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Search results for: linear-scaling
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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Extended phase diagram of RNiC2 family: Linear scaling of the Peierls temperature
PublicationPhysical properties for the late-lanthanide-based RNiC2 (R = Dy, Ho, Er, and Tm) ternary compounds are reported. All the compounds show antiferromagnetic ground state with the Néel temperature ranging from 3.4 K for HoNiC2 to 8.5 K for ErNiC2. The results of the transport and galvanomagnetic properties confirm a charge density wave state at and above room temperature with transition temperatures TCDW = 284, 335, 366, and 394 K for...
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The potential of imogolite nanotubes as (co-)photocatalysts: a linear-scaling density functional theory study
PublicationWe report a linear-scaling density functional theory (DFT) study of the structure, wall-polarization absolute band-alignment and optical absorption of several, recently synthesized, open-ended imogolite (Imo) nanotubes (NTs), namely single-walled (SW) aluminosilicate (AlSi), SW aluminogermanate (AlGe), SW methylated aluminosilicate (AlSi-Me), and double-walled (DW) AlGe NTs. Simulations with three different semi-local and dispersion-corrected...
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Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublicationWe present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been imple- mented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ...
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Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory
PublicationWe present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such...
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Massively parallel linear-scaling Hartree–Fock exchange and hybrid exchange–correlation functionals with plane wave basis set accuracy
PublicationWe extend our linear-scaling approach for the calculation of Hartree–Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the ONETEP (Order-N Electronic Total Energy Package) density functional theory framework, which employs a basis of non-orthogonal generalized Wannier functions (NGWFs) to achieve...
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublicationWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Raw data for the paper "Mutually polarizable QM/MM model with in situ optimized localized basis functions"
Open Research DataThis dataset contains raw data used to generate plots in the paper Mutually polarizable QM/MM model with in situ optimized localized basis functions. The paper is devoted to a second generation of the TINKTEP model -- an QM/MM approach combining linear-scaling DFT (ONETEP) and a polarizable force field (AMOEBA).
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Efficiency of linear and non-linear classifiers for gas identification from electrocatalytic gas sensor
PublicationElectrocatalytic gas sensors belong to the family of electrochemical solid state sensors. Their responses are acquired in the form of I-V plots as a result of application of cyclic voltammetry technique. In order to obtain information about the type of measured gas the multivariate data analysis and pattern classification techniques can be employed. However, there is a lack of information in literature about application of such...
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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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Chemically Selective Alternatives to Photoferroelectrics for Polarization-Enhanced Photocatalysis: The Untapped Potential of Hybrid Inorganic Nanotubes
PublicationLinear-scaling density functional theory simulation of methylated imogolite nanotubes (NTs) elucidates the interplay between wall-polarization, bands separation, charge-transfer excitation, and tunable electrostatics inside and outside the NT-cavity. The results suggest that integration of polarization-enhanced selective photocatalysis and chemical separation into one overall dipole-free material should be possible.
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Multiple output CMOS current amplifier
PublicationIn this paper the multiple output current amplifier basic cell is proposed. The triple output current mirror and current follower circuit are described in detail. The cell consists of a split nMOS differential pair and accompanying biasing current sources. It is suitable for low voltage operation and exhibits highly linear DC response. Through cell devices scaling, not only unity, but also any current gains are achievable. As...
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Stability analysis of nanobeams in hygrothermal environment based on a nonlocal strain gradient Timoshenko beam model under nonlinear thermal field
PublicationThis article is dedicated to analyzing the buckling behavior of nanobeam subjected to hygrothermal environments based on the principle of the Timoshenko beam theory. The hygroscopic environment has been considered as a linear stress field model, while the thermal environment is assumed to be a nonlinear stress field based on the Murnaghan model. The size-dependent effect of the nanobeam is captured by the nonlocal strain gradient...
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Low-fidelity model considerations for simulation-based optimisation of miniaturised wideband antennas
PublicationHere, variable-fidelity electromagnetic (EM)-based design optimisation of miniaturised antennas is discussed. The authors focus on an appropriate selection of discretisation density of the low-fidelity EM model, which results in good performance of the optimisation algorithm in terms of its computational complexity and reliability. Trust-region gradient search with low-fidelity model corrected by means of non-linear frequency scaling...
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
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Charge density wave and large nonsaturating magnetoresistance in YNiC2 and LuNiC2
PublicationWe report a study of physical properties of two quasi-low-dimensional metals YNiC2 and LuNiC2 including the investigation of transport, magnetotransport, galvanomagnetic, and specific heat properties. In YNiC2 we reveal two subsequent transitions associated with the formation of weakly coupled charge density wave at TCDW=318K and its locking in with the lattice at T1=275K. These characteristic temperatures follow the previously...
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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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Performance assessment of OpenMP constructs and benchmarks using modern compilers and multi-core CPUs
PublicationConsidering ongoing developments of both modern CPUs, especially in the context of increasing numbers of cores, cache memory and architectures as well as compilers there is a constant need for benchmarking representative and frequently run workloads. The key metric is speed-up as the computational power of modern CPUs stems mainly from using multiple cores. In this paper, we show and discuss results from running codes such as:...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Electrochemistry from first-principles in the grand canonical ensemble
PublicationProgress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are...
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Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
PublicationStatistical block copolymers, composed of donor (D) and acceptor (A) blocks, are a novel type of material for organic photovoltaics (OPVs) devices. In particular a new series of polymers based on PBTZT-stat-BDTT-8, recently developed by Merck, offers high solubility in different solvents, and a high power conversion efficiency (PCE) in different device architectures. Although it is known that the electronic properties of these...
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces
PublicationDensity functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign (“jellium”). This artificial neutralization does not occur in reality, where a different...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Scaling of numbers in residue arithmetic with the flexible selection of scaling factor
PublicationA scaling technique of numbers in resudue arithmetic with the flexible selection of the scaling factor is presented. The required scaling factor can be selected from the set of moduli products of the Residue Number System (RNS) base. By permutation of moduli of the number system base it is possible to create many auxilliary Mixed-Radix Systems associated with the given RNS with respect to the base, but they have different sets...
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Scaling of signed residue numbers with mixed-radix conversion in FPGA with extended scaling factor selection
PublicationA scaling technique of signed residue numbers in FPGA is proposed. The technique is based on conversion of residue numbers to the Mixed-Radix System (MRS). The scaling factor is assumed to be a moduli product from the Residue Number System (RNS) base. Scaling is performed by scaling of MRS terms, the subsequent generation of residue representations of scaled terms, binary addition of these representations and generation of residues...
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Inverse surrogate modeling for low-cost geometry scaling of microwave and antenna structures
PublicationPurpose–The purpose of this paper is to investigate strategies for expedited dimension scaling ofelectromagnetic (EM)-simulated microwave and antenna structures, exploiting the concept of variable-fidelity inverse surrogate modeling.Design/methodology/approach–A fast inverse surrogate modeling technique is described fordimension scaling of microwave and antenna structures. The model is established using referencedesigns obtained...
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At the Limits of Criticality-Based Quantum Metrology: Apparent Super-Heisenberg Scaling Revisited
PublicationWe address the question of whether the super-Heisenberg scaling for quantum estimation is indeed realizable. We unify the results of two approaches. In the first one, the original system is compared with its copy rotated by the parameter-dependent dynamics. If the parameter is coupled to the one-body part of the Hamiltonian, the precision of its estimation is known to scale at most as N−1 (Heisenberg scaling) in terms of the number...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Experimental research on evolutionary path planning algorithm with fitness function scaling for collision scenarios
PublicationThis article presents typical ship collision scenarios, simulated using the evolutionary path planning system and analyses the impact of the fitness function scaling on the quality of the solution. The function scaling decreases the selective pressure, which facilitates leaving the local optimum in the calculation process and further exploration of the solution space. The performed investigations have proved that the use of scaling...
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Pipelined sceling of signed residue numbers with the mixed-radix conversion in the programmable gate array
PublicationIn this work a scaling technique of signed residue numbers is proposed. The method is based on conversion to the Mixed-Radix System (MRS) adapted for the FPGA implementation. The scaling factor is assumed to be a moduli product from the Residue Number System (RNS) base. Scaling is performed by scaling of terms of the mixed-radix expansion, generation of residue reprezentation of scaled terms, binary addition of these representations...
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Comprehensive Comparison of a Few Variants of Cluster Analysis as Data Mining Tool in Supporting Environmental Management
PublicationA few variants of hierarchical cluster analysis (CA) as tool of assessment of multidimensional similarity in environmental dataset are compared. The dataset consisted of analytical results of determination of metals (Na, K, Ca, Sc, Fe, Co, Zn, As, Br, Rb, Mo, Sb, Cs, Ba, La, Ce, Sm, Hf and Th) in ambient air dried and kept alive, by the means of hydroponics, moss baskets collected in 12 locations on the area of Tricity (Poland)....
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Rapid dimension scaling of triple-band antennas by means of inverse surrogate modeling
PublicationGeometry scaling of antennas, i.e., finding optimum dimensions of the structure for given operating conditions and material parameters is an important yet challenging problem. In this paper, we discuss fast dimension scaling of triple-band antennas with respect to operating frequencies. We adopt the inverse surrogate modeling approach where the surrogate model is a function of the three operating frequencies of the antenna and...
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Flow structure, heat transfer and scaling analysis in the case of thermo-magnetic convection in a differentially heated cylindrical enclosure
PublicationThe experimental, numerical and scaling analysis in the case of thermo-magnetic convection in a thermosyphon-like enclosure filled with a paramagnetic fluid is presented. Visualization of temperature field together with the numerical simulation gave an information about the flow structure, which indicated “finger-like” structures of hot and cold streams advecting each other. Their number depended on the Rayleigh number and also...
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Derivation of the scaling laws used in geotechnical centrifuge modelling-application of dimensional analysis and Buckingham Π theorem
PublicationGeotechnical centrifuge modelling has been a world-wide used technology in physical tests. In this paper a derivation of scaling laws by dimensional analysis for the centrifugal modelling is presented. Basic principles of centrifuge modelling are described. Scaling laws for slow events like consolidation and fast events like dynamic loads are shown. The differences in scale factors for both processes are noticed. The aim of this...
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Design of Microstrip UWB Balun Using Quasi-TEM Approach Aided by the Artificial Neural Network
PublicationThe design procedure for UWB balun realized in the microstrip technology is proposed in the paper. The procedure applies Artificial Neural Network which corrects the dimensions of the approximate design found by appropriate scaling of the dimensions of the prototype. The scale coefficients for longitudinal and transverse dimensions of microstrip lines are determined from electromagnetic modeling based on transmission line equations....
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Fast geometry scaling of UWB band-notch antennas
PublicationImplementation of band-notch capability plays an important role in the design of ultra-wideband (UWB) antennas. At the same time, appropriate sizing of antenna geometry parameters in order to precisely allocate the notch at the required frequency as well as to ensure sufficient reflection level is quite challenging and has to be based—for reliability reasons—on full-wave electromagnetic (EM) simulations of the structure. In this...
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Low-energy positron scattering from gas-phase benzene
PublicationIn this paper we are presenting calculations of the elastic cross section of positrons with gas-phase benzene for the energy range from 0.25 eV to 9.0 eV. The calculations are done with the molecular R-matrix method for positron-scattering from poly-atomic molecules using a scaling factor to scale the electron-positron interaction. The scaling factor influences the position of the poles of the R-matrix. We adjust the scaling factor...
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Expedited two-objective dimension scaling of compact microwave passives using surrogate models
PublicationGeometry scaling of compact microwave structures is a challenging problem because of complex relationships between the physical dimensions and electrical characteristics, mostly caused by considerable cross-couplings in densely arranged layouts. Here, a procedure for expedited dimension scaling of compact microwave couplers with respect to two independent criteria has been presented. Our approach involves inverse surrogate models...
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Fast surrogate-assisted frequency scaling of planar antennas with circular polarisation
PublicationIn this work, the problem of computationally efficient frequency scaling (re-design) of circular polarisation antennas is addressed using surrogate-assisted techniques. The task is challenging and requires the identification of the optimum geometry parameters to enable the operation of the re-designed structure at a selected (required) centre frequency. This involves handling several performance figures such as the antenna gain,...
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Low-cost and reliable geometry scaling of compact microstrip couplers with respect to operating frequency, power split ratio, and dielectric substrate parameters
PublicationA technique for rapid re-design of miniaturised microstrip couplers with respect to operating conditions as well as material parameters of the dielectric substrate is proposed. The dimension scaling process is based on a set of pre-optimised reference designs, obtained for an equivalent circuit model of the coupler at hand. The reference designs are utilised to construct an inverse surrogate model which – upon suitable correction...
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Rapid Microwave Design Optimization in Frequency Domain Using Adaptive Response Scaling
PublicationIn this paper, a novel methodology for cost-efficient microwave design optimization in the frequency domain is proposed. Our technique, referred to as adaptive response scaling (ARS), has been developed for constructing a fast replacement model (surrogate) of the high-fidelity electromagnetic-simulated model of the microwave structure under design using its equivalent circuit (low-fidelity model). The basic principle of ARS is...
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Fast geometry scaling of miniaturized microwave couplers with power split correction
PublicationRedesigning a microwave circuit for various operating conditions is a practically important yet challenging problem. The purpose of this article is development and presentation of a technique for fast geometry scaling of miniaturized microwave couplers with respect to operating frequency. Our approach exploits an inverse surrogate model constructed using several reference designs that are optimized for a set of operating frequencies...
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Music Mood Visualization Using Self-Organizing Maps
PublicationDue to an increasing amount of music being made available in digital form in the Internet, an automatic organization of music is sought. The paper presents an approach to graphical representation of mood of songs based on Self-Organizing Maps. Parameters describing mood of music are proposed and calculated and then analyzed employing correlation with mood dimensions based on the Multidimensional Scaling. A map is created in which...
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Comparison of various speech time-scale modificartion methods
PublicationThe objective of this work is to investigate the influence of the different time-scale modification (TSM) methods on the quality of the speech stretched up using the designed non-uniform real-time speech time-scale modification algorithm (NU-RTSM). The algorithm provides a combination of the typical TSM algorithm with the vowels, consonants, stutter, transients and silence detectors. Based on the information about the content and...
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Accelerated Re-Design of Antenna Structures Using Sensitivity-Based Inverse Surrogates
PublicationThe paper proposes a novel framework for accelerated re-design (dimension scaling) of antenna structures using inverse surrogates. The major contribution of the work is a sensitivity-based model identification procedure, which permits a significant reduction of the number of reference designs required to render the surrogate. Rigorous formulation of the approach is supplemented by its comprehensive numerical validation using a...
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Loudness Scaling Tests in Hearing Problems Detection
PublicationThe number of people using portable audio players has increased significantly over the recent years. This implies the rise in the number of people having hearing loss problems. Therefore, there is a need to find appropriate procedures that simplify the process of the hearing problem detection. Investigations performed show that audiometric tests may not be sufficient to assess hearing in young people. Contrarily, the obtained results...
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Rapid EM-driven antenna dimension scaling through inverse modeling
PublicationIn this letter, a computationally feasible technique for dimension scaling of antenna structures is introduced. The proposed methodology is based on inverse surrogate modeling where the geometry parameters of the antenna structure of interest are explicitly related to the operating frequency. The surrogate model is identified based on a few antenna designs optimized for selected reference frequencies. For the sake of computational...