Amir Kotobi

Building 25B
22607 Hamburg
Room: 033



Dynamic Protein Pattern Recognition in Free-Electron Laser Experiments
Supervisors: Prof. Sadia Bari (DESY), Prof. Robert Meißner (TUHH, Hereon)

Amir obtained his bachelor's degree in 2017 at University of Tehran and his master's degree at Technical University of Munich and Ludwig Maximilian University of Munich in 2019 in materials science for large-scale facilities, with a thesis project at the department of physics at Technical University of Munich. His master thesis research was focused on exploring semiconductor polymers for photovoltaic applications with scattering techniques namely GISAXS and GIWAXS.
The main goal of his PhD project is to gain information about the structure of peptides and proteins and their dynamics with a combination of x-ray scattering and x-ray spectroscopy methods as well as advanced molecular dynamics (MD) simulation. In addition to experimental techniques, machine learning approaches will be implemented in order to get information about the conformational space of the proteins. For instance, pattern recognition algorithms combined with X-ray experiments will be implemented for identification of energetically stable patterns in the conformational space of firstly small peptides. Moreover, charge dynamics involved in small peptides and proteins is of further interest. In this regard, peptides which have sulfur-containing amino acids will be utilized in order to investigate the processes following a localized excitation (e.g. in sulfur or aromatic side chain). For the study of these processes, gas-phase photoionization of these biomolecules will be carried out with the utilization of tandem mass-spectrometers, based on electrospray ionization (ESI) sources and radio-frequency ion traps, with free-electron laser (FEL) and synchrotron beamlines in both the VUV and soft X-ray energy regimes.

Watch Amir explaining his project at the HIDA Annual Conference 2021 here.