Stérin, Tristan (2023) Six Tiles : From Collatz Sequences to Algorithmic DNA Origami. PhD thesis, National University of Ireland Maynooth.
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Abstract
We tile a path from the theoretical world of Collatz sequences, which are fascinating, seemingly undecipherable
mathematical objects, to the experimental wet lab world of algorithmic DNA origami, which is
our proposed technique to run algorithms using self-assembling DNA nanostructures. The common thread
throughout these seemingly unrelated worlds is the use of tile self-assembly models to reason about the
problem at hand.
In the case of Collatz sequences (also known as 3x+1 sequences), we study 6 Wang tiles, which give this
thesis its name, that assemble Collatz sequences in tilings. These Collatz tilings provide a microscope for
studying Collatz sequences symbolically in many bases (base 2, 3, 6, and more) and allow us to interpret
known results in our 2D tiling framework, as well as partially characterising the complexity of predicting
Collatz iterations, Chapter 1.
We then use these 6 tiles to visualise a conjecture by Erdős on powers of two that we encode as the
halting problem (from blank tape) of a 15-state 2-symbol Turing machine. This construction implies that
knowing the busy beaver value BB(15) is at least as hard as solving Erdős’ conjecture, which seems to put
BB(15) out of reach since the conjecture has been open for decades, Chapter 2.
We go on to show that our 6 tiles can simulate arbitrary Boolean circuits in a model of tile assembly
that we introduce: the Maze-Walking Tile Assembly Model. This is when our journey starts entering the
realm of wet lab experiments, as we argue that our Maze-Walking TAM is suited to DNA nanostructure
implementation, Chapter 3.
We make this claim concrete in Chapter 4 by introducing the Scaffolded DNA Computer, a thermodynamically
favoured model of computation very close in spirit to the Maze-Walking TAM. In the wet lab
we implement eight DNA-based programs for this computer (corresponding to over 100 DNA program
executions), including a 7-bit adder running within a DNA origami, or, as we call it, an algorithmic DNA
origami.
Item Type: | Thesis (PhD) |
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Keywords: | Six Tiles; Collatz Sequences; Algorithmic DNA Origami; |
Academic Unit: | Faculty of Science and Engineering > Computer Science Faculty of Science and Engineering > Research Institutes > Hamilton Institute |
Item ID: | 19476 |
Depositing User: | IR eTheses |
Date Deposited: | 11 Feb 2025 10:24 |
URI: | https://mural.maynoothuniversity.ie/id/eprint/19476 |
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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