Wood, Cai (2025) Theory and implementation of a reconfigurable DNA molecular robot. PhD thesis, National University of Ireland Maynooth.
Restricted to Repository staff only until 20 February 2027.
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Abstract
Molecular robots are nanoscale devices that take input from the environment
(senses) and process the information (computes) to inform an
actuation. Despite a multitude of interesting molecular robots made of
DNA, implementing dynamic state information is a major challenge.
This thesis aims to leverage computational model-driven design principles
for reconfigurable molecular robotics. We study two theoretical
models consisting of monomer units that are globally connected and
encode simple state information: Turning Machines utilise integer state
information to control local rotations of robotic units to fold into target
shapes. Despite the intended simplicity of the model, the state
information and characteristic motion proved conceptually challenging to
implement experimentally. We then propose the Tethered Tile Bot model,
which consists of a chain of ‘tethered’ square tiles that encode target
bonds as ‘glues’ on tile edges and use two rule types for reconfiguration:
‘bond break’ and ‘bond form’ rules.
We implement Tethered Tile Bots using double-layered DNA origami
tiles that are tethered to each other by a long single-strand of 360 DNA
bases. Reconfiguration is realised as a two-step process. First, bonds
between tiles are broken via toehold-mediated strand displacement. Then,
bonds for the target configuration are formed via hybridisation. The
tethers between tiles ensure the tiles do not fully dissociate into the liquid
environment, allowing the original material to be reconfigured. Tethered
Tile Bot configurations correspond to paths in the plane Z2, represented
by a series of forward, left and right moves.
Lastly, we implement a form of memory that encodes the target
shape during the anneal, via custom designed sequences (memory domains).
When precisely the same ‘information’ (DNA strands) is added
to samples with different target shapes encoded, we observe different behaviours
(target configurations) during the reconfiguration process. This
serves as a step towards using computation to drive robotic molecular
reconfiguration.
| Item Type: | Thesis (PhD) |
|---|---|
| Keywords: | Theory and implementation; reconfigurable DNA molecular robot; |
| Academic Unit: | Faculty of Science and Engineering > Computer Science Faculty of Science and Engineering > Research Institutes > Hamilton Institute |
| Item ID: | 20686 |
| Depositing User: | IR eTheses |
| Date Deposited: | 13 Oct 2025 10:11 |
| Funders: | European Research Council |
| Use Licence: | This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here |
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