Work

Lattice Microbe: Prochlorococcus Whole-Cell Model Integration Workflow

Year: 2025

Type: book

Abstract: For simulation of a Prochlorococcus marinus MED4 (CCMP1986) cell under various light conditions. Can be extended to simulate a whole cell model for a target organism under different environment perturbations or stress conditions. Key Features Simulates the 4D intracellular environment of Prochlorococcus marinus MED4, a minimal photoautotroph. Simulations include: Cell boundary, thylakoid, ribosomes, DNA. Genome-scale metabolism. Spatially resolved transcription (including RNAP-DNA binding), translation (including mRNA-ribosome binding), and protein diffusion for 15 key genes. Light-driven post-translational modification of key CBC enzyme that controls formation of the "dark complex" and initiation/cessation of carbon fixation. Funding Acknowledgements The source code described was supported by the Pacific Northwest National Laboratory (PNNL) Northwest Biopreparedness Research Virtual Environment (NW-BRaVE) project funded by the U. S. Department of Energy (DOE), Office of Science, Biological and Environmental Research Program, under the award FWP 81832. PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RL01830.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.18025764

Authors: Rozum, Jordan C., Johnson, Connah G., George, August D., Chan, Aaron, Cheung, Margaret S.

Institutions: Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, University of Illinois Urbana-Champaign

Language: enc

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: Biological and Environmental Research

Award: G1230889638