UCSD - University of California - San Diego

01/15/2026 | Press release | Distributed by Public on 01/15/2026 10:22

By Building Virtual Cells, Researchers Aim to Design Better Microbes and Drugs

Published Date

January 15, 2026

Article Content

With new funding provided by prime contractor CFD Research Corporation as part of a new Defense Advanced Research Projects Agency (DARPA) program, bioengineers at the University of California San Diego Jacobs School of Engineering are taking computational biology to the next level: creating comprehensive digital twins of bacterial cells and putting them to practical use. These virtual microbes will be used to understand more about how to engineer strains that can sustainably produce valuable chemicals, as well as understand the effects of antibiotics in order to combat drug-resistant bacteria.

The $4.1 million project, led by CFD Research Corporation and involving researchers at the UC San Diego Future Biomanufacturing Center, is part of DARPA's Simulating Microbial Systems program. The effort aims to build, test and apply a whole cell model of Escherichia coli, the workhorse of biology labs and biomanufacturing worldwide. Unlike conventional simulations that capture only fragments of a cell's activity, a whole cell model integrates every known cellular process into a single, comprehensive framework.

The result, explained Daniel Zielinski, a project scientist in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering, is a digital twin of life at the microbial scale - a companion computational simulation that is capable of predicting how an actual bacterium behaves under different conditions. "Whole cell models are a sophisticated type of digital twin in that they capture all cellular processes," Zielinski said. "They could be used to understand and improve these processes."

Zielinski is one of the researchers working on the project with Bernhard Palsson, Y.C. Fung Endowed Chair in Bioengineering and professor in the Shu Chien-Gene Lay Department of Bioengineering at UC San Diego. Palsson, a pioneer of large-scale cell simulation, is leading the academic side of the project, while CFD Research Corporation contributes industrial expertise in advanced engineering simulations. Together, the team aims to transform whole cell modeling from a theoretical possibility into a practical tool.

"Until now, researchers have demonstrated that such models are feasible, but none have been applied to solve real-world problems," Zielinski said. "This will be the first such effort."

As a proof of concept, the team will pursue two applications of their whole cell model. First, they will design an E. coli strain that can produce valuable chemicals from plant biomass byproducts. This approach could lead to renewable chemical manufacturing processes. Second, they will use the model to predict how E. coli responds to antibiotics. Their goal is to combat antibiotic resistance and guide the design of new drugs.

Being able to run those experiments entirely in silico could significantly cut the time and cost of discovery. "The dream is to design better antibiotics all within a computer," Zielinski said.

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