THESES

PhD Theses

Molecular dynamics and interactions of murine guanylate binding proteins and a bacterial dynamin like protein
PhD thesis, Wibke Schumann, Heinrich Heine University Düsseldorf, 2023.

Network Models and Structural Characteristics of Oligomer Formation of Amyloid-β Peptides and Huntingtin Proteins Based on Microsecond Timescale Molecular Dynamics Simulations
PhD thesis, Mohammed Khaled, Heinrich Heine University Düsseldorf, 2023.

Computer simulations of amyloid aggregation considering in vivo conditions
PhD thesis, Hebah Fatafta, Heinrich Heine University Düsseldorf, 2022.

Understanding the aggregation of sickle hemoglobin (HbS) and identification of HbS aggregation inhibitors
PhD thesis, Maryam Olangunju, Heinrich Heine University Düsseldorf, 2022.

The effects of dimerization and membrane binding on protein dynamics: the cases of GABARAP and guanylate binding proteins
PhD thesis, Xue Wang, 2022.

Essays on the interplay between glycosaminoglycans and amyloid-β peptides
PhD thesis, Suman Samantha, RWTH Aachen, 2021.

Computational enzyme evolution and design: studies of protein dynamics and substrate binding
PhD thesis, Dusan Petrovic, Heinrich Heine University Düsseldorf, 2018.

On the combined power of simulation and experiment to model protein structure, dynamics, function and assembly mechanisms.
PhD thesis, Oliver Schillinger, Heinrich Heine University Düsseldorf, 2017.

Atomistic simulations of amyloidogenic peptides and their aggregation.
PhD thesis, Martin Carballo Pacheco, RWTH Aachen, 2017.

Application of coarse grained force fields for protein-protein docking.
PhD thesis, Philipp Kynast, Heinrich Heine University Düsseldorf, 2016.

Role of Cu2+ in the conformational transitions and dimerization of amyloid-β peptide and its implications in Alzheimer’s disease
PhD thesis, Qinghua Liao, Heinrich Heine University Düsseldorf, 2016.

Protein structure prediction using global optimization by basin-hopping.
PhD thesis, Falk Hoffmann, Heinrich Heine University Düsseldorf, 2014.

Interaction of amyloid peptides with biomembranes and its implications in Alzheimer’s disease and type II diabetes.
PhD thesis, Chetan Poojari, Heinrich Heine University Düsseldorf, 2013.

Investigation of the interaction between Alzheimer’s Abeta peptide and aggregation inhibitors using molecular simulations.
PhD thesis, Olujide O. Olubiyi, RWTH Aachen, 2013.

Master Theses

Engineering of an organic solvent-tolerant esterase by modifying surface charges following simulation-based predictions
MSc thesis, Lara Scharbert, Heinrich Heine University Düsseldorf, 2021

Simulation study of the interaction of synthetic peptides with an amyloid-β fibril
MSc thesis, Monika Keutmann, Heinrich Heine University Düsseldorf, 2020.

Comparison of Transition Networks and Markov State Models for Describing Peptide Dynamics and Aggregation
MSc thesis, Alexander-Marice Illig, RWTH Aachen University, 2020.

Computational analyses towards the mechanism behind resistance to organic solvent and sodium dodecyl sulfate of a novel esterase
MSc thesis, Anna Jäckering, University of Cologne, 2020.

A Molecular Dynamics Study of the Early Steps of Functional CsgA Amyloid Formation
MSc thesis, Wibke Schumann, Heinrich Heine University Düsseldorf, 2019.

Building Markov state models and hidden Markov models from molecular dynamics data of the amyloid-beta peptide
MSc thesis, Marco Anteghini, University of Bologna (Italy), 2019.

Automated Markov state models for macromolecular simulations
MSc thesis, Ushnish Sengupta, RWTH Aachen University, 2018.

Characterizing the dynamics of the murine guanylate binding protein 2 by molecular modeling
MSc thesis, Matthias Henzgen, Heinrich Heine University Düsseldorf, 2015.

Membrane perturbation by the antimicrobial peptide [KIGAKI]3: a simulation study
MSc thesis, Marianne Schulte, Heinrich Heine University Düsseldorf, 2014.

Protein Structure and Dynamics of Bacillus Subtilis Lipase LipA Fused to the Ligand-Binding Domain of Sensor Histidine Kinase CitA.
MSc thesis, Oliver Schillinger, RWTH Aachen University, 2013.

Extension of the FACTS implicit solvation model to membranes.
MSc thesis, Martin Carballo Pacheco, RWTH Aachen University, 2013.

Comparison of force fields to test the membrane adsorption of the amyloid-like [KIGAKI]3peptide.
MSc thesis, Nam Bao Hoang, RWTH Aachen University, 2013.

Driving Forces Of Amyloid Aggregation: Database Analysis, Coarse-Grained and All Atom Simulations.
MSc thesis, Purbaj Pant, University of Bonn, 2012.

Membrane adsorption and insertion of the amyloid-β peptide: a coarse-grained simulation study.
MSc thesis, Gourav Sansanwal, University of Bonn, 2012.

Exploring the GABARAP dimer using molecular simulations.
MSc thesis, Manoj Rangan, University of Bonn, 2010.

Bachelor Theses

Creation and removal of disulfide bridges in two biotechnologically relevant esterases aided by molecular dynamics simulation
BSc thesis, Georg Jannes Pöppich, Technische Universität Dresden, 2023

Evaluation of various machine learning approaches to predicting enzyme mutation data
BSc thesis, Tilman Hoffbauer, RWTH Aachen University, 2021.

In silico identification of peptide inhibitors of the main protease of SARS-CoV-2
BSc thesis, Anton Bleckert, Heinrich Heine University Düsseldorf, 2021.

In silico identification of inhibitors of α-synuclein amyloid fibril elongation
BSc thesis, Anne Bannemann, Heinrich Heine University Düsseldorf, 2021.

Testing lipid-protein complex formation for Alzheimer’s peptide Aβ42 using molecilar simulations
BSc thesis, Bastian Bundschuh, Heinrich Heine University Düsseldorf, 2020.

Molekulare Simulationen zur Charakterisierung der amyloiden Eigenschaften einer Leichtkette
BSc thesis, Andreas Papadopoulos, Heinrich Heine University Düsseldorf, 2015.

Evaluierung des OPEP coarse-grained Kraftfelds für Protein-Protein-Docking
BSc thesis, Kal Nehlsen, Heinrich Heine University Düsseldorf, 2014.

The effect of Gly radicals on the conformation of Amyloid-β peptide.
BSc thesis, Jennifer Schumann, Heinrich Heine University Düsseldorf, 2014.

Simulationsstudie zur Interaktion von EGCG mit sich selbst und dem Amyloid-beta-Peptid
BSc thesis, Jennifer Loschwitz, Heinrich Heine University Düsseldorf, 2014.

Untersuchung der Aggregation amyloider Peptide mittels molekularer Simulationen
BSc thesis, Ekaterina Ponomareva, Heinrich Heine University Düsseldorf, 2014.

Evaluierung von FACTSMEM bezüglich des Unterscheidungsvermögens für den nativen Zustand von Membranproteinen
BSc thesis, Matthias Henzgen, Heinrich Heine University Düsseldorf, 2014.