i 16-członowej. Oba związki krystalizują w układzie jednoskośnym. W komórce elementarnej, w każdym przypadku znajdują się dwie niezależne cząsteczki, różniące się konformacją, szczególnie łańcucha eterowego. Porównując konformacje ''wolnych'' makrocykli z konformacjami ich kompleksów z jonami metali wskazano,...
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Spatiotemporal dynamics of the active perirheic zone in a natural wetland floodplain
PublicationAbstract The ecologically and biogeochemically significant perirheic zone is a part of the floodplain where waters originating from both the river and adjacent floodplain are present. In this study, we investigate the spatiotemporal dynamics of the active perirheic zone, i.e. river and floodplain waters and their transient mixing extent. This is achieved by using the Hydraulic Mixing-Cell method, a complement to a fully integrated...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Simulation of Signal Propagation Along Fractional-Order Transmission Lines
PublicationIn this paper, the simulation method of signal propagation along fractional-order (FO) transmission lines is presented. Initially, fractional calculus and the model of FO transmission line are introduced. Then, the algorithm allowing for simulation of the nonmonochromatic wave propagation along FO transmission lines is presented. It employs computations in the frequency domain, i.e., an analytical excitation is transformed to the...
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Fatty acids as molecular carriers in cleavable antifungal conjugates
PublicationConjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker, demonstrate good in vitro activity against human pathogenic yeasts of Candida spp. The minimal inhibitory concentrations (MIC) values for the most active conjugates containing caprylic...