Algorithmics of motion: From robotics, through structural biology, toward atomic-scale CAD Juan Cortés To cite this version: Juan Cortés. Algorithmics of motion: From robotics, through structural biology, toward atomic-scale CAD. Robotics [cs.RO]. Universite Toulouse III Paul Sabatier, 2014. tel-01110545 HAL Id: tel-01110545 https://tel.archives-ouvertes.fr/tel-01110545 Submitted on 28 Jan 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Habilitation a Diriger des Recherches (HDR) delivr´eepar l'Universit´ede Toulouse pr´esent´eeau Laboratoire d'Analyse et d'Architecture des Syst`emes par : Juan Cort´es Charg´ede Recherche CNRS Algorithmics of Motion: From Robotics, Through Structural Biology, Toward Atomic-Scale CAD Soutenue le 18 Avril 2014 devant le Jury compos´ede : Michael Nilges Institut Pasteur, Paris Rapporteurs Fr´ed´ericCazals INRIA Sophia Antipolis-Mediterrane St´ephane Doncieux ISIR, UPMC-CNRS, Paris Oliver Brock Technische Universit¨atBerlin Examinateurs Jean-Pierre Jessel IRIT, UPS, Toulouse Jean-Paul Laumond LAAS-CNRS, Toulouse Pierre Monsan INSA, Toulouse Membre invit´e Thierry Sim´eon LAAS-CNRS, Toulouse Parrain Contents Curriculum Vitæ1 1 Research Activities5 1.1 Introduction...................................5 1.2 Methodological advances............................6 1.2.1 Algorithmic developments in a general framework...........6 1.2.2 Methods for molecular modeling and simulation............ 13 1.3 Applications in robotics............................ 17 1.3.1 Manipulation and Grasping....................... 17 1.3.2 Motion planning for aerial robots.................... 19 1.4 Applications in structural biology, biotechnology and materials science................................ 21 1.4.1 Modeling conformational transitions of proteins and peptides.... 21 1.4.2 Analyzing and predicting molecular interactions........... 24 1.4.3 Polymer modeling............................ 26 2 Other Activities 27 2.1 Teaching and Advising Activities....................... 27 2.1.1 Teaching................................. 27 2.1.2 Advising.................................. 28 2.2 Organizational and Editorial Activities.................... 29 2.2.1 Chairing activities, organization de conferences et workshops.... 29 2.2.2 Editorial activities............................ 30 2.2.3 Other organizational and evaluation duties.............. 30 2.3 Projects and collaborations.......................... 30 2.3.1 Contractual projects........................... 30 2.3.2 Other collaborations........................... 32 2.4 Mobility..................................... 34 2.4.1 Disciplinary mobility........................... 34 2.4.2 Geographic mobility........................... 34 2.5 Software development............................. 35 2.5.1 Move3D.................................. 35 2.5.2 MoMA................................... 35 2.6 Technology transfer, industrial relationships................. 36 3 Research Project 37 3.1 Overview.................................... 37 3.2 Methodological developments......................... 38 3.3 Robotics applications: motion planning and control of aerial robots................. 39 3.4 Towards integrative approaches in structural biology............ 40 3.5 Computational Protein Design........................ 41 ii Contents 3.6 Towards atomic-scale CAD.......................... 42 4 List of Publications 45 Annex 1: Selected Publications 51 Curriculum Vitæ Full name: Juan Cort´es-Mastral Date of birth: 15/08/1974 Place of birth: Zaragoza, Spain Marital status: Married, 1 child Professional address: LAAS-CNRS 7 Av. Colonel Roche, F-31400 Toulouse, France Phone: +33 5 61 33 63 45 Fax: +33 5 61 33 64 55 E-mail: [email protected] Web: http://homepages.laas.fr/jcortes/ Professional Experience CNRS Researcher at LAAS-CNRS (Toulouse) From Oct. 2004 • Area: Algorithmics of motion, with applications in robotics, structural biology, biotechnology and materials science Invited Professor at IRI (CSIC-UPC, Barcelona) Nov. 2008 - Nov. 2009 • Subject: New approaches to peptide and polymer modeling Post-doctoral Researcher at UFIP (Univ. Nantes-CNRS) Mar. 2004 - Sep. 2004 • Subject: Computational prediction and analysis of protein loop motions PhD thesis preparation at LAAS-CNRS (Toulouse) Oct. 2000 - Dec. 2003 • Subject: Motion planning algorithms for close-chain mechanisms Undergrad. Research Assistant at LAAS-CNRS (Toulouse) Aug. 1999 - Sep. 2000 • Subject: Participation to the development of Move3D: a generic path-planning software platform Education PhD - Computer science / Robotics December 2003 • Institut National Polytechnique de Toulouse (France) Dipl^omed'Etudes Approfondies (Master) - Control / Robotics July 2000 • Institut National Polytechnique de Toulouse (France) Engineering Degree - Specialization in Control and Robotics June 2000 • Centro Polit´ecnicoSuperior - Universidad de Zaragoza (Spain) Awards Prix Jean Lagasse : Award to the best PhD theses of the CNRS STIC department, 2004 • Prix L´eopold Escande : Award to the best PhD theses of the INP Toulouse, 2004 • 2 Curriculum Vitæ Summary of Research and Teaching Activities Research Topics Basic research, Robotics: Algorithmics of motion. Motion computation and analysis for • complex systems. Applications in robotics, mainly to motion planning and manipulation task planning. Interdisciplinary research: Development of computational methods to study protein flex- • ibility and interactions, for protein design, and polymer modeling. Applications in structural biology, biotechnology and materials science. Publications 20 articles in scientific journals on robotics (IEEE Trans. Robot., Int. J. Robot. Res.), • bioinformatics and theoretical physical chemistry (Bioinformatics, J. Comput. Chem., Proteins, Polymer, Nucl. Acids Res., among others). 4 book chapters. • 23 publications in proceedings of international conferences and workshops. • 5 invited talks, and 9 seminars in French and foreign universities. • Google Scholar h-index = 20 ; 1133 citations. • Advising activities Advisor or co-advisor of 8 PhD students and 6 post-docs. • Advisor of 12 undergraduate students. • Scientific advisor of 1 CNRS Research Engineer. • Teaching Co-organizer and teacher of the international, interdisciplinary school \Algorithms in • Structural Bioinformatics", 2012, 2013. ( http://algosb.sciencesconf.org/ ) Member of the teaching team of the master program \Ing´enieriede la Mati`ere: Mod´elisa- • tion des Processus Physiques", Universit´ede Toulouse, since 2008. Teacher in the \Master en Simulaci´onde Pol´ımerosy Biopol´ımeros", Universidad Poli- • t`ecnicade Catalunya (Barcelona, Spain), 2011. Teacher in the \Master en Syst`emesAutomatiques, Informatiques et D´ecisionnels", • Universit´ede Toulouse, 2008-2010. Teacher in the \Master de Rob´otica"of the Universidad Polit´ecnicade Valencia (Spain), • 2008. Teacher in the \Summer School on Image & Robotics", CIC Mexico, 2007. • 3 Organizational and editorial activities Co-chair of the IEEE RAS Technical Committee on Algorithms for Planning and Control • of Robot Motion, since 2009. Co-organizer of the AAAI Workshop on “Artificial Intelligence and Robotics Methods • in Computational Biology", 2013. Co-organizer of the ACM-BCB Tutorial \From Robot Motion Planning to Modeling • Structures and Motions of Biological Molecules", 2013. Co-organizer of the RSS Workshop \Motion Planning: From Theory to Practice", 2010. • Program Committee Member of the Computational Structural Bioinformatics Workshop • (CSBW), 2011-2013. Program Committee Member of the international conference ECAI 2008, 2010. • Associated Editor of the IEEE international conferences ICRA and IROS, 2009-2013. • Reviewer of : IEEE Journals and Conferences (T-RO, T-ASE, ICRA, IROS, ...), The • International Journal of Robotics Research, Workshop on the Algorithmic Foundations of Robotics, Journal of Computations Chemistry, Journal of Chemical Theory and Com- putation, Bioinformatics, Archives of Biochemistry and Biophysics, ... Software development Coordinator of the developments of MoMA, a software platform for molecular modeling. • Participation in the development of Move3D, a generic motion planning software. • Mobility Disciplinary mobility: Being robotics my basic research area, I am interested in the de- • velopment of methods in structural biology and materials science, as well as in applications to biotechnologies and nanotechnologies. Geographic mobility: One-year stay (Nov. 2008 - Nov. 2009) at the l'Universidad • Polit´ecnicade Catalunya (Barcelona, Spain), in the framework of international mobility pro- grams of the CNRS and the INPT. Participation in projets Robotics projects: 6 European projects (ARCAS, SAPHARI, DEXMART, PHRIENDS, • MOVIE, MOLOG), 1 French national project (IRASIS). Computational biology / Molecular modeling projects: 3 French national projects • (ProtiCAD, GlucoDesign, NanoBioMod), 1 regional project (AMYLO), 1 trans-regional project (AMOBIO), 3 local projects (ITAV-ALMA, OTIMASU, AMORO), 1 CNRS project (BioMove3D), 1 ADEME project.