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DNA machine: building computers and robots out of DNA

Damien Woods, Maynooth University
1-2pm  1st Nov 2024

Abstract

We're all familiar with DNA's simple double-helical structure. It turns out that DNA can be coaxed into forming much more intricate structures and devices by leveraging its information-bearing capabilities, chemical characteristics and our imaginations. We design nanoscale DNA computers that live in a test tube, without need of enzymes nor external chemical fuel--the system is energetically driven by DNA hybridisation, with a bit of external warmth to jiggle the molecules out of kinetic traps, and a lot of mathematical theory for intellectual guidance. We're much better at doing this with DNA than other information-bearing polymers like RNA and protein, so far anyway.

The talk will show how we design and build molecular computers using DNA self-assembly to execute algorithms [1]. We will then leverage ideas from physics to design and build DNA computers that are thermodynamically favoured [2]: the correct output of a computation is energetically preferred over all else. Beyond the conceptual innovation, such devices facilitate simple experimental protocols, progammability, resuable programs and in-built error correction, with future potential for energy-efficient DNA data storage.

Short Bio

Damien Woods' team at the Hamilton Institute, Maynooth University, mixes theory and experiment. Experimentally, the focus is on building nanoscale computers, robots and structures out of DNA. That work is driven by solid theory: the team develop algorithms for better prediction of thermodynamics and kinetics of DNA interactions, define new models of computation, and prove mathematical results about the capabilities of molecular computers [3]. The work draws on ideas from computer science, mathematics, physics, chemistry, biology and engineering, and is funded by the European Research Council (ERC), Science foundation Ireland (SFI) and the European Innovation Council (EIC).

Damien travelled for a bit, doing research in Inria (France, 2016-2018), Caltech (USA, 2009-2016), University of Seville (Spain) and University College Cork (Ireland).  His PhD is from Maynooth University. He enjoys whiteboarding, pipetting, AFMing and other scientific sports.
Recent news coverage in advertisement https://www.rte.ie/news/business/2024/1021/1476530-maynooth-dna-project/
Group website: dna.hamilton.ie/<http://dna.hamilton.ie/>

Venue

Atrium of the Smurfit Institute of Genetics