Powers and Behaviors of Directed Self-assembly

In nature there are a variety of self-assembling systems occurring at varying scales which give rise to incredibly complex behaviors. Theoretical models of self-assembly allow us to gain insight into the fundamental nature of self-assembly independent of the specific physical implementation. In Winfree\u27s abstract tile assembly model (aTAM), the atomic components are unit square tiles which have glues on their four sides. Beginning from a seed assembly, these tiles attach one at a time during the assembly process in an asynchronous and nondeterministic manner. We can gain valuable insights into the nature of self-assembly by comparing different models of self-assembly which use fundamentally different mechanisms for local interactions. A powerful notion which allows us to compare models of self-assembly is simulation. The first result of this thesis examines the role of non-determinism in simulation. It shows that the universal simulation of directed aTAM systems requires undirectedness. A tile assembly model is said to be directed if it always assembles the same final assembly. We distinguish between two types of aTAM systems: cooperative systems and non-cooperative systems. In cooperative aTAM systems, we are able to enforce that in order for a tile to attach to an assembly, the glues of a tile must match two or more glues of neighboring tiles. On the other hand, in non-cooperative aTAM systems, tiles are able to attach to an assembly provided that one of the tile\u27s glues match an exposed glue on the assembly. It is well known that the cooperative aTAM is computationally universal, and it is conjectured that the non-cooperative aTAM is not computationally universal. For our second result, we show that if we allow tiles to be polygons with six or more sides, then the class of non-cooperative systems is capable of universal computation. On the other hand, we show that the class of systems consisting of polygons with six or less sides is not capable of computing using any of the currently known methods

The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum β-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 2000-2011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBL-resistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen