Staff Dr. Jan Hamaekers

Address:
Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI
Friedrich-Hirzebruch-Allee 7
53115 Bonn
Phone: +49 228 73-69771
Office: FHA7 2.011
E-Mail: ed tod refohnuarf tod iacs ta srekeamah tod naja tod b@foo tod de

Affiliated to Fraunhofer SCAI

Research Interests

  • Application of new numerical methods for high dimensional problems to the Schrödinger equation.
Potential (unit cell)
Potential (unit cell)
Symmetric groundstate
Symmetric groundstate
Antisymmetric groundstate
Antisymmetric groundstate
Antisymmetric groundstate for N=2
Antisymmetric groundstate for N=2
Antisymmetric groundstate for N=3
Antisymmetric groundstate for N=3
Excited state (2p) of H atom
Excited state (2p) of H atom
Rank-1 approximation of He
Rank-1 approximation of He
Adaptive sparse grid for two electron correlation
Adaptive sparse grid for two electron correlation
Groundstate of He
Groundstate of He
  • Application of QM and MM methods for problems in chemistry, biochemistry, molecular physics, solid state physics, material science and nanotechnology.
GaAs unit cell
GaAs unit cell
C-Nanotube + H<sub>2</sub>
C-Nanotube + H2
NaPO unit cell
NaPO unit cell
C-NT in polyethylene with cross-links
C-NT in polyethylene with cross-links
Functionalized BN-NT
Functionalized BN-NT
BN-NT in Si<sub>3</sub>B<sub>3</sub>N<sub>7</sub>
BN-NT in Si3B3N7
Cementitious silicate hydrate (C-S-H) gels
Cementitious silicate hydrate (C-S-H) gels
Growth of amorphous Si-O NT on functionalized BN-NT
Growth of amorphous Si-O NT on functionalized BN-NT
Benzene droplet on SiO<sub>2</sub>
Benzene droplet on SiO2

Teaching

Summer semester 2021

Summer semester 2020

  • Practical Lab Numerical Simulation Particle methods and meshless discretizations Practical Lab, module P4E1.
  • Programmierpraktikum numerische Algorithmen Partikelmethoden und gitterlose Diskretisierungen Practical Lab, module P2E1.

Research Projects

Current

Molecular Dynamics Simulations for Material Science Applications

Completed

A dimension-adaptive sparse grid method for the Schrödinger equation

DFG priority program 1145.

Homepage.

CODICE - Computationally Driven design of Innovative Cement-based materials

EU FP7.

Homepage.

Cooperation with Asociacion CIC nanoGUNE - Self-Assembly

Homepage.

Cooperation with Labein Centro Tecnologico, Bilbao, Spain

Homepage.

Development of efficient algorithms for nanoscale dynamics simulations based on first principles methods

Hide description.

ESPACK: A parallel electronic structure dynamics software package

High-dimensional problems and multi-scale methods

Project Area J, Cluster of Excellence.

Homepage.

Multiscale QM/MM simulations of the growth process and the material properties of inorganic nanotubes and nanotube composites

DFG priority program 1165.

Homepage.

Parallel methods for short- and long-ranged potentials in Molecular Dynamics

TREMOLO - a parallel molecular dynamics software package

Homepage.

Publications

  1. On multilevel energy-based fragmentation methods. J. Barker, M. Griebel, and J. Hamaekers. Available as INS Preprint No. 2403, 2024. BibTeX PDF
  2. Confrank: improving gfn-ff conformer ranking with pairwise training. C. Hölzer, R. Oerder, S. Grimme, and J. Hamaekers. ChemRxiv, 2024. BibTeX DOI
  3. Generalized sparse grid interpolation based on the fast discrete Fourier transform. M. Griebel and J. Hamaekers. In Sparse Grids and Applications - Munich 2018, volume 144 of Lecture Notes in Computational Science and Engineering, pages 53–68. Springer International Publishing, 2022. BibTeX PDF DOI
  4. Rapid prescreening of organic compounds for redox flow batteries: a graph convolutional network for predicting reaction enthalpies from smiles. L.-S. Berg, J. Hamaekers, J. Barker, and A. Maass. Batteries & Supercaps, 2021. BibTeX
  5. Similarity of particle systems using an invariant root mean square deviation measure. J. Bulin and J. Hamaekers. arXiv preprint, 2021. BibTeX arXiv
  6. An adaptive multiscale approach for electronic structure methods. M. Griebel, J. Hamaekers, and R. Chinnamsetty. Multiscale Modeling & Simulation, 16(2):752–776, 2018. Also available as INS Preprint No. 1601. BibTeX PDF DOI
  7. Insights into the folding of disulfide-rich µ-conotoxins. A. A. Paul George, P. Heimer, A. Maaß, J. Hamaekers, M. Hofmann-Apitius, A. Biswas, and D. Imhof. ACS Omega, 3(10):12330–12340, 2018. BibTeX DOI
  8. LC-GAP: Localized Coulomb descriptors for the Gaussian Approximation Potential. J. Barker, J. Bulin, J. Hamaekers, and S. Mathias. In M. Griebel, A. Schüller, and M. A. Schweitzer, editors, Scientific Computing and Algorithms in Industrial Simulations: Projects and Products of Fraunhofer SCAI, pages 25–42. Springer International Publishing, Cham, 2017. BibTeX PDF
  9. The octet rule in chemical space: generating virtual molecules. R. Israels, A. Maaß, and J. Hamaekers. Molecular diversity, 21(4):769–778, 2017. BibTeX DOI
  10. ATK-ForceField: a new generation molecular dynamics software package. J. Schneider, J. Hamaekers, S. Chill, S. Smidstrup, J. Bulin, R. Thesen, A. Blom, and K. Stokbro. Modelling and Simulation in Materials Science and Engineering, 25(8):085007, 2017. BibTeX
  11. A multilevel approach to the evolutionary generation of polycrystalline structures. J. Barker, G. Bollerhey, and J. Hamaekers. Computational Materials Science, 114:54–63, 2016. Also available as INS Preprint No. 1525. BibTeX PDF
  12. A finite element study on the effect of curvature on the reinforcement of matrices by randomly distributed and curved nanotubes. C. Diedrich, D. Dijkstra, J. Hamaekers, B. Henninger, and M. Randrianarivony. Journal of Computational and Theoretical Nanoscience, 12:2108–2116, 2015. BibTeX PDF
  13. Fast discrete Fourier transform on generalized sparse grids. M. Griebel and J. Hamaekers. In Sparse grids and Applications, volume 97 of Lecture Notes in Computational Science and Engineering, pages 75–108. Springer, 2014. BibTeX PDF
  14. A bond order dissection ANOVA approach for efficient electronic structure calculations. M. Griebel, J. Hamaekers, and F. Heber. In Extraction of Quantifiable Information from Complex Systems, volume 102 of Lecture Notes in Computational Science and Engineering, pages 211–235. Springer, 2014. BibTeX PDF
  15. Multiscale simulation of ion migration for battery systems. C. Neuen, M. Griebel, and J. Hamaekers. MRS Online Proceedings Library, 2013. Also available as INS Preprint no. 1208. BibTeX PDF DOI
  16. The nano-branched structure of cementitious calcium-silicate-hydrate gel. J. S. Dolado, M. Griebel, J. Hamaekers, and F. Heber. Journal of Materials Chemistry, 21:4445–4449, 2011. BibTeX PDF DOI Link
  17. BOSSANOVA - A bond order dissection approach for efficient electronic structure calculations. M. Griebel, J. Hamaekers, and F. Heber. Oberwolfach Report, 32:1804–1808, 2011. BibTeX DOI
  18. Tensor product multiscale many-particle spaces with finite-order weights for the electronic Schrödinger equation. M. Griebel and J. Hamaekers. In M. Dolg, editor, Modern and Universal First-principles Methods for Many-electron Systems in Chemistry and Physics, volume 3 of Progress in Physical Chemistry, pages 237–253. Oldenbourg Wissenschaftsverlag GmbH, München, 2010. BibTeX
  19. Tensor product multiscale many-particle spaces with finite-order weights for the electronic Schrödinger equation. M. Griebel and J. Hamaekers. Zeitschrift für Physikalische Chemie, 224:527–543, 2010. Also available as INS Preprint no 0911. BibTeX PDF
  20. Sparse Grids for the Electronic Schrödinger Equation: Construction and Application of Sparse Tensor Product Multiscale Many-Particle Spaces with Finite-Order Weights for Schrödinger's Equation. J. Hamaekers. Südwestdeutscher Verlag für Hochschulschriften, Saarbrücken, 2010. ISBN 978-3-8381-1578-8. BibTeX
  21. Biomolecules as soft matter surfaces. A. M. Bittner, F. Heber, and J. Hamaekers. Surface Science, 603:1922–1925, 2009. BibTeX DOI
  22. A molecular dynamics study on the impact of defects and functionalization on the Young modulus of boron-nitride nanotubes. M. Griebel, J. Hamaekers, and F. Heber. Computational Materials Science, 45(4):1097–1103, 2009. BibTeX PDF
  23. Tensor Product Multiscale Many–Particle Spaces with Finite–Order Weights for the Electronic Schödinger Equation. J. Hamaekers. Dissertation, Institut für Numerische Simulation, Universität Bonn, jul 2009. BibTeX Read
  24. BOSSANOVA: A bond order dissection approach for efficient electronic structure calculations. M. Griebel, J. Hamaekers, and F. Heber. INS Preprint 0704, Institut für Numerische Simulation, Universität Bonn, 2008. BibTeX PDF
  25. A molecular dynamics study of the aluminosilicate chains structure in Al-rich calcium silicate hydrated (C-S-H) gels. H. Manzano, J. Dolado, M. Griebel, and J. Hamaekers. physica status solidi (a) - applications and materials science, 205(6):1324–1329, 2008. Also as INS Preprint No. 0707. BibTeX PDF DOI
  26. A molecular dynamics study of cementitious silicate hydrate (C-S-H) gels. J. S. Dolado, M. Griebel, and J. Hamaekers. Journal of the American Ceramic Society, 90(12):3938–3942, 2007. Also as INS Preprint No. 0701. BibTeX PostScript PDF
  27. Molecular dynamics simulations of boron-nitride nanotubes embedded in amorphous Si-B-N. M. Griebel and J. Hamaekers. Computational Materials Science, 39(3):502–517, 2007. Also as INS Preprint No. 0501. BibTeX PostScript PDF
  28. Sparse grids for the Schrödinger equation. M. Griebel and J. Hamaekers. Mathematical Modelling and Numerical Analysis, 41(2):215–247, 2007. Special issue on Molecular Modelling. Also as INS Preprint No. 0504. BibTeX PostScript PDF
  29. A wavelet based sparse grid method for the electronic Schrödinger equation. M. Griebel and J. Hamaekers. In M. Sanz-Solé, J. Soria, J. Varona, and J. Verdera, editors, Proceedings of the International Congress of Mathematicians, volume III, 1473–1506. Madrid, Spain, August 22–30 2006. European Mathematical Society. Also as INS Preprint No. 0603. BibTeX PDF
  30. Molecular dynamics simulations of the mechanical properties of polyethylene-carbon nanotube composites. M. Griebel and J. Hamaekers. In M. Rieth and W. Schommers, editors, Handbook of Theoretical and Computational Nanotechnology, volume 9, chapter 8, pages 409–454. American Scientific Publishers, 2006. BibTeX PostScript PDF Link
  31. Molecular dynamics simulations of the influence of chemical cross-links on the elastic moduli of polymer-carbon nanotube composites. M. Griebel, J. Hamaekers, and R. Wildenhues. In J. Sanchez, editor, Proceedings 1st Nanoc-Workshop. LABEIN, Bilbao, Spain, 2005. Also as INS Preprint No. 0503. BibTeX PDF
  32. Molecular dynamics of mechanical properties of boron-nitride nanotubes embedded in Si-B-N ceramics. M. Griebel and J. Hamaekers. In N. M. Ghoniem, editor, Conference Proceedings, Second International Conference on Multiscale Materials Modeling, 51–55. Mechanical and Aerospace Engineering Department, University of California Los Angeles, October 11–15 2004. BibTeX PostScript PDF
  33. Molecular dynamics simulations of the elastic moduli of polymer-carbon nanotube composites. M. Griebel and J. Hamaekers. Computer Methods in Applied Mechanics and Engineering, 193(17–20):1773–1788, 2004. BibTeX PostScript PDF
  34. Molecular dynamics simulations of the elastic moduli of polymer-carbon nanotube composites. M. Griebel and J. Hamaekers. In D. Hui, editor, ICCE-10, 213–214. College of Engineering, University of New Orleans, July 20–26 2003. International Community for Composites Engineering. BibTeX PostScript PDF
  35. Ebene-Wellen basiertes, adaptives und paralleles Verfahren für die Dichtefunktionaltheorie. J. Hamaekers. Diplomarbeit, Institut für Angewandte Mathematik, Universität Bonn, Bonn, Germany, 2002. BibTeX PostScript PDF