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Search results for: MOLECULAR DYNAMICS SIMULATIONS
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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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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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Antenna Modeling Using Variable-Fidelity EM Simulations and Constrained Co-Kriging
PublicationUtilization of fast surrogate models has become a viable alternative to direct handling of fullwave electromagnetic (EM) simulations in EM-driven design. Their purpose is to alleviate the difficulties related to high computational cost of multiple simulations required by the common numerical procedures such as parametric optimization or uncertainty quantification. Yet, conventional data-driven (or approximation) modeling techniques...
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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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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublicationRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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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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Prediction of ship resistance with the use of Full-scale CFD simulations
PublicationIn recent years, the IMO has introduced new regulations to reduce the negative impact of ships on the natural environment. A particularly important step forcing technological innovations is the increasing requirement of ship energy efficiency. It is expressed by the Energy Efficiency Design Index (EEDI). Another important step towards green shipping is rising the required quality of fuel used for propulsion, so called Tier limits....
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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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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublicationSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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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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Ampacity of power cables exposed to solar radiation – recommendations of standards vs. CFD simulations
PublicationThe aim of the paper is to evaluate the ampacity of a low-voltage single power cable according to: 1) recommendations of the standard IEC 60287, 2) a Computational Fluid Dynamics method, implemented in Ansys software; and comparison of the results obtained for these two cases. Moreover, limitations of recommendations of the above mentioned standard are indicated.
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Au–Si plasmonic platforms: synthesis, structure and FDTD simulations
PublicationPlasmonic platforms based on Au nanostructures have been successfully synthesized by directional solidification of a eutectic from Au and the substrate. In order to determine homogeneous shape and space distribution, the influence of annealing conditions and the initial thickness of the Au film on the nanostructures was analyzed. For the surface morphology studies, SEM and AFM measurements were performed. The structure of platforms...
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FDTD Method for Electromagnetic Simulations in Media Described by Time-Fractional Constitutive Relations
PublicationIn this paper, the finite-difference time-domain (FDTD) method is derived for electromagnetic simulations in media described by the time-fractional (TF) constitutive relations. TF Maxwell’s equations are derived based on these constitutive relations and the Grünwald–Letnikov definition of a fractional derivative. Then the FDTD algorithm, which includes memory effects and energy dissipation of the considered media, is introduced....
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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...
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Bio‐polyols synthesized by liquefaction of cellulose: Influence of liquefaction solvent molecular weight
PublicationCurrently, the plastics industry including polyurethanes is based on the use of petrochemicals. For this reason, scientists are looking for new types of renewable resources for the substitution of petrochemical substances. This work aims to evaluate the effect of polyethylene glycols (PEG) with different molecular mass impact on properties of bio-based polyols synthesized via biomass liquefaction of cellulose. To date, research...
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Molecular Biology of Meniscal Healing: A Narrative Review
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Numerical simulations of a triaxial test in granular bodies using discrete particle simulations with contact moments
PublicationW artykule przedstawiono wyniki symulacji badania trójosiowego dla materiałów granulowanych. Obliczenia wykonano przy zastosowaniu metody DEM. Pokazano wpływ momentów kontaktowych na wytrzymałość próbki. Zbadano wpływ parametrów mikroskopowych.
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Beyond the helium buffer: 12C−2 rotational cooling in cold traps with H2 as a partner gas: interaction forces and quantum dynamics
Publicationabstract = { The scattering cross-sections and corresponding rate coefficients for rotationally inelastic collisions of $^{12}$C$_2$^-$ ($^2 \Sigma_g^+$) with H$_2$ ($^1 \Sigma_g^+$) are presented over a broad range of cold-trap temperatures. They have been calculated using quantum scattering theory that employs a new ab initio potential energy surface. The rate coefficients for the inelastic processes in the anionic partner are...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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Dynamics of Topology-dependent Water Purification by Siliceous Zeolite Membranes
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Quantum corrections to 4 model solutions and applications to Heisenberg chain dynamics
PublicationThe Heisenberg spin chain is considered in φ^4 model approximation. Quantum corrections to classical solutions of the one-dimensional φ^4 model within the correspondent physics are valuated with account of rest d − 1 dimensions of a d-dimensional theory. A quantization of the model is considered in terms of space- time functional integral. The generalized zeta-function formalism is used to renormalize and evaluate the functional...
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BIOGAS PRODUCTION FROM BAKERY WASTES -DYNAMICS, RETENTION TIME AND BIOGAS POTENTIAL
PublicationThis paper presents results of bakery-waste methane-fermentation. The scope of the study covers the determination of basic physicochemical parameters, process dynamics and retention time as well as biogas composition and biogas efficiency. Methane fermentation process was carried out in accordance with German Standard DIN 38414 S8 and under condition of 38°C. Conclusion: bakery wastes have big potential for biogas production.
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Non-uniqueness of fracture parameter choice in simulations of concrete cracking at mesoscale level
PublicationIn the paper a non-uniqueness of fracture parameter choice in simulations of cracking process in plain concrete specimens at mesoscale level under monotonic static loading is analysed. The Finite Element Method is used, where cracks are defined in a discrete way using interface cohesive elements with nonlinear material law including softening. The concrete mesostructure (such as: cement matrix, air voids, aggregates, and Interfacial...
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Periodic Properties of 1D FE Discrete Models in High Frequency Dynamics
PublicationFinite element discrete models of various engineering 1D structures may be considered as structures of certain periodic characteristics. The source of this periodicity comes from the discontinuity of stress/strain field between the elements. This behaviour remains unnoticeable, when low frequency dynamics of these structures is investigated. At high frequency regimes, however, its influence may be strong enough to dominate calculated...
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Dynamics of the small-span railway bridge under moving loads
PublicationThe paper presents the results of dynamic analysis of the small-span railway bridge, subjected to an action of moving trains. Numerical simulations were performed using three different load models: series of moving forces, series of moving single-mass and double-mass oscillators. The parameters of the vehicle were taken from the existing EN57 train. The parameters of the bridge were taken from the existing steel span of 10,24 m...
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Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
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A Comprehensive Review: Applications of the Kozeny–Carman Model in Engineering with Permeability Dynamics
PublicationIn this review article, we investigate the dynamic nature of the Kozeny–Carman Model concerning permeability and its application in engineering contexts. Providing insights into the changing dynamics of permeability within mining, petroleum, and geotechnical engineering, among other engineering applications. While some are complex and require additional modifcations to be applicable, others are simple and still function in specifc...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Fast Multi-Objective Antenna Design Through Variable-Fidelity EM Simulations
PublicationA technique for fast multi-objective antenna optimization is introduced. A kriging interpolation surrogate constructed from sampled coarse-mesh EM simulations is utilized by multi-objective evolutionary algorithm (MOEA) to obtain the initial Pareto front approximation. The surrogate is defined in a subset of the original design space, determined by means of independently optimized individual objectives. Response correction techniques...
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Modelling and simulations in time-fractional electrodynamics based on control engineering methods
PublicationIn this paper, control engineering methods are presented with regard to modelling and simulations of signal propagation in time-fractional (TF) electrodynamics. That is, signal propagation is simulated in electromagnetic media described by Maxwell’s equations with fractional-order constitutive relations in the time domain. We demonstrate that such equations in TF electrodynamics can be considered as a continuous-time system of...
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Chitosan-Based Membranes as Gentamicin Carriers for Biomedical Applications — Influence of Chitosan Molecular Weight
PublicationOver the past decade, much attention has been paid to chitosan as a potential drug carrier because of its non-toxicity, biocompatibility, biodegradability and antibacterial properties. The effect of various chitosan characteristics on its ability to carry different antibiotics is discussed in the literature. In this work, we evaluated the influence of the different molecular weights of this polymer on its potential as an antibacterial...
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Using River Formation Dynamics Algorithm in Mobile Robot Navigation
PublicationRiver Formation Dynamics is a heuristic optimization algorithm based on the manner, in which drops of water form the river bed. The idea is to imitate the movement of drops on the edges between given nodes thus performing a search based on their height, which is modified through the mechanism of soil erosion and sediment deposition. In this way decreasing gradients are constructed, and these are followed by subsequent drops to...
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Dynamics of Changes in The Urban Space
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Microarrays and Dynamics of Fluorescent Dyes
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Dynamics of surface floating objects
PublicationPrezentowana praca stanowi wstępne rozeznanie w dziedzinie badań dynamiki konstrukcji pływających z zastosowaniem teorii procesu dyfuzji. W pracy rozpatrywane są modele fizyczne jednostek wielokadłubowych oraz modele matematyczne. Spośród modeli jednostek wielokadłubowych wyróżnia się modele deterministyczne oraz modele stochastyczne.
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Statistical Dynamics of the Rolling Mills
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Lattice dynamics of CuAu-orderedCuInSe2
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Maxillary sinus aeration analysis using computational fluid dynamics
PublicationThe maxillary sinus aeration using the computational fluid dynamics (CFD) method based on individual adult patients’ computed tomography (CT) scans were analyzed. The analysis was based on CT images of 4 patients: one with normal nose anatomy and three with nasal septal deviation (NSD) and concha bullosa (CB). The CFD simulation was performed using the Reynolds-Average Simulation approach and turbulence closure based on linear...
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INFORMATION ABOUT DYNAMICS OF THE SEA SURFACE AS A MEANS TO IMPROVE SAFETY OF THE UNMANNED VESSEL AT SEA
PublicationOne of the fundamental states of the sea surface is its heave. Despite of years of the intense scientific inquiry, no clear understanding of the influence of this aspect on the dynamics of the sea environment has emerged. The separation of two nearby fluid elements which one may observed for example as a free floating of small objects on the sea surface (rescuers on the rough sea or small research vessels) is caused by the interaction...
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Improvement of ships seakeeping performance by application of the Full-scale CFD simulations – case study
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 reflects very difficult operational con-ditions 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,...
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Numerical Simulations and Tracer Studies as a Tool to Support Water Circulation Modeling in Breeding Reservoirs
PublicationThe article presents a proposal of a method for computer-aided design and analysis of breeding reservoirs in zoos and aquariums. The method applied involves the use of computer simulations of water circulation in breeding pools. A mathematical model of a pool was developed, and a tracer study was carried out. A simplified model of two-dimensional flow in the form of a biharmonic equation for the stream function (converted into...
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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublicationIn the paper experimental tests and numerical simulations of a full cross-section segment of ultimately designed foot-and cycle-bridge are presented. The experimental tests were conducted on element with length reduced to 3 m and unchanged (target) cross-section dimensions. The external skin of structure is GFRP laminate while internal core is PET foam. Several quasi-static tests were performed using hydraulic cylinder to generate...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Simulations CAE of wood pellet machine
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Measurements and Simulations of Engineered Ultrasound Loudspeakers
PublicationSimulation and measurement results of the sound emitted from an ultrasound custom-made system with high spatial directivity are presented. The proposed system is using modulated ultrasound waves which demodulate in nonlinear medium resulting in audible sound. The system is aimed at enhancing the users’ personal audio space, therefore the measurements are performed using the Head and Torso Simulator which provides realistic reproduction...
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FE simulations of a soil structure interface.
PublicationPrzedstawiono warunki brzegowe do opisu szorstkości ściany konstrukcji w kontakcie z gruntem. Wykonano doświadczenia i symulacje MES na bazie mikropolarnego prawa hipoplastycznego.
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Molecular Umbrellas Modulate the Selective Toxicity of Polyene Macrolide Antifungals
PublicationAntifungal polyene macrolide antibiotics Amphotericin B (AmB) and Nystatin (NYS) were conjugated through the ω-amino acid linkers with diwalled “molecular umbrellas” composed of spermidine-linked deoxycholic or cholic acids. The presence of “umbrella” substituents modulated biological properties of the antibiotics, especially their selective toxicity. Some of the AmB-umbrella conjugates demonstrated antifungal in vitro activity...
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FDTD Simulations on Disjoint Domains with the Use of Discrete Green's Function Diakoptics
PublicationA discrete Green's function (DGF) approach to couple disjoint domains in the finite-difference time-domain (FDTD) grid is developed. In this method, total-field/scattered-field (TFSF) FDTD domains are associated with simulated objects whereas the interaction between them is modeled with the use of the DGF propagator. Hence, source and scatterer are simulated in separate domains and updating of vacuum cells, being of little interest,...
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High frequency dynamics of an isotropic Timoshenko periodic beam by the use of the Time-domain Spectral Finite Element Method
PublicationIn this work results of numerical simulations and experimental measurements related to the high frequency dynamics of an aluminium Timoshenko periodic beam are presented. It was assumed by the authors that the source of beam structural periodicity comes from periodical alterations to its geometry due to the presence of appropriately arranged drill-holes. As a consequence of these alterations dynamic characteristics of the beam...
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Real-Time PCR: molecular technique of many applications
PublicationReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...