Three researchers at Ireland’s Hamilton Institute have devised a molecular computer, leveraging interacting DNA strands suspended in water, capable of multiplication, division and addition.
The team, Professor Damien Woods, Assistant Professor Dr. Abeer Eshra, and Dr Tristan Stérin, have published their findings in a Nature journal paper. They state this research unlocks new avenues for long-term data storage, energy-efficient computing, and eventually molecular systems operating inside cells for use cases including disease detection.
Maynooth DNA researchers
The concept appears surprisingly simple in overview yet highly intricate in implementation. Researchers placed a drop of salty water inside a test tube together with short DNA fragments and a longer DNA scaffold. Heating then cooling the mixture triggers the DNA to carry out computation. Woods commented: “The molecules interact, form a structure and that structure is the answer. One key innovation is that the system naturally finds that answer without continuous energy inputs.”
Dubbed the Scaffolded DNA Computer (SDC), it uses long scaffold DNA strands as a backbone. Hundreds of shorter strands attach at pre-designed binding sites to encode bits. These bindings may be altered to edit data as input for molecular programs. DNA interactions behave predictably, similar to Lego bricks or DNA origami, and the same wet hardware can execute distinct molecular programs.
Cooling drives the system toward a thermodynamically stable equilibrium state encoding algorithm outputs. Computation occurs automatically as the system reaches equilibrium. Researchers note this eliminates separate error-correction subsystems, as the system naturally settles into the target output state.
The team ran ten programs, including:
---Multiplication-by-3,
---Division-by-2,
---8-bit parity-detection,
---Addition of 25-bit numbers — a 100-bit computation.
By silicon standards, computation remains slow, though it sets new speed benchmarks within DNA computing. One experiment adding numbers ranging roughly from 11 million to 34 million took up to 14 hours to return results, while calculating 10 plus 3 finished in 30 seconds. Researchers report the SDC can complete non-trivial computations in as little as 30 seconds to one minute, matching the speed limits of their lab equipment and representing the fastest such programs documented in DNA computing literature.
Dr Eshra said: “The reaction happens fast in the test tube, but not as fast as silicon, nor is it intended to be. But compared to other DNA computers, ours is the fastest.”
The device is also described as robust and reusable, completing up to 25 sequential distinct calculations.
The complexity of this work can be seen in diagrams featured within their Nature paper;
Viewing the full diagram helps illustrate its scope.
The researchers write in their Nature paper: “Thermodynamic computing principles could enable robust DNA data storage.” While theoretically feasible, slow data access and system complexity make widespread DNA storage impractical. Claims that silicon computing, even with constant power draw, faces threat from this publicly funded research are clearly overstated. Still, molecular DNA computing may prove valuable for reprogramming human cells, an exciting prospect.
Professor Woods noted: “This is blue skies science. We don’t know where the future is going to take us.”
Tristan Stérin shared a detailed account of the research and its origins.
Bootnotes
This DNA computer research receives EU funding under the DISCO project, DNA-based Infrastructure for Storage and Computation. The initiative explores DNA technologies for novel computing and data storage methods. Funded via the European Innovation Council Pathfinder Challenge on DNA-based digital data storage, the project holds roughly €4 million ($4.6 million). Coordinated by Professor Woods and the TAPDANCE group at Maynooth University, its partners include Tilibit of Munich specialising in DNA origami and Paris-based PRGM.dev / Major Groove.
TAPDANCE is the Theory And Practice of DNA Computing Engines research group within Maynooth University’s Hamilton Institute and Department of Computer Science, led by Professor Woods.
Maynooth University is a constituent school of the National University of Ireland based in Maynooth, County Kildare, Ireland, roughly 15 miles west of Dublin.
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