Jean-Noël Grad

Jean-Noël Grad
Postdoc

Office:	1.041
Phone:	+49 711 685-67715
Fax:	+49 711 685-63658
Email:	jgrad _at_ icp.uni-stuttgart.de
Address:	Jean-Noël Grad Institute for Computational Physics Universität Stuttgart Allmandring 3 70569 Stuttgart Germany

Research software engineer

ORCID: 0000-0002-5821-4912

GitHub: jngrad

Publications

• Rudolf Weeber, Jean-Noël Grad, David Beyer, Pablo M. Blanco, Patrick Kreissl, Alexander Reinauer, Ingo Tischler, Peter Košovan, Christian Holm.
  ESPResSo, a Versatile Open-Source Software Package for Simulating Soft Matter Systems.
  In Comprehensive Computational Chemistry, pages 578–601. Edited by Manuel Yáñez, Russell J. Boyd. Edition 1.
  Elsevier, Oxford, 2024. ISBN: 978-0-12-823256-9.
  [PDF] (3.7 MB) [DOI]

• Jean-Noël Grad, Rudolf Weeber.
  Report on the current scalability of ESPResSo and the planned work to extend it.
  MultiXscale Deliverable, EuroHPC Centre of Excellence MultiXscale, Zenodo, 2023.
  [PDF] (1.2 MB) [DOI]

• Shoaib Sufi, Carlos Martinez-Ortiz, Peter Doorn, Jessica Farrell, Michelle Barker, Daniel S. Katz, Adam Jackson, Alexander Struck, Andrew Sandeman, Andrew Stewart, Andy R. Terrel, Ben Companjen, Carina Haupt, Carly Strasser, Carole Goble, Christina Von Flach Garcia Chavez, Colin Venters, Dianne Dietrich, Elena Colón-Marrero, Emma Irwin, Euan Cochrane, Fakhereh (Sarah) Alidoost, Fotis Psomopoulos, Gerard Coen, Hilary Szu Yin Shiue, Ignacio Blanquer, Jean-Noël Grad, Jesse de Vos, Jessica Meyerson, Kelly Rosa Braghetto, Konstantinos Repanas, Martin Hammitzsch, Meta Keijzer-de Ruijter, Michael Courtney, Morane Gruenpeter, Mustafa Doğan, Neil Chue Hong, Nicolas M. Thiéry, Otigbu Austine, Pamela Nye, Patricia Falcão, Paula Andrea Martinez, Rachael Ainsworth, Raniere Silva, Scott Kirycki, Stian Soiland-Reyes, Tom Honeyman, Vicky Rampin.
  Report on the Workshop on Sustainable Software Sustainability 2021 (WoSSS21).
  Zenodo, 2023.
  [PDF] (13 MB) [DOI]

• Anna-Lena Lamprecht, Carlos Martinez-Ortiz, Michelle Barker, Sadie L. Bartholomew, Justin Barton, Neil Chue Hong, Jeremy Cohen, Stephan Druskat, Jeremy Forest, Jean-Noël Grad, Daniel S. Katz, Robin Richardson, Robert Rosca, Douwe Schulte, Alexander Struck, Marion Weinzierl.
  What Do We (Not) Know About Research Software Engineering?
  Journal of Open Research Software 10(1):11, 2022.
  [PDF] (1.1 MB) [Preprint] [DOI]

• Neda Rafieiolhosseini, Matthias Killa, Thorben Neumann, Niklas Tötsch, Jean-Noël Grad, Alexander Höing, Thies Dirksmeyer, Jochen Niemeyer, Christian Ottmann, Shirley K. Knauer, Michael Giese, Jens Voskuhl, Daniel Hoffmann.
  Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups.
  Beilstein Journal of Organic Chemistry 18(1):1322–1331, 2022.
  [PDF] (3.4 MB) [Preprint] [DOI]

• Kai Szuttor, Florian Weik, Jean-Noël Grad, Christian Holm.
  Modeling the current modulation of bundled DNA structures in nanopores.
  The Journal of Chemical Physics 154(5):054901, 2021.
  [PDF] (3.0 MB) [Preprint] [DOI]

• Annika Meiners, Sandra Bäcker, Inesa Hadrović, Christian Heid, Christine Beuck, Yasser B. Ruiz-Blanco, Joel Mieres-Perez, Marius Pörschke, Jean-Noël Grad, Cecilia Vallet, Daniel Hoffmann, Peter Bayer, Elsa Sánchez-García, Thomas Schrader, Shirley K. Knauer.
  Specific inhibition of the Survivin–CRM1 interaction by peptide-modified molecular tweezers.
  Nature Communications 12(1):1505, 2021.
  [PDF] (2.5 MB) [DOI]

• Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojciech Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Jan Hegewald, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H.C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Joerg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekermann, Stefan Unger, Rudolf Weeber.
  An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved].
  F1000Research 9(295), 2021.
  [PDF] (912 KB) [Preprint] [DOI]

• Bernd Flemisch, Sibylle Hermann, Christian Holm, Miriam Mehl, Guido Reina, Benjamin Uekermann, David Boehringer, Thomas Ertl, Jean-Noël Grad, Dorothea Iglezakis, Alexander Jaust, Timo Koch, Anett Seeland, Rudolf Weeber, Florian Weik, Kilian Weishaupt.
  Umgang mit Forschungssoftware an der Universität Stuttgart.
  Technical report, Universität Stuttgart, 2020.
  [PDF] (134 KB) [DOI]

• Daniel Smolin, Niklas Tötsch, Jean-Noël Grad, Jürgen Linders, Farnusch Kaschani, Markus Kaiser, Michael Kirsch, Daniel Hoffmann, Thomas Schrader.
  Accelerated trypsin autolysis by affinity polymer templates.
  RSC Advances 10(48):28711-28719, 2020.
  [PDF] (1000 KB) [DOI]

• Alba Gigante, Jean-Noël Grad, Jeroen Briels, Maria Bartel, Daniel Hoffmann, Christian Ottmann, Carsten Schmuck.
  A new class of supramolecular ligands stabilizes 14-3-3 protein–protein interactions by up to two orders of magnitude.
  Chemical Communications 55(1):111-114, 2019.
  [PDF] (2.1 MB) [DOI]

• Jean-Noël Grad, Alba Gigante, Christoph Wilms, Jan Nikolaj Dybowski, Ludwig Ohl, Christian Ottmann, Carsten Schmuck, Daniel Hoffmann.
  Locating Large, Flexible Ligands on Proteins.
  Journal of Chemical Information and Modeling 58(2):315–327, 2018.
  [PDF] (4.8 MB) [Preprint] [DOI]

• Martin Ehlers, Jean-Noël Grad, Sumit Mittal, David Bier, Marcel Mertel, Ludwig Ohl, Maria Bartel, Jeroen Briels, Marius Heimann, Christian Ottmann, Elsa Sanchez-Garcia, Daniel Hoffmann, Carsten Schmuck.
  Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein.
  ChemBioChem 19(6):591-595, 2018.
  [PDF] (1.2 MB) [DOI]

Workshops

As a co-organizer:

• Simulating energy materials with ESPResSo and waLBerla, October 9th-13th 2023, Institute for Computational Physics, University of Stuttgart, Germany, hybrid event.
• Simulating the dynamics of soft matter with ESPResSo, PyStencils and LbmPy, October 10th-14th 2022, Institute for Computational Physics, University of Stuttgart, Germany, hybrid event.
• Combining particle-based and continuum modelling in soft matter physics with ESPResSo, PyStencils, and LbmPy, October 11th-15th 2021, Institute for Computational Physics, University of Stuttgart, Germany, hybrid event.
• ESPResSo and Python: Versatile Tools for Soft Matter Research, October 5th-9th 2020, Institute for Computational Physics, University of Stuttgart, Germany, online event.

As an attendee:

• International Conference on Data-Integrated Simulation Science (SimTech2023), October 4th-6th 2023, University of Stuttgart, Germany.
  • poster: Jean-Noël Grad, Alexander Reinauer, Christian Holm, Rudolf Weeber, ESPResSo – An open source package for simulating coarse-grained models, in: Theme 4 - Knowledge, Data & Software (abstract, poster)
• FAIR and TRUE Data Processing for Soft Matter Simulations, September 25th-27th 2023, Max Planck Institute for Polymer Research, Mainz, Germany.
  • talk: Jean-Noël Grad, Simulation data management in ESPResSo (talk slides)
• un-deRSE23 – Unconference for Research Software Engineering in Germany, September 26th-28th, Dornburger Schlösser, Jena, Germany.
• deRSE23 – Conference for Research Software Engineering in Germany, February 20th-22nd 2023, Heinz Nixdorf Forum, Paderborn, Germany.
  • talk: Jean-Noël Grad, Alexander Reinauer, Markus Holzer, Christian Holm, Rudolf Weeber, ESPResSo and LbmPy: Re-usable and modular interface between particle-based and lattice-based simulation codes, in: Session Integration vs. Modularity (talk slides).
• Day of Teaching and Learning, “University of Stuttgart beyond THE LÄND!”, November 30th 2022, Gießelmann, Wieprecht (organizers), University of Stuttgart, Germany.
  • talk: Jean-Noël Grad, Rudolf Weeber, Christian Holm, Teaching soft matter physics to an international audience, in: Track 1 Courses taught in English (talk slides)
• Managing Research Software, September 15th-16th 2022, DINI/nestor workshop, University of Stuttgart, Germany (hybrid event).
  • talk: Jean-Noël Grad, Alexander Reinauer, Rudolf Weeber, Christian Holm, Managing sustainable and community-driven research software in physics (talk slides, workshop program)
• Software Engineering (SE) '22, February 21th-25th 2022, Department of Computer Science, Humboldt University of Berlin, Germany (online event).
  • talk: Jean-Noël Grad, Rudolf Weeber, Markus Holzer, Christian Holm, Making use of established codes instead of re-inventing the wheel: Using lattice-based methods from waLBerla into ESPResSo, in: Track rSE 22 (talk slides).
• WoSSS21 - Workshop on Sustainable Software Sustainability, October 6th-8th 2021, Online.
  • notes published in Sufi et al. Report on the Workshop on Sustainable Software Sustainability 2021. Zenodo, 2023.
• What do we (not) know about RSE?, October 30th 2020, Lamprecht, Barker, Martinez (organizers), International Series of Online Research Software Events (SORSE).
  • notes published in Lamprecht et al. What Do We (Not) Know About Research Software Engineering?. JORS, 2022.
• FAIR 4 Research Software, November 19th 2020, Lamprecht, Katz, Psomopoulos et al. (organizers), International Series of Online Research Software Events (SORSE).
  • notes published in Gruenpeter et al. SORSE2020 outputs for the FAIR4RS workshop. Zenodo, 2020.
• Nachhaltigkeit von Forschungssoftware, November 7th-8th 2019, DFG-Rundgespräch, Loewe, Bach, Druskat, Renard, Seemann (organizers), Robert Koch-Institut, Berlin, Germany.
  • notes published in Struck et al. A Guide for Publishing, Using, and Licensing Research Software in Germany, Zenodo, 2020.
  • de-RSE Position 001 published in Anzt et al. An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved], F1000Research, 2021.
• Herausforderungen für die nachhaltige Entwicklung, Bereitstellung und Pflege von Forschungssoftware in Deutschland, June 5th 2019, Loewe, Katerbow, Seemann, Bach, Druskat (organizers), deRSE19, Albert Einstein Science Park, Potsdam, Germany.
• deRSE19 - Conference for Research Software Engineers in Germany, June 4th-6th 2019, Albert Einstein Science Park, Potsdam, Germany.
  • poster: Jean-Noël Grad, Rudolf Weeber, Florian Weik, Kai Szuttor, Christian Holm, ESPResSo: Experiences in lowering the entry barrier for new developers in a particle-based simulation package (abstract)

Teaching

• ESPResSo Block course (WiSe 23/24)
• ESPResSo Block course (WiSe 22/23)
• ESPResSo Block course (WiSe 21/22)
• ESPResSo Block course (WiSe 20/21)