Date of Graduation

5-2013

Document Type

Thesis

Degree Name

Master of Science in Computer Science (MS)

Degree Level

Graduate

Department

Computer Science & Computer Engineering

Advisor

Russell Deaton

Committee Member

Gordon Beavers

Second Committee Member

Wing Ning Li

Keywords

Applied sciences; Abstract tile assembly model; Percolation theory; Self assembly

Abstract

Self-assembly is a process by which simple components build complex structures through local interactions. Directed percolation is a statistical physical model for describing competitive spreading processes on lattices. The author describes an algorithm which can transform a tile assembly system in the abstract Tile Assembly Model into a directed percolation problem, and then shows simulations of the aTAM which support this algorithm. The author also investigates two new constructs designed for Erik Winfree's abstract Tile Assembly Model called the NULL tile and temperature 1.5. These constructs aid the translation between self-assembly and directed percolation and may assist self-assembly researchers in designing tilesets in the aTAM with non-deterministic local properties, but guaranteed global properties. Temperature 1.5 results indicate the brittleness of the standard temperature 2 tile assembly system, and the NULL tile is shown to assist simulations of large assembly processes while also reinforcing the need for variable temperature models to more closely simulate laboratory self-assembly.