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Danny E. P. Vanpoucke

Publications and source records attributed to Danny E. P. Vanpoucke.

At least 19 recordsLinked to original sources

Predictive Inorganic Synthesis based on Machine Learning using Small Data sets: a case study of Hydrodynamic Diameter-controlled Cu Nanoparticles

Cu NPs have a broad applicability, yet their synthesis is sensitive to subtle changes in reaction parameters. This sensitivity, combined with the time- and resource-intensive nature of experimental optimization, poses a major challenge in achieving reproducible and size-controlled synthesis. While ML shows promise in materials research, its application is often limited by scarcity of large high-quality experimental data sets. This study explores ML to predict the DLS-derived hydrodynamic diameter of Cu NPs using a small data set of 25 syntheses. Latin Hypercube Sampling is used to efficiently cover the parameter space while creating the experimental data set. Ensemble regression models successfully predict hydrodynamic diameters with good predictive performance given the limited dataset. Since quantitative regression requires a unique DLS-derived hydrodynamic diameter, the regression model is restricted to mono-modal DLS distributions, while a complementary classification model identifies synthesis conditions for which quantitative prediction is applicable. Using equivalent out-of-sample validation, the ML and DoE models showed comparable generalization. The final ensemble model achieved an R2=0.74 compared to 0.60 for the DoE model, while retaining the complete synthesis parameter space, making it better suited for synthesis guidance. Additionally, classification models using both random forests and LLMs are evaluated to distinguish between large and small particles. These classification models exhibited only modest predictive performance, indicating that this small dataset is insufficient to fully exploit the capabilities of complex LLMs. Overall, this study demonstrates that carefully curated small data sets, paired with robust classical ML, can effectively support the synthesis of Cu NPs and highlights that for lab-scale studies, complex models like LLMs may offer limited benefits.

cond-mat.mtrl-sci↗

Modeling the Zero-Phonon Line of Strained SnV Centers in Diamond; Including Reflections on Computational Cost and Accuracy

Among the group-IV vacancy color centers in diamond, the SnV holds promise for photonics based quantum applications. In this work, the Tin-Vacancy (SnV) zero-phonon line (ZPL) and its pressure coefficient are calculated using first principles approaches. The predicted absolute ZPL position is shown to be strongly influenced by the method and supercell size used. The results are therefore extrapolated to the dilute limit allowing for direct comparison with experiments. The importance of identifying the color-center related Kohn--Sham states is highlighted, as well as the shifting of these states due to electron excitations as well as supercell size and k-point position. In contrast to the absolute ZPL positions, the relative position of the SnV$^0$ ZPL is consistently redshifted about $43$ nm compared to the SnV$^-$ ZPL. In addition, the pressure coefficient is shown to be very robust over different methods, always resulting in a value of about $1.4$ nm/GPa, for both SnV$^0$ and SnV$^-$. Finally, the computational accuracy and cost are put into perspective.

cond-mat.mtrl-sci↗

The impact of strain on the GeV-color center in diamond

Color centers in diamond, such as the GeV center, are promising candidates for quantum-based applications. Here, we investigate the impact of strain on the zero-phonon line (ZPL) position of GeV$^0$. Both hydrostatic and linear strain are modeled using density functional theory for GeV$^0$ concentrations of $1.61$ \% down to $0.10$ \%. We present qualitative and quantitative differences between the two strain types: for hydrostatic tensile and compressive strain, red-and blue-shifted ZPL positions are expected, respectively, with a linear relation between the ZPL shift and the experienced stress. By calculating the ZPL shift for varying GeV$^0$ concentrations, a shift of $0.15$ nm/GPa ($0.38$ meV/GPa) is obtained at experimentally relevant concentrations using a hybrid functional. In contrast, only red-shifted ZPL are found for tensile and compressive linear strain along the $\langle100\rangle$ direction. The calculated ZPL shift exceeds that of hydrostatic strain by at least one order of magnitude, with a significant difference between tensile and compressive strains: $3.2$ and $4.8$ nm/GPa ($8.1$ and $11.7$ meV/GPa), respectively. In addition, a peak broadening is expected due to the lifted degeneracy of the GeV$^0$ $e_g$ state, calculated to be about $6$ meV/GPa. These calculated results are placed in perspective with experimental observations, showing values of ZPL shifts and splittings of comparable magnitude.

cond-mat.mtrl-sci↗

First-principles investigation of hydrogen-related reactions on (100)--(2$\times$1)$:$H diamond surfaces

Hydrogen radical attacks and subsequent hydrogen migrations are considered to play an important role in the atomic-scale mechanisms of diamond chemical vapour deposition growth. We perform a comprehensive analysis of the reactions involving H-radical and vacancies on H-passivated diamond surfaces exposed to hydrogen radical-rich atmosphere. By means of first principles calculations -- density functional theory and climbing image nudged elastic band method -- transition states related to these mechanisms are identified and characterised. In addition, accurate reaction rates are computed using variational transition state theory. Together, these methods provide -- for a broad range of temperatures and hydrogen radical concentrations -- a picture of the relative likelihood of the migration or radical attack processes, along with a statistical description of the hydrogen coverage fraction of the (100) H-passivated surface, refining earlier results via a more thorough analysis of the processes at stake. Additionally, the migration of H-vacancy is shown to be anisotropic, and occurring preferentially across the dimer rows of the reconstructed surface. The approach used in this work can be generalised to other crystallographic orientations of diamond surfaces or other semiconductors.

cond-mat.mtrl-sci↗

How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

In the past decades many density-functional theory methods and codes adopting periodic boundary conditions have been developed and are now extensively used in condensed matter physics and materials science research. Only in 2016, however, their precision (i.e., to which extent properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. We discuss here general recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z=1 to 96 and characterizing 10 prototypical cubic compounds for each element: 4 unaries and 6 oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Such effort is facilitated by deploying AiiDA common workflows that perform automatic input parameter selection, provide identical input/output interfaces across codes, and ensure full reproducibility. Finally, we discuss the extent to which the current results for total energies can be reused for different goals (e.g., obtaining formation energies).

cond-mat.mtrl-sci↗

Assigning probabilities to non-Lipschitz mechanical systems

We present a method for assigning probabilities to the solutions of initial value problems that have a Lipschitz singularity. To illustrate the method, we focus on the following toy example: $\frac{d^2r(t)}{dt^2} = r^a$, $r(t=0) =0$, and $\frac{dr(t)}{dt}\mid_{r(t=0)} =0$, with $a \in ]0,1[$. This example has a physical interpretation as a mass in a uniform gravitational field on a frictionless, rigid dome of a particular shape; the case with $a=1/2$ is known as Norton's dome. Our approach is based on (1) finite difference equations, which are deterministic; (2) elementary techniques from alpha-theory, a simplified framework for non-standard analysis that allows us to study infinitesimal perturbations; and (3) a uniform prior on the canonical phase space. Our deterministic, hyperfinite grid model allows us to assign probabilities to the solutions of the initial value problem in the original, indeterministic model.

physics.class-ph↗

Linker Functionalization in MIL-47(V)-R Metal-Organic Frameworks: Understanding the Electronic Structure

Metal-Organic Frameworks (MOFs) have gained much interest due to their intrinsic tunable nature. In this work, we study how linker functionalization modifies the electronic structure of the host MOF, more specifically the MIL-47(V)-R (R=-F, -Cl, -Br, -OH, -CH$_3$, -CF$_3$, and -OCH$_3$). It is shown that the presence of a functional group leads to a splitting of the $π$-orbital on the linker. Moreover, the upward shift of the split-off $π$-band correlates well with the electron withdrawing/donating nature of the functional groups. For halide functional groups the presence of lone-pair back donation is corroborated by calculated Hirshfeld-I charges. In case of the ferromagnetic configuration of the host MIL-47(V$^{\mathrm{+IV}}$) material a half-metal to insulator transition is noted for the -Br, -OCH$_3$, and -OH functional groups, while for the anti-ferromagnetic configuration only the hydroxy-group results in an effective reduction of the band gap.

cond-mat.mtrl-sci↗

Fingerprinting defects in diamond: Partitioning the vibrational spectrum

In this work, we present a computational scheme for isolating the vibrational spectrum of a defect in a solid. By quantifying the defect character of the atom-projected vibrational spectra, the contributing atoms are identified and the strength of their contribution determined. This method could be used to systematically improve phonon fragment calculations. More interestingly, using the atom-projected vibrational spectra of the defect atoms directly, it is possible to obtain a well-converged defect spectrum at lower computational cost, which also incorporates the host-lattice interactions. Using diamond as the host material, four test case defects, each presenting a distinctly different vibrational behaviour, are considered: a heavy substitutional dopant (Eu), two intrinsic defects (neutral vacancy and split interstitial), and the negatively charged N-vacancy center. The heavy dopant and split interstitial present localized modes at low and high frequencies, respectively, showing little overlap with the host spectrum. In contrast, the neutral vacancy and the N-vacancy center show a broad contribution to the upper spectral range of the host spectrum, making them challenging to extract. Independent of the vibrational behaviour, the main atoms contributing to the defect spectrum can be clearly identified. Recombination of their atom-projected spectra results in the isolated defect spectrum.

cond-mat.mtrl-sci↗

Can Europium Atoms form Luminescent Centres in Diamond: A combined Theoretical-Experimental Study

The incorporation of Eu into the diamond lattice is investigated in a combined theoretical-experimental study. The large size of the Eu ion induces a strain on the host lattice, which is minimal for the Eu-vacancy complex. The oxidation state of Eu is calculated to be 3+ for all defect models considered. In contrast, the total charge of the defect-complexes is shown to be negative -1.5 to -2.3 electron. Hybrid-functional electronic-band-structures show the luminescence of the Eu defect to be strongly dependent on the local defect geometry. The 4-coordinated Eu substitutional dopant is the most promising candidate to present the typical Eu3+ luminescence, while the 6-coordinated Eu-vacancy complex is expected not to present any luminescent behaviour. Preliminary experimental results on the treatment of diamond films with Eu-containing precursor indicate the possible incorporation of Eu into diamond films treated by drop-casting. Changes in the PL spectrum, with the main luminescent peak shifting from approximately 614 nm to 611 nm after the growth plasma exposure, and the appearance of a shoulder peak at 625 nm indicate the potential incorporation. Drop-casting treatment with an electronegative polymer material was shown not to be necessary to observe the Eu signature following the plasma exposure, and increased the background luminescence.

cond-mat.mtrl-sci↗

Probability of Inconsistencies in Theory Revision: A multi-agent model for updating logically interconnected beliefs under bounded confidence

We present a model for studying communities of epistemically interacting agents who update their belief states by averaging (in a specified way) the belief states of other agents in the community. The agents in our model have a rich belief state, involving multiple independent issues which are interrelated in such a way that they form a theory of the world. Our main goal is to calculate the probability for an agent to end up in an inconsistent belief state due to updating (in the given way). To that end, an analytical expression is given and evaluated numerically, both exactly and using statistical sampling. It is shown that, under the assumptions of our model, an agent always has a probability of less than 2% of ending up in an inconsistent belief state. Moreover, this probability can be made arbitrarily small by increasing the number of independent issues the agents have to judge or by increasing the group size. A real-world situation to which this model applies is a group of experts participating in a Delphi-study.

physics.soc-ph↗

Aliovalent Doping of CeO$_2$: DFT-study of Oxidation State and Vacancy Effects

The modification of the properties of CeO$_2$ through aliovalent doping are investigated within the \emph{ab-initio} density functional theory framework. Lattice parameters, dopant atomic radii, bulk moduli and thermal expansion coefficients of fluorite type Ce$_{1-x}$M$_{x}$O$_{2-y}$ (with M$ = $ Mg, V, Co, Cu, Zn, Nb, Ba, La, Sm, Gd, Yb, and Bi)are presented for dopant concentrations in the range $0.00 \leq x \leq 0.25$. The stability of the dopants is compared and 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, but are shown to present no simple trend. The previously observed inverse relation between the thermal expansion coefficient and the bulk modulus is shown to persist independent of the inclusion of charge compensating vacancies.

cond-mat.mtrl-sci↗

Tuning of CeO$_2$ buffer layers for coated superconductors through doping

The appearance of microcracks in CeO$_2$ buffer layers, as used in buffer layer architectures for coated superconductors, indicates the presence of stress between this buffer layer and the substrate. This stress can originate from the differences in thermal expansion or differences in lattice parameters between the CeO$_2$ buffer layer and the substrate. In this article, we study, by means of \textit{ab initio} density functional theory calculations, the influence of group IV doping elements on the lattice parameter and bulk modulus of CeO$_2$. Vegard's law behavior is found for the lattice parameter in systems without oxygen vacancies, and the Shannon crystal radii for the doping elements are retrieved from the lattice expansions. We show that the lattice parameter of the doped CeO$_2$ can be matched to that of the La$_2$Zr$_2$O$_7$ coated NiW substrate substrate for dopant concentrations of about $5\%$, and that bulk modulus matching is either not possible or would require extreme doping concentrations.

cond-mat.mtrl-sci↗

Modeling 1D structures on semiconductor surfaces: Synergy of theory and experiment

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 a 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 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.

cond-mat.mtrl-sci↗

Models and Simulations in Material Science: Two Cases Without Error Bars

We discuss two research projects in material science in which the results cannot be stated with an estimation of the error: a spectro- scopic ellipsometry study aimed at determining the orientation of DNA molecules on diamond and a scanning tunneling microscopy study of platinum-induced nanowires on germanium. To investigate the reliability of the results, we apply ideas from the philosophy of models in science. Even if the studies had reported an error value, the trustworthiness of the result would not depend on that value alone.

cond-mat.mtrl-sci↗

DFT study of Pt-induced Ge(001) reconstructions

Pt deposited on a Ge(001) surface spontaneously forms nanowire arrays. These nanowires are thermodynamically stable and can be hundreds of atoms long. The nanowires only occur on a reconstructed Pt-Ge-surface where they fill the troughs between the dimer rows on the surface. This unique connection between the nanowires and the underlying substrate make a thorough understanding of the latter necessary for understanding the growth of the nanowires. In this paper we study possible surface reconstructions containing 0.25 and 0.5 of a monolayer of Pt. Comparison of calculated STM images to experimental STM images of the surface reconstruction reveal that the Pt atoms are located in the top layer, creating a structure with rows of alternating Pt-Ge and Ge-Ge dimers in a c(4x2) arrangement. Our results also show that Pt atoms in the second or third layer can not be responsible for the experimentally observed STM images.

cond-mat.mtrl-sci↗

Pt-induced nanowires on Ge(001): a DFT study

We study formation of the nanowires formed after deposition of Pt on a Ge(001) surface. The nanowires form spontaneously after high temperature annealing. They are thermodynamically stable, only one atom wide and up to a few hundred atoms long. Ab initio density functional theory calculations are performed to identify possible structures of the Pt-Ge (001) surface with nanowires on top. A large number of structures is studied. With nanowires that are formed out of Pt or Ge dimers or mixed Pt-Ge dimers. By comparing simulated scanning tunneling microscopy images with experimental ones we model the formation of the nanowires and identify the geometries of the different phases in the formation process. We find that the formation of nanowires on a Pt-Ge(001) surface is a complex process based on increasing the Pt density in the top layers of the Ge(001) surface. Most remarkably we find the nanowires to consist of germanium dimers placed in troughs lined by mixed Pt-Ge dimer rows.

cond-mat.mtrl-sci↗

CO adsorption on Pt induced Ge nanowires

Using density functional theory, we investigate the possible adsorption sites of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001). Calculated STM images are compared to experimental STM images to identify the experimentally observed adsorption sites. The CO molecules are found to adsorb preferably onto the Pt atoms between the Ge nanowire dimer segments. This adsorption site places the CO in between two nanowire dimers, pushing them outward, blocking the nearest equivalent adsorption sites. This explains the observed long-range repulsive interaction between CO molecules on these Pt induced nanowires.

cond-mat.mtrl-sci↗

The Formation of Self-Assembled Nanowire Arrays on Ge(001): a DFT Study of Pt Induced Nanowire Arrays

Nanowire (NW) arrays form spontaneously after high temperature annealing of a submonolayer deposition of Pt on a Ge(001) surface. These NWs are a single atom wide, with a length limited only by the underlying beta-terrace to which they are uniquely connected. Using ab-initio density functional theory (DFT) calculations we study possible geometries of the NWs and substrate. Direct comparison to experiment is made via calculated scanning tunneling microscope (STM) images. Based on these images, geometries for the beta-terrace and the NWs are identified, and a formation path for the nanowires as function of increasing local Pt density is presented. We show the beta-terrace to be a dimer row surface reconstruction with a checkerboard pattern of Ge-Ge and Pt-Ge dimers. Most remarkably, comparison of calculated to experimental STM images shows the NWs to consist of germanium atoms embedded in the Pt-lined troughs of the underlying surface, contrary to what was assumed previously in experiments.

cond-mat.mtrl-sci↗