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High quality speech coding using combined parametric and perceptual modules. [Kodowanie sygnału mowy z zachowaniem wysokiej jakości przy wykorzystaniu modułu parametrycznego i perceptualnego]
PublicationW komunikacie zaprezentowano nową metodę hybrydowego kodowania sygnału mowy. Techniki kodowania parametrycznego oraz perceptualnego zostały wykorzystane w celu zapewnienia wysokiej jakości kodowania sygnału mowy. Przedstawiono wyniki badań dla dwóch architektur kodeka. Jedna z nich bazuje na algorytmie pozwalajacym wyodrębnić składowe dźwięczne, bezdźwięczne oraz transjenty. Składowe dźwięczne kodowane są metodą perceptualną, bezdźwięczne...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublicationThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor−Acceptor Dye Assisted by Resonance Raman Spectroscopy
PublicationThe excitation energies and gradients in the ground and the first excited state of a novel donor−(π- bridge)−acceptor 4-methoxy-1,3-thiazole-based chromophore were investigated by means of MS-RASPT2/RASSCF and TDDFT in solution. Within both methods, the excitation energies strongly depend on the employed equilibrium structures, whose differences can be rationalized in terms of bond length alternation indexes. It is shown that functionals with...
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A multithreaded CUDA and OpenMP based power‐aware programming framework for multi‐node GPU systems
PublicationIn the paper, we have proposed a framework that allows programming a parallel application for a multi-node system, with one or more GPUs per node, using an OpenMP+extended CUDA API. OpenMP is used for launching threads responsible for management of particular GPUs and extended CUDA calls allow to manage CUDA objects, data and launch kernels. The framework hides inter-node MPI communication from the programmer who can benefit from...
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Natural Deep Eutectic Solvents as Agents for Improving Solubility, Stability and Delivery of Curcumin
PublicationPurpose Study on curcumin dissolved in natural deep eutectic solvents (NADES) was aimed at exploiting their beneficial properties as drug carriers. Methods The concentration of dissolved curcumin in NADES was measured. Simulated gastrointestinal fluids were used to determine the concentration of curcumin and quantum chemistry computations were performed for clarifying the origin of curcumin solubility enhancement in NADES. Results NADES...
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Analytical Estimation of Power Losses in a Dual Active Bridge Converter Controlled with a Single-Phase Shift Switching Scheme
PublicationMicro-grid solutions around the world rely on the operation of DC/DC power conver- sion systems. The most commonly used solution for these topologies is the use of a dual active bridge (DAB) converter. Increasing the efficiency and reliability of this system contributes to the improvement in the stability of the entire microgrid. This paper discussed an analytical method of energy efficiency and power loss estimation in a single...
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Construction of phylogenetic trees with topological constraints
PublicationThis paper proposes a method of reconstruction of phylogenetic trees based on heuristic search with topological constraints. Using topological constraints it is possible to reduce the set of solutions as well as to enforce that the result is consistent with a given hypothesis about the evolution process within some group of species. Along with this work a number of algorithms used for phylogenetic analysis were implemented. Those...
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Efficiency of gas detection algorithms using fluctuation enhanced sensing
PublicationEfficiency of various gas detection algorithms by applying fluctuation enhanced sensing method was discussed. We have analyzed resistance noise observed in resistive WO3- nanowires gas sensing layers. Power spectral densities of the recorded noise were used as the input data vectors for two algorithms: the principal component analysis (PCA) and the support vector machine (SVM). The data were used to determine gas concentration...
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Accuracy of Differential Phase Delay Estimation for GPS Spoofing Detection
PublicationGPS spoofing is an attack based on transmission of false signals to target receivers, in order to force the computation of incorrect time, position or velocity information. It is a threat which is recently considered with continuously growing awareness. There is a need for effective way of GPS spoofing detection. Many groups of methods are proposed in the literature. Spatial processing methods are considered to be robust in a wide...
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Fast Full-Wave Multilevel Zero-Pole Optimization of Microwave Filters
PublicationA new concept is proposed for the full-wave computer-aided design of microwave filters. The method consists of two stages and operates on the zeros and poles of the transfer function and their derivatives. These quantities are evaluated from the response computed by a full-wave electromagnetic solver with two levels of accuracy. The two stages make use of different models that are optimized using a low-accuracy electromagnetic...
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Computational complexity and length of recorded data for fluctuation enhanced sensing method in resistive gas sensors
PublicationThis paper considers complexity and accuracy of data processing for gas detection using resistance fluctuation data observed in resistance gas sensors. A few selected methods were considered (Principal Component Analysis – PCA, Support Vector Machine – SVM). Functions like power spectral density or histogram were used to create input data vector for these algorithms from the observed resistance fluctuations. The presented considerations...
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Local Mesh Deformation for accelerated parametric studies based on the Finite Element Method
PublicationThis paper presents an approach for enhancing the efficiency of two-dimensional Finite Element Method analysis in parametric studies or optimisation process of microwave components. The new approach involves local mesh deformation applied near the elements that are modified during computations. Since in the proposed approach the topology of the mesh remains unchanged, a new mesh does not have to be generated from scratch when the...
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Local basis function estimators for identification of nonstationary systems
PublicationThe problem of identification of a nonstationary stochastic system is considered and solved using local basis function approximation of system parameter trajectories. Unlike the classical basis function approach, which yields parameter estimates in the entire analysis interval, the proposed new identification procedure is operated in a sliding window mode and provides a sequence of point (rather than interval) estimates. It is...
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Modeling of Performance, Reliability and Energy Efficiency in Large-Scale Computational Environment
PublicationLarge scale of complexity of distributed computational systems imposes special challanges for prediction of quality in such systems.Existing quality models for lower-scale systems include functionality,performance,reliability,flexibility and usability.Among these attributes,performance and reliability have a particular significance to the large-scale systems computing quality modeling due to their strong dependence on the system...
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Automated Reduced Model Order Selection
PublicationThis letter proposes to automate generation of reduced-order models used for accelerated -parameter computation by applying a posteriori model error estimators. So far,a posteriori error estimators were used in Reduced Basis Method (RBM) and Proper Orthogonal Decomposition (POD) to select frequency points at which basis vectors are generated. This letter shows how a posteriori error estimators can be applied to automatically select...
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Accuracy Analysis of Determination the Vertical Displacements in Unstable Reference System
PublicationMeasurements of horizontal and vertical displacements are carried out mostly based on reference points identified as fixed. In surveying practice there may be some situations in which there is not possible to perform the measurements with reference to stable points or the difficulties in identification of points’ stability may arise. Accuracy analysis based on the covariance matrices have a special role in this process. In presented...
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A subdomain model for armature reaction field and open‐circuit field prediction in consequent pole permanent magnet machines
PublicationIn this paper, the machine quantity, such as electromagnetic torque, self and mutual inductances, and electromotive force, is analytically calculated for non-overlapping winding consequent pole slotted machine for open-circuit field and armature reaction. The sub-domain approach of (2-D) analytical model is developed using Maxwell's equations and divide the problem into slots, slot-openings, airgap and magnets region, the magnet...
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Efficient analysis of structures with rotatable elements using model order reduction
PublicationThis paper presents a novel full-wave technique which allows for a fast 3D finite element analysis of waveguide structures containing rotatable tuning elements of arbitrary shapes. Rotation of these elements changes the resonant frequencies of the structure, which can be used in the tuning process to obtain the S-characteristics desired for the device. For fast commutations of the response as the tuning elements are rotated, the...
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OPTIMIZATION OF THE LAST STAGE OF GAS-STEAM TURBINE USING A HYBRID METHOD
PublicationThis paper relates to the CFD calculation of a new turbine type which is in the phase of theoretical analysis, because the working fluid is a mixture of steam and gas generated in wet combustion chamber. At first, this article concentrates on a possibility of streamlining the flow efficiency of a last stage of axial turbine working on gas-steam mixture using a hybrid of the particle swarm optimization algorithm with the Nelder-Mead...
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Performance Models of a Multidomain IMS/NGN Service Stratum
PublicationThis paper quantifies call processing performance (CPP) of a multidomain IMS/NGN architecture, which was proposed to deliver current and future telecommunication services with strict quality requirements, independently of the transport network technologies. A realistic simulation model is used as a reference for evaluation of the analytical results, in which vari-ous types of queuing systems are applied to model the opera-tion...
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Simplified probabilistic analysis of settlement of cyclically loaded soil stratum using point estimate method
PublicationThe paper deals with the probabilistic analysis of settlement of a non-cohesive soil layer subjected to cyclic loading. Originally, the settlement assessment is based on deterministic compaction model which requires integration of a set of differential equations. However, making use of the Bessel functions the settlement of the soil stratum can be calculated by means of simplified algorithm. The compaction model parameters were...
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An absorbing set for the Chialvo map
PublicationThe classical Chialvo model, introduced in 1995, is one of the most important models that describe single neuron dynamics. In order to conduct effective numerical analysis of this model, it is necessary to obtain a rigorous estimate for the maximal bounded invariant set. We discuss this problem, and we correct and improve the results obtained by Courbage and Nekorkin (2010). In particular, we provide an explicit formula for an...
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Modeling of Performance, Reliability and Energy Efficiency in Large-Scale Computational Environments
PublicationLarge scale of complexity of distributed computational systems imposes special challenges for prediction of quality in such systems. Existing quality models for lower-scale systems include functionality, performance, reliability, flexibility and usability. Among these attributes, performance and reliability have a particular significance to the large-scale systems computing quality modeling due to their strong dependence on the...
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The concept of a new two-stage fuse for high power pulse forming
PublicationThis manuscript introduces the concept, physical operating principle and studies on a new and unique two stage forming fuse (TSFF) with interstage spark gap commutation and presents its application for forming high power pulses of extreme parameters. The paper classifies TSFF performance and compares it with conventional single-stage forming fuses. The conclusions are supported by analytical and experimental studies in laboratory...
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FEM simulations applied to the failure analysis of RC structure under the influence of municipal sewage pressure
PublicationThe paper discusses a failure mechanism of reinforced concrete (RC) structure with steel cover that failed under the influence of municipal sewage pressure. To explain the reasons of failure, in-situ measurements, laboratory experiments and comprehensive Finite Element Method (FEM) computations were performed. Non-destructive in-situ scanning tests were carried out to determine quantity and cover thickness of embedded reinforcement...
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Improving Effectiveness of SVM Classifier for Large Scale Data
PublicationThe paper presents our approach to SVM implementation in parallel environment. We describe how classification learning and prediction phases were pararellised. We also propose a method for limiting the number of necessary computations during classifier construction. Our method, named one-vs-near, is an extension of typical one-vs-all approach that is used for binary classifiers to work with multiclass problems. We perform experiments...
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Parallelization of Selected Algorithms on Multi-core CPUs, a Cluster and in a Hybrid CPU+Xeon Phi Environment
PublicationIn the paper we present parallel implementations as well as execution times and speed-ups of three different algorithms run in various environments such as on a workstation with multi-core CPUs and a cluster. The parallel codes, implementing the master-slave model in C+MPI, differ in computation to communication ratios. The considered problems include: a genetic algorithm with various ratios of master processing time to communication...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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Distributed state estimation using a network of asynchronous processing nodes
PublicationWe consider the problem of distributed state estimation of continuous-time stochastic processes using a~network of processing nodes. Each node performs measurement and estimation using the Kalman filtering technique, communicates its results to other nodes in the network, and utilizes similar results from the other nodes in its own computations. We assume that the connection graph of the network is not complete, i.e. not all nodes...
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Performance evaluation of the parallel object tracking algorithm employing the particle filter
PublicationAn algorithm based on particle filters is employed to track moving objects in video streams from fixed and non-fixed cameras. Particle weighting is based on color histograms computed in the iHLS color space. Particle computations are parallelized with CUDA framework. The algorithm was tested on various GPU devices: a desktop GPU card, a mobile chipset and two embedded GPU platforms. The processing speed depending on the number...
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Distributed state estimation using a network of asynchronous processing nodes
PublicationWe consider the problem of distributed state estimation of continuous-time stochastic processes using a~network of processing nodes. Each node performs measurement and estimation using the Kalman filtering technique, communicates its results to other nodes in the network, and utilizes similar results from the other nodes in its own computations. We assume that the connection graph of the network is not complete, i.e. not all nodes...
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Fast implementation of FDTD-compatible green's function on multicore processor
PublicationIn this letter, numerically efficient implementation of the finite-difference time domain (FDTD)-compatible Green's function on a multicore processor is presented. Recently, closed-form expression of this discrete Green's function (DGF) was derived, which simplifies its application in the FDTD simulations of radiation and scattering problems. Unfortunately, the new DGF expression involves binomial coefficients, whose computations...
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Estimation of the steam condensation flow via CFD methods
PublicationThe results of numerical simulations to predict the performance of different steam models have been presented. All of the considered models of steam condensation have been validated on the base of benchmark experiment employing expansion in nozzle and next on the low pressure part of the steam turbine stage. For numerical analysis three models have been finally used – the ideal steam model without condensation, an equilibrium steam...
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Fracture mechanics model of cutting power versus widespread regression equations while wood sawing with circular saw blades
PublicationA comparison of the theoretical cutting power consumption results forecasted with the model (FM_CM model) which include work of separation (fracture toughness) in addition to plasticity and friction, and two widespread regression equations while wood sawing with circular saw blades has been described. in and cutting power consumption forecasted. In computations of the cutting power consumption during rip sawing of Scots pine wood...
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Empirical verification in industrial conditions of fracture mechanics models of cutting power prediction
PublicationA comparison of experimental results obtained in the industrial conditions at a sawmill located in the Baltic Natural Forest Region (PL) and theoretical cutting power consumption forecasted with the models which include work of separation (fracture toughness) in addition to plasticity and friction has been described. In computations of cutting power consumption during rip sawing of Scots pine wood (Pinus sylvestris L.) values of...
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FDTD-Compatible Green's function based on scalar discrete Green's function and multidimensional Z-transform
PublicationIn this contribution, a new formulation of the discrete Green's function (DGF) is presented for the finitedifference time-domain (FDTD) grid. Recently, dyadic DGF has been derived from the impulse response of the discretized scalar wave equation (i.e., scalar DGF) with the use of the multidimensional Z-transform. Its software implementation is straightforward because only elementary functions are involved and a single function...
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Analytical fluctuation enhanced sensing by resistive gas sensors
PublicationResistance fluctuations across polarised resistive gas sensors were studied in detail to evaluate sensor working conditions for detecting methane and ammonia at various concentrations. The 1/f noise component typically dominates other noise sources up to a few kHz and can be utilised to improve gas selectivity when compared with measurements of the sensor DC resistance. The Arrhenius plot was created and the activation energy for...
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Convergence of Monte Carlo algorithm for solving integral equations in light scattering simulations
PublicationThe light scattering process can be modeled mathematically using the Fredholm integral equation. This equation is usually solved after its discretization and transformation into the system of algebraic equations. Volume integral equations can be also solved without discretization using the Monte Carlo (MC) algorithm, but its application to the light scattering simulations has not been sufficiently studied. Here we present implementation...
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Optimization of Execution Time under Power Consumption Constraints in a Heterogeneous Parallel System with GPUs and CPUs
PublicationThe paper proposes an approach for parallelization of computations across a collection of clusters with heterogeneous nodes with both GPUs and CPUs. The proposed system partitions input data into chunks and assigns to par- ticular devices for processing using OpenCL kernels defined by the user. The sys- tem is able to minimize the execution time of the application while maintaining the power consumption of the utilized GPUs and...
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Modeling SPMD Application Execution Time
PublicationParallel applications in a Single Process Multiple Data paradigm assume splitting huge amounts of data to multiple processors working in parallel at small data packets. As the individual data packets are not independent, the processors must interact with each other to exchange results of the calculations with their adjacent partners and take these results into account in their own computations. An example of SPMD is geometric parallelism...
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Estimation of fracture toughness and shear yield stress of orthotropic materials in cutting with rotating tools
PublicationThe cutting force is an energetic effect of splitting material, and might be considered from a point of view of modern fracture mechanics. Forecasting of the shear plane angle in cutting broaden possibilities for modelling of the cutting process even for thin uncut chips. Such mathematical model has been developed here for description of the orthotropic materials’ cutting on the base of fracture theory, and includes work of separation...
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A New Type of Macro-Elements for Efficient Two-Dimensional FEM Analysis
PublicationThis letter deals with a model order reduction technique applicable for driven and eigenvalue problems solved using the finite element method (FEM). It allows one to efficiently compute electromagnetic parameters of structures comprising small features that require strong local mesh refinement. The subdomains of very fine mesh are separated from the global domain as so called macro-elements that undergo model reduction. The macro-elements...
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Fluid–Structure Interaction methods for the progressive anatomical and artificial aortic valve stenosis
PublicationCardiovascular system diseases, as aortic valve stenosis, are the main cause of mortality and morbidity among patients. There is still a room for enhancement of the diagnostic and therapeutic procedures, which will lead to improvement of the treatment. One of the remedies are the computer tools to support the medical diagnoses and prostheses design. The development of a procedure for modeling the aortic valves: anatomical tricuspid...
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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....