Plate Nº 74 · recorded October 10, 2026
Biology & EvolutionReported finding
New 'Computational Microscope' Simulates DNA Packaging at 10x Previous Scale
OpenCGChromatin, a new open-source 'computational microscope,' simulates DNA packaging systems ten times larger than earlier models, revealing how chromatin folds.
By Marcus Bennett4 min read741 words
In brief
- OpenCGChromatin simulates chromatin systems more than 10 times larger than previous models at comparable resolution.
- The tool can model assemblies containing hundreds of nucleosomes, the basic units of DNA packaging.
- The study, first-authored by Kieran Russell, was published in Nature Communications in 2026 (DOI: 10.1038/s41467-026-78050-6).
- The software was developed by a team led by IRB Barcelona, the University of Cambridge, UT Southwestern Medical Center and the Howard Hughes Medical Institute.
- OpenCGChromatin is released as open-source software for the research community.
Researchers have built a "computational microscope" that can simulate DNA packaging at more than ten times the scale of previous models while keeping comparable molecular resolution. The tool, called OpenCGChromatin, lets scientists watch chromatin — the compact structure our DNA forms inside the cell nucleus — fold, flex and reorganize in simulations that were previously out of reach.
An international team led by IRB Barcelona, the University of Cambridge, UT Southwestern Medical Center and the Howard Hughes Medical Institute developed the software. The findings appeared in the journal Nature Communications in 2026, with first author Kieran Russell.
Why does DNA packaging matter?
Inside each of our cells, roughly two meters of DNA must fit into a nucleus far too small to see. To manage this, DNA wraps around spool-like proteins called histones, forming units called nucleosomes. These nucleosomes then organize into a larger structure called chromatin.
How chromatin is arranged matters beyond storage. Its organization influences how easily genes can be read and how DNA damage gets repaired. But the molecular movements and interactions that drive these arrangements are extremely difficult to capture with experiments alone. That is where simulation comes in.
What does the new tool actually do?
OpenCGChromatin combines two things that rarely go together: a detailed representation of DNA and proteins, and high computational efficiency. The payoff is scale. Researchers can now study chromatin systems containing hundreds of nucleosomes — more than ten times larger than what earlier models could handle at a similar level of detail.
Crucially, the simulations are not flying blind. They reproduce observations from microscopy and biochemical experiments. At the same time, they reveal something experiments struggle with: the movements of flexible histone regions that are hard to resolve in the lab.
"The challenge is to connect interactions between individual molecules with the behavior of much larger stretches of chromatin. This tool allows us to study both within the same framework and understand how small molecular changes can alter DNA packaging," said Dr. Modesto Orozco, head of the Molecular Modeling and Bioinformatics Laboratory at IRB Barcelona, an ICREA Academia researcher and a professor at the University of Barcelona, who co-led the study.
Who built it, and how?
The project drew directly on experimental work. "OpenCGChromatin was inspired by beautiful cryo-ET experimental work from professor Michael Rosen's group at UT Southwestern Medical Center and the Howard Hughes Medical Institute, who co-led this study with us," said professor Rosana Collepardo-Guevara of the University of Cambridge, who co-led the study alongside Orozco. Cryo-ET, or cryo-electron tomography, is an imaging technique that captures 3D snapshots of frozen biological structures.
Collepardo-Guevara praised the first author's contribution in unusually strong terms. "What Kieran Russell, first author of this study, has achieved is remarkable. He has pushed the state of the art in chromatin modeling, allowing us to simulate systems at a scale and level of molecular detail that were previously out of reach," she said.
What questions can it answer?
The tool works across scales, from single molecular interactions up to gene-sized structures and biomolecular condensates — membraneless droplet-like compartments that concentrate molecules inside cells.
"We can now connect the chemical makeup of chromatin to its organization across scales — from molecular interactions to gene-sized structures and biomolecular condensates — while remaining closely grounded in experiment. I am very excited because OpenCGChromatin opens up a completely new range of questions that we can now address computationally," Collepardo-Guevara said.
The simulations already offer practical insight into how chromatin behaves. "The simulations help us understand why changing the spacing between nucleosomes, or adding chemical modifications to histones, can make chromatin behave differently," explained David Farré-Gil, an author of the paper.
What are the limitations?
As with any simulation study, the results depend on how faithfully the model captures molecular physics. The team anchored its work in experimental data — reproducing microscopy and biochemical observations — but simulations remain approximations of reality, and findings from in-silico chromatin will need continued experimental validation as researchers apply the tool to new questions.
Can other researchers use it?
Yes. OpenCGChromatin is available as open-source software, meaning any research group can download it, inspect the code and use it to investigate the physical principles underlying genome organization.
Publication details: Kieran Russell et al., "Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation," Nature Communications (2026). DOI: 10.1038/s41467-026-78050-6
via Phys.org Biology (Source)
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