Simulation model of DNA tile self-assembly
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 temperature, 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 average 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.