Circuits with broken fibration symmetries perform core logic computations in biological networks

PLoS Comput Biol. 2020 Jun 17;16(6):e1007776. doi: 10.1371/journal.pcbi.1007776. eCollection 2020 Jun.

Abstract

We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks in biological networks, and present a systematic route to design synthetic biological circuits.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Arabidopsis
  • Bacillus subtilis
  • Computational Biology / methods*
  • Computer Simulation
  • Electronics
  • Escherichia coli
  • Gene Regulatory Networks*
  • Humans
  • Models, Theoretical
  • Mycobacterium tuberculosis
  • Oscillometry
  • Salmonella
  • Synthetic Biology / methods*