Multiscale Simulations on Biological Energy Catalysis

NAISS 2024/1-28


NAISS 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 chemical and light energy and transduces this into other energy forms. This NAISS project is a continuation of our 2023 Large Computing project in which we studied molecular principles of proteins that catalyze chemical and light-driven energy transduction in cellular respiration and photosynthesis, with exciting results from the last funding round. We tackle these systems by multi-scale simulations that range from hybrid quantum/classical (QM/MM) approaches to classical atomistic and coarse-grained simulations to obtain a detailed understanding of the structure, energetics, and dynamics of these proteins on a broad range of timescales and spatial resolutions. The simulations are further integrated and validated by biochemical, biophysical, and structural experiments. The project aims to link the molecular structure and dynamics with the biological function and, based on these, derive a molecular understanding of how enzymes generate electrochemical energy gradients across biological membranes. Our work focuses on 1) mechanisms of long-range redox-coupled proton/ion-transport in the Complex I superfamily; 2) the functional role of membrane-bound supercomplexes; 3) the functional dynamics of light-driven ion pumps and photosynthesis, and 4) principles of charge transfer reactions in biocatalysis. This computational consortium involves around 20 researchers (one professor, one staff scientist, 4 post-doctoral fellows, 8 PhD students, 3 master students, and several external collaborators) currently supported by the KAW foundation, VR, and the collaborative research center SFB1078 (Berlin).