A team of researchers has succeeded in simulating the complete life cycle of a living cell for the first time on a computer – from DNA replication to cell division. The detailed model makes it possible to track the behavior of thousands of molecules inside the cell in real time and simultaneously examine many biological processes.
A team of researchers has succeeded in simulating the complete life cycle of a living cell for the first time on a computer – from DNA replication to cell division. The detailed model makes it possible to track the behavior of thousands of molecules inside the cell in real time and examine many biological processes simultaneously.
Researchers at the University of Illinois at Urbana-Champaign have successfully simulated the life cycle of a basic bacterial cell—from DNA replication to protein translation and metabolism to cell division. The work opens a new window into understanding the fundamental processes of life at unprecedented resolution.
The study, led by Prof. Zan Luthey-Schulten from the university's Department of Chemistry, was published in the journal Cell.
This required years of work, vast computing resources, large experimental data sets, and a combination of advanced experimental and computational methods. The researchers had to take into account every gene, protein, RNA molecule, and chemical reaction that occurs in a cell to reproduce the precise timing of cellular events. For example, the model had to accurately reflect the process by which a cell doubles in size before dividing.
To make the task more feasible, the researchers used a “minimal” living cell developed at the J. Craig Venter Institute in California. The cell chosen for the study, JCVI-syn3A, or Syn3A for short, is a bacterium that has been genetically engineered so that its genome includes only the genes necessary for life – DNA replication, growth, division and most basic biological functions.
According to Lotay-Schulten:
“This is a fully dynamic 3D model of a living cell with only essential functions, mimicking what happens in a real cell. Such a comprehensive project was only possible thanks to a broad collaboration between researchers at the University of Illinois and Harvard Medical School.”
The Syn3A cell has fewer than 500 genes, all of which are located on a single circular strand of DNA. The laboratories of researchers Angad Mehta of the University of Illinois and Taekjip Ha of Boston Children's Hospital and Harvard Medical School provided additional experimental data that allowed the simulation to be refined and various aspects of the cell's activity to be verified.
According to Lotei-Schulten, these data allowed for a better understanding of the extent of DNA replication and the fact that Syn3A cell division is symmetrical.
The simulations themselves were performed by Zane Thornburg, a postdoctoral fellow at the Beckman Institute for Advanced Science and Technology, and Andrew Maytin, a graduate student in Lotay-Schulten's lab.
Like other bacteria, the Syn3A cell does not have a nucleus. All of the molecules that make up it are located in the cytoplasm, in the outer membrane, or arrive from the outside through transport mechanisms. The cell is so densely packed with molecules that when the researchers created high-resolution images of the simulation, they had to hide some of the components to allow other structures to be seen. For example, when they “hidden” the proteins from the simulation, it was possible to see how the chromosome tangled up within the dense cell space.
The researchers discovered that some processes in the cell require much more computational power than others. For example, chromosome replication significantly slowed down the simulation, nearly doubling the computational time. The solution was to assign a dedicated graphics processing unit (GPU) to DNA replication, while another GPU handled all other cellular processes. This allowed the team to simulate a complete 105-minute cell cycle in just six days of computing time.
According to Thornburg, one of the biggest challenges was to simulate processes that occur simultaneously in different areas of the cell.
“You can’t overstate the difficulty of simulating things that are constantly moving – and doing it in 3D for a whole cell was a major achievement,” he said. “One of the final challenges that Andrew and I had to solve was understanding how the membrane and DNA interact with each other when they are both in motion.”
Although the model does not simulate each individual atom but uses average values for molecular dynamics, it was able to reproduce the timing of cellular processes quite accurately. In repeated simulations of cells with slightly different starting conditions, the simulated cell cycle occurred on average only about two minutes later than the real cycle. Throughout, the simulations were checked against real experimental data, which allowed the model to be gradually improved.
Lutey-Schulten says that the ability to accurately simulate the changing conditions inside a living cell opens up new research possibilities.
“We have a whole-cell model that predicts many cellular properties at once,” she said. “If you want to know what’s happening in nucleotide metabolism, for example, you can also see what’s happening in DNA replication or ribosome formation. That means the simulation can provide results from hundreds of experiments at once.”
The study's authors also include University of Illinois graduates Benjamin Gilbert and John Glass, who leads the synthetic biology group at the J. Craig Venter Institute.
The research was carried out within the framework of the National Science Foundation's (NSF) Quantitative Cell Biology Science and Technology Center. The calculations were conducted using the advanced computing system: Delta, operated in collaboration with the University of Illinois and the National Center for Supercomputing Applications.
the article:
"Bringing the genetically minimal cell to life on a computer in 4D"
Journal: Cell
DOI: 10.1016/j.cell.2026.02.009
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One response
This is an achievement, but it seems to me that in the not-so-distant future it will be dwarfed by what AI will do in this regard with AlphaCell or something similar.
I feel a bit like I read that there is a new version of Deep Blue with an ELO rating of 3500.