Multiscale Simulations on Biological Energy Catalysis
Title: Multiscale Simulations on Biological Energy Catalysis
SNIC Project: SNIC 2019/2-3
Project Type: SNIC Large Compute
Principal Investigator: Ville Kaila <>
Affiliation: Stockholms universitet
Duration: 2020-01-01 – 2020-07-01
Classification: 10602 10603 10407


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 aim of this project is to elucidate molecular principles of proteins catalyzing 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) and free energy methods 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, catalyzed by a chemical or light-triggered reaction in the active center of the proteins. 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, two visiting professors, a staff scientist, four post-doctoral fellows, 8 PhD students, and two students) in projects that are supported by the ERC and the KAW foundation.