For a short CV and my publication list see my ORCID page
Using atomistic simulations, my research interests are directed to understanding the properties of soft matter, in particular those of peptides and proteins. My work concentrates on the calculation of free energy differences based on molecular dynamics simulations. My current focus is on the calculation of absolute binding free energies and the application of free energy simulations in systems fully described by neural network potential (NNP).
The motivation driving my research are threefold. First, I develop novel and/or optimize existing methods. My second aim is to complement experimental work and to aid in the interpretation of experimental data by the microscopic view made possible by computer simulation. Third, the results should help elucidate questions relevant to chemistry and/or biology. Worfklows we develop should be suitable for applied research.
News
I recently revisited my older work on absolute binding free energies (ABFE), which underlies all current large-scale ABFE workflows. Together with a team from Exscientia/Recursion, this has resulted in an industrial-strength ABFE workflow. You can find the details in this JCTC publication.
Yes, one can calculate alchemical free energy differences directly using an all NNP description of systems! Keep in mind though that condensed phase properties obtained from transferable NNPs are currently poor (see the preprint of the manuscript under review at JCIM.
Martin Karplus, my thesis advisor, passed away peacefully on December 28, 2024. Thank you, Martin,
for being my scientific mentor. Like many fellow Karplusians, I have asked myself more than once: How
would Martin approach this question? As we kept in touch over the years, I came to a
appreciate you as a man of many facets who was truly a role model, both as a scientist and
as a fellow human being.
The German version of Martin's Nobel lecture, translated by me
for Angewandte
Chemie, can be accessed here. I also was the scientific editor of his scientific autobiography, Martin Karplus, Facetten meines Lebens. My obituary can be found here.
CHARMM turned 45 and the developers celebrated with the third CHARMM publiction.
Our recent two publications describing indirect free energy simulations reweigthing to the NNP/MM level of theory, gas phase and solvation free energies, show what can and yet cannot be achieved by NNP/MM.
Here are the slides of my talk "Have Alchemical Free Energy Simulations Come of Age?" held at the ACS Spring conference 2024, New Orleans.
Congratulations and a big thank you to all who contributed / are contributing to transformato. The proof of concept paper is here; we have applied transformato to relative binding and absolute solvation free energy studies. I presented our work at the 2024 Workshop on Free Energy Methods in Drug Design; the recording is available on youtube. The meeting also featured the insightful keynote presentation by Max Welling, Free Energy is all you need.
Links to older news and activities
Slides from my presentation at the EUROPIN Summer School on Drug Design - Vienna (2021) are available here. Note that text in blue is clickable links which should take you to the original references. As mentioned in my talk, mail me questions which may arise and were not answered.
Just back from the 2021 CECAM CHARMM-GUI school in Toulouse. All slides and recordings of the lectures are publically available (click on 'Documents'!).
Our manuscript on the correct treatment of dummy atoms in free energy simulations, on occasion referred to as "Dummy atoms for Dummies", has been published.
With a grave heart, I mourn the passing away of my colleague and friend, Walther Schmid --- RIP!
Organization of the 2015 "CHARMM meeting" in Vienna (July 17-19, 2015)
