A quarter of a petabyte of data closer to discovering the physical principles of information storage in DNA

Date added: 2026-07-17

A quarter of a petabyte of data closer to discovering the physical principles of information storage in DNA

In the photo, from the left: Michał Jurkowski, MSc, Eng., and Miłosz Wieczór, PhD, Eng. Photo: Krzysztof Mystkowski / Gdańsk Tech

Researchers have performed one of the most extensive studies to date using computer simulations to investigate how different DNA sequences behave. The data obtained help to get a better understanding of how DNA works and provide a vast, publicly accessible resource for further scientific research. The findings of the study, co-authored by researchers from the Gdańsk University of Technology, were published in Nature Communications.

Fourteen research groups affiliated with the ABC (Ascona B-DNA Consortium) took part in the study. This is the latest initiative by this research consortium, and it aimed to examine in detail the mechanical properties of various DNA sequences using computational methods. The results of earlier stages of this multi-year project have enabled the development of tools for, among other things, predicting nucleosome positioning and calculating the deformation cost of any DNA sequence, whilst the latest results improve the accuracy of these methods. Based on these findings, it will be possible to create more accurate models and develop AI-based tools. Furthermore, each successive research cycle sets new standards for DNA structure analysis and visualisation.

The research findings were published in the journal Nature Communications. The paper’s co-authors are four researchers affiliated with Gdańsk Tech: Miłosz Wieczór, PhD, Eng. (second author; at the time of publication at IRB Barcelona, currently at the Department of Physical Chemistry, Faculty of Chemistry, Gdańsk Tech), Prof. Jacek Czub, PhD, Eng., and Michał Jurkowski, MSc, Eng. (Faculty of Physical Chemistry, Faculty of Chemistry, Gdańsk Tech, Doctoral School at Gdańsk Tech), and Kazi Amirul Hossein, PhD (PhD completed at Gdańsk Tech in 2023; at IRB Barcelona at the time of publication; currently at Schrödinger, Inc).

Monitoring processes that take place in a fraction of a second

This is one of the most extensive studies to date in this field. The researchers collected a total of 0.25 petabytes of data (250 terabytes), enabling them to describe events occurring on a timescale of up to 0.1 seconds whilst maintaining extremely high temporal and spatial precision.

“The simulations recreate the course of the process under investigation on a femtosecond timescale, enabling us to observe structural changes occurring at the atomic level. However, certain elements of the DNA structure change on a micro- or even millisecond timescale, and it takes months of simulation to describe these relatively rare phenomena in statistical terms,” said Miłosz Wieczór, PhD, Eng., the paper’s second author.

The data are organised according to a standardised format, which is important in the context of, for example, machine learning, and all simulations are available in an open database, meaning they can be used for further analysis.

The contribution of the Gdańsk Tech team involved conducting part of the simulations within the consortium, as well as analysing and visualising large structural datasets with innovative deep learning tools.

“Our work on simulations of systems containing nucleic acids began around 13–14 years ago. Since then, we have been making a consistent contribution to the development and refinement of new standards, a key aspect of which is our long-term collaboration with the group led by Prof. Modesto Orozco at the University of Barcelona and Prof. Gulia Palermo at the University of California, Los Angeles,” added Miłosz Wieczór, PhD, Eng.

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