Publications

Articles pdf are posted for educational purposes only. Publishers own copyright for all articles.

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Molecular programming

33. A. Zambrano, A. Zadorin, Y. Rondelez, A. Estévez-Torres, J.-C. Galas, Pursuit-and-evasion Reaction-diffusion Waves In Micro-reactors with Tailored Geometry Journal of Physical Chemistry B 10.1021/jp509474w (2015)

32. Synthesis of Programmable Reaction-Diffusion Fronts Using DNA Catalyzers. A. S. Zadorin, Y. Rondelez, J.-C. Galas, A. Estevez-Torres, Phys. Rev. Lett, 114, 068301 (2015).

Highlighted in Physics: Making Waves with DNA Irving R. Epstein, Physics 8, 12 (2015).

Highlighted in Nature Nanotech: http://www.nature.com/nnano/reshigh/2015/0315/full/nnano.2015.44.html

31. Automated Design of Programmable Enzyme-Driven DNA Circuits. H. van Roekel, L. Meijer; S. Masroor, G. Zandra, A. Estévez-Torres, Y. Rondelez, A. Zagaris, M. Peletier, P. Hilbers, T. de Greef. ACS Synthetic Biology, DOI: 10.1021/sb500300d (2014)

30. Dynamic DNA reaction network: a walkthrough.  A. Baccouche, K. Montagne, A. Padirac, Y. Rondelez. Methods, (2014).

29. Computer Assisted Design for Scaling Up Systems based on DNA Reaction Networks, N. Aubert, T. Fujii, M. Hagiya, Y. Rondelez , J. R. Soc. Interface, 11 (93) 20131167, 2014.

28. An Effective Method for Evolving Reaction Network in Synthetic Biochemical Systems, D. Q. Huy, N. Aubert, N. Noman, T. Fujii, Y. Rondelez, H. Iba, IEEE Transaction on Evolutionary Computations, (2014). 10.1109/TEVC.2014.2326863

27. High-throughput observation of compartmentalized biochemical oscillators, K. Hasatani, M. Leocmach, A. J. Genot, A. Estevez-Torres, T. Fujii, Y. Rondelez,  Chem. Commun., 49 (73), 8090 – 8092 (2013)

26. Enforcing delays in DNA computing systems, N. Aubert, Y. Rondelez, T. Fujii, M. Hagiya, Natural Computing, in press.

25. Spatial Waves in Synthetic Biochemical Networks, A. Padirac, T. Fujii, A. Estévez-Torres, Y. Rondelez, J. Am. Chem. Soc., 135 (39), pp 14586–14592  (2013).

24. Scaling down DNA circuits with competitive neural networks, A Genot, T. Fujii & Y. Rondelez, J. R. Soc. Interface, 10, 20130212 (2013).

23.  In vitro regulatory models for systems biology, A. Genot, T. Fujii & Y. Rondelez, Journal of Biotechnology Advances, (2013).

22. Predator-Prey molecular ecosystems, T. Fujii & Y. Rondelez,  ACS nano, 7 27-34 (2013)

21. Nucleic acids for the rational design of reaction circuits, A. Padirac, T. Fujii & Y. Rondelez. Curr. Op. Biotech. 24 1-6 (2012)

20.Bottom-up construction of in vitro switchable memories, A. Padirac, T. Fujii & Y. Rondelez,  PNAS 109, E3212–E3220 (2012)

19. A microfluidic device for on-chip agarose microbeads generation with ultralow reagent consumption. L. Desbois, A. Padirac, S. Kaneda, Y. Rondelez, D. Hober, D. Collard & T. Fujii,  Biomicrofluidics. 6, 044101 (2012)

18. Computing with Competition in Biochemical Networks. A. Genot, T. Fujii & Y. Rondelez, Phys. Rev. Let. 109 208102 (2012)

17. Quencher-free multiplexed monitoring of DNA reaction circuits. A. Padirac, T. Fujii & Y. Rondelez, Nucleic Acid Research, 1-7 (2012)

16. Competition for Catalytic Resources Alters Biological Network DynamicsY. Rondelez, Phys. Rev. Let. 108, 018102 (2012)

15. Programming an in vitro DNA oscillator using a molecular networking strategy . K. Montagne, R. Plasson, Y. Sakai, T. Fujii & Y. Rondelez, Molecular System Biology 7:466 (2011)

 

Book Chapter

 

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. link.

 

Previous work

 

14. R. Iino, L. Lam, K. V. Tabata, Y. Rondelez & H. Noji, Single-molecule assay of biological reaction in femtoliter chamber array. Japanese Journal of Applied Physics, 48 (8), 08JA04 (2009)

13. 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 regulation J. Am. Chem. Soc., 129 (28), 8801 -8810, (2007)

12. D. Coquière, H. Cadeau, Y. Rondelez, M. Giorgi, O. Reinaud. Ipso-chlorosulfonylation of calixarenes: A powerful tool for the selective functionalization of the large rim. J. Org. Chem. 71(11), 4059 -4065 (2006).

11. H. Arata, Y. Rondelez, H. Noji & H. Fujita, Temperature alternation by an on-chip microheater to reveal enzymatic activity of beta-galactosidase at high temperatures. Anal. Chem. 77, 15, 4810 (2005).

10. R. Iino, Y. Rondelez, M. Yoshida , H. Noji. Chemomechanical coupling in single-molecule F-type ATP synthase. J. Bioenerg. Biomembr. 37(6), 451-4 (2005).

9. 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).

8. Y. Rondelez, G. Tresset, T. Nakashima, Y. Kato-Yamada, H. Fujita, S. Takeuchi, H. Noji. Highly coupled ATP synthesis by F1-ATPase single molecules. Nature 433, 773-777 (2005).

7. Y. Rondelez, G. Tresset, K. V. Tabata, H. Arata, H. Fujita, S. Takeuchi, H. Noji. Microfabricated arrays of femtoliter chambers allow single molecule enzymology. Nature Biotech. 23, 361-365 (2005).

6. 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 core. Tet. Letters 45(24), 4669-72 (2004).

5. 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 metalloenzymes. Angewandte Chem. 41(6) 1044-6 (2002).

4. 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 sites J. Am. Chem. Soc. 124(7), 1334-40 (2002).

3. 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 environment Eur. J. Inorg. Chem. 10, 2597-04 (2001).

2. 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 system Chem. Eur. J. 6, 4218-4226 (2000).

1. 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 catalysis C. R. Acad. Sci. Paris, Série IIc, Chimie / Chemistry. 3, 811-819 (2000).

 

Conference Proceedings

 

1. Evolving cheating DNA networks: a Case Study with the Rock–Paper–Scissors Game N. Aubert, Q. H. Dinh, M. Hagiya, T. Fujii, H. Iba, N. Bredeche, Y. Rondelez , ECAL 2013 proceedings.

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