Nicolas SCHABANEL Directeur de recherches au CNRS — LIP — École Normale Supérieure de Lyon 46 allée d'Italie 69364 Lyon Cedex 07 France Office: GN1.330S (Site Monnod - Main building - 3rd floor - South) Phone: +33 4 72 72 80 00 / +33 4 26 73 14 55 Resident member of the Rhône-Alpes Complex Systems Institute (IXXI)

My current researches cover:

• DNA Computing: Algorithmic self-assembly, Molecular folding, Experiments
• DNA nanostructures: Automated DNA origami design and algorithms, ENSnano software development, Curved DNA nanostructures, Experiments (design, assembly, atomic force microscopy (AFM) imaging)
• Algorithms: biomolecular, approximation, randomized, online, distributed,...
• Complex systems such as:
  • Complex networks: clustering and drawing of dynamical networks
  • Stochastic cellular automata: definition, analysis, intrinsic simulations, local probabilistic correlations,...
  • Small world phenomenon: analysis, algorithms design, modelization,...
  • Random systems

Grants

My work is supported by the "projet à risque" CalcADN (2025-2030), ANR Scalmazène (2022-2026), NanoShapeLearn (2023-2027), the LIP Installation BQR (2017-18), MoPrExProgMol (2018) and AMARP (2018-20) by CNRS Mission pour l'interdisplinarité, and IXXI CalcASMol (2018-19) grants.

Students

• Pacôme Perrotin (Post-doc, 2025-26)
• Yarong Shi (Post-doc, 2024-26)
• Eliott Mercier Del Forno (Stage ingénieur, 2025)
• Axel Brisse (Stage ingénieur, 2025-26)
• Gwendal Ducloz (M2, 2025)
• Marie de Sainte Marie (M2, 2024)
• Samuel Gardenne (M2, 2024)
• Octave Hazard (M2, 2021; PhD advisor 2022-2025)
• Nicolas Levy (M2, 2020; PhD advisor 2020-2023)
• Pierre Marcus (M2, 2020; 4A, 2021; PhD Advisor 2022-2024)
• Amaury Jacques (M1, 2021)
• Daria Pchelina (M1, 2019) [ Report ]
• Enka (Nikola) Blanchard (M2, 2015; PhD co-advisor with Ted Selker 2016-2019) Prix de thèse PSL SHS Interface Sciences/Humanités [ web | Remise du prix ]
• Alberto Vera Azócar (U. Chile, several research internships 2013, 2015)
• Damien Regnault (PhD co-advisor with Éric Thierry, 2005-2008)
• Julien Robert (PhD advisor, 2006-2009)
• Emmanuelle Lebhar (PhD co-advisor with Michel Morvan, 2003-2005)
• Sandeep Dey (Master thesis advisor, 2005)

Teaching

• Mastère 2 M2ICA CR16: Molecular programming: Theory & wet-lab experiments [ web ]
• Cours 3ème année STA et TYLA à l’EPITA Lyon

Softwares

• ENSnano: our 3D DNA nanostructure design software for Windows, Mac OS and linux. Codeveloped with Nicolas Levy, 2021 [ website | youtube channel ]
• OS simulator: a fast and memory-efficient iPad app that simulates arbitrary Oritatami Systems (works with limitations on Apple silicon Mx too), 2021 [ website | download ]
• CAOS simulator: an iOS app implementing our Oritatami cellular automata simulation, 2020 [ source code ]
• Scary Pacman: an iOS app implementing our Oritatami scaling algorihms, 2018 [ source code ]
• Clean scan: an iOS app to take printable pictures of white, green and black board, 2015

Publications

• 2025
• Algorithm-driven DNA nanostructure design for advanced functionality
  Nicolas Levy and Julie Finkel, Allan Mills, Gerrit Wilkens, Anjelica Kucinic, Aurelie Ancelin, Pierre Marcus, Octave Hazard, Joris Picot, Daria Pchelina, Gaëtan Bellot* and Nicolas Schabanel*. In review at Nature Nanotechnology, 2025. [ Article (12 pages) | Supplementary Informations (127 pages) ]
• 2023
• Ok: A Kinetic Model for Locally Reconfigurable Molecular Systems
  Pierre Marcus, Nicolas Schabanel and Shinnosuke Seki. In: Jonoska, N., Winfree, E. (eds) Visions of DNA Nanotechnology at 40 for the Next 40. Natural Computing Series. Springer, Singapore.
• 2022
• Rule-of-thumb-free geometry-driven design of arbitrary complex curved DNA origami with ENSnano (Abstract)
  Nicolas Levy, Allan Mills, Gaëtan Bellot*, Nicolas Schabanel*. DNA28, New Mexico, Aug. 2022.
  
• Turedo a new computational model for molecular nanobots?, Nicolas Schabanel.
  Invited talk at the special session «Computing with bio-molecules» at CiE 2022, Swansea, Jul 2022.
• Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)
  Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier. STACS, 26:1-23, 2022.
  Supplementary material: [ Turedo2oritatami compiler | Full version ]
• 2021
• ENSnano: a 3D modeling software for DNA nanostructures
  Nicolas Levy, Nicolas Schabanel. In DNA27, LIPIcs, vol. 205, pp.5:1-23, doi:10.4230/LIPIcs.DNA.27.5, 2021.
  :!: best student paper & best presentation award.
  :!: Download ENSnano at: [ ENSnano website ] [ Youtube channel ]
• 2020
• Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model [ Full version ]
  Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata. In LATIN, LNCS 12118:425-436, Sao Paulo, 2020. doi:10.1007/978-3-030-61792-9_34 hal-02410874
  Download the iOS app CAOS simulator implementing our simulation [ source code ]
• 2019
• Oritatami: A Computational Model for Molecular Co-Transcriptional Folding [ PDF & supplementary materials ]
  Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. IJMS (Int. J. of Molecular Sciences), Special Issue Nucleic Acid Nanotechnology, 2019, 20(9), 2259.
  DOI
• 2018
• Proving the Turing Universality of Oritatami Co-Transcriptional Folding [ Supplementary materials ]
  Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. ISAAC 2018, LIPIcs.ISAAC.2018.23:1-23:13, Jiaoxi, Yilan County, Taiwan, Dec. 2018. [ Arxiv ]
• Know When to Fold ’Em: Self-Assembly of Shapes by Folding in Oritatami
  Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thomas. DNA24, LNCS 11145:19-36, Jinan, China, Oct. 2018.
  Invited talk at UCNC2018 Self-assembly, geometry and computation workshop, Fontainebleau, June 2018.
  Download the iOS app Scary Pacman implementing our algorithms [ source code ]
• 2017
• Dynamic Facility Location: Minimizing the Sum of Radii
  Nicolas K. Blanchard, Nicolas Schabanel. WALCOM, LNCS 10167:30-41, march 2017.
• 2016
• Oritatami systems: a computational model for co-transcriptional folding
  Nicolas Schabanel. Invited plenary talk at Automata, Jun. 2016.
• Programming biomolecules that fold greedily during transcription
  Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. MFCS, LIPIcs 58, 43:1-43:14, Aug. 2016.
• Folding Turing is hard but feasible
  Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki.HALG, Jun. 2016.
• 2015
• Efficient universal computation by molecular co-transcriptional folding (Short announcement)
  Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. DNA21, 1 page, 2015.
• Facility Location in Evolving Metrics
  with David Eisenstat and Claire Mathieu. ICALP, pages 459-470, 2014.
• 2013
• Stochastic Cellular Automata: Correlations, Decidability and Simulations
  with Pablo Arrighi and Guillaume Theyssier. Fundamenta Informaticæ, 126:121-156, 2013.
• 2012
• Intrinsic simulations between stochastic cellular automata
  with Pablo Arrighi and Guillaume Theyssier. AUTOMATA & JAC, EPTCS, 90:208–224, 2012.
• Randomness + Determinism = Progresses: Why random processes could be favored by evolution
  Progress in Biophysics and Molecular Biology (Special edition on the conference ”Chance at the heart of the cell”), 110(1):129–136, 2012.
• 2011
• Les complexités : point de vue d’un institut des systèmes complexes (in French)
  with Éric Bertin, Guillaume Beslon, Olivier Gandrillon, Sébastian Grauwin, and Pablo Jensen. Hermès, 60:145–150, 2011.
• Optimal path search in small worlds: Dimension matters
  with George Giakkoupis. STOC, 43:393–402, 2011.
• Analyzing search algorithms in smallworlds
  TERANET (colocated with DISC), 4 pages, Roma, Italy, Sep. 2011.
• 2010
• Minimizing Maximum Flowtime of Jobs with Arbitrary Parallelizability
  with Kirk Pruhs and Julien Robert. WAOA, LNCS 6534:237–248, 2010.
• Systèmes complexes & algorithmes (in French)
  Habilitation à diriger des recherches, Université Paris Diderot, 2010. Slides
• On the analysis of “simple” 2D stochastic cellular automata
  with Damien Regnault and Éric Thierry. Invited publication to the special issue of DMTCS in honor of Philippe Flajolet, 12(2):263–294, 2009.
• 2009
• Progresses in the analysis of stochastic 2D cellular automata: a study of asynchronous 2D Minority
  with Damien Regnault and Éric Thierry. TCS, 410(47-49):4844-4855S, 2009. doi:10.1016/j.tcs.2009.06.024
• 2008
• Non-Clairvoyant Scheduling with Precedence Constraints
  with Julien Robert. SODA, 491-500, Jan. 2008.
• On the analysis of ”simple” 2D stochastic cellular automata
  with Damien Regnault and Éric Thierry. LATA, LNCS 5196:452-463, Mar. 2008.
• Time optimal self-assembling of 2D and 3D shapes: the case of squares and cubes
  with Florent Becker and Éric Rémila. DNA14, LNCS 5347:144–155, June 2008.
• Graph augmentation via metrics embedding
  with Emmanuelle Lebhar. OPODIS, LNCS 5401:217-225, Dec. 2008.
• 2007
• Non-clairvoyant batch sets scheduling: Fairness is fair enough
  with Julien Robert. ESA, LNCS 4698:742-753, Oct. 2007.
• Progresses in the analysis of stochastic 2D cellular automata: a study of asynchronous 2D Minority
  with Damien Regnault and Éric Thierry. MFCS, LNCS 4708:320-332, Aug. 2007.
• Small alliances in graphs
  with Rodolfo Carvajal, Martín Matamala, and Iván Rapaport. MFCS, LNCS 4708:218-227, Aug. 2007.
• Pull-Based Data Broadcast with Dependencies: Be Fair to Users, not to Items
  with Julien Robert. SODA, p. 238-247, Jan. 2007.
• 2006
• Customized Newspaper Problem: Data Broadcast with dependancies
  with Sandeep Dey. LATIN, LNCS 3887:362-373, Valdivia, march 2006.
• Asynchronous behavior of double-quiescent elementary cellular automata
  with Nazim Fatès, Damien Regnault and Éric Thierry. LATIN, LNCS 3887:455-466, Valdivia, march 2006.
• Could any graph be turn into a smallworld?
  with Philippe Duchon, Nicolas Hanusse and Emmanuelle Lebhar. TCS, 355(1):96-103, 2006.
• Towards small world emergence
  with Philippe Duchon, Nicolas Hanusse and Emmanuelle Lebhar.SPAA, 225-232, july 2006.
• Fully asynchronous behavior of double-quiescent elementary cellular automata
  with Nazim Fatès, Michel Morvan, Éric Thierry.TCS, 362(1-3):1-16, 2006.
• 2005
• Close to optimal decentralized routing in long-range contact networks
  with Emmanuelle Lebhar. TCS, 348:294–310, 2005.
• Could any graph be turn into a smallworld?
  with Philippe Duchon, Nicolas Hanusse and, Emmanuelle Lebhar. DISC, LNCS 3724:512-513, Cracow, september 2005.
• Fully asynchronous behavior of double-quiescent elementary cellular automata
  with Nazim Fatès, Michel Morvan and Éric Thierry. MFCS, LNCS 3618:316-327, Gdansk, september 2005.
• 2004
• Almost optimal decentralized routing in long-range contact networks
  with Emmanuelle Lebhar. ICALP, Turku, Finland, july 2004. Full
• An Internet Graph Model based on trade-off optimization
  with José-Ignacio Alvarez-Hamelin. European Physical Journal B (EPJB), 38(2):231-238, 2004.
  A preliminary version of the paper was presented at the Conference on Growing Networks and Graphs in Statistical Physics, Finance, Biology and Social Systems, Rome, 1-5 Sep. 2003.
• 2003
• The data broadcast problem with non-uniform transmission times
  with Claire Kenyon. Algorithmica, 35:146-175, February 2003.
  A preliminary version of this paper was published in SODA 1999, pages 547-556.
• 2000
• Algorithmes d'approximation pour les télécommunications sans fil : Ordonnancement pour la dissémination de données et Allocation statique de fréquences (in French) PDF
  PhD Thesis, École normale supérieure de Lyon, 2000. Advisors: Claire Kenyon and Stéphane Ubéda (local advisor).
• Polynomial-Time Approximation Scheme for Data Broadcast
  with Claire Kenyon and Neal E. Young. STOC, pages 659-666, May 2000.
• The databroadcast problem with preemption
  STACS, LNCS 1770:181-192, Lille, February 2000. Full
• 1999
• The data broadcast problem with non-uniform transmission times
  with Claire Kenyon. SODA, pp.547–556. SIAM, Jan. 1999.
• A randomized BSP algorithm for the maximal independent set problem
  with Afonso Ferreira. In PPL, 9(3):411-422, 1999.
  A preliminary version was published in I-SPAN'99, pages 284-289, june 1999.
• 1998 and beyond
• Parallel algorithm for the optimization of the span of an hexagonal frequency planning graph
  with Stéphane Ubéda and Janez Žerovnik. Telepar, pages 237-241, Boston, Avril 1998. SCS.
• Concurrent rebalancing of AVL trees: a fine-grained approach
  with Luc Bougé, J. Gabarro, and X. Messeguer. Euro-Par, LNCS 1300:421-429, Août 1997. Full
• Basic linear algebra operations in SLI arithmetic
  with M. A. Anuta, D. W. Lozier, and Peter R. Turner. Euro-Par, LNCS 1124:193-202, Août 1996.