Submitted in accompaniment with final year report of MEng Project.



DNA tile self-assembly is the spontaneous assembly of nano-structures made from short single-

stranded DNA sequences. Successful assembly occurs within a narrow parameter window. This

project presents a model with which DNA self-assembly is simulated. Simulations for different tem-

perature, sequence binding specificity and DNA tile concentrations indicate that: the growth rate

of assemblies from uniform strand solutions is linear and highly temperature dependent; the aver-

age nucleation times of assembly increase exponentially with temperature; high binding strengths

of boundary strands improve the stability of the complete assembly; locally high concentrations of

strands seed the growth of the assembly; and locally low strand concentrations spatially direct the

growth of the assembly. The source code is written in C.