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Search results for: DAMPING, DYNAMICS, DIFFERENTIAL EQUATIONS, LOWERING A LIFEBOAT, NUMERICAL SIMULATIONS
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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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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Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity
PublicationWe demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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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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Verification of the method of reconstructing convective velocity fields on the basis of temperature fields in vertical, differential and equally heated, open and closed channels
PublicationThis paper describes a method of reconstructing velocity fields, i.e. a numerical reconstruction procedure (NRP) that involves the numerical processing of experimentally measured temperature distributions in free convection heat transfer. The NRP consists in solving only the continuity and Navier–Stokes equations with an additional source term. This term is proportional to a known temperature (e.g. from a thermal imaging camera)...
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Structural response of existing spatial truss roof construction based on Cosserat rod theory
PublicationPaper presents the application of the Cosserat rod theory and newly developed associated finite elements code as the tools that support in the expert-designing engineering practice. Mechanical principles of the 3D spatially curved rods, dynamics (statics) laws, principle of virtual work are discussed. Corresponding FEM approach with interpolation and accumulation techniques of state variables are shown that enable the formulation...
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Mechanical properties of Precontraint 1202S coated fabric under biaxial tensile test with different load ratios
PublicationThe paper describes a method of laboratory tests necessary for identifying the mechanical properties of polyester coated fabrics named Precontraint 1202S with PVDF surface treatment. Two sets of initial material parameters for dense net model and orthotropic model are specified. Material parameters for Precontraint 1202S coated fabric are specified on the basis of the biaxial tensile tests for different load ratios. In order to...
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An Innovative Floating System with a Savonius Rotor as a Horizontal-Axis Wind Turbine
PublicationIn this project, an innovative wind turbine was designed for a floating plant. A large Savonius rotor was replaced with a double-rotor wind turbine implemented as a horizontal-axis turbine. This double rotor was positioned on the tip of a thrust plate and fixed to the deck of a catamaran. Simple 2D numerical simulations were performed to confirm the effectiveness of the concept. An analysis of the floating system configuration...
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Study on 19th-century cast iron columns from the former financial office building in Kwidzyn
PublicationThe article presents the results for cast iron columns used as floor supports in the former financial office building in Kwidzyn (Poland).The stocktaking drawings provided the general and detailed data about the 19th century designer’s decisions. During the research, architectural and structural analysis was carried out. The graphics were used as a starting material for preparing 3D calculation models. The FEM-based numerical simulations...
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FE analysis of a coupled energetic-statistical size effect in plain concrete beams with varying material properties.
PublicationThe numerical FE investigations of a coupled energetic-statistical size effect in unnotched concrete beams of similar geometry under quasi-static three point bending were performed within elasto-plasticity with non-local softening. The stochastic FE analyses were carried out with three different beam sizes. Deterministic calculations were performed with the uniform distribution of a uniaxial tensile strength. In statistical calculations...
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On the influence of shell element properties on the response of car model in crash test
PublicationIt goes without saying that numerical simulations play important role in the modern engineering practice. Contemporary CAD environments combined with FEM solvers, along with computer power of modern processors, give the engineer fast and efficient tool. Ultimately, however it is the user alone who is responsible for the correctness of the results. As long as the FEM calculations remain in the sphere of academic exercise, the inevitable...
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Improved finite element method for flow, heat and solute transport of Prandtl liquid via heated plate
PublicationIn the current study, a vertical, 3D-heated plate is used to replicate the generation of heat energy and concentration into Prandtl liquid. We discuss how Dufour and Soret theories relate to the equations for concentration and energy. In order to see how efectively particles, interact with heat and a solvent, hybrid nanoparticles are used. It does away with the phenomena of viscous dissipation and changing magnetic felds. The motivation...
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NUMERICAL MODEL QUALITY ASSESSMENT OF OFFSHORE WIND TURBINE SUPPORTING STRUCTURE BASED ON EXPERIMENTAL DATA
PublicationAs a structure degrades some changes in its dynamical behavior can be observed, and inversely, observation and evaluation of these dynamical changes of the structure can provide information of structural state of the object. Testing of the real structure, besides of being costly, can cover only limited working states. It is particularly considerable in case of hardly accessible, and randomly/severely dynamically loaded offshore...
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SPECTRAL RESPONSE OF STATIONARY JACK-UP PLATFORMS LOADED BY SEA WAVES AND WIND USING PERTURBATION METHOD
PublicationThe paper addresses non-linear vibrations of offshore jack-up drilling platforms loaded by sea waves and wind in their stationary condition using the perturbation method. Non-linearity of dynamic equations of motion for fixed offshore platforms yields from two factors. The first is load excitation generating non-linear velocity coupling in a dynamic system. This coupling is inherent in the modified Morison equation, involving the...
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Temperature Evolution, Material Flow, and Resulting Mechanical Properties as a Function of Tool Geometry during Friction Stir Welding of AA6082
PublicationThe friction stir welding process was simulated for joining AA6082 aluminum alloy with the use of the computational fluid dynamics method. Two different tool geometries were used—a tapered cylindrical pin (simple pin) and a hexagonal pin with grooves (complex pin). The analysis of the simulations performed was discussed in terms of temperature evolution during the process, total heat input, residual stresses and material flow....
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Numerical simulation of cold flow and combustion in a swirl stabilized combustor
PublicationA numerical simulation model was developed to investigate the cold flow and combustion using Ansys FLUENT 2021R1. The governing equations were solved using the pressure-based method, and pressure–velocity coupling was performed using the SIMPLE method. To model the turbulent process, the RSM model was used. Non-premixed model is chosen to solve the chemical kinetics between fuel and oxigen. Radiation heat transfer was calculated...
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PROBLEMS OF THE STARTING AND OPERATING OF HYDRAULIC COMPONENTS AND SYSTEMS IN LOW AMBIENT TEMPERATURE (PART IV) MODELLING THE HEATING PROCESS AND DETERMINING THE SERVICEABILITY OF HYDRAULIC COMPONENTS DURING THE STARTING-UP IN LOW AMBIENT TEMPERATURE
PublicationDesigners of hydraulically driven machines and devices are obliged to ensure during design process their high service life with taking into account their operational conditions. Some of the machines may be started in low ambient temperature and even in thermal shock conditions (due to delivering hot working medium to cold components). In order to put such devices into operation appropriate investigations, including experimental...
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The use of a two-phase Monte Carlo material model to reflect the dispersion of asphalt concrete fracture parameters
PublicationThe work covers comprehensive laboratory tests of semi-circular bending (SCB) of asphalt concrete samples. The results of two test series, including four and 32 SCB specimens, indicate a substantial scatter of force–deflection (F-d) histories. The numerical analysis is aimed to reflect the maximum breaking load and fracture energy of the samples, pointing out their random character. The original simulation-based fictitious Monte...
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Detection and Imaging of Debonding in Adhesive Joints of Concrete Beams Strengthened with Steel Plates Using Guided Waves and Weighted Root Mean Square
PublicationStrengthening of engineering structures is an important issue, especially for elements subjected to variable loads. In the case of concrete beams or slabs, one of the most popular approaches assumes mounting an external reinforcement in the form of steel or composite elements by structural adhesives. A significant disadvantage of adhesive joints is the lack of access to the adhesive film for visual condition assessment, thus, there...
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Numerical Simulation of Catastrophic Flood: the Case Study of Hypothetical Failure of the Bielkowo Hydro–Power Plant Reservoir
PublicationThe numerical modeling of flood wave propagation following the hypo-thetical breaks of the embankments of the Bielkowo hydro–power plant storage reservoir (Kolbudy II Reservoir) on the Radunia River in Poland have been presented. The results of computations were used to estimate the parameters of the flood waves, which are indispensable for the flood zone determination and mapping and then for the flood risk analysis. When estimating...
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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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Experimental and numerical investigation of mercury removal from flue gas by sorbent polymer composite
PublicationThis paper presents an experimental and numerical investigation of the performance of a sorbent polymer composite (SPC) material used for removing mercury from the flue gases in a full-scale industrial installation. The investigated material is an attractive alternative to activated carbon, which is commonly used for this purpose. While the application of the SPC is characterized by high capital expenditures, this technology offers...
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A model development and experimental verification for a vapour microturbine with a permanent magnet synchronous generator
PublicationVapour microturbines with permanent magnet synchronous generators are implemented in micropower plants for dispersed power generation systems. The dynamic model of such a microturbine set was developed and presented. The developed relations result from the generic equations. Experimental data for two different working medium were used for model verification. A microturbine set model was tested during the changes in the parameters...
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TIME- AND FREQUENCY-DOMAIN QUASI-2D SMALL-SIGNAL MOSFET MODELS
PublicationA novel approach to small-signal MOSFET modeling is presented in this book. As a result, time- and frequency-domain physics-based quasi-2D NQS four-terminal small-signal MOSFET models are proposed. The time-domain model provides the background to a novel DIBL-included quasi‑2D NQS four-terminal frequency-domain small-signal MOSFET model. Parameters and electrical quantities of the frequency-domain model are described by explicit...
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Badania eksperymentalne i analiza numeryczna sklepień ceglanych. Wzmocnienie sklepień z wykorzystaniem struktur tensegrity.
PublicationCelem pracy jest opracowanie wzmocnienia zabytkowych sklepień murowych prętowo-cięgnowymi strukturami tensegrity. W tym celu przeanalizowano zagadnienia uszkodzeń, analizy oraz wzmacniania kopuł i sklepień murowych. W kolejnej części rozprawy przedstawiono prace badawczo-rozwojowe zakończone skutecznym wdrożeniem typoszeregu hal namiotowych o konstrukcji prętowo-cięgnowej typu tensegrity. Przeprowadzono badania dynamiczne oraz...
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Numerical investigation on dynamic performance of a multi-storey steel structure model and comparison with experimental results
PublicationShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
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Numerical Investigation on Dynamic Performance of a Multi-storey Steel Structure Model and Comparison with Experimental Results
PublicationShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
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Thermal buckling of functionally graded piezomagnetic micro- and nanobeams presenting the flexomagnetic effect
PublicationGalerkin weighted residual method (GWRM) is applied and implemented to address the axial stability and bifurcation point of a functionally graded piezomagnetic structure containing flexomagneticity in a thermal environment. The continuum specimen involves an exponential mass distributed in a heterogeneous media with a constant square cross section. The physical neutral plane is investigated to postulate functionally graded material...
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Applications of Tensor Analysis in Continuum Mechanics
PublicationA tensor field is a tensor-valued function of position in space. The use of tensor fields allows us to present physical laws in a clear, compact form. A byproduct is a set of simple and clear rules for the representation of vector differential operators such as gradient, divergence, and Laplacian in curvilinear coordinate systems. The tensorial nature of a quantity permits us to formulate transformation rules for its components...
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Full scale CFD seakeeping simulations for case study ship redesigned from V-shaped bulbous bow to X-bow hull form
PublicationIncreasing propulsion efficiency, safety, comfort and operability are of the great importance, especially for small ships operating on windy sites like the North Sea and the Baltic Sea. Seakeeping performance of ships and offshore structures can be analysed by different methods and the one that is becoming increasingly important is CFD RANS. The recent development of simulation techniques together with rising HPC accessibility...
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On instabilities and post-buckling of piezomagnetic and flexomagnetic nanostructures
PublicationWe focus on the mechanical strength of piezomagnetic beam-like nanosize sensors during post-buckling. An effective flexomagnetic property is also taken into account. The modelled sensor is selected to be a Euler-Bernoulli type beam. Long-range interactions between atoms result in a mathematical model based on the nonlocal strain gradient elasticity approach (NSGT). Due to possible large deformations within a post-buckling phenomenon,...
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Generalized Chebyshev Bandpass Filters With Frequency-Dependent Couplings Based on Stubs
PublicationThis paper presents an accurate synthesis method for inline and cross-coupled generalized Chebyshev bandpass filters with frequency-dependent couplings implemented via open and short stubs. The technique involves the synthesis of a lumped-element prototy pe in the form of a coupling matrix with a frequency-dependent term and the conversion of this prototype to a distributed-element mode l composed of sections of TEM lines. This...
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JMATRIX - a package for relativistic J-matrix calculations in elastic scattering of electrons from model potentials
PublicationWe present a software package JMATRIX, consisting of two computer codes written in FORTRAN 95 and parallelized with OpenMP, implementing the so-called J-matrix method, applied to elastic scattering of electrons on the radial potential, vanishing faster than Coulomb one. In the J-matrix method, physical scattering problem is replaced by using well-defined model, which is solved analytically. Presented software implements both non-relativistic...
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Integration of Multi-Source Geospatial Data from GNSS Receivers, Terrestrial Laser Scanners, and Unmanned Aerial Vehicles
PublicationThe analysis based on geospatial data from different measurement systems now constitutes a complex numerical and practical enterprise. The dynamic development of modern technologies enables rapid and precise acquisition of such data. Nonetheless, the diversity of reference systems is today one of the main challenges for their correct interpretation. The combined use of the processed measurement results and archival data in paper...
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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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Pedestrian on footbridges, vertical loads and response
PublicationThe paper is a synthesis of the experimental and theoretical investigations on dynamics of pedestrian bridges under vertical load The subject is divided into four issues.1) The pedestrian as a vertical dynamic load on footbridges, theoretic load function for walking and crouching.2) Crowd walking on the footbridge - pedestrian flow.3) Vertical lock-in effect.4) Response of the footbridge - numeric and side test results, -...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublicationThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Simulation of unsteady flow over floodplain using the diffusive wave equation and the modified finite element method
PublicationWe consider solution of 2D nonlinear diffusive wave equation in a domain temporarily covered by a layer of water. A modified finite element method with triangular elements and linear shape functions is used for spatial discretization. The proposed modification refers to the procedure of spatial integration and leads to a more general algorithm involving a weighting parameter. The standard finite element method and the finite difference...
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Nonlinear Free and Forced Vibrations of a Hyperelastic Micro/Nanobeam Considering Strain Stiffening Effect
PublicationIn recent years, the static and dynamic response of micro/nanobeams made of hyperelasticity materials received great attention. In the majority of studies in this area, the strain-stiffing effect that plays a major role in many hyperelastic materials has not been investigated deeply. Moreover, the influence of the size effect and large rotation for such a beam that is important for the large deformation was not addressed. This...
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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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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Application of the finite element methods in long-term simulation of the multi-physics systems with large transient response differences
PublicationApplication of the Finite Element Method (FEM) and the Multibody Dynamics Method allows analyzing of complex physical systems. Complexity of the system could be related both to the geometry and the physical description of phenomenon. The metod is the excellent tool for analyzing statics or dynamics of the mechanical systems, and permits tracking of Multi Body System (MBS) transient response for the long-term simulations and application...
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Influence of the air phase on water flow in dikes
PublicationNumerical models are often used to describe flow and deformation processes occurring in dikes during flood events. Modeling of such phenomena is a challenging task, due to the complexity of the system, consisting of three material phases: soil skeleton, pore water and pore air. Additional difficulties are transient loading caused by variable in time water levels, heterogeneity of the soil or air...
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A benchmark for particle shape dependence
PublicationParticle shape is a major parameter for the space-filling and strength properties of granular materials. For a systematic investigation of shape effect, a numerical benchmark test was set up within a collaborative group using different numerical methods and particles of various shape characteristics such as elongation, angularity and nonconvexity. Extensive 2D shear simulations were performed in this framework and the shear strength...
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Efficient Gradient-Based Algorithm with Numerical Derivatives for Expedited Optimization of Multi-Parameter Miniaturized Impedance Matching Transformers
PublicationFull-wave electromagnetic (EM) simulation tools have become ubiquitous in the design of microwave components. In some cases, e.g., miniaturized microstrip components, EM analysis is mandatory due to considera¬ble cross-coupling effects that cannot be accounted for otherwise (e.g., by means of equivalent circuits). These effects are particularly pronounced in the structures in¬volving slow-wave compact cells and their numerical...