Computational Physics and Biophysics

Concerning the quantum dynamics in molecular systems, the group develops and applies a variety of approaches. These schemes range from purely quantum mechanical approaches on model systems to multi-scale approaches in which we derive the parameters for the model systems from atomistic simulations. Examples in this direction, on which the Kleinekathöfer group has focused, are the excitation energy transfer in biological light-harvesting systems and the charge transfer through molecular junctions, i.e., molecules between two leads. 

Over the last few years, the group has also performed various molecular dynamics simulations on proteins in bacterial membranes. We had a special focus on the membrane pores through which antibiotics need to enter bacteria to destroy them. The poor understanding of these permeation processes leads to serious problems in the development of new antibiotics. In close collaboration with the group of Prof. Mathias Winterhalter at Constructor University, we are studying these and other topics in the area of nanopore permeation. Other areas include substrate transport, the electroosmotic flow which pushes neutral substrate through pores, the identification of chiral isomers, and the assembly of transmembrane pores from mirror-image peptides.

• Photosynthesis — Due to the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated in a combined quantum-classical description. We used Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics fashion for the ground state followed by excitation energy calculations. By now, this scheme has been tested for several light-harvesting complexes. The spectral densities, in particular, show an excellent agreement with experimental findings. In addition, we showed that the obtained results for the fluctuating site energies and couplings can be used to estimate the excitation energy transfer dynamics.
• Transport through nanopores — Researchers are using the voltage-dependent transport through biological and artificial nanopores in many applications such as DNA or protein sequencing and sensing. The primary approach to determine the transport has been to measure the temporal ion current fluctuations caused by solutes when applying external voltages. The electroosmotic flow is a voltage-dependent ion-associated flow of water molecules. In a joint study with the Winterhalter group, we have investigated the electroosmotic flow by probing the transport of cyclodextrin molecules through the ΔCymA channel.
• Nanopore sensing — Chirality is essential in nearly all biological organization and chemical reactions but is rarely considered due to technical limitations. Using OmpF, a membrane channel from the bacterium E. coli with an electrostatically asymmetric constriction zone, we were able to determine chiral amino acids in a single peptide. Using a statistical analysis of the respective ion current variations, we were able to distinguish the presence and position of each chiral amino acid.

In 2022, the Computational Physics and Biophysics Group consisted of six PhD students and two postdocs, funded through the German Science Foundation, DFG, the German Academic Exchange Service, DAAD, and the Federal Office for Radiation Protection, BfS. The group is part of the DFG Research Training Group “Quantum Mechanical Materials Modeling” and of the DFG Priority Programme “Molecular Machine Learning”.

• R. S. Krishnan, K. Jana, A. H. Shaji, K. S. Nair, A. D. Das, D. Vikraman, H. Bajaj, U. Kleinekathöfer and K. R. Mahendran, Assembly of Transmembrane Pores from Mirror-Image Peptides, Nat. Commun. 13, 5377 (2022).
• J. Wang, J. D. Prajapati, F. Gao, Y.-L. Ying, U. Kleinekathöfer, M. Winterhalter and Y.-T. Long, Identification of Single Amino Acid Chiral and Positional Isomers Using an Electrostatically Asymmetric Nanopore, J. Am. Chem. Soc. 144, 15 072–15 078 (2022).
• P. Sarngadharan, S. Maity, U. Kleinekathöfer, Spectral Densities and Absorption Spectra of the Antenna Complex CP43 from Photosystem II, J. Chem. Phys. 156, 215 101 (2022).
• J. D. Prajapati, S. Pangeni, M. A. Aksoyoglu, M. Winterhalter and U. Kleinekathöfer, Changes in Salt Concentration Modify the Translocation of Neutral Molecules through a ΔCymA Nanopore in a Non-Monotonic Manne r, ACS Nano 16, 7701–7712 (2022).
• L. Mejía, U. Kleinekathöfer and I. Franco, Coherent and Incoherent Contributions to Molecular Electron Transport, J. Chem. Phys. 156, 094 302 (2022).