Simulation and analysis of the cell nucleus
Code for molecular dynamics simulations of the whole cell nucleus, including chromatin, actin, RNA binding proteins and transcription (“WholeNucleusProject”): https://github.com/ezingrebe/WholeNucleusProject/
Analysis code for genome wide transposon insertion patterns: https://github.com/aaron-gad/Transposon_Clustering. Code for molecular dynamics simulations of chromatin unfolding and transposon insertion: https://zenodo.org/records/14788016. Both used in Prizak et al Biophysical Journal, 2025.
Molecular Dynamics Simulations of Enhancer-Promoter Interactions in a Model Shoe Box, repository with ongoing code development: https://github.com/lhilbert/EnhancerShoeBox
Simulation and analysis of synthetic DNA systems
Code to run and evaluate DNA nanomotif simulations using oxDNA or ReaDDy and to carry out Bayesian parameter optimization with BoTorch: https://github.com/aaron-gad/DNA_Nanomotif_ML_MD. Used in Gadzekpo et al. Advanced Functional Materials, 2025
Code to run and evaluate coarse-grained molecular dynamics simulations of phase separation and of surface condensation on polymer strands: https://github.com/aaron-gad/Condensate_BD_Sim. Used in Hilbert et al. Annals of the New York Academy of Sciences, 2025
Image analysis
MatLab scripts to segment and analyse polymerase clusters in 3D microscopy image stacks: https://github.com/lhilbert/NuclearObjects_ImageAnalysis
Scripts for the interactive choice and fine-tuning of image segmentation algorithms, as shown in Hajiabadi et al. Journal of Systems and Software, 2024: https://doi.org/10.5281/zenodo.10687188
3D-printing
3D-printing model for a stamp to create imaging wells in agarose for the microscopy of zebrafish embryos https://doi.org/10.5281/zenodo.10797918
Videos
Video of a developing one-cell-stage to 21-somite-stage development of a zebrafish embryo: https://doi.org/10.5281/zenodo.12547356
Teaching
Lecture Notes “Basics of Image Processing, using Cell Profiler”, view-only link for Overleaf: https://www.overleaf.com/read/gsnnthgrtwhf#73dfb7
Overleaf template for Bachelor and Master theses: https://www.overleaf.com/read/qtyvbxjkwnzp#46450b