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Search results for: Molecular dynamics simulations
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublicationMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Numerical simulations of novel GFRP sandwich footbridge
PublicationIn the following paper some aspects of numerical analysis and designing stages of a footbridge made of composite materials are elucidated. Because of the used materials the design process in this case is not ordinary and requires the development of concepts, material selections, identification of material properties, numerical simulations, strength calculations, serviceability and durability analyses. This contribution presents...
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Circular saw vibrations or dynamics of the spindle
PublicationSawing of wood with circular saws is a typical example of cutting with multi-blade tools. In that kind of cutting, theposition accuracy of following tool blades is a crucial factor which affects the cutting process and machining final effects.Position tooth errors may cause deterioration in cutting conditions, changes in loads of individual teeth and the tool as a whole,and also a decrease in accuracy and surface quality after...
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MOLECULAR PHARMACEUTICS
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Mesoscopic simulations of crack propagation in concrete using cohesive elements
PublicationThe paper presents results of two-and three-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 3-phase material composed of aggregate grains placed in the cement matrix with Interfacial Transitional Zones (ITZs) between then. In 2D simulations macro-voids were also taken into account. The particle distribution was taken from real concrete beams...
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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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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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International Review on Modelling and Simulations (IREMOS)
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Some Optimization Methods for Simulations in Volunteer and Grid Systems
PublicationIn this chapter, some optimization methods have been presented for improving performance of simulations in the volunteer and grid computing system called Comcute. Some issues related to the cloud computing can be solved by presented approaches as well as the Comcute platform can be used to simulate execution of expensive and energy consuming long-term tasks in the cloud environment. In particular, evolutionary algorithms as well...
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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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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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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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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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Discussing daylight simulations in a proposal for online daylighting education.
PublicationThere is increasing interest concerning daylighting in the building sector. However, such knowledge is difficult to penetrate the curricula of architects and designers as existing educational programmes often do not provide sufficient training on BPS. This also leads to superficial use of daylight simulations. This paper presents a proposal for a needs-based education package on daylighting design, that mixes modular eLearning...
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Acceleration of Electromagnetic Simulations on Reconfigurable FPGA Card
PublicationIn this contribution, the hardware acceleration of electromagnetic simulations on the reconfigurable field-programmable-gate-array (FPGA) card is presented. In the developed implementation of scientific computations, the matrix-assembly phase of the method of moments (MoM) is accelerated on the Xilinx Alveo U200 card. The computational method involves discretization of the frequency-domain mixed potential integral equation using...
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Searching for Critical Conditions During Lifeboat Launching – Simulations
PublicationThe article describes numerical simulations of the process of lifeboat launching at the ship’s side. The research is aimed at finding the values of ship motion parameters which appear to be most dangerous for people in the lowered lifeboat due to the generated accelerations. The simplified model of ship hull motion adopted at this research stage bases on a superposition of harmonic motions with given amplitudes and periods in six...
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Introduction in to tyre simulations
PublicationW artykule przedstawiono wyniki symulacji komputerowej zachowania się opony w czasie badania jej oporów toczenia w oparciu o program LMS Virtual Lab. Przedstawiono także wnioski wynikające z przeprowadzonej symulacji.
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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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Molecular properties with dual basis set methods
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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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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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A NUMERICAL STUDY ON THE DYNAMICS OF DENGUE DISEASE MODEL WITH FRACTIONAL PIECEWISE DERIVATIVE
PublicationThe aim of this paper is to study the dynamics of Dengue disease model using a novel piecewise derivative approach in the sense of singular and non-singular kernels. The singular kernel operator is in the sense of Caputo, whereas the non-singular kernel operator is the Atangana–Baleanu Caputo operator. The existence and uniqueness of a solution with piecewise derivative are examined for the aforementioned problem. The suggested...
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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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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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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublicationMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Structural Change and Economic Dynamics
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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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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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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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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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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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Improvement of ships seakeeping performance by application of the full-scale cfd simulations
PublicationThe ship’s fuel economy is increasingly important. The paper presents the effect of redesigning a case study ship for increasing seakeeping performance. Selected wave parameters reflect very difficult operational conditions existing on the North Sea and the Baltic Sea. The analyzed variants of a case study ship represent the latest developments of modern hull forms. The concepts similar to V-shaped bulbous bow, X-bow, X-aft, B-bow...
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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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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...
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A Subspace-Splitting Moment-Matching Model-Order Reduction Technique for Fast Wideband FEM Simulations of Microwave Structures
PublicationThis article describes a novel model-order reduction (MOR) approach for efficient wide frequency band finite-element method (FEM) simulations of microwave components. It relies on the splitting of the system transfer function into two components: a singular one that accounts for the in-band system poles and a regular part that has no in-band poles. In order to perform this splitting during the reduction process, the projection...
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Simulations of air and water flow in a model dike during overflow experiments
PublicationFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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Membrane model of human abdominal wall. Simulations vs. in vivo measurements
PublicationThe study presents a methodology of defining a numerical model of human abdominal wall based on the experimentally registered data of the abdomen geometry due to variations of the intraabdominal pressure. The abdominal wall is modelled here as a simple homogeneous membrane structure made of linear orthotropic material The displacements registered during the increase of pressure are compared with the re-sults of the model static...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Simulations of Shear Zones and Cracks in Engineering Materials Using eXtended Finite Element Method
PublicationNumerical simulations of cracks and shear zones in quasi-brittle materials are presented. Extended Finite Element Method is used to describe both cracks and shear zones. In a description of tensile cracks, a Rankine criterion is assumed. A discrete Mohr-Coulomb law is adopted for simulations of shear zones. Results of simple numerical tests: unixial tension, bending and biaxial compression are demonstrated.
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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From flow to jamming: Lattice Gas Automaton simulations in granular materials
PublicationWe introduce the first extension of a Lattice Gas Automaton (LGA) model to accurately replicate observed emergent phenomena in granular materials with a special focus on previously unexplored jamming transitions by incorporating gravitational effects, energy dissipation in particle collisions, and wall friction. We successfully reproduce flow rate evolution, density wave formation, and jamming transition observed in experiments....
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Experimental and numerical analysis of the pyrolysis dynamics of a single wood particle: presentation of the radiographic technique
PublicationPyrolysis is an oxygen-free process for the thermal decomposition of raw materials. The heat conduction and flow of pyrolysis products (i.e., the gas fraction and liquid vapour generated during pyrolysis) influence the process and products. In this work, the influence of the orientation of wooden particle fibres with respect to the direction of the heat source on the dynamics of the process was investigated, where there were two...
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Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublicationThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
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Experimental investigations and simulations of the microturbine unit with permanent magnet generator
PublicationIn dispersed power generation, low power devices are used for local combined generating of heat end electric power. There are developing concepts of micropower plants with electric generators driven by steam or gas microturbines. The paper presents the results of an experimental investigations of the microturbine set consists of the turbine with partial admission, permanent magnet generator and three phase AC-to-DC rectifier. The...
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Systematic Management of Simulation State for Multi-Branch Simulations in Simulink
PublicationSystematic simulation is a technique related and motivated by the formal analysis of hybrid dynamic systems. It combines the exhaustive and conservative nature of traditional model checking with numerical simulation for providing efficient algorithms to manage simulations. Multi-branch simulation is the concept advancing simulation efficiency by reducing the number of state transitions. This paper introduces an approach to implement...
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Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates
PublicationInefficient transportation of polar metabolic inhibitors through cell membranes of eukaryotic and prokaryotic cells precludes their direct use as drug candidates in chemotherapy. One of the possible solutions to this problem is application of the ‘Trojan horse’ strategy, i.e. conjugation of an active substance with a molecular carrier of organic or inorganic nature, facilitating membrane penetration. In this work, the synthetic...