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Danny Vanpoucke
Author's posts
Jan 02 2015
First light
Happy 2015!
A new year goes hand in hand with new beginnings and resolutions for the coming year. For me, the new beginning is this new version of my personal webpage, and the resolution is my intent to launch this blog.
As you may have read on the frontpage of this website; I am a computational scientist with a background in both physics and chemistry. In addition, to being spread out between physics and chemistry, and between theory and experiment, I am also spread out in the real space we all live in, since I am always traveling between work and family. This lack of clear position in life and research makes me feel a bit like a delocalized particle: I am a delocalized Physicist.
On this blog you will be able to read:
- What the life of such a delocalized physicist looks like (or a modern academic).
- About scientific programming and computational science.
- About the physics of/in nature.
Permanent link to this article: https://dannyvanpoucke.be/first-light/
Permanent link to this article: https://dannyvanpoucke.be/paper2014_comment-en/
Oct 28 2014
Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles
| Authors: | Danny E. P. Vanpoucke, Jan W. Jaeken, Stijn De Baerdemacker, Kurt Lejaeghere and Veronique Van Speybroeck |
| Journal: | Beilstein J. Nanotechnol. 5, 1738-1748 (2014) |
| doi: | 10.3762/bjnano.5.184 |
| IF(2014): | 2.670 |
| export: | bibtex |
| pdf: | <Beilstein> (open access) |
 |
| Graphical Abstract: The MIL-47(V) MOF has one unpaired electron per V site. As a result, different spin configurations are possible, several of which lead to an anti-ferromagnetic state. The spin density of an antiferromagnetic state, containing only ferromagnetic chains is shown on the left. On the right, the electronic band structure of the same system is presented. |
Abstract
The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials.
Permanent link to this article: https://dannyvanpoucke.be/paper2014_mil47beil-en/
Oct 28 2014
Aliovalent Doping of CeO2: DFT study of oxidation state and vacancy effects
| Authors: | Danny E. P. Vanpoucke, Patrick Bultinck, Stefaan Cottenier, Veronique Van Speybroeck, and Isabel Van Driessche, |
| Journal: | J. Mater. Chem. A 2(33), 13723-13737 (2014) |
| doi: | 10.1039/C4TA02449D |
| IF(2014): | 7.443 |
| export: | bibtex |
| pdf: | <JMaterChemA> <arXiv> |
Abstract
The modification of CeO2 properties by means of aliovalent doping is investigated within the ab initio density functional theory framework. Lattice parameters, dopant atomic radii, bulk moduli and thermal expansion coefficients of fluorite type Ce1-xMxO2-y (with M = Mg, V, Co, Cu, Zn, Nb, Ba, La, Sm, Gd, Yb, and Bi) are presented for 0.00 ≤ x ≤ 0.25. The relative stability of the doped systems is discussed, and the influence of oxygen vacancies is investigated. It is shown that oxygen vacancies tend to increase the lattice parameter, and strongly decrease the bulk modulus. Defect formation energies are correlated with calculated crystal radii and covalent radii of the dopants, and are shown to present no simple trend. The previously observed inverse relationship between the thermal expansion coefficient and the bulk modulus in group IV doped CeO2 [J. Am. Ceram. Soc. 97(1), 258 (2014)] is shown to persist independent of the inclusion of charge compensating vacancies.
Permanent link to this article: https://dannyvanpoucke.be/paper2014_ceo2alio-en/
Oct 28 2014
Tetravalent Doping of CeO2: The impact of valence electron character on group IV dopant influence
| Authors: | Danny E. P. Vanpoucke, Stefaan Cottenier, Veronique Van Speybroeck, Isabel Van Driessche, and Patrick Bultinck |
| Journal: | J. Am. Ceram. Soc. 97(1), 258-266 (2014) |
| doi: | 10.1111/jace.12650 |
| IF(2014): | 2.610 |
| export: | bibtex |
| pdf: | <J.Am.Ceram.Soc.> <arXiv> |
Abstract
Fluorite CeO2 doped with group IV elements is studied within the density functional theory (DFT) and DFT + U framework. Concentration-dependent formation energies are calculated for Ce1−xZxO2 (Z = C, Si, Ge, Sn, Pb, Ti, Zr, Hf) with 0 ≤ x ≤ 0.25 and a roughly decreasing trend with ionic radius is observed. The influence of the valence and near valence electronic configuration is discussed, indicating the importance of filled d and f shells near the Fermi level for all properties investigated. A clearly different behavior of group IVa and IVb dopants is observed: the former are more suitable for surface modifications and the latter are more suitable for bulk modifications. For the entire set of group IV dopants, there exists an inverse relation between the change, due to doping, of the bulk modulus, and the thermal expansion coefficients. Hirshfeld-I atomic charges show that charge-transfer effects due to doping are limited to the nearest-neighbor oxygen atoms.
Permanent link to this article: https://dannyvanpoucke.be/paper2014_ceo2group4-en/
Oct 28 2014
Modeling 1D structures on semiconductor surfaces: Synergy of theory and experiment
| Authors: | Danny E. P. Vanpoucke |
| Journal: | J. Phys.: Condens. Matter 26(13), 133001 (2014) |
| doi: | 10.1088/0953-8984/26/13/133001 |
| IF(2014): | 2.346 |
| export: | bibtex |
| pdf: | <J.Phys.Condens.Matter> <arXiv> |
Abstract
Atomic scale nanowires attract enormous interest in a wide range of fields. On the one hand, due to their quasi-one-dimensional nature, they can act as an experimental testbed for exotic physics: Peierls instability, charge density waves, and Luttinger liquid behavior. On the other hand, due to their small size, they are of interest not only for future device applications in the micro-electronics industry, but also for applications regarding molecular electronics. This versatile nature makes them interesting systems to produce and study, but their size and growth conditions push both experimental production and theoretical modeling to their limits. In this review, modeling of atomic scale nanowires on semiconductor surfaces is discussed, focusing on the interplay between theory and experiment. The current state of modeling efforts on Pt- and Au-induced nanowires on Ge(001) is presented, indicating their similarities and differences. Recently discovered nanowire systems (Ir, Co, Sr) on the Ge(001) surface are also touched upon. The importance of scanning tunneling microscopy as a tool for direct comparison of theoretical and experimental data is shown, as is the power of density functional theory as an atomistic simulation approach. It becomes clear that complementary strengths of theoretical and experimental investigations are required for successful modeling of the atomistic nanowires, due to their complexity.
Permanent link to this article: https://dannyvanpoucke.be/paper2014_reviewnw-en/
Oct 28 2014
Rationality: A Social-Epistemology Perspective
| Authors: | Sylvia Wenmackers, Danny E. P. Vanpoucke, and Igor Douven |
| Journal: | Front. Psychol. 5, 581 (2014) |
| doi: | 10.3389/fpsyg.2014.00581 |
| IF(2014): | 2.560 |
| export: | bibtex |
| pdf: | <Front.Psychol.> (open Access) |
Abstract
Both in philosophy and in psychology, human rationality has traditionally been studied from an ‘individualistic’ perspective. Recently, social epistemologists have drawn attention to the fact that epistemic interactions among agents also give rise to important questions concerning rationality. In previous work, we have used a formal model to assess the risk that a particular type of social-epistemic interactions lead agents with initially consistent belief states into inconsistent belief states. Here, we continue this work by investigating the dynamics to which these interactions may give rise in the population as a whole.
Permanent link to this article: https://dannyvanpoucke.be/paper2014_frontpsychol-en/
Oct 28 2014
Cover Image of Journal of Computational Chemistry : Extending Hirshfeld-I
| Authors: | Danny E. P. Vanpoucke |
| Journal: | J. Comput. Chem. 34(5), i-ii (2013) |
| doi: | 10.1002/jcc.23239 |
| IF(2013): | 3.601 |
| export: | bibtex |
| pdf: | <J.Comput.Chem.> |
Abstract
The image shows an isosurface of Hirshfeld-I “atoms in molecules” for Ti-doped CeO2, taken at an electron density of 0.03e/Å3, as presented by Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche on page 405. The cubic Ce0.75Ti0.25O2 unit cell is shown along the 111 direction. The different atoms are still clearly distinguishable at this iso-surface level, and show the Ti atom in the corners to be much smaller than the Ce atoms on the sides. In this issue, this implementation of the Hirshfeld- I method for solids is published back to back with a Comment from Thomas A. Manz and the authors’ Reply.
Permanent link to this article: https://dannyvanpoucke.be/paper2013_hicover-en/
Oct 28 2014
Reply to ‘Comment on “Extending Hirshfeld-I to bulk and periodic materials” ‘
| Authors: | Danny E. P. Vanpoucke, Isabel Van Driessche, and Patrick Bultinck |
| Journal: | J. Comput. Chem. 34(5), 422-427 (2013) |
| doi: | 10.1002/jcc.23193 |
| IF(2013): | 3.601 |
| export: | bibtex |
| pdf: | <J.Comput.Chem.> <arXiv> |
 |
Graphical Abstract:The issues raised in the preceding comment are addressed. It is shown why Hirshfeld-I is, from a theoretical point of view, a good method for defining AIM and obtaining charges. Charges for a set of ionic systems are calculated using our presented method and shown to be chemically feasable. Comparison of pseudo-density to all-electron based results shows the pseudo-densities to be sufficient to obtain all-electron quality results. Timing results for systems containing hundreds of atoms. |
Abstract
The issues raised in the comment by Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO3, and La2Ce2O7, using our previously presented method for calculating Hirshfeld-I charges in solids (Vanpoucke et al., J. Comput. Chem. doi: 10.1002/jcc.23088). It is shown that the use of pseudovalence charges is sufficient to retrieve the full all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over 200 atoms, underlining the relatively low cost for large systems. A number of theoretical issues are formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on “expectations” for atomic charges.
Permanent link to this article: https://dannyvanpoucke.be/paper2013_hireply-en/
Oct 28 2014
Extending Hirshfeld-I to bulk and periodic materials
| Authors: | Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche, |
| Journal: | J. Comput. Chem. 34(5), 405-417 (2013) |
| doi: | 10.1002/jcc.23088 |
| IF(2013): | 3.601 |
| export: | bibtex |
| pdf: | <J.Comput.Chem.> <arXiv> |
 |
Graphical Abstract: The Hirshfeld-I method is extended to solids, allowing for the partitioning of a solid density into constituent atoms. The use of precalculated density grids makes the implementation code independent, and the use of pseudo-potential based electron density distributions is shown to give qualitatively the same results as all electron densities. Results for some simple solids/periodic systems like cerium oxide and graphene are presented. |
Abstract
In this work, a method is described to extend the iterative Hirshfeld-I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudopotential-based electron density distributions, and it is shown that high-quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of grids containing (precalculated) electron densities makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems. The conceptual issue of obtaining reference densities for anions is discussed, and the delocalization problem for anionic reference densities originating from the use of a plane wave basis set is identified and handled.
Permanent link to this article: https://dannyvanpoucke.be/paper2013_hipaper-en/
Oct 28 2014
Comment on ‘Europium doping induced symmetry deviation and its impact on the second harmonic generation of doped ZnO nanowires’
October 28, 2014
Abstract
In Dhara et al. 2014 Nanotechnology 25 225202, the authors reported on the synthesis of Eu-doped ZnO nanowires (NWs) and investigated the influence of Eu doping on the second harmonic generation (SHG). Maximum SHG was found to correlate strongly with the structural deformation attributed to Eu3+ doping. In this comment, we show the deformation of interest is due to the presence of Eu2+ dopants, based on both the experimental data presented by Dhara et al. and ab-initio density functional theory calculations.