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“Seeing and measuring in 3D with electrons”. Bals S, Goris B, Altantzis T, Heidari H, Van Aert S, Van Tendeloo G, Comptes rendus : physique 15, 140 (2014). http://doi.org/10.1016/j.crhy.2013.09.015
Abstract: Modern TEM enables the investigation of nanostructures at the atomic scale. However, TEM images are only two-dimensional (2D) projections of a three-dimensional (3D) object. Electron tomography can overcome this limitation. The technique is increasingly focused towards quantitative measurements and reaching atomic resolution in 3D has been the ultimate goal for many years. Therefore, one needs to optimize the acquisition of the data, the 3D reconstruction techniques as well as the quantification methods. Here, we will review a broad range of methodologies and examples. Finally, we will provide an outlook and will describe future challenges in the field of electron tomography.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.048
Times cited: 15
DOI: 10.1016/j.crhy.2013.09.015
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“Shaping electron beams for the generation of innovative measurements in the (S)TEM”. Verbeeck J, Guzzinati G, Clark L, Juchtmans R, Van Boxem R, Tian H, Béché, A, Lubk A, Van Tendeloo G, Comptes rendus : physique 15, 190 (2014). http://doi.org/10.1016/j.crhy.2013.09.014
Abstract: In TEM, a typical goal consists of making a small electron probe in the sample plane in order to obtain high spatial resolution in scanning transmission electron microscopy. In order to do so, the phase of the electron wave is corrected to resemble a spherical wave compensating for aberrations in the magnetic lenses. In this contribution, we discuss the advantage of changing the phase of an electron wave in a specific way in order to obtain fundamentally different electron probes opening up new applications in the (S)TEM. We focus on electron vortex states as a specific family of waves with an azimuthal phase signature and discuss their properties, production and applications. The concepts presented here are rather general and also different classes of probes can be obtained in a similar fashion, showing that electron probes can be tuned to optimize a specific measurement or interaction.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.048
Times cited: 22
DOI: 10.1016/j.crhy.2013.09.014
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“A versatile lab-on-chip test platform to characterize elementary deformation mechanisms and electromechanical couplings in nanoscopic objects”. Pardoen T, Colla M-S, Idrissi H, Amin-Ahmadi B, Wang B, Schryvers D, Bhaskar UK, Raskin J-P, Comptes rendus : physique 17, 485 (2016). http://doi.org/10.1016/j.crhy.2015.11.005
Abstract: A nanomechanical on-chip test platform has recently been developed to deform under a variety of loading conditions freestanding thin films, ribbons and nanowires involving submicron dimensions. The lab-on-chip involves thousands of elementary test structures from which the elastic modulus, strength, strain hardening, fracture, creep properties can be extracted. The technique is amenable to in situ transmission electron microscopy (TEM) investigations to unravel the fundamental underlying deformation and fracture mechanisms that often lead to size-dependent effects in small-scale samples. The method allows addressing electrical and magnetic couplings as well in order to evaluate the impact of large mechanical stress levels on different solid-state physics phenomena. We had the chance to present this technique in details to Jacques Friedel in 2012 who, unsurprisingly, made a series of critical and very relevant suggestions. In the spirit of his legacy, the paper will address both mechanics of materials related phenomena and couplings with solids state physics issues.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.048
Times cited: 7
DOI: 10.1016/j.crhy.2015.11.005
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“Applications of synchrotron X-ray nano-probes in the field of cultural heritage”. Cotte M, Genty-Vincent A, Janssens K, Susini J, Comptes rendus : physique 19, 575 (2018). http://doi.org/10.1016/J.CRHY.2018.07.002
Abstract: Synchrotron-based techniques are increasingly used in the field of cultural heritage, and this review focuses notably on the application of nano-beams to access high-spatial-resolution information on fragments sampled in historical or model artworks. Depending on the targeted information, various nano-analytical techniques can be applied, providing both identification and localization of the various components. More precisely, nano-X-ray fluorescence probes elements, nano-X-ray diffraction identify crystalline phases, and nano X-ray absorption spectroscopy is sensitive to speciation. Furthermore, computed tomography-based techniques can provide useful information about the morphology and in particular the porosity of materials. (C) 2018 Academie des sciences. Published by Elsevier Masson SAS.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 2.048
Times cited: 3
DOI: 10.1016/J.CRHY.2018.07.002
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“Corrélations chimiques-géothermométriques des paramètres microchimiques des hydrothermes profonds”. Pentcheva E, Van 't dack L, Veldeman E, Gijbels R, Comptes rendus de l'Académie bulgare des sciences 49, 61 (1996)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Sur les processus, controlant le caractère hydrochimique des eaux thermales profondes (Bulgarie Méridionale)”. Pentcheva E, Veldeman E, Van 't dack L, Gijbels R, Comptes rendus de l'Académie bulgare des sciences 44, 51 (1991)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Development of a ReaxFF reactive force field for intrinsic point defects in titanium dioxide”. Huygh S, Bogaerts A, van Duin ACT, Neyts EC, Computational materials science 95, 579 (2014). http://doi.org/10.1016/j.commatsci.2014.07.056
Abstract: A reactive ReaxFF force field is developed for studying the influence of intrinsic point defects on the chemistry with TiO2 condensed phases. The force field parameters are optimized to ab initio data for the equations of state, relative phase stabilities for titanium and titanium dioxide, potential energy differences for (TiO2)n-clusters (n = 116). Also data for intrinsic point defects in anatase were added. These data contain formation energies for interstitial titanium and oxygen vacancies, diffusion barriers of the oxygen vacancies and molecular oxygen adsorption on a reduced anatase (101) surface. Employing the resulting force field, we study the influence of concentration of oxygen vacancies and expansion or compression of an anatase surface on the diffusion of the oxygen vacancies. Also the barrier for oxygen diffusion in the subsurface region is evaluated using this force field. This diffusion barrier of 27.7 kcal/mol indicates that the lateral redistribution of oxygen vacancies on the surface and in the subsurface will be dominated by their diffusion in the subsurface, since both this barrier as well as the barriers for diffusion from the surface to the subsurface and vice versa (17.07 kcal/mol and 21.91 kcal/mol, respectively, as calculated with DFT), are significantly lower than for diffusion on the surface (61.12 kcal/mol as calculated with DFT).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.292
Times cited: 15
DOI: 10.1016/j.commatsci.2014.07.056
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“Stability and structures of the CFCC-TmC phases : a first-principles study”. Fang CM, van Huis MA, Zandbergen HW, Computational materials science 51, 146 (2012). http://doi.org/10.1016/j.commatsci.2011.07.017
Abstract: The η-M6C, γ-M23C6, and π-M11C2 phases (M = Cr, Mn and Fe) have complex cubic lattices with lattice parameters of approximately 1.0 nm. They belong to the CFCC-TmC family (complex face-centered cubic transition metal carbides), display a rich variety of crystal structures, and play in important role in iron alloys and steels. Here we show that first-principles calculations predict high stability for the γ-M23C6 and η-M6C phases, and instability for the π-M11C2 phases, taking into account various compositional and structural possibilities. The calculations also show a wide variety in magnetic properties. The Cr-containing phases were found to be non-magnetic and the Fe-phases to be ferromagnetic, while the Mn-containing phases were found to be either ferrimagnetic or non-magnetic. Details of the local atomic structures, and the formation and stability of these precipitates in alloys are discussed.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.292
Times cited: 18
DOI: 10.1016/j.commatsci.2011.07.017
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“Structural, mechanical and electronic properties of two-dimensional structure of III-arsenide (111) binary compounds: An ab-initio study”. Gonzalez-Garcia A, Lopez-Perez W, Rivera-Julio J, Peeters FM, Mendoza-Estrada V, Gonzalez-Hernandez R, Computational materials science 144, 285 (2018). http://doi.org/10.1016/J.COMMATSCI.2017.12.050
Abstract: Structural, mechanical and electronic properties of two-dimensional single-layer hexagonal structures in the (111) crystal plane of IIIAs-ZnS systems (III = B, Ga and In) are studied by first-principles calculations based on density functional theory (DFT). Elastic and phonon dispersion relation display that 2D h-IIIAs systems (III = B, Ga and In) are both mechanical and dynamically stable. Electronic structures analysis show that the semiconducting nature of the 3D-IIIAs compounds is retained by their 2D single layer counterpart. Furthermore, density of states reveals the influence of sigma and pi bonding in the most stable geometry (planar or buckled) for 2D h-IIIAs systems. Calculations of elastic constants show that the Young's modulus, bulk modulus and shear modulus decrease for 2D h-IIIAs binary compounds as we move down on the group of elements of the periodic table. In addition, as the bond length between the neighboring cation-anion atoms increases, the 2D h-IIIAs binary compounds display less stiffness and more plasticity. Our findings can be used to understand the contribution of the r and p bonding in the most stable geometry (planar or buckled) for 2D h-IIIAs systems. Structural and electronic properties of h-IIIAs systems as a function of the number of layers have been also studied. It is shown that h-BAs keeps its planar geometry while both h-GAs and h-InAs retained their buckled ones obtained by their single layers. Bilayer h-IIIAs present the same bandgap nature of their counterpart in 3D. As the number of layers increase from 2 to 4, the bandgap width for layered h-IIIAs decreases until they become semimetal or metal. Interestingly, these results are different to those found for layered h-GaN. The results presented in this study for single and few-layer h-IIIAs structures could give some physical insights for further theoretical and experimental studies of 2D h-IIIV-like systems. (C) 2017 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.292
Times cited: 3
DOI: 10.1016/J.COMMATSCI.2017.12.050
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“Effects of silicon doping on strengthening adhesion at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study”. Grubova IY, Surmeneva MA, Huygh S, Surmenev RA, Neyts EC, Computational materials science 159, 228 (2019). http://doi.org/10.1016/J.COMMATSCI.2018.12.026
Abstract: In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.292
Times cited: 1
DOI: 10.1016/J.COMMATSCI.2018.12.026
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“Accelerated molecular dynamics simulation of large systems with parallel collective variable-driven hyperdynamics”. Fukuhara S, Bal KM, Neyts EC, Shibuta Y, Computational Materials Science 177, 109581 (2020). http://doi.org/10.1016/j.commatsci.2020.109581
Abstract: The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diffusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diffuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.3
DOI: 10.1016/j.commatsci.2020.109581
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“Validation of inter-atomic potential for WS2 and WSe2 crystals through assessment of thermal transport properties”. Mobaraki A, Kandemir A, Yapicioglu H, Gulseren O, Sevik C, Computational materials science 144, 92 (2018). http://doi.org/10.1016/J.COMMATSCI.2017.12.005
Abstract: In recent years, transition metal dichalcogenides (TMDs) displaying astonishing properties are emerged as a new class of two-dimensional layered materials. The understanding and characterization of thermal transport in these materials are crucial for efficient engineering of 2D TMD materials for applications such as thermoelectric devices or overcoming general overheating issues. In this work, we obtain accurate Stillinger-Weber type empirical potential parameter sets for single-layer WS2 and WSe2 crystals by utilizing particle swarm optimization, a stochastic search algorithm. For both systems, our results are quite consistent with first-principles calculations in terms of bond distances, lattice parameters, elastic constants and vibrational properties. Using the generated potentials, we investigate the effect of temperature on phonon energies and phonon linewidth by employing spectral energy density analysis. We compare the calculated frequency shift with respect to temperature with corresponding experimental data, clearly demonstrating the accuracy of the generated inter-atomic potentials in this study. Also, we evaluate the lattice thermal conductivities of these materials by means of classical molecular dynamics simulations. The predicted thermal properties are in very good agreement with the ones calculated from first-principles. (C) 2017 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
DOI: 10.1016/J.COMMATSCI.2017.12.005
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“Chlorinated phosphorene for energy application”. Hassani N, Yagmurcukardes M, Peeters FM, Neek-Amal M, Computational materials science 231, 112625 (2024). http://doi.org/10.1016/J.COMMATSCI.2023.112625
Abstract: The influence of decoration with impurities and the composition dependent band gap in 2D materials has been the subject of debate for a long time. Here, by using Density Functional Theory (DFT) calculations, we systematically disclose physical properties of chlorinated phosphorene having the stoichiometry of PmCln. By analyzing the adsorption energy, charge density, migration energy barrier, structural, vibrational, and electronic properties of chlorinated phosphorene, we found that (I) the Cl-P bonds are strong with binding energy Eb =-1.61 eV, decreases with increasing n. (II) Cl atoms on phosphorene have anionic feature, (III) the migration path of Cl on phosphorene is anisotropic with an energy barrier of 0.38 eV, (IV) the phonon band dispersion reveal that chlorinated phosphorenes are stable when r <= 0.25 where r = m/n, (V) chlorinated phosphorenes is found to be a photonic crystal in the frequency range of 280 cm-1 to 325 cm-1, (VI) electronic band structure of chlorinated phosphorenes exhibits quasi-flat bands emerging around the Fermi level with widths in the range of 22 meV to 580 meV, and (VII) Cl adsorption causes a semiconducting to metallic/semi-metallic transition which makes it suitable for application as an electroactive material. To elucidate this application, we investigated the change in binding energy (Eb), specific capacity, and open-circuit voltage as a function of the density of adsorbed Cl. The theoretical storage capacity of the chlorinated phosphorene is found to be 168.19 mA h g-1with a large average voltage (similar to 2.08 V) which is ideal number as a cathode in chloride-ion batteries.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.3
Times cited: 2
DOI: 10.1016/J.COMMATSCI.2023.112625
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“Two new members of the covalent organic frameworks family : crystalline 2D-oxocarbon and 3D-borocarbon structures”. Hassani N, Movafegh-Ghadirli A, Mahdavifar Z, Peeters FM, Neek-Amal M, Computational materials science 241, 1 (2024). http://doi.org/10.1016/J.COMMATSCI.2024.113022
Abstract: Oxocarbons, known for over two centuries, have recently revealed a long-awaited facet: two-dimensional crystalline structures. Employing an intelligent global optimization algorithm (IGOA) alongside densityfunctional calculations, we unearthed a quasi -flat oxocarbon (C 6 0 6 ), featuring an oxygen -decorated hole, and a novel 3D-borocarbon. Comparative analyses with recently synthesized isostructures, such as 2D -porous carbon nitride (C 6 N 6 ) and 2D -porous boroxine (B 6 0 6 ), highlight the unique attributes of these compounds. All structures share a common stoichiometry of X 6 Y 6 (which we call COF-66), where X = B, C, and Y = B, N, O (with X not equal Y), exhibiting a 2D -crystalline structure, except for borocarbon C 6 B 6 , which forms a 3D crystal. In our comprehensive study, we conducted a detailed exploration of the electronic structure of X 6 Y 6 compounds, scrutinizing their thermodynamic properties and systematically evaluating phonon stability criteria. With expansive surface areas, diverse pore sizes, biocompatibility, pi-conjugation, and distinctive photoelectric properties, these structures, belonging to the covalent organic framework (COF) family, present enticing prospects for fundamental research and hold potential for biosensing applications.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.3
DOI: 10.1016/J.COMMATSCI.2024.113022
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“Accurate pseudopotential description of the GW bandstructure of ZnO”. Dixit H, Saniz R, Lamoen D, Partoens B, Computer physics communications 182, 2029 (2011). http://doi.org/10.1016/j.cpc.2011.02.001
Abstract: We present the GW band structure of ZnO in its wurtzite (WZ), zincblende (ZB) and rocksalt (RS) phases at the Γ point, calculated within the GW approximation. We have used a Zn20+ pseudopotential which is essential for the adequate treatment of the exchange interaction in the self-energy. The accuracy of the pseudopotential used is also discussed. The effect of the pd hybridization on the GW corrections to the band gap is correlated by comparing the ZB and RS phase.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT)
Impact Factor: 3.936
Times cited: 18
DOI: 10.1016/j.cpc.2011.02.001
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“MsSpec-1.0 : a multiple scattering package for electron spectroscopies in material science”. Sébilleau D, Natoli C, Gavaza GM, Zhao H, da Pieve F, Hatada K, Computer physics communications 182, 2567 (2011). http://doi.org/10.1016/j.cpc.2011.07.012
Abstract: We present a multiple scattering package to calculate the cross-section of various spectroscopies namely photoelectron diffraction (PED), Auger electron diffraction (AED), X-ray absorption (XAS), low-energy electron diffraction (LEED) and Auger photoelectron coincidence spectroscopy (APECS). This package is composed of three main codes, computing respectively the cluster, the potential and the cross-section. In the latter case, in order to cover a range of energies as wide as possible, three different algorithms are provided to perform the multiple scattering calculation: full matrix inversion, series expansion or correlation expansion of the multiple scattering matrix. Numerous other small Fortran codes or bash/csh shell scripts are also provided to perform specific tasks. The cross-section code is built by the user from a library of subroutines using a makefile.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.936
Times cited: 6
DOI: 10.1016/j.cpc.2011.07.012
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“An efficient finite-difference scheme for computation of electron states in free-standing and core-shell quantum wires”. Arsoski VV, Čukarić, NA, Tadic MZ, Peeters FM, Computer physics communications 197, 17 (2015). http://doi.org/10.1016/j.cpc.2015.08.002
Abstract: The electron states in axially symmetric quantum wires are computed by means of the effective-mass Schrodinger equation, which is written in cylindrical coordinates phi, rho, and z. We show that a direct discretization of the Schrodinger equation by central finite differences leads to a non-symmetric Hamiltonian matrix. Because diagonalization of such matrices is more complex it is advantageous to transform it in a symmetric form. This can be done by the Liouville-like transformation proposed by Rizea et al. (2008), which replaces the wave function psi(rho) with the function F(rho) = psi(rho)root rho and transforms the Hamiltonian accordingly. Even though a symmetric Hamiltonian matrix is produced by this procedure, the computed wave functions are found to be inaccurate near the origin, and the accuracy of the energy levels is not very high. In order to improve on this, we devised a finite-difference scheme which discretizes the Schrodinger equation in the first step, and then applies the Liouville-like transformation to the difference equation. Such a procedure gives a symmetric Hamiltonian matrix, resulting in an accuracy comparable to the one obtained with the finite element method. The superior efficiency of the new finite-difference scheme (FDM) is demonstrated for a few p-dependent one-dimensional potentials which are usually employed to model the electron states in free-standing and core shell quantum wires. The new scheme is compared with the other FDM schemes for solving the effective-mass Schrodinger equation, and is found to deliver energy levels with much smaller numerical error for all the analyzed potentials. It also gives more accurate results than the scheme of Rizea et al., except for the ground state of an infinite rectangular potential in freestanding quantum wires. Moreover, the PT symmetry is invoked to explain similarities and differences between the considered FDM schemes. (C) 2015 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.936
Times cited: 4
DOI: 10.1016/j.cpc.2015.08.002
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“Tight-binding studio : a technical software package to find the parameters of tight-binding Hamiltonian”. Nakhaee M, Ketabi SA, Peeters FM, Computer Physics Communications 254, 107379 (2020). http://doi.org/10.1016/J.CPC.2020.107379
Abstract: We present the Tight-Binding Studio (TB Studio) software package that calculates the different parameters of a tight-binding Hamiltonian from a set of Bloch energy bands obtained from first principle theories such as density functional theory, Hartree-Fock calculations or semi-empirical band-structure theory. This will be helpful for scientists who are interested in studying electronic and optical properties of structures using Green's function theory within the tight-binding approximation. TB Studio is a cross-platform application written in C++ with a graphical user interface design that is user-friendly and easy to work with. This software is powered by Linear Algebra Package C interface library for solving the eigenvalue problems and the standard high performance OpenGL graphic library for real time plotting. TB Studio and its examples together with the tutorials are available for download from tight-binding.com. Program summary Program Title: Tight-Binding Studio Program Files doi:http://dx.doi.org/10.17632/j6x5mwzm2d.1 Licensing provisions: LGPL Programming language: C++ External routines: BLAS, LAPACK, LAPACKE, wxWidgets, OpenGL, MathGL Nature of problem: Obtaining Tight-Binding Hamiltonian from a set of Bloch energy bands obtained from first-principles calculations. Solution method: Starting from the simplified LCAO method, a tight-binding model in the two-center approximation is constructed. The Slater and Koster (SK) approach is used to calculate the parameters of the TB Hamiltonian. By using non-linear fitting approaches the optimal values of the SK parameters are obtained such that the TB energy eigenvalues are as close as possible to those from first-principles calculations. We obtain the expression for the Hamiltonian and the overlap matrix elements between the different orbitals of the different atoms in an orthogonal or non-orthogonal basis set. (C) 2020 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 6.3
Times cited: 27
DOI: 10.1016/J.CPC.2020.107379
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“RAMS and WRF sensitivity to grid spacing in large-eddy simulations of the dry convective boundary layer”. Ercolani G, Gorle C, Garcia Sánchez C, Corbari C, Mancini M, Computers and fluids 123, 54 (2015). http://doi.org/10.1016/j.compfluid.2015.09.009
Abstract: Large-eddy simulations (LESS) are frequently used to model the planetary boundary layer, and the choice of the grid cell size, numerical schemes and sub grid model can significantly influence the simulation results. In the present paper the impact of grid spacing on LES of an idealized atmospheric convective boundary layer (CBL), for which the statistics and flow structures are well understood, is assessed for two mesoscale models: the Regional Atmospheric Modeling System (RAMS) and the Weather Research and Forecasting model (WRF). Nine simulations are performed on a fixed computational domain (6 x 6 x 2 km), combining three different horizontal (120, 60, 30 m) and vertical (20, 10, 5 m) spacings. The impact of the cell size on the CBL is investigated by comparing turbulence statistics and velocity spectra. The results demonstrate that both WRF and RAMS can perform LES of the CBL under consideration without requiring extremely high computational loads, but they also indicate the importance of adopting a computational grid that is adequate for the numerical schemes and subgrid models used. In both RAMS and WRF a horizontal cell size of 30 m is required to obtain a suitable turbulence reproduction throughout the CBL height. Considering the vertical grid spacing, WRF produced similar results for all the three tested values, while in RAMS it should be ensured that the aspect ratio of the cells does not exceed a value of 3. The two models were found to behave differently in function of the grid resolution, and they have different shortcomings in their prediction of CBL turbulence. WRF exhibits enhanced damping at the smallest scales, while RAMS is prone to the appearance of spurious fluctuations in the flow when the grid aspect ratio is too high. (C) 2015 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.313
Times cited: 3
DOI: 10.1016/j.compfluid.2015.09.009
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“Effect of plasma-induced oxidative stress on the glycolysis pathway of Escherichia coli”. Ranjbar S, Shahmansouri M, Attri P, Bogaerts A, Computers In Biology And Medicine 127, 104064 (2020). http://doi.org/10.1016/j.compbiomed.2020.104064
Abstract: Antibiotic resistance is one of the world’s most urgent public health problems. Due to its antibacterial properties, cold atmospheric plasma (CAP) may serve as an alternative method to antibiotics. It is claimed that oxidative stress caused by CAP is the main reason of bacteria inactivation. In this work, we computationally investigated the effect of plasma-induced oxidation on various glycolysis metabolites, by monitoring the production of the biomass. We observed that in addition to the significant reduction in biomass production, the rate of some reactions has increased. These reactions produce anti-oxidant products, showing the bacterial defense mechanism to escape the oxidative damage. Nevertheless, the simulations show that the plasma-induced oxidation effect is much stronger than the defense mechanism, causing killing of the bacteria.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.7
DOI: 10.1016/j.compbiomed.2020.104064
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Oliveira MC, Yusupov M, Cordeiro RM, Bogaerts A (2021) Unraveling the permeation of reactive species across nitrated membranes by computer simulations. 104768
Abstract: Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the permeation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hydrophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hydrophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignificant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies.
Keywords: A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 1.836
DOI: 10.1016/j.compbiomed.2021.104768
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“Substrate-induced proximity effect in superconducting niobium nanofilms”. Rezvani SJ, Perali A, Fretto M, De Leo N, Flammia L, Milošević, M, Nannarone S, Pinto N, Condensed Matter 4, 4 (2018). http://doi.org/10.3390/CONDMAT4010004
Abstract: Structural and superconducting properties of high-quality niobium nanofilms with different thicknesses are investigated on silicon oxide (SiO2) and sapphire substrates. The role played by the different substrates and the superconducting properties of the Nb films are discussed based on the defectivity of the films and on the presence of an interfacial oxide layer between the Nb film and the substrate. The X-ray absorption spectroscopy is employed to uncover the structure of the interfacial layer. We show that this interfacial layer leads to a strong proximity effect, especially in films deposited on a SiO2 substrate, altering the superconducting properties of the Nb films. Our results establish that the critical temperature is determined by an interplay between quantum-size effects, due to the reduction of the Nb film thicknesses, and proximity effects. The detailed investigation here provides reference characterizations and has direct and important implications for the fabrication of superconducting devices based on Nb nanofilms.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Times cited: 3
DOI: 10.3390/CONDMAT4010004
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“Transition metal dichalcogenides as strategy for high temperature electron-hole superfluidity”. Conti S, Neilson D, Peeters FM, Perali A, Condensed Matter 5, 22 (2020). http://doi.org/10.3390/CONDMAT5010022
Abstract: Condensation of spatially indirect excitons, with the electrons and holes confined in two separate layers, has recently been observed in two different double layer heterostructures. High transition temperatures were reported in a double Transition Metal Dichalcogenide (TMD) monolayer system. We briefly review electron-hole double layer systems that have been proposed as candidates for this interesting phenomenon. We investigate the double TMD system WSe2/hBN/MoSe2, using a mean-field approach that includes multiband effects due to the spin-orbit coupling and self-consistent screening of the electron-hole Coulomb interaction. We demonstrate that the transition temperature observed in the double TMD monolayers, which is remarkably high relative to the other systems, is the result of (i) the large electron and hole effective masses in TMDs, (ii) the large TMD band gaps, and (iii) the presence of multiple superfluid condensates in the TMD system. The net effect is that the superfluidity is strong across a wide range of densities, which leads to high transition temperatures that extend as high as TBKT=150 K.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Times cited: 13
DOI: 10.3390/CONDMAT5010022
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“Study of rechargeable batteries using advanced spectroscopic and computational techniques”. Barbiellini B, Kuriplach J, Saniz R, Condensed Matter 6, 26 (2021). http://doi.org/10.3390/CONDMAT6030026
Abstract: Improving the efficiency and longevity of energy storage systems based on Li- and Na-ion rechargeable batteries presents a major challenge. The main problems are essentially capacity loss and limited cyclability. These effects are due to a hierarchy of factors spanning various length and time scales, interconnected in a complex manner. As a consequence, and in spite of several decades of research, a proper understanding of the ageing process has remained somewhat elusive. In recent years, however, combinations of advanced spectroscopy techniques and first-principles simulations have been applied with success to tackle this problem. In this Special Issue, we are pleased to present a selection of articles that, by precisely applying these methods, unravel key aspects of the reduction-oxidation reaction and intercalation processes. Furthermore, the approaches presented provide improvements to standard diagnostic and characterisation techniques, enabling the detection of possible Li-ion flow bottlenecks causing the degradation of capacity and cyclability.
Keywords: Editorial; Electron microscopy for materials research (EMAT)
DOI: 10.3390/CONDMAT6030026
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“Effect of mismatched electron-hole effective masses on superfluidity in double layer solid-state systems”. Conti S, Perali A, Peeters FM, Neilson D, Condensed Matter 6, 14 (2021). http://doi.org/10.3390/CONDMAT6020014
Abstract: Superfluidity has been predicted and now observed in a number of different electron-hole double-layer semiconductor heterostructures. In some of the heterostructures, such as GaAs and Ge-Si electron-hole double quantum wells, there is a strong mismatch between the electron and hole effective masses. We systematically investigate the sensitivity to unequal masses of the superfluid properties and the self-consistent screening of the electron-hole pairing interaction. We find that the superfluid properties are insensitive to mass imbalance in the low density BEC regime of strongly-coupled boson-like electron-hole pairs. At higher densities, in the BEC-BCS crossover regime of fermionic pairs, we find that mass imbalance between electrons and holes weakens the superfluidity and expands the density range for the BEC-BCS crossover regime. This permits screening to kill the superfluid at a lower density than for equal masses.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Times cited: 1
DOI: 10.3390/CONDMAT6020014
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“Impact of calibrated band-tails on the subthreshold swing of pocketed TFETs”. Bizindavyi J, Verhulst AS, Sorée B, Groeseneken G, Conference digest
T2 –, 76th Device Research Conference (DRC), JUN 24-27, 2018, Santa Barbara, CA (2018)
Keywords: P1 Proceeding; Condensed Matter Theory (CMT)
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“Impact of calibrated band-tails on the subthreshold swing of pocketed TFETs”. Bizindavyi J, Verhulst AS, Sorée B, Groeseneken G, Conference digest
T2 –, 76th Device Research Conference (DRC), JUN 24-27, 2018, Santa Barbara, CA (2018). http://doi.org/10.1109/DRC.2018.8442246
Keywords: P1 Proceeding; Condensed Matter Theory (CMT)
DOI: 10.1109/DRC.2018.8442246
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“In-situ HREM irradiation study of point defect clustering in strained GexSi1-x/(001)Si heterostructure”. Fedina L, Lebedev OI, Van Tendeloo G, van Landuyt J, Conference series of the Institute of Physics 157, 55 (1997)
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Times cited: 1
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“Morphology and defects in shallow trench isolation structures”. Stuer C, van Landuyt J, Bender H, Rooyackers R, Badenes G, Conference series of the Institute of Physics 164, 443 (1999)
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Times cited: 1
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“New intermediate defect configuration in Si studied by in situ HREM irradiation”. Fedina L, Gutakovskii A, Aseev A, van Landuyt J, Vanhellemont J, Conference series of the Institute of Physics 157, 43 (1997)
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
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