![\"Simulating](\"https:\/\/www.newsbeep.com\/au\/wp-content\/uploads\/2026\/03\/Simulating-A-Living-Cell.png\")
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\n A simulated cell in the early stages of division. Left half shows membrane (green cubes), and ribosomes (yellow\/purple) interwoven through in the cell\u2019s chromosome (red). Right side shows all the proteins (grey) and RNA (orange) inside the cell with a small cutaway to show a second copy of the cell\u2019s chromosome (blue). From Figure 1 of the paper, \u201cBringing the genetically minimal cell to life on a computer in 4D.\u201d Journal: Cell. DOI: 10.1016\/j.cell.2026.02.009 Credit Graphic by Zane Thornburg <\/p>\n
By simulating the life cycle of a minimal bacterial cell \u2014 from DNA replication to protein translation to metabolism and cell division \u2014 scientists have opened a new frontier of computer vision into the essential processes of life.<\/p>\n
The researchers, led by chemistry professor Zan Luthey-Schulten at the University of Illinois Urbana-Champaign, present their findings in the journal Cell. In two videos, researchers describe the work and walk viewers through the simulation of a full cell cycle.<\/p>\n
The team simulated a living cell at nanoscale resolution and recapitulated how every molecule within that cell behaved over the course of a full cell cycle. The work took many years, vast computer resources, large experimental datasets, a suite of experimental and computational techniques and an understanding of the roles, behaviors and physical interactions of thousands of molecular players. The researchers had to account for every gene, protein, RNA molecule and chemical reaction occurring within the cell to recreate the timing of cellular events. For example, their model had to accurately reflect the processes that allow the cell to double in size prior to cell division.<\/p>\n<\/p>\n
First-ever whole cell 4D simulation shows everything everywhere all at once \u2013 Illinois researchers discuss their first-ever whole cell simulation of a living cell in four dimensions. The simulation represents the entire life cycle of the JCVI-syn3A minimal bacteria as it grows and divides over its two-hour life cycle.<\/p>\n
To make the task more manageable, the team used a living \u201cminimal cell\u201d developed at the J. Craig Venter Institute in California. The version of the cell used in the new study, JCVI-syn3A \u2014 \u201cSyn3A\u201d for short \u2014 is a modified bacterium with a pared-down genome that carries only the genes needed to replicate its DNA, grow, divide and perform most of the other functions that make life possible.<\/p>\n
\u201cThis is a three-dimensional, fully dynamic kinetic model of a living minimal cell that mimics what goes on in the actual cell,\u201d Luthey-Schulten said. \u201cSuch a comprehensive undertaking was only possible through the combined efforts of a host of collaborators at the U. of I. as well as Harvard Medical School, where we systematically modeled the essential metabolism and other subcellular networks through a series of publications starting in 2018.\u201d<\/p>\n
The Syn3A cell has fewer than 500 genes, all of which reside on a single circular strand of DNA. The laboratories of study co-authors Angad Mehta, a professor of chemistry at the U. of I., and Taekjip Ha, of Boston Children\u2019s Hospital and Harvard Medical School, generated additional experimental data that allowed the team to accurately simulate and validate numerous aspects of cell function.<\/p>\n
\u201cMost importantly, their work revealed the extent of DNA replication and that Syn3A\u2019s cell division is symmetrical,\u201d Luthey-Schulten said.<\/p>\n
Both factors guided and validated the simulations performed by Zane Thornburg, a postdoctoral fellow at the Beckman Institute for Advanced Science and Technology and the Cancer Center at Illinois, and Andrew Maytin, a graduate student in Luthey-Schulten\u2019s lab.<\/p>\n
Like other bacterial cells, Syn3A has no nucleus. Every molecule that comprises and sustains it is either a component of its outer membrane, is transported into it from outside the cell or is assembled in the cytoplasm. The cell is so jam-packed with molecular players that, when creating high-resolution cartoons and animations of their computer simulations, the researchers had to render some of the components invisible. Making all the cellular proteins invisible, for example, allowed the scientists to see how Syn3A\u2019s chromosome threads through the cell\u2019s crowded interior.<\/p>\n<\/p>\n
A simulation of the entire cell life cycle of the JCVI-syn3A minimal bacterial cell. This is the first 4D whole-cell model of a complete cell life cycle.<\/p>\n
Some processes were more computationally expensive than others, the team discovered. For example, Maytin realized that chromosome replication was slowing the whole simulation to a crawl, nearly doubling the time it took to capture the whole cell cycle. He determined that efficiently simulating the cell\u2019s DNA replication process required its own dedicated graphics processing unit, while another GPU handled all other cellular dynamics. This allowed the team to simulate the full, 105-minute cell cycle in just six days of computer time.<\/p>\n
Thornburg and Maytin struggled with the challenge of simulating cellular events occurring at the same time in various parts of the cell.<\/p>\n
\u201cI can\u2019t overstate how hard it is to simulate things that are moving \u2014 and doing it in 3D for an entire cell was \u2026 triumphant,\u201d Thornburg said. \u201cOne of the last big hurdles that Andrew and I had to solve was understanding how the membrane and the DNA talk to one another when both are moving.\u201d<\/p>\n
While the simulated cell cycle has its limitations \u2014 this was not an atom-by-atom simulation but instead averaged the dynamics of individual molecules \u2014 it yielded a surprisingly accurate accounting of the timing of cellular processes. In repeated simulations involving individual cells with slightly varying start conditions, the simulated cell cycle occurred, on average, within two minutes of the real-world cell cycle, Thornburg said. The work was repeatedly guided and tested against actual experimental outcomes, a process that allowed the scientists to refine their simulations.<\/p>\n
The ability to accurately capture the ever-changing conditions within a living cell opens a new window on the foundations of living systems, Luthey-Schulten said.<\/p>\n
\u201cWe have a whole-cell model that predicts many cellular properties simultaneously,\u201d she said. \u201cIf you want to know what\u2019s going on, say, in nucleotide metabolism, you can also look at what\u2019s going on in DNA replication and the biogenesis of ribosomes. So the simulations can give you the results of hundreds of experiments simultaneously.\u201d<\/p>\n
Study co-authors also include Illinois chemistry alumnus Benjamin Gilbert and John Glass, who leads the J. Craig Venter Institute Synthetic Biology Group.<\/p>\n
This work was conducted in the National Science Foundation\u2019s Science and Technology Center for Quantitative Cell Biology at the U. of I. Luthey-Schulten also is a professor of physics and a professor in the Beckman Institute at the U. of I. The research was conducted using the Delta advanced computing and data resource, which is supported by the NSF and the state of Illinois. Delta is a joint effort of the U. of I. and its National Center for Supercomputing Applications.<\/p>\n
Astrobiology,<\/p>\n","protected":false},"excerpt":{"rendered":"A simulated cell in the early stages of division. Left half shows membrane (green cubes), and ribosomes (yellow\/purple)…\n","protected":false},"author":2,"featured_media":533843,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[256,64,63,23014,1115,133061,8054,264915,264916,264917,92752,264918,128,21041,112944],"class_list":{"0":"post-533842","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-ai","9":"tag-au","10":"tag-australia","11":"tag-cell-biology","12":"tag-dna","13":"tag-dna-replication","14":"tag-genomics","15":"tag-j-craig-venter-institute","16":"tag-jcvi-syn3a-minimal-bacteria","17":"tag-modelling","18":"tag-national-science-foundation","19":"tag-protein-translation","20":"tag-science","21":"tag-simulation","22":"tag-university-of-illinois-at-urbana-champaign"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts\/533842","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/comments?post=533842"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts\/533842\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/media\/533843"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/media?parent=533842"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/categories?post=533842"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/tags?post=533842"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}