Feb 14 2025

No boundaries and naturally-defined boundaries obtained via the electrostatic potential

Authors: Goedele Roos, Danny E.P. Vanpoucke, and Jane S. Murray
Journal: ChemPhysChem XX, e202401065 (2025)
doi: 10.1002/cphc.202401065
IF(2023): 2.3
export: bibtex
pdf: <ChemPhysChem_XX>

 

Graphical Abstract: Schematic representation of the electrostatic potential within a water molecule along the lines between the atoms. The color background shows the electrostatic potential on the 0.001 a.u. contour of the density. The Vs,min and Vs,max points on the surface are indicated.

Abstract

This paper discusses the use of the electrostatic potential in both recent and older literature, with an emphasis upon a 2022 Molecular Physics article by Politzer and Murray entitled “Atoms do exist in molecules: analysis using electrostatic potentials at nuclei“. We discuss electrostatic potentials at nuclei and how they easily lead to atoms in molecules, without physically separating the individual atoms. We further summarize the work by the Politzer group on definitions of atomic radii by means of the electrostatic potential. The earlier studies began in the 1970’s and continued through the 1990’s. Unfortunately, access to these older publications is often limited, cfr. digital libraries often limit the authorized access until a certain publication year, and these papers are often not cited in current publications. Although still being highly interesting and relevant, this older literature is in danger of being lost. Digging into this older literature thus opens up new views. Our feeling is that Peter passed ‘on’ a vision that boundaries do not exist between atoms in molecules, but that some useful and meaningful radii can be obtained using the electrostatic potential between atoms in molecules.

Permanent link to this article: https://dannyvanpoucke.be/2025-paper-esp-politzer-rev-en/

Jan 21 2025

Machine Learning and Artificial Intelligence in modern materials science

  • Filed under blog

  • January 21, 2025

One of the most joyful parts of teaching, is when you read a student paper and see their joy of the research shine through.

This year was the second year I taught the course “Machine Learning and Artificial Intelligence in modern materials science“, an elective course in the second master materiomics program. As with my other computational courses, there is a strong hands-on component present in this course: a semester long homework assignment, culminating in a paper and presentation of the work done. The basic idea behind the assignment is simple: Take the QM9 dataset and study it using machine learning and artificial intelligence, incorporating things you learn during the course. In practice this means a lot of coding with for example scikit-learn in combination with using every ounce of physical and chemical intuition they gathered during their previous courses. The absolute freedom generally results in some initial trepidation, but intermediate feedback and the growing understanding that the journey is the the actual goal results in some amazing work.

At the end of the semester, I had three papers before me, which could only be written by these three students (Materiomics is a new program, so having 3 of the 7 students picking a rather hard core computational course is good 😉 ). You could feel their own backgrounds and interests seeping through, as well as the fun they had doing so. There was the engineer who approached the problem from a pipeline perspective, the chemist comparing the efficacy of various fingerprints as features, and the physicist who build a new small fingerprint from scratch creating a linear regression model that outperformed all else having R² =1. The last one is a very nice example of frugal computing, of which we do need more in a world suffering climate change. It was also interesting to see also how three totally different stories also hint at the same underlying properties of the dataset (same target being the hardest to predict), a consistency which provides a level of meta-validation of the results. The students themselves also learned to be critical of their own work by comparing the results of different methods used to attack their own research question.

At the end of this course, it is clear they learned more about artificial intelligence than what is possible by just reading about it. The understood the entire workflow of which training is merely a small part, they learned directly the importance of having good quality data and features, and most importantly they learned that they themselves need to be the I in AI, to be successful…and finally, maybe us four should put our heads together and combine this work into a real research paper, as to celebrate the great research done as a “mere homework-assignment”.

Permanent link to this article: https://dannyvanpoucke.be/machine-learning-and-artificial-intelligence-in-modern-materials-science/

Jan 09 2025

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

Authors: Thijs G.I. van Wijk, E. Aylin Melan, Rani Mary Joy, Emerick Y. Guillaume, Paulius Pobedinskas, Ken Haenen, and Danny E.P. Vanpoucke
Journal: Carbon 234, 119928 (2025)
doi: 10.1016/j.carbon.2024.119928
IF(2024): 10.5
export: bibtex
pdf: <Carbon>

 

Graphical abstract strained GeV0.
Graphical Abstract: Schematic representation of the impact of hydrostatic and linear strain on the Zero Phonon Line of the neutral GeV defect in diamond.

Abstract

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 GeV0. Both hydrostatic and linear strain are modeled using density functional theory for GeV0concentrations 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 GeV0 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 ⟨100⟩ 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 GeV0 eg 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.

Permanent link to this article: https://dannyvanpoucke.be/2025-paper-strainedgev-en/

Jan 03 2025

New QuATOMs group member: Minh-Thu Bui

Since the first of January 2025, the QuATOMs group has been strengthened with a new member: Minh-Thu Bui.

She is an expert in polymer chemistry, with a MSc in Polymers for advanced Technologies from the university of Grénoble. The coming four years she will be working on the QuantumLignin project. In this project, she’ll investigate the structure-property relations of lignin building blocks, with the aim of creating an additive model suitable for predicting the properties of mixed lignin samples. With her life motto: “Don’t wait for the perfect moment. Take the moment and make it perfect.” I’m sure we can expect great things to happen in the theoretical lignin field, the coming years.

Welcome to the QuATOMs team, we look forward to your enthusiasm and the intuition you bring to the team.

Permanent link to this article: https://dannyvanpoucke.be/new-quatoms-group-member-minh-thu-bui/

Jan 01 2025

Review of 2024

  • Filed under blog

  • January 1, 2025

Happy 2025

2023 and 2024 have been an intense ride, with both the materiomics program, the tenure track and the research group. Since the previous overview in 2022, the QuATOMs group has seen some growth with the arrival of three new members (Pauline Castenetto, Thijs van Wijk, and Aylin Melan). In addition, Emerick Guillaume defended his PhD on the study of diamond growth.

These are not the only things which happened the last two years, so let us look back at 2023 and 2024 one last time, keeping up with  tradition.

1. Publications: +4 (and currently a handful in progress)

2. Cover publication: +1

Cover Nature Reviews Physics: Accuracy of DFT

3. Project proposals accepted: +2

  • QuantumLignin: Elucidating the interactions of lignin building blocks with their environment for the creation of additive models by means of quantum mechanical modelling.
  • AI-accelerated quantum mechanical modelling of the optical properties of semiconductor materials: from colour centres in diamond to transition-metal oxides.

4. Completed refereeing tasks: +20

  • ACS Photon
  • Journal of Physics D: Applied Physics (2x)
  • Philosophical Transactions (2x)
  • Journal of Materials Chemistry A (2x)
  • Journal of Physical Chemistry (3x)
  • Diamond and Related Materials (11x)

5. Conferences & seminars: +7/+1 (Attended & Organised)

  • SBDD XXVII & SBDD XXVIII, Hasselt University, Belgium, March 15th-17th, 2023 & February 28th-March 1st, 2024 [poster presentations, PhD students & MSc student]
  • EAB-workshop on AI in Higher Education, UHasselt, Belgium, April 24th, 2024 [oral presentation]
  • DFT-2024: 20th International Conference on Density Functional Theory and its Applications, Paris, France, August 25th-30th, 2024 [oral presentation]
  • E-MRS Spring meeting 2023 & 2024, Strassbourg, France, May 29th-June 2nd, 2023 & May 27th-31st, 2024 [oral presentations]
  • Summer School: “Materiomics: Innovative Materials From Healthcare Across Quantum To Sustainable Technologies”, UHasselt, Belgium, September 4th-6th, 2024 [member of Organizating Committee; seminar]
  • NISM seminar: “Extreme Machine Learning – When the average model knows best”  (Prof. L. Henrard), UNamur, Belgium, September 12th, 2024 [invited seminar]

6. Supervised students:

  • BSc Projects Physics: 4
  • MSc Projects Materiomics: 3
  • Internships: 2

7. Hive-STM program:

And now, upward and onward, a new year, a fresh start.

Permanent link to this article: https://dannyvanpoucke.be/review-of-2024/

Dec 17 2024

The devil in the details: lessons from Li6PS5X for robust high-throughput workflows

Authors: Asif Iqbal Bhatti, Sandeep Kumar, Catharina Jaeken, Michael Sluydts, Danny E.P. Vanpoucke, and Stefaan Cottenier
Journal: Journal of Materials Chemistry A 13, 526-539 (2025)
doi: 10.1039/D4TA06603K
IF(2024): 10.7
export: bibtex
pdf: <J.Mat.Chem.A>

 

Graphical Abstract: Schematic representation of the LPS material and the variation of results obtained due to slight changes in settings within a High Throughput workflow.

Abstract

High-throughput computational screening has become a powerful tool in materials science for identifying promising candidates for specific applications. However, the effectiveness of these methods relies heavily on the accuracy and appropriateness of the underlying models and assumptions. In this study, we use the popular argyrodite solid-state electrolyte family Li6PS5X (X = Cl, Br, I) as a case study to critically examine key steps in high-throughput workflows and highlight potential pitfalls. We demonstrate some of these pitfalls by highlighting the importance of careful structural considerations, including symmetry breaking and site disorder, and examine the difference between 0 K thermodynamic stability and finite-temperature stability based on temperature-dependent Gibbs free energy calculations. Furthermore, we explore the implications of these findings for the ranking of candidate materials in a mini-throughput study in a search space of isovalent analogs to Li6PS5Cl. As a result of these findings, our work underscores the need for balanced trade-offs between computational efficiency and accuracy in high-throughput screenings, and offers guidance for designing more robust workflows that can better bridge the gap between computational predictions and experimental realities.

Permanent link to this article: https://dannyvanpoucke.be/2025-paper-thedevilinthedetails-en/

Sep 22 2024

End of summer, and the start of a new academic year.

  • Filed under blog

  • September 22, 2024

Mid September in Hasselt means the start of a new academic year. It brings to an end a summer of doing some unrestricted research. Especially the last month has been extremely busy.

  • The DFT2024 conference in Paris from August 25th until 30th, where I presented our recent work on the GeV defect, which we will be submitting shortly.
  • The materiomics summer school, where I gave a lecture on performing practical quantum mechanical calculations,
  • The public PhD defense of Emerick Guillaume (QuATOMs group member) on the growth of diamond: congratulations Emerick!
  • A seminar at UNamur on “extreme machine learning”, discussing our work on small datasets and some of the work I did this summer on a spray coating dataset.

Today the first week of academic year ended, and I already had the pleasure teaching quantum mechanics and modelling courses to chemistry and materiomics students. We also welcome 2 MSc materiomics students to the group: Brent Motmans and Eleonora Thomas. Brent will be working on an experimental-theoretical project, where the theoretical side will focus on machine learning of his experimental data. Eleonora on the other hand will be combining DFT and machine learning in her study of diamond. A very warm welcome to the QuATOMs group for both.

 

Permanent link to this article: https://dannyvanpoucke.be/end-of-summer-and-the-start-of-a-new-academic-year/

Sep 01 2024

New QuATOMs group member

During the last year, Esin Aylin Melan worked hard at her MSc Thesis within the QuATOMs group. Her research focus was centered on the impact of strain on the zero-phonon-line of the GeV color center in diamond. This work she presented, together with Thijs van Wijk, at the SBDD conference in Hasselt, and was presented as well at both the BPS and EMRS spring meeting of 2024. Before the summer she gave her (very good and enthusiastic) final presentation of the MSc thesis results, bringing her first real research project to good end. (Paper will follow later 🙂 )

Recently, she also received the great news that she was awarded a bilateral PhD Scholarship between UHasselt & UNamur. So from September first, she has started working on the modeling of color centers in diamond and oxides for the coming four years. Welcome to the QuATOMs team, and congratulations on the scholarship. We look forward to the enthusiasm and insights you’ll bring to the team.

Permanent link to this article: https://dannyvanpoucke.be/new-quatoms-group-member/

Jun 21 2024

DigiLignin: Consortium Meeting

Today we had our fourth consortium meeting for the DigiLignin project. Things are moving along nicely, with a clear experimental database almost done by VITO, the Machine Learning model taking shape at UMaastricht, and quantum mechanical modeling providing some first insights.

Permanent link to this article: https://dannyvanpoucke.be/digilignin-c4-en/

Mar 06 2024

First-principles investigation of hydrogen-related reactions on (100)–(2×1)∶H diamond surfaces

Authors: Emerick Y. Guillaume, Danny E. P. Vanpoucke, Rozita Rouzbahani, Luna Pratali Maffei, Matteo Pelucchi, Yoann Olivier, Luc Henrard, & Ken Haenen
Journal: Carbon 222, 118949 (2024)
doi: 10.1016/j.carbon.2024.118949
IF(2022): 10.9
export: bibtex
pdf: <Carbon>

 

Graphical Abstract for Carbon publication on the adsorption of H onto diamond.
Graphical Abstract: (left) Ball-and-stick representation of aH adsorption/desorption reaction mediated through a H radical. (right) Monte Carlo estimates of the H coverage of the diamond surface at different temperatures based on quantum mechanically determined reaction barriers and reaction rates.

Abstract

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.

Permanent link to this article: https://dannyvanpoucke.be/2024-paper-hadsorption-emerick-en/