Simulated Photosynthesis

The model of the chromatophore is spherically round, scientists used computers with an enormous capacity to develop it. The simulation behaves in exactly the same way as its counterpart in nature. (Source: C. Maffeo, U. Illinois)

The conversion of sunlight into chemical energy is essential for life. In one of the largest simulations of a biosystem worldwide, scientists have mimicked his complex process for a component of a bacterium atom by atom. The work is an important step towards a better under­standing of photo­synthesis in some biological structures. Headed by the University of Illinois, a team from Jacobs University Bremen was also involved in the inter­national research coopera­tion.

The project was initiated by Klaus Schulten from the University of Illinois, who researched the under­standing and repre­sentation of atomic inter­actions of living systems. His research group modeled the chromato­phore, a light-absorbing part of a cell that releases chemical energy in the form of a ATP-molecule. These chromato­phores are found in plant cells as well as in some bacteria. “They act like a solar cell of the cell. With their antenna complexes, they absorb light and release energy in the form of ATP for all other cell acti­vities,” says Ulrich Kleine­kathöfer. The professor of theoretical physics at Jacobs Uni­versity worked on the project together with his doctoral student Ilaria Mallus. Based on the data of their American colleagues, they performed quantum mechanical calcu­lations for the model.

To find out how this system works, the inter­national research group dissected the chromato­phore with every tool available to science, from labora­tory experiments over atomic force micro­scopy to software innovations. All parts were reassembled in the 136 million atom model, which behaves like its counterpart in nature. This was only possible with the help of enormously powerful supercomputers. “Standard simu­lations work with about 100,000 atoms, this model is 1,000 times larger, it is an advance into new dimensions,” says Kleine­kathöfer.

So far, researchers have usually only been able to simulate indi­vidual proteins. The model shows the interplay of very many proteins along the entire process chain, from light absorption to the production of ATP.  “At some point, we will be able to simulate an entire bacterium or cell,” believes Kleine­kathöfer. “This is an important step towards this goal.” (Source: Jacobs U. Bremen)

Reference: A. Singharoy et al.: Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism, Cell 179, 1098 (2019); DOI: 10.1016/j.cell.2019.10.021

Links: Computational Physics and Biophysics Group (U. Kleinkathöfer), Jacobs University Bremen, Bremen, Germany • Dept. of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, USA

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