Alexandre Baccouche

A.BACCOUCHE.jpg Host Laboratory FUJII LAB.
Position in LIMMS PhD Student
Main Research Topic in LIMMS

Bio-MEMS - Functional Analysis of Artificial DNA Reaction Network


DNA, Reaction networks, Dynamical systems, Confocal Microscopy, Microfludics

Contact LIMMS/CNRS-IIS (UMI 2820)
Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
Phone:+81 (0)3 5452 6036 / Fax:+81 (0)3 5452 6088
E-mail baccouch at
Download icon_pdf.gifAbstract2015_ABaccouche.pdf


Short resume :
2012-now Actual position
2008-2012 Here
2004-2008 Here
2001-2003 Here

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Research Projects in Limms

1- Functional Analysis of Artificial DNA Reaction Network
Context :
Unicellular organisms such as bacteria are computing at the molecular level by processing sets of stimuli into an appropriate response through chemical reactions. Molecular programming reproduces these dynamic molecular circuits, but ex-vivo.  This field is moving from proof-of-principle demonstrations to practical applications. Three-dimensional nanoscale structures, as well as molecular machines or algorithms encoded in the matter itself have been achieved [1]. We are building dynamic DNA reaction circuits from cascadable elementary modules that, once assembled in a given topology, can perform a targeted behaviour. These circuits are made of multiple DNA strands and monitored in real-time thanks to a sequence-specific, non-disruptive detection technique [2,3].
Objectives & Methods:
  • Extend the previous work on in vitro small reaction networks with non-trivial dynamics by developing new modules and assembling them into more and more complex network architectures [4,5], using theoretical and experimental techniques.
  • Explore the behavior of such system in spatially resolved conditions through microscopy, and use microfluidic tools for high-throughput system characterization. 
Results :
We successfully developed a new inhibitory module that leads to non-trivial behaviors such as bi-rhythmicity and hard excitations. We have also obtained high resolution experimental mapping of bifurcation diagrams (Fig. 2).






Fig. 1 Molecular implementation of the new inhibitory architecture exhibiting exotic behaviors.


Fig. 2 Example of experimental bifurcation diagram for predator-prey system, showing the frequency of oscillating cycles (red: high, blue: low) depending on two control parameters of the system.

References :
[1] X. Chen et al., Curr. Opin. Biotechnol., 21, p.392, 2010
[2] A. Baccouche et al, Methods, 67, p.234, 2014
[3] A. Padirac et al, Nucl. Acids Res., 40, 15, 2012 
[4] T. Fujii , Y. Rondelez, ACSnano 2012
[5] A. Padirac et al, PNAS, 109 (47),  p.19047, 2012

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Main publication List (papers, conferences and patent)





  1. A. Baccouche, K. Montagne, A. Padirac, Y. Rondelez, Dynamic DNA reaction network: a walkthrough, Methods 10.1016/j.ymeth.2014.01.015 (2014).


2013 and prior

  1. A. Baccouche, T. Fujii, Y. Rondelez, New inhibitory architecture for in vitro DNA reaction networks DNA19 Tempe, USA, 22-27.09 (2013) Poster
  2. A. Padirac, A. Baccouche, T. Fujii, A. Estevez-Torres and Y. Rondelez, Predator prey molecular landscapes ECAL, Taormine, Italy 2-6.09 (2013).

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