Yannick RONDELEZ, Dr.

 

limms_Rondelez.jpg

 Laboratory Fujii-Lab / Rondelez Group
Position in LIMMS CNRS Researcher (CR1) / Project Associate professor of the University of Tokyo
Main Research Topic in LIMMS

Bio-MEMSArtificial reaction networks for the design of in vitro dynamics

In vitro reaction networks FOR DETAILS VISIT www.yannick-rondelez.com

Keywords

DNA, Molecular programming, Reaction networks, Reaction-diffusion, Chemical systems

Contact LIMMS/CNRS-IIS (UMI 2820)
Institute of Industrial Science, The University of Tokyo, 4-6-1 Komba, Meguro-ku, Tokyo 153-8505, Japan
Phone:+81 (0)3 5452 6213 / Fax:+81 (0)3 5452 6213
E-mail check my papers
Download

icon_pdf.gifAbstract2015_YRondelez.pdf , Abstract2016

 

Resume

Short resume :
2012-now “Habilitation à Diriger des Recherches” at ParisV - CR1
Since Nov. 2008 CNRS researcher in LIMMS/CNRS-IIS, UMI2820 Tokyo : Unconventional computing using microfluidic/biochemical hybrid structures
This project is at the interface between system chemistry, reaction diffusion system and amorphous computing. The goal is to create a tool box of simple chemical reactions that can be easily wired together in order to obtain networks. Like in electronics these networks are able to perform high level functions like information processing, control or sensing.
May 2008 CCRIM consultant. Problem solving, scientific and TRIZ expertise.
April 2002  Post-doc in Nanotech for Biophysics. University of Tokyo. Pr. Noji’s group  |  “Microchambers for the study of mechanically driven ATP synthesis by F1 protein motor.” The goal was to detect the tiny amount of ATP produced from ADP by a single nanometric F1 motor under forced rotation.
Feb. 1999 Ph. D. in Chemistry and Biomimetics. University Paris V. Pr. Reinaud’s group  |  “Supramolecular models of copper-enzymes: behavior in response to bio-active molecules.” Involved skills: organic and inorganic synthesis, metalloenzymes and proteins, NMR, IR and other spectroscopy.

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Research Projects (VISIT MY RESEARCH HOME PAGE HERE)

1- Artificial reaction networks for the design of in vitro dynamics

Context :
Living organisms are chemical objects, but they are fundamentally different from man-made chemistry. This is because living organisms are organized in systems (networks) of chemical transformations and because they process information rather that matter. Another point in that they are evolved rather than designed. We have reported a method to build artificial circuits that mimic biological systems and are now exploring the design process. We target out-of-equilibrium temporal and spatio-temporal (reaction-diffusion) systems, collective behaviours of particles and stochastic dynamics in micro-compartments.
Objectives :
Rationally or stochastically create biochemical circuits to program complex spatiotemporal dynamics.
Methods :
We use DNA amplification reactions to create simple modules, like activation, inhibition or degradation. Then, we use computer assisted design tools1 to guide the experiments toward the realization of a particular function.
Results :
This learning-by-doing approach gives insights about biological networks and provide useful information concerning their design rules2. On the way to artificial morphogenesis, we have recently shown spatiotemporal behaviors3, and compartmentalized molecular programs4.
Booklet_LIMMS2015_YR2.jpeg                                                                                                          Chemical communication in a population of DNA-programmed microscopic particles.
References :
[1] D. Q. Huy et al. An Effective Method for Evolving Reaction Network in Synthetic Biochemical Systems, IEEE Transaction on Evolutionary Computations, (2014). 10.1109/TEVC.2014.2326863.
[2] Rondelez, Y. Competition for Catalytic Resources Alters Biological Network Dynamics. Phys Rev Lett 108, (2012).
[3] A. S. Zadorin, et al.  Synthesis of Programmable Reaction-Diffusion Fronts Using DNA Catalyzers, Phys. Rev. Lett, 114, 068301 (2015).
[4] Hasatani, K. et al. High-throughput and long-term observation of compartmentalized biochemical oscillators. Chem Commun 49, 8090–8092 (2013).

 

2- Chemical reaction networks and their assembly in spatial arrays
YROscillator250px.png YRNetworkofoscills250px.png YRChambersNet250px.png

Context :
Living organisms perform and control complex behaviours by using webs of chemical reactions organized in precise networks. This powerful system concept, which is at the very core of biology, has seldom penetrated the field of chemistry. However, a shift from isolated reactions to supra-reactionnal chemistry (also sometime called system chemistry) would open a completely new array of applications:

  • The possibility to do information processing (or computation) within molecular systems
  • Autonomous molecular robotics
  • models to help our understanding of biological reaction networks.

However, it is still extremely difficult to rationally create such network architectures in artificial, in vitro settings. Our goal is to introduce a method for such a purpose, based on in vitro DNA biochemistry.

We have initially demonstrated this approach by assembling de novo an efficient chemical oscillator: we encode the wiring of the corresponding network in the sequence of small DNA templates, and obtain the predicted dynamics. This show that the rational cascading of standard elements opens the possibility to implement complex behaviours in vitro. Because of the simple and well-controlled environment, the corresponding chemical network is easily amenable to quantitative mathematical analysis. .

Results :
In our recent papers:

  • We describe a new framework to rationally build complex reaction networks, reminiscent of those controlling living organisms, (or built by synthetic biologists), but in vitro. As a proof of concept we present the de novo assembly of a DNA oscillator (MSB 2011) or switchable chemicla memories (PNAS 2012) or the first predator-prey oscillating system (ACSnano 2013). This last system work in a closed environement and has a remarkable efficiency (up to 100 cycles)
  • We take advantage of the relative simplicity of the involved biochemistry to introduce chemically realistic kinetic models, which are fed with independently measured rate constants to yield quantitative predictions. This also stand in contrasts to prior works, both in vivo and in vitro, which uses mostly empirical mathematical modeling.
  • We also develop methods for the building and observation of non-trivial reaction networks. For example, simple and efficient fluorescent monitoring (NAR 2012), droplet-based observation of oscillations (submitted).
  • We have recently expanded this work to the construction of reaction diffusion systems. For example, we have observed travelling waves in the molecular predator-prey system.
  • We also look for the best architectures for the building of molecular systems with complex behaviors. We have proposed the use of competition as a potent non-linear primitive (submitted) for pattern classification. By comparing in vitro and in vivo system we also try to infer the design rules underlying biological information processing (PRL 2012 & PRL 2012)

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Journal Papers (for latest papers and downloads, visit here)

Original Papers on in vitro networks and theoretical biology

  1. A Genot, T. Fujii & Y. Rondelez, Scaling down molecular computers using competitive kinetics, submitted.
  2. K. Hasatani, M. Leocmach, A. J. Genot, A. Estevez-Torres, T. Fujii, Y. Rondelez, High-throughput observation of compartmentalized biochemical oscillators, Submitted
  3. N. Aubert, T. Fujii, M. Hagiya, Y. Rondelez, Computer Assisted Design for Scaling Up Systems based on DNA Reaction Networks, in preparation
  4. N. Aubert, Y. Rondelez, T. Fujii, M. Hagiya Enforcing delays in DNA computing systems, Submitted
  5. T. Fujii & Y. Rondelez, Predator-prey molecular ecosystems. ACS nano, 7 27-34 (2013)
  6.  A. Padirac, T. Fujii & Y. Rondelez, Nucleic acids for the rational design of reaction circuits. Curr. Op. Biotech. 24 1-6 (2012)
  7. A. Padirac, T. Fujii & Y. Rondelez, Bottom-up construction of in vitro switchable memories. PNAS 109, E3212–E3220 (2012)
  8. A. Genot, T. Fujii & Y. Rondelez, Competition and computation in biomolecular networks. Phys. Rev. Let. 109 208102 (2012)
  9. A. Padirac, T. Fujii & Y. Rondelez, Quencher-free multiplexed monitoring of DNA reaction circuits. Nucleic Acid Research, 1-7 (2012)
  10. Y. Rondelez, Competition for catalytic resources alters biological networks dynamics. Phys. Rev. Let. 108, 018102 (2012) icon_pdf.gifarticle
  11. Y. RondelezBreaking down complexity Physics, 4, 8 (2011) icon_pdf.gifarticle
  12. K. Montagne, R. Plasson, Y. Sakai, T. Fujii & Y. Rondelez, Programming an in vitro DNA oscillator using a molecular networking strategy Molecular System Biology 7 (1) (2011) icon_pdf.gifarticle

 

Journal Papers

  • 2016
  1. K. Montagne, G. Gines, T. Fuji, Y. Rondelez, Creative destruction: Boosting functionality of synthetic DNA circuits with tailored deactivation, Nature Communication, in press.
  2. A. Genot, A. Baccouche, R. Sieskind, N. Aubert-Kato, N. Bredeche, J.F. Bartolo, V. Taly, T. Fujii, Y. Rondelez, High-resolution mapping of bifurcations in nonlinear biochemical circuits, Nature Chemistry (2016).
  3. Highlighted in: Wang, Fei, and Chunhai Fan. "DNA reaction networks: Providing a panoramic view." Nature Chemistry 8.8 (2016): 738-740.
  4. G. Perret, P. Ginet, M. C. Tarhan, A. Baccouche, T. Lacornerie, M. Kumemura, L. Jalabert et al., Nano systems and devices for applications in biology and nanotechnology, Solid-State Electronics 115, 66-73 (2016).
  • 2015
  • 2014
  1. A. Baccouche, K. Montagne, A. Padirac, Y. Rondelez, Dynamic DNA reaction network: a walkthrough, Methods 10.1016/j.ymeth.2014.01.015 (2014).
  2. N. Aubert, T. Fujii, M. Hagiya, Y. Rondelez, Computer Assisted Design for Scaling Up Systems based on DNA Reaction Networks, J. R. Soc. Interface, 11 20131167 (2014). (Commented in http://eandt.theiet.org/news/2014/jan/bio-computing-cad.cfm)
  3. D. Q. Huy, N. Aubert, N. Noman, T. Fujii, Y. Rondelez, H. Iba, An Effective Method for Evolving Reaction Network in Synthetic Biochemical Systems, IEEE Transaction on Evolutionary Computations, in press.
  4. K. Hasatani, M. Leocmach, A. J. Genot, A. Estevez-Torres, T. Fujii, Y. Rondelez, High-throughput observation of compartmentalized biochemical oscillators, Chem. Commun.,49 (73), 8090 - 8092 (2013)
  5. N. Aubert, Y. Rondelez, T. Fujii, M. Hagiya, Enforcing delays in DNA computing systems, Natural Computing, in press (2014).
  • 2013
  1. A. Padirac, T. Fujii, A. Estévez-Torres, Y. Rondelez, Spatial waves in synthetic biochemical networks, J. Am. Chem. Soc., 135 (39), 14586–14592 (2013).
  2. A Genot, T. Fujii & Y. Rondelez, Scaling down DNA circuits with competitive neural networks, J. R. Soc. Interface, 10, 20130212 (2013). 
  3. A. Genot, T. Fujii & Y. Rondelez, In vitro regulatory models for systems biology. Journal of Biotechnology Advanceshttp://dx.doi.org/10.1016/ j.biotechadv.2013.04.008 (2013).
  4. T. Fujii & Y. Rondelez, Predator-prey molecular ecosystems. ACS nano,7, 27-34 (2013) (Commented by F. Simmel in ACS Nano, Paper focus in La Recherche, etc) 
  • 2012
  1. A. Padirac, T. Fujii & Y. Rondelez. Nucleic acids for the rational design of reaction circuits. Curr. Op. Biotech. 24 1-6 (2012) Invited
  2. A. Padirac, T. Fujii & Y. Rondelez, Bottom-up construction of in vitro switchable memories. PNAS 109, E3212–E3220 (2012)
  3. L. Desbois, A. Padirac, S. Kaneda, Y. Rondelez, D. Hober, D. Collard & T. Fujii, A microfluidic device for on-chip agarose microbeads generation with ultralow reagent consumption. Biomicrofluidics. 6, 044101 (2012); doi: 10.1063/1.4758460
  4. A. Genot, T. Fujii & Y. Rondelez, Computing with Competition in Biochemical Networks. Phys. Rev. Let. 109 208102 (2012)
  5. A. Padirac, T. Fujii & Y. Rondelez, Quencher-free multiplexed monitoring of DNA reaction circuits. Nucleic Acid Research, 1-7 (2012)
  6. Y. Rondelez, Competition for catalytic resources alters biological network dynamics. Phys. Rev. Let. 108, 018102 (2012)
  • 2011 and prior

  1. Ryota Iino, Liza Lam, Kazuhito V. Tabata, Yannick Rondelez, Hiroyuki Noji Single-molecule assay of biological reaction in femtoliter chamber arrayJapanese Journal of Applied Physics, 48 (8), 08JA04 (2009).
  2. N. Le Poul, M. Campion, B. Douziech, Y. Rondelez, L. Le Clainche, O. Reinaud, Y. Le Mest. Monocopper center embedded in a biomimetic cavity: From supramolecular control of copper coordination to redox regulationJ. Am. Chem. Soc., 129 (28), 8801 -8810, (2007).
  3. D. Coquière, H. Cadeau, Y. Rondelez, M. Giorgi, O. Reinaud. Ipso-chlorosulfonylation of calixarenes: A powerful tool for the selective functionalization of the large rimJ. Org. Chem., 71(11), 4059 -4065 (2006).
  4. H. Arata, Y. Rondelez, H. Noji, and H. Fujita. Temperature alternation by an on-chip microheater to reveal enzymatic activity of beta-galactosidase at high temperaturesAnal. Chem., 77, 15, 4810 (2005).
  5. Ryota Iino , Yannick Rondelez, Masasuke Yoshida , Hiroyuki Noji. Chemomechanical coupling in single-molecule F-type ATP synthaseJ Bioenerg Biomembr. 37(6), 451-4 (2005).
  6. H. Noji, Y. Rondelez, T. Nakashima, G. Tresset, K. Tabata, Y. Kato-Yamada, H. Fujita and S. Takeuchi. Ultra-small chamber for single-molecule detection of biological reaction. e-Journal of Surface Science and Nanotechnology 3, 79-81(2005).
  7. Y. Rondelez, G. Tresset, T. Nakashima, Y. Kato-Yamada, H. Fujita, S. Takeuchi, H. Noji. Highly coupled ATP synthesis by F-1-ATPase single moleculesNature 433, 773-777 (2005).
  8. Y. Rondelez, G. Tresset, K. V. Tabata, H. Arata, H. Fujita, S. Takeuchi, H. Noji. Microfabricated arrays of femtoliter chambers allow single molecule enzymologyNature Biotech. 23, 361-365 (2005).
  9. Y. Rondelez, Y. Li, O. Reinaud. An efficient route to disymmetrically substituted calix[6]arenes. Synthesis of novel ligands presenting a N2S or N3CO2 binding coreTet. Letters 45(24), 4669-72 (2004).
  10. Y. Rondelez, G. Bertho, O. Reinaud. The first water-soluble copper(I) calix[6]arene complex presenting a hydrophobic ligand binding pocket: A remarkable model for active sites in metalloenzymesAngew. Chem.. 41(6) 1044-6 (2002).
  11. Y. Rondelez, M.-N. Rager, A. Duprat, O. Reinaud. Calix[6]arene-based cuprous "funnel complexes": A mimic for the substrate access channel to metalloenzyme active sitesJ. Am. Chem. Soc. 124(7), 1334-40 (2002).
  12. O. Sénèque, Y. Rondelez, L. Le Clainche, C. Inisan, M.-N. Rager,M. Giorgi, O. Reinaud. Calix[6]arene-based N-3-donors - A versatile supramolecular system with tunable electronic and steric properties - Study on the formation of tetrahedral dicationic zinc complexes in a biomimetic environmentEur. J. Inorg. Chem. 10, 2597-04 (2001).
  13. Y. Rondelez, O. Sénèque, M.-N. Rager, A. Duprat, O. Reinaud. Biomimetic Copper(I)-CO complexes: A structural and dynamic study of a calix[6]arene-based supramolecular systemChem. Eur. J. 6, 4218-4226 (2000).
  14. L. Le Clainche, Y. Rondelez, O. Sénèque, S. Blanchard, M. Campion, M. Giorgi, A. Duprat, Y. Le Mest. O. Reinaud. Calix[6]arene-based models for mono-copper enzymes: a promising supramolecular system for oxidation catalysisC. R. Acad. Sci. Paris, Série IIc, Chimie / Chemistry., 3, 811-819 (2000).

 

Book chapters

  • Dinh, Q. H., Aubert, N., Noman, N., Iba, H., & Rondelez, Y., "EVOLVING GRN-INSPIRED IN VITRO OSCILLATORY SYSTEMS." (Wiley; Evolutionary Computation in Gene Regulatory Network Research) 2016, p269.
  • (Edition) Lecture Notes in Computer Science: DNA Computing and Molecular Programming 22nd International Conference, DNA 22, Munich, Germany, September 4-8, 2016. Proceedings; Editors: Rondelez, Yannick, Woods, Damien (Eds.) ISBN 978-3-319-43994-5.
  • T. Plasson & Y. Rondelez. Synthetic biochemical dynamic circuits, in “Multiscale Analysis and Nonlinear Dynamics: From Molecules to the Brain”, edited by M. Pesenson. (Wiley Series: Reviews of Nonlinear Dynamics and Complexity). ISBN-10: 3527411984 ISBN-13: 978-3-527-41198-6. www.wiley-vch.de/publish/dt/books/bySubjectPH00/ISBN3-527-41198-4

Patents

  • Yannick Rondelez, Kevin Montagne, Guillaume Gines, Teruo Fujii. METHOD OF ELIMINATING BACKGROUND IN ISOTHERMAL AMPLIFICATION, Filled 16.02.2015 PCT/FR2016/050357 and PCT/IB2016/000352 applications, by the University of Tokyo and CNRS.
  • Yannick Rondelez, Guillaume Gines, Teruo Fujii. MOLECULAR COMPUTING COMPONENT AND METHOD OF MOLECULAR COMPUTING, Filled 16.02.2016; PCT/ FR2016/050356, IB2016/000419 by the University of Tokyo and CNRS.

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Talks and conferences

Conference proceeding

  •  N. Aubert, Q. H. Dinh, M. Hagiya, T. Fujii, H. Iba, N. Bredeche, Y. Rondelez "Evolution of Cheating DNA-based Agents Playing the Game of Rock-Paper-Scissors." In Advances in Artificial Life, ECAL, vol. 12, pp. 1143-1150 (2013).

 

Invited international conferences & workshops

  • 2016
  1. Journes de la matiere condensed (JMC), “Research and technological developments using DNA and RNA: algorithmic materials for self-assembly and self-organization,” 22-26-.08.2016, Bordeaux.
  2. Colloque, “Art et sciences : de nouveaux domaines pour l'informatique”. Informatique et ADN, College de France, Paris, France, 27.05.2016.
  3. Fnano 2016: A. Estevez-Torres, J. Lee Tin Wah, A. Zadorina, Y. Rondelez, J.-C. Galas, Controlling molecular organization across scales: from DNA origami folding to pattern formation, keynote lecture.
  4. 11th IEEE International Conference on Nano/Micro Engineered and Molecular Systems (IEEE NEMS), Molecular robotics workshop, Collective behaviors encoded by DNA, 17-20 April 2016 in Matsushima/Sendai, Japan.
  5. aSSB-Evry'16 Thematic Research School, "Advances in Systems and Synthetic Biology" (epigenomique.free.fr/en/programme.php), Paris, March 21-25, 2016.
  • 2015
  • 2014
  1. Workshop on Mathematics and its applications to complex phenomena arising in biology, chemistry and medicine, TBA, Marseille, 3-5 June (2014)
  2. DNATEC 2014 DNA-Based Nanotechnology: Digital Chemistry, Y. Rondelez, Parameter landscapes for dynamical reaction networks programs. Dresden 5-9.05 (2014)
  3. Gordon Research Conference on Oscillations & Dynamic Instabilities: Y. Rondelez, Rational building of molecular programs with DNA, Spain 13-18.08 (2014).
  • 2013
  1. Advances in Molecular Programming and Computing, Y. Rondelez, Rational design of temporal and spatiotemporal emergence, Copenhaguen 2-4.05 (2013)
  2. Frontiers of nanoscience and biosystems, LIMMS workshop, Y. Rondelez, Building emergent chemical systems, 16-17.05 (2013)
  3. Solvay Workshop on Patterns and Hydrodynamic Instabilities in Reactive Systems, Y. Rondelez, Rational encoding of reaction- and reaction-diffusion networks using DNA. Bruxelles 15-17.05 (2013)
  4. DNA19 Conference. Y. Rondelez, Molecular programming with the DNA toolbox. Tempe Arizona (US) 22-27.09 (2013) Keynote!
  5. French-Japanese Workshop on Bioinspired Methods & applications, Y. Rondelez, Is molecular programming a good model of biological circuits? Tokyo 4-6.02 (2013).
  • 2012
  1. Workshop on Bio-inspired Computing and Architectures Y. Rondelez, Designing in vitro reaction circuits, IRCICA, Lille 14.12 (2012)
  2. International Workshop on Quantitative Biology, Y. Rondelez, In vitro models of gene regulatory networks, Tokyo (Japan) 22.11 (2012)
  3. Solvay Workshop on Patterns and Hydrodynamic Instabilities in Reactive Systems, Bruxelles 15-17.05 (2012)
  4. IBS2012 A. Genot, T. Fujii, Y. Rondelez, An in-vitro toolbox to model gene regulatory networks Daegu (Korea) 16-21.09 (2012)
  5. Molecular Programming Retreat Y. Rondelez, Dynamic DNA circuits and ecosystems California (US) 19-21.08 (2012)
  6. Society for evolutionary studies Symposium A. Padirac, Y Rondelez, DNA predators and their preys in complex in vitro ecosystems 21-24.08 (2012)
  7. FNANO2012 Yannick Rondelez Emerging temporal patterns from DNA networks. Snowbird, USA 16-19.04.2012 Keynote!
  8. FNANO2012 A. Genot, J. Bath, T. Fujii, Y. Rondelez, A. Turberfield Programming matter(s): from Turing to Kirby and back to E.Coli Snowbird, USA 16-19.04 (2012).
  • 2011
  1. Annual meeting of Systems Information Division of SICE, K. Montagne, Y. RondelezProgramming complex in vitro behaviours using oligonucleotides Tokyo, 23.11 (2011).
  2. Annual Meeting of Cell Synthesis Research. In vitro dynamic networks, Osaka, Japan, 27-28.10.2011
  3. 3rd workshop on Stochasticity in Biochemical Reaction NetworksIn vitro minimal universal networks, Banff, Canada 11-16.09 (2011)  3rd Workshop on Stochasticity in Biochemical Reaction Networks
  4. The 49th Annual Meeting of the Biological Society of Japan: Building complex dynamic behaviors in a tubeA. Padirac, K. Montagne, R. Plasson, T. Fujii, Y. Rondelez Himeji. Japan16-18.09 (2011) The 49th Annual Meeting of the Biological Society of Japan,
  5. The Society for Biotechnology of Japan, 2011 Meeting: DNA-based reaction networks with complex behaviors, K. Montagne, A. Padirac, T. Fujii, R. Plasson, Y. Rondelez, Tokyo, Japan, 26-28.09 (2011)
  6. Annual Symposium of the Belgian Biophysical Society: Mechanically driven ATP synthesis by single F1-ATPase, Brussels, Belgium. Oral. 16.12 (2005).

 

 Other invited seminars & talks

  1. Building molecular programs. UC Riverside US 21.03 (2014)
  2. Experimental landscapes of molecular programs. Molecular Programming Project, Caltech US 27.02 (2014)
  3. Generating populations of biochemical oscillators. FIRST, Aihara Innovative Mathematical Modelling Project, Tokyo University (2014)
  4. Dynamic DNA circuits and ecosystems Molecular Programming Retreat, Oxnard (US) 19-21.08 (2012)
  5. DNA predators and their preys in complex in vitro ecosystems. Meeting of the Japanese Society for Evolutionary Studies 2012, A. Padirac & Y. Rondelez, Tokyo (Japan) 21-24.08 (2012)
  6. Building complex dynamic behaviors in a tube. The 49th Annual Meeting of the Biological Society of Japan, A. Padirac, K. Montagne, R. Plasson, T. Fujii, Y. Rondelez, Himeji (Japan) 16-18.09 (2011)
  7. DNA-based reaction networks with complex behaviors. The Society for Biotechnology of Japan, 2011 Meeting. K. Montagne, A. Padirac, T. Fujii, R. Plasson, Y. Rondelez, Tokyo (Japan) 26-28.09 (2011).

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Other International Conferences

  • 2016

  • A. Drame-Maigne, A. Kazuaki, D. Kiga, T. Fujii, Y. Rondelez. Self-Selection Using Artificial Networks: An Adaptive Tool for Directed Evolution, SEED2016, 18-21.07.2016, Boston, US (Poster)
  • A. Drame-Maigne, K. Amikura, D. Kiga, T. Fujii, Y. Rondelez. Artificial networks implementing selection functions for directed evolution, DNA22, 4-9.09.2016, Munich, Germany (Poster)
  • 2015

  • 2014

  • 2013

  1. A. Estévez-Torres, L. Mzali, A. Kalley, A. Zadorin, Y. Rondelez, J.-C. Galas Microfluidic to explore spatial behavior of synthetic biochemical networks microTAS Freiburg Germany (2013) Oral
  2. A. Vlandas, A. Padirac, Y. Rondelez, A. Estevez-Torres Switching a bistable DNA circuit electrically DNA19 Tempe, USA, 22-27.09 (2013) Poster
  3. A. Baccouche, T. Fujii, Y. Rondelez, New inhibitory architecture for in vitro DNA reaction networks DNA19 Tempe, USA, 22-27.09 (2013) Poster
  4. N. Aubert, T. Fujii, M. Hagiya, Y. Rondelez, A Computer Assisted Design Tool for Dynamic DNA Computation Systems DNA19 Tempe, USA, 22-27.09 (2013) Poster
  5. A. Padirac, J-C. Galas, A. Zadorin, A. Kalley, Y. Rondelez, A. Estévez-Torres. DNA molecular programming goes spatial DNA19 Tempe, USA, 22-27.09 (2013) Oral
  6. N. Aubert, H. D. Quang, M. Hagiya, H. Iba, T. Fujii, Y. Rondelez, Evolution of Cheating DNA-Based Agents Playing the Game of Rock–Paper–Scissors. ECAL, Taormine, Italy, 2-6.09 (2013) Oral
  7. A. Padirac, A. Baccouche, F. Teruo, A. Estevez-Torres and Y. Rondelez, Predator prey molecular landscapes ECAL, Taormine, Italy 2-6.09 (2013) Poster.
  • 2012
  1. A. Padirac, A. Estevez-Torres, T. Fujii, Y. Rondelez, DNA-based Molecular Ecosystem on a Chip, MicroTAS 2012, Okinawa (Japan) 28-01.11 (2012) Oral.
  2. Linda Desbois, Adrien Padirac, Yannick Rondelez and Teruo Fujii, Push-pull generated agarose microdroplets for on-chip real time detectable DNA isothermal amplification MicroTAS 2012, Okinawa (Japan) 28-01.11 (2012), Poster.
  3. T. Fujii, Y. Rondelez Predator-Prey DNA oscillators DNA18 Aarhus (Denmark) 13-17.08 (2012) Oral.
  4. N. Aubert, Y. Rondelez, T. Fujii, M. Hagiya, Enforcing delays in DNA computing systems DNA18 Aarhus (Denmark) 13-17.08 (2012) Oral.
  5. A. Padirac, A. Estévez-Torres, T. Fujii, Y. Rondelez Spatially-resolved DNA ecosystem DNA18 Aarhus (Denmark) 13-17.08 (2012) Poster.
  6. A. Genot, T. Fujii & Y. Rondelez, Molecular computations with competitive neural networks that exploit linear and nonlinear kinetics, Turing 100, Manchester, 22-25.06 (2012). Poster.
  • 2011
  1. R. Plasson, K. Montagne, A. Padirac, T. Fujii & Yannick RondelezA DNA toolbox for the design of in vitro complex reaction networks. Systems Chemistry III, Oral, Crete, Greece, 23-28.11 (2011)
  2. Kevin Montagne, R. Plasson, A. Padirac, T. Fujii & Y. RondelezA toolbox to build time-responsive in vitro DNA networksOral DNA17, Caltech USA 19-23.09 (2011)
  3. A. Padirac, T. Fujii & Y. Rondelez De novo construction of a DNA-based bistable switch. DNA17, Poster, Caltech USA 19-23.09 (2011). Best poster award!
  4. A DNA toolbox for engineering in vitro life-like behaviors, R. Plasson, K. Montagne, A. Padirac, T. Fujii & Y. Rondelez, European Conference on Artificial Life 2011, Oral, Paris, France (2011).  European Conference on Artificial Life 2011
  5. A DNA toolbox for engineering in vitro life-like behaviors, R. Plasson, K. Montagne, A. Padirac, T. Fujii & Y. Rondelez, Origin2011, Oral, Montpelier France (2011). Origin2011.
  • 2010 and prior

  1. S. Kim, Y. Rondelez, S. Takeuchi, S. Yoshizawa, D. Fourmy and T. Fujii Microchamber array for cell-free protein synthesis from single DNA molecules, Poster, PacifiChem, Hawaii, USA (2010).
  2. An experimental batch oscillator encoded by DNA oligonucleotides K. Montagne, Y. Sakai, T. Fujii & Y. Rondelez DNA16 Oral, 123 (2010).
  3. Electroactive microwell array for trapping and lysing single E. Coli cells, Micro Total Analysis Systems 2009, Jejun, Korea. Poster (2009).
  4. Winding up Single F1-Motor Protein in Femtoliter Chambers: The Molecular Pull-Back Car.Micro Total Analysis Systems 2004, Malmö, Sweden. Oral. 5-9.09 (2004)
  5. Activity Measurement at High Temperature by Momentary Heating with On-Chip Micro Heater, Micro Total Analysis Systems 2004, Malmö, Sweden. Poster. 5-9.09 (2004)
  6. Micro-Electro Mechanical Systems 2004. Maastricht, The Netherlands. Poster. 25-29.1 (2004)
  7. Femtoliters chambers for the study of mechanically-driven ATP synthesis by F1 protein motor. Micro Total Analysis Systems 2003, California, USA. Poster. 5-9.09 (2003)
  8. 10th International Conference on Bioinorganic Chemistry. Calixarene-based supramolecular models for mono-copper and zinc enzymes: the "Funnel Complexes. Poster. Calix[6]arene based Cu(I) complexes. Supramolecular control of a biomimetic receptor. Poster. 26-31.08 Florence, Italy (2001).

 

Domestic Conferences

  1. A molecular networking strategy to build artificial complex behaviours. K. Montagne, R. Plasson, T. Fujii & Y. Rondelez, Saibo o tsukuru kai third meeting, Tokyo, Japan (2010).
  2. Journée Science Francophone 2003. Tokyo. Un bio-moteur rotatif de 10 nm. Plenary session. 24.11.03
  3. 41st Annual Meeting of the Biophysical Society of Japan. Niigata, Japan. Poster. 23-26.09.03
  4. 7th Meeting of the Society for Chemistry and Micro-Nano Systems Sapporo, Japan Enclosing femtoliters volumes of liquids. Rotation of single F1 in PDMS microchambres. Poster. 11-12.04.03
  5. Meeting of the French Bioinorganic Network. Autrans, France. Oral. 4-7.03.01
  6. 2nd MSG Meeting for Organic and Bio-Organic Chemistry. Institut Curie, Paris. Oral. 19.05.99.

 

Teaching

  • BIOMOD international undergraduate competition on biomolecular design 2012 (http://biomod.net/). see the wiki on the DNA Tablet at http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba.

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