Department of Applied Physics
KTH Royal Institute of Technology
anton.jansen@scilifelab.se
Project:
During my PhD in Stockholm, Sweden, I have helped to implement a constant-pH molecular dynamics (CpHMD) algorithm in GROMACS. Furthermore, I have developed a tool that automates the set up process of such simulations, and I have applied our novel CpHMD implementation to study proton-dependent conformational states of the GLIC and sTeLIC ligand-gated ion channels (in collaboration with the Lindahl group at KTH).
Publications:
- Ida Ygland, Anton Jansen, Emelia Karlsson, Erik Lindahl, Rebecca Howard, Berk Hess, Molecular Dynamics of an Alkaline-Gated Ion Channel Using Constant-pH Simulations (preprint).
- Anton Jansen, Paul Bauer, Rebecca Howard, Berk Hess, Erik Lindahl, Constant-pH MD simulations of progressive activation in a proton-gated ion channel (preprint).
- Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess, phbuilder: A Tool for Efficiently Setting up Constant pH MD Simulations in GROMACS, JCIM, 2024.
- Pavel Buslaev, Noora Aho, Anton Jansen, Paul Bauer, Berk Hess, Gerrit Groenhof, Best Practices in Constant pH MD Simulations: Accuracy and Sampling, JCTC, 2022.
- Noora Aho, Pavel Buslaev, Anton Jansen, Paul Bauer, Gerrit Groenhof, Berk Hess, Scalable Constant pH Molecular Dynamics in GROMACS, JCTC, 2022.
Also:
- Invited speaker at the 2023 Advanced Methods in MD conference in Copenhagen.
- Awarded poster prize at the 2023 European Biophysics Conference (EBSA).
- Platform speaker at the 2022 Biophysical Society in San Francisco.
- Supervised a master student on a constant-pH MD project.
- Authored a Python package for setting up constant-pH MD simulations.
- Teaching assistant (2x) for the Simulation and Modeling course at KTH.
Other experience:
- Teaching assistant (5x bachelor courses), University of Groningen (2015-2019).
- Chairman of the Board, study association for Engineering Physics, UG (2016-2017).
Education:
- MSc Physics (cum laude), University of Groningen (2020).
- Honours College, University of Groningen (2019).
- BSc Physics, University of Groningen (2017).
Profiles:
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