Efficient in-message computation of prevalent mathematical operations in DNA-based nanonetworks

摘要

One of the most important research issues in the field of nanonetworks is the problem of constructingreal networks in practice. To build such networks, one needs to create the nano-devices themselvesas well as a computing and a communication mechanism. We already have developed such a conceptbased on DNA building blocks (so called DNA tiles), which is able to generate all three mechanismsby self-construction, basically by providing a sufficiently large number of specific DNA buildingblocks. Such networks are Turing complete; however, as we demonstrate in this paper, the numberof required building blocks to execute computations by simulating Turing machines is large. We willshow in this paper that the number can be reduced by using specific, more efficient sets of buildingblocks for problems that can be modeled as boolean formulas. For specific mathematical operationslike And or Add, even smaller solutions/message molecules can be created.This paper presents small message molecules for frequently requested mathematical problems.We present nanonetworks for the Thres and Add operations. Thres operations can be used toregister if critical concentrations of disease markers have been reached. Add forms the basis formany advanced communication protocols. Furthermore, message molecules for Mult, Xor and Incare conceptualized. The presented message molecules are smaller and less error prone compared tothe tilesets that result from more generic approaches. It is therefore more likely that they can beemployed in groundbreaking wet-lab experiments in the near future.