HINSEN Konrad

 

email : konrad.hinsen@cnrs-orleans.fr

Phone : +33 2.38.25.78.42

Researcher and co-coordinator of the thematic group “Statistical and computational physics of biomolecular systems”

 



71 documents

Article dans une revue

  • Gerald R. Kneller, Konrad Hinsen. Memory effects in a random walk description of protein structure ensembles. Journal of Chemical Physics, American Institute of Physics, 2019, 150 (6), pp.064911. ⟨10.1063/1.5054887⟩. ⟨hal-02117662⟩
  • Konrad Hinsen. Dealing With Software Collapse. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2019, 21 (3), pp.104-108. ⟨10.1109/MCSE.2019.2900945⟩. ⟨hal-02117588⟩
  • Konrad Hinsen. Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface. PeerJ Computer Science, PeerJ, 2018, 4, pp.e158. ⟨10.7717/peerj-cs.158⟩. ⟨hal-02068574⟩
  • Konrad Hinsen. Domain-Specific Languages in Scientific Computing. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2018, 20 (1), pp.88-92. ⟨10.1109/MCSE.2018.011111130⟩. ⟨hal-01966145⟩
  • Konrad Hinsen. Reusable vs. re-editable code. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2018, 20 (3), pp.78-83. ⟨10.1109/MCSE.2018.03202636⟩. ⟨hal-01966146⟩
  • Nicolas P. Rougier, Konrad Hinsen. Correspondance. Code review poses extra challenges. Nature, Nature Publishing Group, 2018, pp.309. ⟨10.1038/d41586-018-04628-w⟩. ⟨hal-01773411⟩
  • Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, et al.. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, Elsevier, 2017, ⟨10.1016/j.future.2017.01.012⟩. ⟨hal-01516082⟩
  • Nicolas Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena Barba, et al.. Sustainable computational science: the ReScience initiative. PeerJ Computer Science, PeerJ, 2017, 3. ⟨hal-01592078⟩
  • Konrad Hinsen. A Dream of Simplicity: Scientific Computing on Turing Machines. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2017, 19 (3), pp.78-85. ⟨10.1109/MCSE.2017.39⟩. ⟨hal-02117720⟩
  • Konrad Hinsen. A Dream of Simplicity: Scientific Computing on Turing Machines. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2017, 19 (3), pp.78 - 85. ⟨10.1109/mcse.2017.39⟩. ⟨hal-01618280⟩
  • Konrad Hinsen. The Roles of Code in Computational Science. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2017, 19 (1), pp.78 - 82. ⟨10.1109/MCSE.2017.18⟩. ⟨hal-01618279⟩
  • Christophe Pouzat, Andrew P. Davison, Konrad Hinsen. La recherche reproductible : une communication scientifique explicite. Statistique et Société, Société française de statistique, 2016, Deux débats sur les données, 3 (1). ⟨hal-01478360⟩
  • Konrad Hinsen, Gérald Kneller. Communication: A multiscale Bayesian inference approach to analyzing subdiffusion in particle trajectories. Journal of Chemical Physics, American Institute of Physics, 2016, 145 (15), pp.151101. ⟨10.1063/1.4965881⟩. ⟨hal-02154066⟩
  • Konrad Hinsen. The Power to Create Chaos. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2016, 18 (4), pp.75-79. ⟨10.1109/MCSE.2016.67⟩. ⟨hal-02071770⟩
  • Konrad Hinsen. ActivePapers: a platform for publishing and archiving computer-aided research.. F1000Research, Faculty of 1000, 2015, pp.doi:10.12688/f1000research.5773.2. ⟨10.12688/f1000research.5773.2.⟩. ⟨hal-01171263⟩
  • Konrad Hinsen, Aurore Vaitinadapoule, Mariano A. Ostuni, Catherine Etchebest, Jean-Jacques Lacapere. Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data.. Biochimica et Biophysica Acta:Biomembranes, Elsevier, 2015, 1848 (2), pp.568-580. ⟨10.1016/j.bbamem.2014.10.028.⟩. ⟨hal-01171268⟩
  • Konrad Hinsen. Technical Debt in Computational Science. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2015, 17 (6), pp.103-107. ⟨10.1109/MCSE.2015.113⟩. ⟨hal-02072258⟩
  • Gerald Kneller, Konrad Hinsen. Protein secondary-structure description with a coarse-grained model. Acta Crystallographica Section D: Biological Crystallography, International Union of Crystallography, 2015, 71 (7), pp.1411-1422. ⟨10.1107/s1399004715007191⟩. ⟨hal-02072279⟩
  • Konrad Hinsen. The Approximation Tower in Computational Science: Why Testing Scientific Software Is Difficult. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2015, 17 (4), pp.72-77. ⟨10.1109/MCSE.2015.75⟩. ⟨hal-01171382⟩
  • Konrad Hinsen. Writing Software Specifications. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2015, 17 (3), pp.54-61. ⟨10.1109/MCSE.2015.64⟩. ⟨hal-01171458⟩
  • Konrad Hinsen. Computational science: shifting the focus from tools to models. F1000Research, Faculty of 1000, 2014, 3, pp.101. ⟨10.12688/f1000research.3978.2⟩. ⟨hal-01175456⟩
  • Konrad Hinsen. MOSAIC: A Data Model and File Formats for Molecular Simulations. Journal of Chemical Information and Modeling, American Chemical Society, 2014, 54 (1), pp.131-137. ⟨10.1021/ci400599y⟩. ⟨hal-01179151⟩
  • Guillaume Chevrot, Konrad Hinsen, Gerald Kneller. Model-free simulation approach to molecular diffusion tensors. Journal of Chemical Physics, American Institute of Physics, 2013, 139 (15), pp.154110. ⟨10.1063/1.4823996⟩. ⟨hal-02070748⟩
  • Konrad Hinsen, Shuangwei Hu, Gerald R. Kneller, Antti J. Niemi. A comparison of reduced coordinate sets for describing protein structure. Journal of Chemical Physics, American Institute of Physics, 2013, 139 (12), pp.124115. ⟨10.1063/1.4821598⟩. ⟨hal-01528424⟩
  • Edvin Fuglebakk, Nathalie Reuter, Konrad Hinsen. Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions. Journal of Chemical Theory and Computation, American Chemical Society, 2013, 9 (12), pp.5618-5628. ⟨10.1021/ct400399x⟩. ⟨hal-02070831⟩
  • Konrad Hinsen. Daydreaming about Scientific Programming. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2013, 15 (5), pp.77-79. ⟨10.1109/MCSE.2013.104⟩. ⟨hal-02070862⟩
  • Konrad Hinsen. Software Development for Reproducible Research. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2013, 15 (4), pp.60-63. ⟨10.1109/MCSE.2013.91⟩. ⟨hal-02070857⟩
  • Konrad Hinsen. A Glimpse of the Future of Scientific Programming. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2013, 15 (1), pp.84-88. ⟨hal-00817458⟩
  • Konrad Hinsen. Managing State. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2012, 14 (1), pp.80-86. ⟨10.1109/MCSE.2012.11⟩. ⟨hal-00726599⟩
  • Konrad Hinsen. Caring for Your Data. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2012, 14 (6), pp.70-74. ⟨10.1109/MCSE.2012.108⟩. ⟨hal-00817362⟩
  • Alexandre Giuliani, Aleksandar R Milosavljević, Konrad Hinsen, Francis Canon, Christophe Nicolas, et al.. Structure and Charge-State Dependence of the Gas-Phase Ionization Energy of Proteins.. Angewandte Chemie (English Edition), John Wiley & Sons, 2012, epub ahead of print. ⟨10.1002/anie.201204435⟩. ⟨hal-00727349⟩
  • Christopher Ing, Konrad Hinsen, Jing Yang, Toby Zeng, Hui Li, et al.. A path-integral Langevin equation treatment of low-temperature doped helium clusters.. Journal of Chemical Physics, American Institute of Physics, 2012, 136 (22), pp.224309-224312. ⟨10.1063/1.4726507⟩. ⟨hal-00726222⟩
  • Gerald R Kneller, Konrad Hinsen, Paolo Calligari. Communication: a minimal model for the diffusion-relaxation backbone dynamics of proteins.. Journal of Chemical Physics, American Institute of Physics, 2012, 136 (19), pp.191101. ⟨10.1063/1.4718380⟩. ⟨hal-00726225⟩
  • Konrad Hinsen, Eric Pellegrini, Sławomir Stachura, Gerald R Kneller. nMoldyn 3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations.. Journal of Computational Chemistry, Wiley, 2012, 33 (25), pp.2043-2048. ⟨10.1002/jcc.23035⟩. ⟨hal-00721865⟩
  • Guillaume Chevrot, Paolo Calligari, Konrad Hinsen, Gerald R Kneller. Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules.. Journal of Chemical Physics, American Institute of Physics, 2011, 135 (8), pp.084110. ⟨10.1063/1.3626275⟩. ⟨hal-00720598⟩
  • Vania Calandrini, E. Pellegrini, Paolo Calligari, Konrad Hinsen, Gerald R. Kneller. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. Collection SFN, 2011, 12, pp.201-232. ⟨10.1051/sfn/201112010⟩. ⟨hal-00720549⟩
  • Konrad Hinsen. A scientific model for free will is impossible. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2010, 107 (38), pp.E149. ⟨10.1073/pnas.1010609107⟩. ⟨hal-00602371⟩
  • Konrad Hinsen, Edward Beaumont, Bertrand Fournier, Jean-Jacques Lacapère. From electron microscopy maps to atomic structures using normal mode-based fitting. Methods in Molecular Biology, Humana Press/Springer Imprint, 2010, 654, pp.237-258. ⟨10.1007/978-1-60761-762-4_13⟩. ⟨hal-00609503⟩
  • Konrad Hinsen. Computer code: incentives needed. Nature, Nature Publishing Group, 2010, 468, pp.370. ⟨10.1038/468037b⟩. ⟨hal-00726320⟩
  • Konrad Hinsen. Economic growth: indicators not targets.. Nature, Nature Publishing Group, 2010, 468, pp.897. ⟨10.1038/468897a⟩. ⟨hal-00726312⟩
  • G.K. Thiruvathukal, Konrad Hinsen, Konstantin Laufer, Joe Kaylor. Virtualization for computational scientists. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2010, 12 (4), pp.52-61. ⟨hal-00602510⟩
  • Konrad Hinsen. Physical arguments for distance-weighted interactions in elastic network models for proteins. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2009, 106 (45), pp.E128. ⟨10.1073/pnas.0909385106⟩. ⟨hal-00522452⟩
  • Konrad Hinsen. The promises of functional programming. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2009, 11 (4), pp.86-90. ⟨hal-00522448⟩
  • Konrad Hinsen, Konstantin Laeufer, K. Thiruvathukal George. Essential tools: version control systems. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2009, 11 (6), pp.84-90. ⟨hal-00522455⟩
  • Gerald R. Kneller, Konrad Hinsen. Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study. Journal of Chemical Physics, American Institute of Physics, 2009, 131 (4), pp.045104. ⟨10.1063/1.3170941⟩. ⟨hal-00522467⟩
  • Konrad Hinsen, Gérald Kneller. Solvent effects in the slow dynamics of proteins. Proteins - Structure, Function and Bioinformatics, Wiley, 2008, 70 (4), pp.1235-1242. ⟨10.1002/prot.21655⟩. ⟨hal-00176279⟩
  • Gerald R. Kneller, Konrad Hinsen, Godehard Sutmann, Vania Calandrini. Scaling laws and memory effects in the dynamics of liquids and proteins. Physics of Particles and Nuclei Letters, 2008, 5 (3), pp.189-195. ⟨10.1134/S1547477108030114⟩. ⟨hal-00518138⟩
  • Konrad Hinsen. Structural flexibility in proteins: impact of the crystal environment. Bioinformatics, Oxford University Press (OUP), 2008, 24 (4), pp.521-528. ⟨10.1093/bioinformatics/btm625⟩. ⟨hal-00283340⟩
  • Konrad Hinsen. Parallel scripting with python. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2007, 9 (6), pp.82-89. ⟨hal-00282403⟩
  • Véronique Hamon, Paolo Calligari, Konrad Hinsen, Gerald R. Kneller. Simulation studies of structural changes and relaxation processes in lysozyme under pressure. Journal of Non-Crystalline Solids, Elsevier, 2006, 352, pp.4417-4423. ⟨hal-00388010⟩
  • Konrad Hinsen, Nathalie Reuter, Jorge Navaza, David L. Stokes, Jean-Jacques Lacapère. Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase. Biophysical Journal, Biophysical Society, 2005, 88, pp.818. ⟨10.1529/biophysj.104.050716⟩. ⟨hal-00015408⟩
  • Gerald Kneller, Konrad Hinsen. Fractional Brownian dynamics in proteins. Journal of Chemical Physics, American Institute of Physics, 2004, 121, pp.10278. ⟨10.1063/1.1806134⟩. ⟨hal-00015422⟩
  • G. Kneller, Konrad Hinsen, G. Sutmann. Mass and size effects on the memory function of tracer particles. Journal of Chemical Physics, American Institute of Physics, 2003, 118 (12), pp.5283-5286. ⟨10.1063/1.1562620⟩. ⟨hal-02154086⟩
  • Konrad Hinsen. High-Level Parallel Software Development with Python and BSP. Parallel Processing Letters, World Scientific Publishing, 2003, 13, pp.473. ⟨hal-00015424⟩
  • Nathalie Reuter, Konrad Hinsen, Jean-Jacques Lacapère. Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study. Biophysical Journal, Biophysical Society, 2003, 85, pp.2186. ⟨hal-00015419⟩
  • T. Róg, K. Murzyn, Konrad Hinsen, G. Kneller. n Moldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations. Journal of Computational Chemistry, Wiley, 2003, 24 (5), pp.657-667. ⟨10.1002/jcc.10243⟩. ⟨hal-02154080⟩
  • G. Kneller, Konrad Hinsen. Computing memory functions from molecular dynamics simulations. Journal of Chemical Physics, American Institute of Physics, 2001, 115 (24), pp.11097-11105. ⟨10.1063/1.1421361⟩. ⟨hal-02155436⟩
  • Konrad Hinsen, Gérald Kneller. Projection Methods for the Analysis of Complex Motions in Macromolecules. Molecular Simulation, Taylor & Francis, 2000, 23 (4-5), pp.275-292. ⟨10.1080/08927020008025373⟩. ⟨hal-02155531⟩
  • Konrad Hinsen, Andrei-Jose Petrescu, Serge Dellerue, Marie-Claire Bellissent-Funel, Gérald Kneller. Harmonicity in slow protein dynamics. Chemical Physics, Elsevier, 2000, 261 (1-2), pp.25-37. ⟨10.1016/S0301-0104(00)00222-6⟩. ⟨hal-02155521⟩
  • D. Viduna, Konrad Hinsen, G. Kneller. Influence of molecular flexibility on DNA radiosensitivity: a simulation study. Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 2000, 62 (3 Pt B), pp.3986-3990. ⟨10.1103/PhysRevE.62.3986⟩. ⟨hal-02155461⟩
  • Konrad Hinsen, Gérald Kneller. A simplified force field for describing vibrational protein dynamics over the whole frequency range. Journal of Chemical Physics, American Institute of Physics, 1999, 111 (24), pp.10766-10769. ⟨10.1063/1.480441⟩. ⟨hal-02155539⟩
  • Konrad Hinsen, Gérald Kneller. Sedimentation of Clusters of Spheres. I. Unconstrained. Journal of Molecular Modeling, Springer Verlag (Germany), 1996, 2 (9), pp.227-238. ⟨10.1007/s0089460020227⟩. ⟨hal-02155706⟩
  • Gérald Kneller, Konrad Hinsen. Sedimentation of Clusters of Spheres II. Constrained systems. Journal of Molecular Modeling, Springer Verlag (Germany), 1996, 2 (9), pp.239-250. ⟨10.1007/s0089460020239⟩. ⟨hal-02155702⟩
  • Konrad Hinsen, Gérald Kneller. Influence of constraints on the dynamics of polypeptide chains.. Physical Review E , American Physical Society (APS), 1995, 52 (6), pp.6868-6874. ⟨10.1103/PhysRevE.52.6868⟩. ⟨hal-02155715⟩
  • Gérald Kneller, Konrad Hinsen. Generalized Euler equations for linked rigid bodies.. Physical Review E , American Physical Society (APS), 1994, 50 (2), pp.1559-1564. ⟨10.1103/PhysRevE.50.1559⟩. ⟨hal-02155721⟩

Communication dans un congrès

  • Konrad Hinsen, Nicolas P. Rougier. ReScience. Open science, transparence et évaluation. Perspectives et enjeux pour les chercheurs, URFIST Bordeaux, Apr 2017, Bordeaux, France. ⟨hal-01573262⟩
  • Konrad Hinsen, Nicolas P. Rougier. ReScience: Reproducible Science is good. Replicated Science is better.. Retour d’expéRiences sur la Recherche Reproductible, Konrad HINSEN, Andrew DAVISON, Christophe POUZAT, Dec 2015, Orléans, France. ⟨hal-01237835⟩
  • Alexandre Giuliani, Alexandre R. Milosavljević, Konrad Hinsen, Francis Canon, Christophe Nicolas, et al.. Ionization energy of gas phase protein cations and its dependence on charge state_and structure. Synchrotron SOLEIL Users Meeting, Jan 2013, Orsay, France. ⟨hal-01573564⟩
  • Konrad Hinsen. A data and code model for reproducible research and executable papers. International Conference on Computational Science, Jun 2011, Singapour, Singapore. pp.579, ⟨10.1016/j.procs.2011.04.061⟩. ⟨hal-00626032⟩

Chapitre d'ouvrage

  • Konrad Hinsen. Problem-Specific Analysis of Molecular Dynamics Trajectories for Biomolecules. Kitzes, J. Turek, D. Deniz, F. The Practice of Reproducible Research : Case Studies and Lessons from the Data-Intensive Sciences, University of California Press, pp.254-260, 2017, 978-0520294752. ⟨hal-02071690⟩
  • Konrad Hinsen, Edward Beaumont, Bertrand Fournier, Jean-Jacques Lacapère. From Electron Microscopy Maps to Atomic Structures Using Normal Mode-Based Fitting. Lacapère Jean-Jacques. Membrane Protein Structure Determination: Methods and Protocols, Springer-Verlag, pp.237-258, 2010, Methods in Molecular Biology, ⟨10.1007/978-1-60761-762-4_13⟩. ⟨hal-00610003⟩