TY - JOUR

T1 - Design and fabrication of networks for bacterial computing

AU - Van Delft, Falco C.M.J.M.

AU - Sudalaiyadum Perumal, Ayyappasamy

AU - Van Langen-Suurling, Anja

AU - De Boer, Charles

AU - Kašpar, Ondřej

AU - Tokárová, Viola

AU - Dirne, Frank W.A.

AU - Nicolau, Dan V.

PY - 2021

Y1 - 2021

N2 - Non-deterministic polynomial (NP-) complete problems, whose number of possible solutions grows exponentially with the number of variables, require by necessity massively parallel computation. Because sequential computers, such as solid state-based ones, can solve only small instances of these problems within a reasonable time frame, parallel computation using motile biological agents in nano- and micro-scale networks has been proposed as an alternative computational paradigm. Previous work demonstrated that protein molecular motors-driven cytoskeletal filaments are able to solve a small instance of an NP complete problem, i.e. the subset sum problem, embedded in a network. Autonomously moving bacteria are interesting alternatives to these motor driven filaments for solving such problems, because they are easier to operate with, and have the possible advantage of biological cell division. Before scaling up to large computational networks, bacterial motility behaviour in various geometrical structures has to be characterised, the stochastic traffic splitting in the junctions of computation devices has to be optimized, and the computational error rates have to be minimized. In this work, test structures and junctions have been designed, fabricated, tested, and optimized, leading to specific design rules and fabrication flowcharts, resulting in correctly functioning bio-computation networks.

AB - Non-deterministic polynomial (NP-) complete problems, whose number of possible solutions grows exponentially with the number of variables, require by necessity massively parallel computation. Because sequential computers, such as solid state-based ones, can solve only small instances of these problems within a reasonable time frame, parallel computation using motile biological agents in nano- and micro-scale networks has been proposed as an alternative computational paradigm. Previous work demonstrated that protein molecular motors-driven cytoskeletal filaments are able to solve a small instance of an NP complete problem, i.e. the subset sum problem, embedded in a network. Autonomously moving bacteria are interesting alternatives to these motor driven filaments for solving such problems, because they are easier to operate with, and have the possible advantage of biological cell division. Before scaling up to large computational networks, bacterial motility behaviour in various geometrical structures has to be characterised, the stochastic traffic splitting in the junctions of computation devices has to be optimized, and the computational error rates have to be minimized. In this work, test structures and junctions have been designed, fabricated, tested, and optimized, leading to specific design rules and fabrication flowcharts, resulting in correctly functioning bio-computation networks.

KW - biocomputation

KW - e-beam lithography

KW - E. coli

KW - microfluidics

KW - motile bacteria

KW - nanofabrication

UR - http://www.scopus.com/inward/record.url?scp=85115168902&partnerID=8YFLogxK

U2 - 10.1088/1367-2630/ac1d38

DO - 10.1088/1367-2630/ac1d38

M3 - Article

AN - SCOPUS:85115168902

VL - 23

JO - New Journal of Physics

JF - New Journal of Physics

SN - 1367-2630

IS - 8

M1 - 085009

ER -