Periodic Reporting for period 2 - DISCO (DNA Infrastructure for Storage and Computation)
Periodo di rendicontazione: 2024-10-01 al 2026-01-31
Funded by the European Innovation Council PATHFINDER Challenge on DNA-based digital data storage, DISCO aims to create a new method of storing data and computing on that data, all in DNA. The work addresses the significant and growing gap between data generation and global storage capacity in a way that is scalable, environmentally sustainable and increases the integrity and is reliable over time. The project is coordinated by Prof Damien Woods who leads the TAPDANCE Research Group at Maynooth University.
Throughout evolution, Biology has found an almost-perfect molecule to pass information down through the millennia. Whether, for a simple bacterium or the largest whale, DNA achieves high information density while permitting cellular machinery rapid random access retrieval to decode everything from a single protein to the development of an entire human brain. Humanity’s rapidly growing data storage and computing needs make it tempting to exploit optimised biological molecules and processes, but biology is messy, poorly understood and much more specialised for life than it is for our needs — we propose to use DNA for storage together with a rationally designed, well-characterised and robust molecular computing architecture.
The DISCO project will address the challenge of engineering a programmable and robust DNA storage and computing platform. DISCO combines powerful molecular-algorithmic ideas from DNA computing with notions of thermodynamic stability from DNA nanostructures, to provide an expressive and robust system design. The project proposes the use of long DNA scaffold strands, upon which hundreds of smaller strands bind to store data, which can be later read, erased, rewritten and computed upon.
Throughout evolution, Biology has found an almost-perfect molecule to pass information down through the millennia. Whether, for a simple bacterium or the largest whale, DNA achieves high information density while permitting cellular machinery rapid random access retrieval to decode everything from a single protein to the development of an entire human brain. Humanity’s rapidly growing data storage and computing needs make it tempting to exploit optimised biological molecules and processes, but biology is messy, poorly understood and much more specialised for life than it is for our needs — we propose to use DNA for storage together with a rationally designed, well-characterised and robust molecular computing architecture.
The DISCO project will address the challenge of engineering a programmable and robust DNA storage and computing platform. DISCO combines powerful molecular-algorithmic ideas from DNA computing with notions of thermodynamic stability from DNA nanostructures, to provide an expressive and robust system design. The project proposes the use of long DNA scaffold strands, upon which hundreds of smaller strands bind to store data, which can be later read, erased, rewritten and computed upon.
To date we have filled one patent, and a number of papers are ether published, under review, or in preparation, including:
- Stérin*, Eshra*, Adio, Evans, Woods. A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable. *Joint lead co-authors. 2025, bioarxiv https://www.biorxiv.org/content/10.1101/2025.07.16.664196v1(si apre in una nuova finestra)
- Shalaby, Thachuk, Woods. Minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded DNA computer. DNA29: The 29th International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:1:1--1:22, 2023.
- Shalaby, Woods. An efficient algorithm to compute the minimum free energy of interacting nucleic acid strands. ICALP: The 52nd EATCS International Colloquium on Automata, Languages, and Programming Leibniz International Proceedings in Informatics (LIPIcs). Volume 334, pp. 130:1-130:20. 2025. Best paper award.
- Ducloz, Shalaby, Woods. Algorithmic hardness of the partition function for nucleic acid strands. DNA31: The 31st International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs 347:1:1-1:23, 2025
As well as other publications that are in preparation or more tangentially related.
- Stérin*, Eshra*, Adio, Evans, Woods. A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable. *Joint lead co-authors. 2025, bioarxiv https://www.biorxiv.org/content/10.1101/2025.07.16.664196v1(si apre in una nuova finestra)
- Shalaby, Thachuk, Woods. Minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded DNA computer. DNA29: The 29th International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:1:1--1:22, 2023.
- Shalaby, Woods. An efficient algorithm to compute the minimum free energy of interacting nucleic acid strands. ICALP: The 52nd EATCS International Colloquium on Automata, Languages, and Programming Leibniz International Proceedings in Informatics (LIPIcs). Volume 334, pp. 130:1-130:20. 2025. Best paper award.
- Ducloz, Shalaby, Woods. Algorithmic hardness of the partition function for nucleic acid strands. DNA31: The 31st International Conference on DNA Computing and Molecular Programming Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs 347:1:1-1:23, 2025
As well as other publications that are in preparation or more tangentially related.
1 patent has been filed in Reporting Period 1. To be updated in subsequent review periods.