Hi there👋,
I am a physics Ph.D. student in my final year at Moldyn Freiburg. In the field of analysing and modeling of MD protein simulation🧬🔬💻, my research focuses on Markov state modeling of fast folding peptides. Unlike most existing approaches, I focus not only on identifying metastable states, but also that they are of biochemical relevance.
Otherwise, I am a big fan and advocate of open-source software. Besides a few scientific Python packages and C++ programs, I always try to challenge myself with other programming languages. Since 2018, I am the maintainer of ameixa one of the most popular FOSS Android icon themes. My newest language is Dart/Flutter where I will soon release my first own app. So stay tuned.
publications 📚
You can also check out my google scholar for an up-to-date list.
D. Nagel, G. Diez, and G. Stock, Accurate estimation of the normalized mutual information of multidimensional data, J. Chem. Phys., 161, 054108, 2024
D. Nagel, S. Sartore, and G. Stock, Towards a Benchmark for Markov State Models: The Folding of HP35, J. Phys. Chem. Lett, 14, 31, 2023
D. Nagel and G. Stock, msmhelper: A Python package for Markov state modeling of protein dynamics, J. Open Source Soft., 8, 5339, 2023
D. Nagel, S. Sartore, and G. Stock, Selecting Features for Markov Modeling: A Case Study on HP35, J. Chem. Theory Comput., 19, 3391, 2023
G. Diez, D. Nagel, and G. Stock, Correlation-Based Feature Selection to Identify Functional Dynamics in Proteins, J. Chem. Theory Comput., 18, 5079, 2022
D. Nagel, A. Weber, and G. Stock, MSMPathfinder: Identification of Pathways in Markov State Models, J. Chem. Theory Comput., 16, 7874, 2020
D. Nagel, A. Weber, B. Lickert, and G. Stock, Dynamical coring of Markov state models, J. Chem. Phys., 150, 094111, 2019
software 💿
The following list is not complete. Please refer to my Github/Gitlab pages for more details.
a wrapper for creating easily beautiful matplotlib figures
#python #matplotlib
a time sequence analysis tool for employing Markov state models
#python #markovchain #numba #dataanalysis
a generalized Kraskov estimator for estimating normalized MI
#python #dataanalysis #ml
2023 © Daniel Nagel