Design of network-based biocomputation circuits for the exact cover problem

Till Korten, Stefan Diez, Heiner Linke, Dan V. Nicolau, Hillel Kugler

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Exact cover is a non-deterministic polynomial time (NP)-complete problem that is central to optimization challenges such as airline fleet planning and allocation of cloud computing resources. Solving exact cover requires the exploration of a solution space that increases exponentially with cardinality. Hence, it is time- and energy consuming to solve large instances of exact cover by serial computers. One approach to address these challenges is to utilize the inherent parallelism and high energy efficiency of biological systems in a network-based biocomputation (NBC) device. NBC is a parallel computing paradigm in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. The network is then explored in parallel using a large number of biological agents, such as molecular-motor-propelled protein filaments. The answer to the combinatorial problem can then be inferred by measuring the positions through which the agents exit the network. Here, we (i) show how exact cover can be encoded and solved in an NBC device, (ii) define a formalization that allows to prove the correctness of our approach and provides a mathematical basis for further studying NBC, and (iii) demonstrate various optimizations that significantly improve the computing performance of NBC. This work lays the ground for fabricating and scaling NBC devices to solve significantly larger combinatorial problems than have been demonstrated so far.

Original languageEnglish
Article number085004
JournalNew Journal of Physics
Volume23
Issue number8
DOIs
StatePublished - Aug 2021

Bibliographical note

Publisher Copyright:
© 2021 The Author(s).

Keywords

  • Biological computation
  • Exact cover
  • NP-complete problems
  • Network based biocomputation

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