Daniel Nagel

@braniii

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, 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.

prettypyplot

#creator

a wrapper for creating easily beautiful matplotlib figures

#python #matplotlib

msmhelper

#creator

a time sequence analysis tool for employing Markov state models

#python #markovchain #numba #dataanalysis

MoSAIC

#creator

a correlation-based feature selection method

#python #feature-selection #ml

ameixa

#maintainer

a minimalistic Material Design inspired icon pack for android

#icontheme #android

dcTMD

#co-creator

analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations

#python #targetedMD #dcTMD

MSMPathfinder

#creator

a cpp proof-of-concept implementation of pathway-analysis of Markov state models

#cpp #dataanalysis

robust density clustering

#maintainer

a cpp framework providing an density-based clustering algorithm including helpful tools

#cpp #clustering