Publications
Data Science
At the first international symposium on the science of data science, organised as a satellite event of the Swiss conference on Data Science in 2022, we had intense discussions on the scientific nature of data science as a discipline and various special topics, such as explainability, rationality, trust and education vs. technical skills. The following article, together with David Kempf, summarises my contribution:
- Is It Ops That Make Data Science Scientific? Archives of Data Science, Series A, vol 8, p. 12, 2022. doi:10.5445/IR/1000150238
Computational Chemistry
This is an overview of the topics I worked on during my time as a computational chemist - most of the publications were written during my dissertation at the École Polytechnique Fédérale de Lausanne (EPFL) under the supervision of Ursula Röthlisberger.
The research activities in the laboratoire the chimie et biochimie computationelle at the time are summarised here:
- Pushing the frontiers of first-principles based computer simulations of chemical and biological systems. Chimia, vol. 65, p. 667, 2011. doi: 10.2533/chimia.2011.667
My PhD thesis - Approaches to Increase the Accuracy of Molecular Dynamics Simulations: From Classical to Tight Binding and First Principles Methods - can be accessed online.
Low energy structure of small biomolecules in the gas phase
A collaboration with the group of Thomas Rizzo (EPFL), who recorded conformer-specific vibrational spectra of small protonated biomolecules in the gas phase at low temperature. Employing a combination of computational methods we determined the molecular structures giving rise to the experimental spectra.
Furthermore, we used the high-resolution experimental benchmark data to asses various computational methods to predict the correct relative energetics of low energy structures.
- Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy. J Phys Chem Lett., vol 14, p.6037, 2023. doi:10.1021/acs.jpclett.3c01239
- Photodynamics of Lys+-Trp Protein Motifs: Hydrogen Bonds Ensure Photostability, Faraday Discuss., vol. 163, p. 189, 2013. doi:10.1039/C3FD00037K
- Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide, Int. J. Quantum Chem., vol. 113, p. 808, 2013. doi:10.1002/qua.24085
- Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide, Angew. Chem. Int. Ed., vol. 50, p. 5383, 2011. doi:10.1002/anie.201100702
Deriving improved classical force field parameters by QM/MM force matching
With the goal to increase the accuracy of classical molecular mechanics force fields we implemented the recently developed force-matching protocol for an automated parametrisation of biomolecular force fields from mixed quantum mechanics/molecular mechanics (QM/MM) reference calculations in the CPMD software package. Such a force field has an accuracy that is comparable to the QM/MM reference, but at the greatly reduced computational cost of the MM approach. We have applied this protocol to derive in situ FF parameters for the retinal chromophore in rhodopsin embedded in a lipid bilayer.
See the QM/MM force matching page at lcbc.epfl.ch – Research – QM/MM force matching
- Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin, J. Chem. Theory Comput., vol. 10, p. 412, 2014. doi:10.1021/ct400697n
Parameterisation of repulsive potentials for the self-consistent charge density functional tight-binding (SCC-DFTB) method
We employed iterative Boltzmann inversion to derive repulsive potentials for SCC-DFTB. We used reference data at the DFT/PBE level to derive highly accurate parameters for liquid water at ambient conditions, a particularly challenging case for conventional SCC-DFTB. The newly determined parameters significantly improved the structural and dynamical properties of liquid water at the SCC-DFTB level.
- In Situ Parameterization of SCC-DFTB Repulsive Potentials by Iterative Boltzmann Inversion, Mol. Phys., vol. 111, p. 3595, 2013. doi:10.1080/00268976.2013.842011
Understanding the dynamics in water
A number of methodological and technical developments in my wowk were applied to the elucidation of new aspects of the highly complex solvation dynamics in liquid water. Related discussions with Thomas Kühne on his findings led to the following article, which attempts to put the scientific observations and technical developments into a generally understandable form (in German):
- Tetraedrisch, wenn flüssig. Nachr. Chem., vol. 61, p. 1203, 2013. doi:10.1002/nadc.201390399
Dispersion-corrected atom-centered potentials (DCACPs) for the halogens
DCACPs are a recently developed method to cure the failure of DFT methods within the generalised gradient approximation to describe dispersion interactions. We complemented the existing library of DCACP parameters by the halogens and compared the performance of various dispersion corrected DFT methods in reproducing high-level benchmark calculations on weakly bound prototype complexes involving halogen atoms.
See the DCACP page at lcbc.epfl.ch – Research - DCACPs
- Intricacies of Describing Weak Interactions involving Halogen Atoms within Density Functional Theory, J. Chem. Theory Comput., vol. 9, p. 955, 2013. doi:10.1021/ct3007524
- Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation, Chem. Phys., vol. 410, p. 25, 2013. doi:10.1016/j.chemphys.2012.10.008
Classical force fields to study excited states-dynamics
During my master’s thesis (2008) I developed classical force fields for molecular dynamics simulations on coupled electronic states, employing trajectory surface hopping. My supervisors were Kim Baldridge (Zürich University) and Daniele Passerone at the federal institute for material science (EMPA): A Force Field Approach to Photochemical cis-trans Isomerization.
