Multiscale Simulations on Biological Energy Catalysis

SNIC 2020/1-38


SNIC Large Compute

Principal Investigator:

Ville Kaila


Stockholms universitet

Start Date:


End Date:


Primary Classification:

10602: Biochemistry and Molecular Biology

Secondary Classification:

10603: Biophysics

Tertiary Classification:

10407: Theoretical Chemistry



The molecular basis of life is established by a complex membrane-bound protein machinery that efficiently captures and converts chemical and light energy and transduces this into other energy forms. The continued SNIC project aims to elucidate molecular principles of proteins that catalyze chemical and light-driven energy transduction in aerobic cell respiration and photosynthesis. We tackle these principles by integrating state-of-the-art computational multi-scale simulations that ranges from classical and coarse-grained simulations to hybrid quantum/classical (QM/MM) approaches (DFT and correlated ab initio) to obtain a detailed understanding of the structure, energetics, and dynamics of the proteins on a broad range of timescales and spatial resolutions. The molecular simulations are further integrated and validated by cryo-electron microscopy (cryo-EM) and biophysical experiments. The project aims to link the molecular structure and dynamics with the biological function and, based on these, derive a molecular understanding on how enzymes generate electrochemical energy across biological membranes. The projects studied here focus on 1) mechanisms of long-range proton-electron transport in the complex I superfamily; 2) the functional role of membrane-bound supercomplexes; and 3) the functional dynamics of light-driven energy conversion in photosystem II at the far-red light limit. This computational consortium involves around 20 researchers (one professor, one visiting professors, a staff scientist, four post-doctoral fellows, 9 PhD students, and six students) in projects that are supported by the ERC and the KAW foundation.