Dimensions of Copeland-Erdos Sequences

The base-$k$ {\em Copeland-Erd\"os sequence} given by an infinite set $A$ of positive integers is the infinite sequence \CE_k(A) formed by concatenating the base-$k$ representations of the elements of $A$ in numerical order. This paper concerns the following four quantities. The {\em finite-state dimension} \dimfs (\CE_k(A)), a finite-state version of classical Hausdorff dimension introduced in 2001. The {\em finite-state strong dimension} \Dimfs(\CE_k(A)), a finite-state version of classical packing dimension introduced in 2004. This is a dual of \dimfs(\CE_k(A)) satisfying \Dimfs(\CE_k(A)) \geq \dimfs(\CE_k(A)). The {\em zeta-dimension} \Dimzeta(A), a kind of discrete fractal dimension discovered many times over the past few decades. The {\em lower zeta-dimension} \dimzeta(A), a dual of \Dimzeta(A) satisfying \dimzeta(A)\leq \Dimzeta(A). We prove the following. \dimfs(\CE_k(A))\geq \dimzeta(A). This extends the 1946 proof by Copeland and Erd\"os that the sequence \CE_k(\mathrm{PRIMES}) is Borel normal. \Dimfs(\CE_k(A))\geq \Dimzeta(A). These bounds are tight in the strong sense that these four quantities can have (simultaneously) any four values in $[0,1]$ satisfying the four above-mentioned inequalities.Comment: 19 page

Self-Assembly of Infinite Structures

We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent various notions of computation self-assemble. Several open questions are also presented and motivated

Approximate Self-Assembly of the Sierpinski Triangle

The Tile Assembly Model is a Turing universal model that Winfree introduced in order to study the nanoscale self-assembly of complex (typically aperiodic) DNA crystals. Winfree exhibited a self-assembly that tiles the first quadrant of the Cartesian plane with specially labeled tiles appearing at exactly the positions of points in the Sierpinski triangle. More recently, Lathrop, Lutz, and Summers proved that the Sierpinski triangle cannot self-assemble in the "strict" sense in which tiles are not allowed to appear at positions outside the target structure. Here we investigate the strict self-assembly of sets that approximate the Sierpinski triangle. We show that every set that does strictly self-assemble disagrees with the Sierpinski triangle on a set with fractal dimension at least that of the Sierpinski triangle (roughly 1.585), and that no subset of the Sierpinski triangle with fractal dimension greater than 1 strictly self-assembles. We show that our bounds are tight, even when restricted to supersets of the Sierpinski triangle, by presenting a strict self-assembly that adds communication fibers to the fractal structure without disturbing it. To verify this strict self-assembly we develop a generalization of the local determinism method of Soloveichik and Winfree

Dimensions of Copeland-Erdos Sequences

The base-k Copeland-Erdös sequence given by an infinite set A of positive integers is the infinite sequence CEk(A) formed by concatenating the base-k representations of the elements of A in numerical order. This paper concerns the following four quantities. • The finite-state dimension dimFS(CEk(A)), a finite-state version of classical Hausdorff dimension introduced in 2001. • The finite-state strong dimension DimFS(CEk(A)), a finite-state version of classical packing dimension introduced in 2004. This is a dual of dimFS(CEk(A)) satisfying DimFS(CEk(A)) ≥ dimFS(CEk(A)). • The zeta-dimension Dimζ(A), a kind of discrete fractal dimension discovered many times over the past few decades. • The lower zeta-dimension dimζ(A), a dual of Dimζ(A) satisfying dimζ(A) ≤ Dimζ(A). We prove the following. 1. dimFS(CEk(A)) ≥ dimζ(A). This extends the 1946 proof by Copeland and Erdös that the sequence CEk(PRIMES) is Borel normal. 2. DimFS(CEk(A)) ≥ Dimζ(A). 3. These bounds are tight in the strong sense that these four quantities can have (simultane-ously) any four values in [0, 1] satisfying the four above-mentioned inequalities

Representation of maxitive measures: an overview

Idempotent integration is an analogue of Lebesgue integration where $\sigma$-maxitive measures replace $\sigma$-additive measures. In addition to reviewing and unifying several Radon--Nikodym like theorems proven in the literature for the idempotent integral, we also prove new results of the same kind.Comment: 40 page

Contributions to computational phylogenetics and algorithmic self-assembly

This dissertation addresses some of the algorithmic and combinatorial problems at the interface between biology and computation. In particular, it focuses on problems in both computational phylogenetics, an area of study in which computation is used to better understand evolutionary relationships, and algorithmic self-assembly, an area of study in which biological processes are used to perform computation. The first set of results investigate inferring phylogenetic trees from multi-state character data. We give a novel characterization of when a set of three-state characters has a perfect phylogeny and make progress on a long-standing conjecture regarding the compatibility of multi-state characters. The next set of results investigate inferring phylogenetic supertrees from collections of smaller input trees when the input trees do not fully agree on the relative positions of the taxa. Two approaches to dealing with such conflicting input trees are considered. The first is to contract a set of edges in the input trees so that the resulting trees have an agreement supertree. The second is to remove a set of taxa from the input trees so that the resulting trees have an agreement supertree. We give fixed-parameter tractable algorithms for both approaches. We then turn to the algorithmic self-assembly of fractal structures from DNA tiles and investigate approximating the Sierpinski triangle and the Sierpinski carpet with strict self-assembly. We prove tight bounds on approximating the Sierpinski triangle and exhibit a class of fractals that are generalizations of the Sierpinski carpet that can approximately self-assemble. We conclude by discussing some ideas for further research