DREAMY - Distributed Algorithms for Microbiological Systems

ANR-funded research project

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Objective

A key advantage of biological computing devices is their ability to sense, compute, and especially to respond to their biological environment, e.g., bacteria can be programmed to act as autonomous robots within the human body. Local presence of certain molecules in the environment allows sensing of neighboring cell types and acting accordingly, e.g., by activating an immune response. Current designs of synthetic circuits in bacteria, however, face severe resource limitations: each genetic part added to the cell imposes an additional burden, becoming progressively toxic for the cell.

The most common design techniques for biological logic gates rely on gene regulation via DNA-binding proteins, nucleic acid (DNA/RNA) interactions, or more recently the CRISPR machinery. Each comes with its own constraints: like limited availability of orthogonal signals for use within the cell (DNA-binding), small dynamic range (RNA-based), or reduced growth rates (the CRISPR machinery). This has led to recent efforts to distribute circuits among several cells to reduce the resource load per cell, taking the formative steps towards distributed bacterial circuits.

The DREAMY research project seeks to develop innovative solutions to the problem of building distributed circuits in bacteria from an algorithmic, theoretical perspective that contributes to real-world implementable solutions.

News

Joining the project team:

We are hiring postdocs and PhD students in the DREAMY project:
Description of the PostDoc positions
Description of the PhD position

For more information, please contact the coordinators: Matthias Függer, Thomas Nowak, and Manish Kushwaha.

Activities

We organize the following related workshops and seminar series:

Project members

Matthias's photo
Matthias Függer

Principal Investigator
Local Coordinator @ LMF
chip design, distributed algorithms

Thomas's photo
Thomas Nowak

Principal Investigator
Local Coordinator @ LISN
distributed algorithms, stochastic processes

Manish's photo
Manish Kushwaha

Local Coordinator @ Micalis
genetic circuits, phage communication

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Joffroy Beauquier

Project Member
population protocols

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Catherine Bonnet

Project Member
control theory

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Janna Burman

Project Member
population protocols

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Arnaud Casteigts

Project Member
dynamic networks

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Thomas Chatain

Project Member
timed concurrency, process mining

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Fabricio Cravo

PhD Student
data analysis

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Jean-Loup Faulon

Project Member
bio-retrosynthesis, biosensors

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Laurent Fribourg

Project Member
hybrid systems

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Cristina Stoica Maniu

Project Member
control theory, cooperative control of multi-agent systems

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Gayathri Prakash

Intern
genetic circuits

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Abhinav Vinayak Pujar

PhD Student
genetic circuits

Publications

Publications will be announced here.

Funding

We are grateful for the funding provided by ANR, CNRS, Digicosme, INRAe, Institut Farman, RFSI, and Université Paris-Saclay.