PNNL-QCB collaboration produces first 4D whole-cell model of a photosynthetic microbe
October 22, 2026
Researchers at Pacific Northwest National Laboratory teamed up with QCB scientists to create the first 4D whole-cell model of how a photosynthetic microbe responds to changing light.
The model by Margaret Cheung’s team at PNNL used the Lattice Microbes simulation software developed by QCB Director Zaida (Zan) Luthey-Schulten’s group to build a four-dimensional model—three-dimensional space plus time—of Prochlorococcus marinus MED4. The team combined detailed cellular images with measurements of molecular changes to investigate how the bacterium regulates carbon fixation, the process of incorporating carbon dioxide into organic molecules.
The model revealed how the cell’s internal organization and the assembly and disassembly of protein complexes help regulate this process as light conditions change. Published in Biophysical Journal, the research demonstrates how whole-cell modeling can connect molecular interactions to cellular behavior, extending the reach of QCB’s computational tools to photosynthetic organisms.
According to PNNL, “this model gives researchers a new way to examine how cell structure, gene activity, proteins, and metabolism work together over time. It showed that small cellular components can adjust cell activity as light conditions change. This knowledge could inspire biotechnology and biomanufacturing approaches that use microbes to produce fuels, chemicals, materials, and other products. The detailed cell maps may also inform research that requires precise control of biological components. For example, it could be relevant for potential quantum technology applications. Lastly, the multiomics data used by the researchers show gene and protein activity over time. These data provide a resource for building and testing other models that could lead to new discoveries.”
Image caption: A computer model of the photosynthetic marine microbe Prochlorococcus marinus MED4, built using detailed three-dimensional microscopy images and a modeled arrangement of its DNA. This reconstruction provides the starting point for simulations that help researchers understand how the cell’s internal organization influences its response to changing light.