DREAMY - Distributed Algorithms for Microbiological Systems
ANR-funded research project
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.
Joining the project team:
We are hiring interns, postdocs, and PhD students in the DREAMY project.
Internship [open 2023]: AI for microfluidic microscopy
Internship [open 2023]: Microfluidics for Algae Bacteria Interactions
Internship [open 2023]: Controlled Microfluidic Syringe Pump
We organize the following related workshops and seminar series:
- CELLS - Workshop on Computing among Cells: co-located with the International Symposium on DIStributed Computing (DISC)
- HicDiesMeus - Working Group on Highly Constrained Discrete Agents for Modeling Natural Systems: seminar series on problems from physical, biological, and sociological domains within a distributed computing context
Local Coordinator @ LMF
chip design, distributed algorithms
Local Coordinator @ LISN
distributed algorithms, stochastic processes
Local Coordinator @ Micalis
genetic circuits, phage communication
timed concurrency, process mining
dynamical systems, control theory
concurrency, partial orders, systems biology, ecology
control theory, cooperative control of multi-agent systems
Abhinav Vinayak Pujar
Letícia Levin Diniz
bio simulation, full stack web development
microfluidics, embedded systems
- Matthias Függer, Christoph Lenzen, Ulrich Schmid: On Specifications and Proofs of Timed Circuits. arXiv, 2022.
- Amit Pathania, Corbin Hopper, Amir Pandi, Matthias Függer, Thomas Nowak, Manish Kushwaha: A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission. bioRxiv, 2022.
- Fabricio Cravo, Matthias Függer, Thomas Nowak, and Gayathri Prakash. Mobspy: A meta-species language for chemical reaction networks. Computational Methods in Systems Biology, 2022.
- Victoria Andaur, Janna Burman, Matthias Függer, Manish Kushwaha, Bilal Manssouri, Thomas Nowak, Joel Rybicki: Reaching Agreement in Competitive Microbial Systems. arXiv, 2021.
- Da-Jung Cho, Matthias Függer, Corbin Hopper, Manish Kushwaha, Thomas Nowak, and Quentin Soubeyran. Distributed computation with continual population growth. Distributed Computing, 2021.
We are grateful for the funding provided by ANR (grant ANR-21-CE48-0003), CNRS, Digicosme, INRAe, Institut Farman, RFSI, and Université Paris-Saclay.