Eric Schulze-Niemand successfully defended his PhD thesis
Research focused on limitations and changes in molecular dynamics simulations
Eric Schulze-Niemand, one of our IMPRS doctoral researchers, successfully defended his PhD thesis on June 27, 2022. He joined the IMPRS in June 2015 and worked in the Group “Molecular Simulations and Design” of Prof. Stein. The title of his thesis is “Molecular Recognition and Selectivity: Computational Investigations on the Dynamics of Non-bonded Interactions”.
Non-covalent interactions give molecules their three-dimensional structure. However, molecules are very flexible under standard conditions and often exist as an ensemble of many different 3D structures (conformations).
Molecular dynamics (MD) simulation is a theoretical method to predict the motion of atoms in molecules. With suitable high-performance computers and a clever choice of simulation parameters, the movement of biological macromolecules such as proteins can be simulated over such long periods of time that the transitions between different conformations become visible. MD can thus be used to identify initially unknown states of molecules and to predict their probability (energy) as well as the energy barrier between the states.
In this work, they have developed optimal protocols for the simulation and evaluation of different types of molecular systems. They combined concepts from the fields of dynamical systems, statistical thermodynamics, and machine learning. That way, they have found out, for example, that sugar chains are not completely flexible but switch between hundreds of distinct states, or that a bacterial enzyme is only activated when it encounters a specific human protein that is only produced during inflammation.
The findings help to better understand the limitations of MD methodology and vividly demonstrate how minute changes at the atomic and molecular level can propagate into drastic differences in the properties of cells and materials.
Congratulations on your successful defence and we wish you all the best!