{"id":333102,"date":"2026-03-17T00:35:13","date_gmt":"2026-03-17T00:35:13","guid":{"rendered":"https:\/\/www.newsbeep.com\/nz\/333102\/"},"modified":"2026-03-17T00:35:13","modified_gmt":"2026-03-17T00:35:13","slug":"digital-twin-of-a-cell-tracks-its-entire-life-cycle-down-to-the-nanoscale","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/nz\/333102\/","title":{"rendered":"Digital Twin of a Cell Tracks Its Entire Life Cycle Down to the Nanoscale"},"content":{"rendered":"

Five years ago, scientists watched in wonder as synthetic bacteria grew and split into daughter cells. The bacteria\u2019s extremely stripped-down genome still supported its entire life cycle<\/a>. It was a crowning achievement in synthetic biology<\/a> that shed light on life\u2019s most basic processes.<\/p>\n

These processes can now be viewed digitally. This month, a team at the University of Illinois at Urbana-Champaign developed a virtual model<\/a> of the bacteria tracking nearly all of a cell’s molecules down to the nanoscale. The researchers made this digital cell by combining several large datasets covering thousands of molecules and then animating them as the bacteria split in two.<\/p>\n

The model is the latest in a growing effort to make digital twins of living cells. Mimicking diseases or treatments in the digital world offers a bird\u2019s-eye view of cellular changes and could speed up drug discovery and help researchers tackle complex diseases like cancer.<\/p>\n

\u201cWe have a whole-cell model that predicts many cellular properties simultaneously,\u201d study author Zan Luthey-Schulten said<\/a> in a press release. The model could provide \u201cthe results of hundreds of experiments\u201d at the same time, she said.<\/p>\n

Digitizing Life<\/p>\n

Every cell is a bustling metropolis. Proteins orchestrate a vast range of cellular responses. RNA molecules carry instructions from genes to the cell\u2019s protein-building factories. Fatty acids in a cell\u2019s membrane rearrange themselves to admit nutrients or ward off invaders. Working in tandem, they all keep the cell humming along.<\/p>\n

This complexity makes cells hard to simulate. But with large datasets charting the genome, gene expression, and proteins alongside sophisticated AI<\/a>, scientists have built static virtual cells that paint a near-complete picture<\/a> with atomic-level resolution. More recent models can even predict molecular movements<\/a> for a short period of time (often less than a second).<\/p>\n

But they can\u2019t simulate \u201cthe mechanics and chemistry that take place over minutes to hours in processes such as gene expression and cell division,\u201d wrote the University of Illinois team.<\/p>\n

Other efforts use physics<\/a> to predict how molecular changes affect behavior in bacteria, yeast, and human cells. These treat cells as a \u201cwell-stirred system\u201d\u2014that is, a cup of molecular soup lacking details about where each molecule sits and how molecules vary from cell to cell.<\/p>\n

But location is key. As cells divide, some proteins gather around DNA to help copy it; others assemble near the membrane to recruit fatty molecules for its growth as the cell splits in two.<\/p>\n

Simulating everything, everywhere, all at once during human cell division is beyond even the most powerful supercomputers. Minimal bacteria offer an alternative. These synthetic bacteria are stripped-down versions of the parasite Mycoplasma mycoides. The team focused on one of these known as JCVI-syn3A. Its 493-gene genome\u2014roughly half the original\u2014is the smallest set of DNA instructions to boot up a living bacteria that can still grow and divide.<\/p>\n

In 2022, the team developed a 3D model<\/a> of the bacteria\u2019s metabolism, genes, and growth. But the software, Lattice Microbes<\/a>, struggled to track division.<\/p>\n

Life in 4D<\/p>\n

The new study added more data to the software. This included membrane changes and information about how ribosomes, the cell\u2019s protein-making machines, assemble and move inside the cell\u2019s gooey interior. They also added stochasticity, or unpredictability, to the model.<\/p>\n

Changes to the location of chromosomes, which house DNA, are random as the cell divides, which makes them difficult to predict. But their position influences DNA replication and gene expression.<\/p>\n

The first update nearly broke the software. It could map molecules involved in cell division, such as an enzyme critical for DNA copying. But adding chromosome location predictions slowed the model to a crawl, even when running on advanced GPUs. Most of the cells died before their simulations were complete.<\/p>\n

Several tweaks helped. One was to add more computational power. The team used a GPU dedicated to chromosomes, while all other details were processed on a separate chip. The model also ran faster by rendering some proteins as inert spheres that could be largely ignored.<\/p>\n

The upgrades worked. Leaving the model running over Thanksgiving, the team returned to find it had completed the bacteria\u2019s whole life cycle. \u201cAll of a sudden, it was just this huge leap,\u201d study author Zane Thornburg told<\/a> Nature.<\/p>\n

The simulation matched many real-world experiments, such as how the cells elongate and bubble into dumbbell-like shapes during division. The model also accurately predicted the length of a cell cycle and captured a wide range of cellular activity.<\/p>\n

\u201cI can\u2019t overstate how hard it is to simulate things that are moving\u2014and doing it in 3D for an entire cell was\u2026triumphant,\u201d said<\/a> Thornburg.<\/p>\n

Every cell is like a snowflake: Although containing similar molecules, the amounts and locations differ. The model easily handled this diversity. Repeated simulations of the bacteria, each starting with slightly different genetic, molecular, and metabolic makeup, resulted in a similar cycle length and movement of chromosomes during division.<\/p>\n

The results came at a cost: Simulating the cell\u2019s 105-minute cycle took up to six days on a supercomputer. But the virtual cell could lend insights into the molecular dance that causes all cells to grow and divide. JCVI-syn3A doesn\u2019t have the smallest genome. Its predecessor<\/a> holds the record, but it also struggles to make normally shaped and functional daughter cells\u2014suggesting some genes are essential for division. Simulation could help us understand why.<\/p>\n

Other efforts using generative AI to build virtual cells are in the works. But because this study\u2019s model was grounded in strict physical and biochemical rules, results could be easily verified in the lab. AI-generated virtual cells, however, are commonly trained on gene expression data<\/a> alone, which is a snapshot of a cell\u2019s state and often fails to predict complex cell responses.<\/p>\n

The two approaches could inspire each other by homing in on principles that make a virtual cell run like the real deal. For example, they could show that capturing each molecule in space and time, rather than as a soup, vastly improves the model.<\/p>\n

Although the model can\u2019t simulate a cell atom-by-atom, the team wrote, it could \u201cilluminate the interwoven nature of the biology, chemistry, and physics that govern life for cells.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"Five years ago, scientists watched in wonder as synthetic bacteria grew and split into daughter cells. The bacteria\u2019s…\n","protected":false},"author":2,"featured_media":333103,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[124271,111,139,69,147],"class_list":{"0":"post-333102","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-feature-photo","9":"tag-new-zealand","10":"tag-newzealand","11":"tag-nz","12":"tag-science"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts\/333102","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/comments?post=333102"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts\/333102\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/media\/333103"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/media?parent=333102"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/categories?post=333102"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/tags?post=333102"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}