Molecular programming of swarms for ALife

Description

The field of Molecular Robotics focuses on implementing computation, sensing and actuation at the molecular scale. The concentration of specific molecules, typically artificial DNA, is used to encode data, and chemical reactions among those molecules implement computational operations. Other molecules are designed to combine and form structures, making up the body of molecular robots. Finally, chemical reactions can also change the shape of those structures, implementing robotic actuation.


Those methods have been used to successfully implement a large variety of in-vitro systems, ranging from the realization of arbitrary chemical reaction networks to the creation of swarms with more than a million individual units. In particular, molecular robotics can provide tools to the Alife community to test theoretical results on the emergence of complex behaviors, and potentially exhibit unexpected ones.


This tutorial session will cover (1) the basics of molecular robotics, (2) modeling, design and simulation of such systems, and (3) methods for the in-vitro implementation of molecular swarms. The basics will introduce the biochemical concepts used to implement computation at the molecular level, and will present an overview of the field. The next part will focus more closely on a specific programming paradigm named the PEN DNA toolbox. It will also present evolutionary optimization-based approaches for the design of molecular robotic controllers. Finally, the last section will show how those theoretical systems can be transferred to the experimental lab.


Code for examples is available at https://bitbucket.org/AubertKato/pentoolboxdesigntutorial



Image credit: Ibuki Kawamata

Image credit: Genot, A. J., et al. "High-resolution mapping of bifurcations in nonlinear biochemical circuits." Nature chemistry 8.8 (2016): 760.


Image credit: Gines, Guillaume, et al. "Microscopic agents programmed by DNA circuits." Nature nanotechnology 12.4 (2017): 351.

How to register / connect:

TBD


Slides:

TBD


Related Papers:

PEN DNA toolbox:

Aubert-Kato, Nathanael, and Leo Cazenille. "Designing Dynamical Molecular Systems with the PEN Toolbox." New Generation Computing (2020): 1-26.

Aubert-Kato, Nathanaël, and Masami Hagiya. "Designing Controllers for Molecular Robots with the PEN DNA Toolbox." Journal of The Society of Instrument and Control Engineers 58, no. 4 (2019): 270-275.

Genot, A. J., et al. "High-resolution mapping of bifurcations in nonlinear biochemical circuits." Nature chemistry 8.8 (2016): 760.

Baccouche, Alexandre, et al. "Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics." nature protocols 12.9 (2017): 1912.

Gines, Guillaume, et al. "Microscopic agents programmed by DNA circuits." Nature nanotechnology 12.4 (2017): 351.

Zadorin, Anton S., et al. "Synthesis and materialization of a reaction–diffusion French flag pattern." Nature chemistry 9.10 (2017): 990.

Fujii, Teruo, and Yannick Rondelez. "Predator–prey molecular ecosystems." ACS nano 7.1 (2013): 27-34.

More general overviews of molecular programming:

Srinivas, Niranjan, et al. "Enzyme-free nucleic acid dynamical systems." Science 358.6369 (2017)

FU, Ting, et al. DNA-based dynamic reaction networks. Trends in biochemical sciences, 43.7 (2018): 547-560.

Padirac, Adrien, Teruo Fujii, and Yannick Rondelez. "Nucleic acids for the rational design of reaction circuits." Current opinion in biotechnology 24.4 (2013): 575-580.

Dalchau, Neil, et al. "Computing with biological switches and clocks." Natural computing 17.4 (2018): 761-779.




Code / git repos:

The Bioneat software used throughout this article is open source and can be obtained at https://bitbucket.org/AubertKato/bioneat/. It contains implementations of the previously described mono-objective and multi-objective optimizers. It makes use of the DACCAD library found at: https://bitbucket.org/AubertKato/daccad

Source codes in Python making use of MAP-Elites to evolve CRNs can be found at https://bitbucket.org/leo-cazenille/daccad-qd.

Tutorial Code: https://bitbucket.org/AubertKato/pentoolboxdesigntutorial


Contacts: