Topology Discovery in Deadlock Free Self-assembled DNA Networks

In this paper we present a novel approach to topology discovery and defect mapping in nano-scale self-assembled DNA networks. The large scale randomness and irregularity of such networks makes it necessary to achieve deadlock freedom without the availability of a topology graph or any other kind of centralized algorithms to configure network paths. Results show how the proposed distributed approach preserves some important properties (coverage, defect tolerance, scalability), reaching a segment-based deadlock freedom while avoiding centralized tree-based broadcasting and hardware node hungry solutions not feasible in such a limited nanoscale scenario. Finally, we quantitatively evaluate an not-optimised gate-level hardware implementation of the required control logic that demonstrates a relatively acceptable impact ranging from 10 to about 17 % of the budget of transistors typically available at each node using such technology.