Analysis of punctures in DNA self-assembly under forward growth

Modeling gross damage in tile-based nanomanufacturing by DNA self-assembly

This paper proposes a novel model for gross damage as occurring in tile-based nanomanufacturing by DNA self-assembly. Gross damage occurs due to exogenous agents (such as radiation and tip-sample interactions) and is modeled as a hole (with a large number of empty tile sites) in the aggregate of the self-assembly. A stochastic analysis based on Markov chains for the tile binding process is pursued for regrowth of the tiles. This analysis establishes resilience as the probability to regrow the target pattern in the area affected by the gross damage. The conditions by which regrowth of a hole is favorable (i.e., at high resilience) compared with normal growth are established by considering temperature of aggregation and bond energy. As examples, two patterns for nano interconnects are analyzed based on the proposed model.

Parallel growth and healing of DNA self-assembly for interconnects

Self-assembly has been employed in nano-technology to build crystals using individual components (commonly referred to as tiles) with limited control. Templates of regular lattice structures for two-dimensional scaffolds and interconnects have been recently implemented by self-assembly. This study proposes a diagonally based growth scheme that is applicable to these templates of interconnects (as an example). Differently from previous techniques (mostly sequential in execution), growth is allowed along two different directions in the aggregate, thus permitting a parallel mode of operation. This is made possible by utilising a tile set and binding scheme to allow multiple seed tiles to grow along the main diagonal of the pattern. The conditions by which this type of new growth is possible at a reduced error occurrence in mismatched tiles, are presented; error tolerance is achieved by employing healing and so-called robust generation of the seed tiles, thus ensuring that pattern growth is controlled along both directions. Simulation results are presented under different scenarios of growth direction (inclusive of backward growth for healing).