PIAZZA Francesco

 

email : francesco.piazza@cnrs-orleans.fr

Phone : +33 2.38.25.56.53 ou +33 6.37.99.38.58

 

Professor, responsible of the group” Statistical Physics of Complex Systems and nanobiotechnology”

 

 

 

 

 



30 documents

Article dans une revue

  • Annise Rivière, Stefano Lepri, Daniele Colognesi, Francesco Piazza. Wavelet imaging of transient energy localization in nonlinear systems at thermal equilibrium: The case study of NaI crystals at high temperature. Physical Review B : Condensed matter and materials physics, American Physical Society, 2019, 99 (2), ⟨10.1103/PhysRevB.99.024307⟩. ⟨hal-02067449⟩
  • A. Sozza, Francesco Piazza, M. Cencini, F. de Lillo, G. Boffetta. Point-particle method to compute diffusion-limited cellular uptake. Physical Review E , American Physical Society (APS), 2018, 97 (2), pp.023301. ⟨hal-01966405⟩
  • Rafael Roa, Stefano Angioletti-Uberti, Yan Lu, Joachim Dzubiella, Francesco Piazza, et al.. Catalysis by Metallic Nanoparticles in Solution: Thermosensitive Microgels as Nanoreactors. Zeitschrift für Physikalische Chemie, Oldenbourg Verlag, 2018, 232 (5-6), pp.773-803. ⟨hal-01966375⟩
  • Cristiano de Michele, Paolo de Los Rios, Giuseppe Foffi, Francesco Piazza, Yanay Ofran. Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces. PLoS Computational Biology, Public Library of Science, 2016, 12 (3), ⟨10.1371/journal.pcbi.1004752⟩. ⟨hal-01406916⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Conformation-controlled binding kinetics of antibodies. Scientific Reports, Nature Publishing Group, 2016, 6, ⟨10.1038/srep18976⟩. ⟨hal-01406993⟩
  • Marta Galanti, Duccio Fanelli, Sergey D. Traytak, Francesco Piazza. Correction: Theory of diffusion-influenced reactions in complex geometries. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (26), pp.17757 - 17757. ⟨10.1039/C6CP90149B⟩. ⟨hal-01408564⟩
  • Marta Galanti, Duccio Fanelli, Sergey D. Traytak, Francesco Piazza. Theory of diffusion-influenced reactions in complex geometries. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (23), pp.15950 - 15954. ⟨10.1039/c6cp01147k⟩. ⟨hal-01406998⟩
  • Marta Galanti, Duccio Fanelli, Stefano Angioletti-Uberti, Matthias Ballauff, Joachim Dzubiella, et al.. Reaction rate of a composite core–shell nanoreactor with multiple nanocatalysts. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (30), pp.20758 - 20767. ⟨10.1039/C6CP01179A⟩. ⟨hal-01407893⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Nonlinear macroscopic transport equations in many-body systems from microscopic exclusion processes. Frontiers in Physics, Frontiers, 2016, 18 (30), pp.20758-20767. ⟨hal-01408558⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Macroscopic Transport Equations in Many-Body Systems from Microscopic Exclusion Processes in Disordered Media: A Review. Frontiers in Physics, Frontiers, 2016, 4, ⟨10.3389/fphy.2016.00033⟩. ⟨hal-02071749⟩
  • Stefano Iubini, Octavi Boada, Yasser Omar, Francesco Piazza. Transport of quantum excitations coupled to spatially extended nonlinear many-body systems. New Journal of Physics, Institute of Physics: Open Access Journals, 2015, 17 (11), pp.113030. ⟨10.1088/1367-2630/17/11/113030⟩. ⟨hal-02072269⟩
  • Jean-Yves Dewavrin, Muhammed Abdurrahiem, Anna Blocki, Mrinal Musib, Francesco Piazza, et al.. Synergistic Rate Boosting of Collagen Fibrillogenesis in Heterogeneous Mixtures of Crowding Agents. Journal of Physical Chemistry B, American Chemical Society, 2015, 119 (12), pp.4350-4358. ⟨10.1021/jp5077559⟩. ⟨hal-02072238⟩
  • Simon Aubailly, Francesco Piazza. Cutoff lensing: predicting catalytic sites in enzymes. Scientific Reports, Nature Publishing Group, 2015, 5 (1), ⟨10.1038/srep14874⟩. ⟨hal-02072226⟩
  • Francesca Di Patti, Duccio Fanelli, Francesco Piazza. Optimal search strategies on complex multi-linked networks. Scientific Reports, Nature Publishing Group, 2015, 5 (1), ⟨10.1038/srep09869⟩. ⟨hal-02072243⟩
  • Francesco Piazza, Sergey Traytak. Diffusion-influenced reactions in a hollow nano-reactor with a circular hole. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2015, 17 (16), pp.10417-10425. ⟨10.1039/c4cp05605a⟩. ⟨hal-02072294⟩
  • Francesco Piazza. Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk.. Physical Biology, Institute of Physics: Hybrid Open Access, 2014, 11 (3), pp.036003. ⟨hal-01180839⟩
  • I.V. Dubinko, Francesco Piazza. On the role of disorder in catalysis driven by discrete breathers. Letters on materials, Elsevier, 2014, 4 (4), pp.273-278. ⟨hal-01178866⟩
  • Enrico Spiga, Luciano A Abriata, Francesco Piazza, Matteo Dal Peraro. Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics.. Journal of Physical Chemistry B, American Chemical Society, 2014, 118 (20), pp.5310-5321. ⟨hal-01180892⟩
  • Marta Galanti, Duccio Fanelli, Amos Maritan, Francesco Piazza. Diffusion of tagged particles in a crowded medium. EPL - Europhysics Letters, European Physical Society/EDP Sciences/Società Italiana di Fisica/IOP Publishing, 2014, 107 (2), pp.20006. ⟨10.1209/0295-5075/107/20006⟩. ⟨hal-01178998⟩
  • Mohamed Naji, Francesco Piazza, Guillaume Guimbretiere, Aurélien Canizares, Yann Vaills. Structural Relaxation Dynamics and Annealing Effects of Sodium Silicate Glass. Journal of Physical Chemistry B, American Chemical Society, 2013, 117 (18), pp.5757-5764. ⟨10.1021/jp401112s⟩. ⟨hal-02070892⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Persistent random walk with exclusion. European Physical Journal B: Condensed Matter and Complex Systems, Springer-Verlag, 2013, 86 (11), ⟨10.1140/epjb/e2013-40838-y⟩. ⟨hal-02070835⟩
  • G Foffi, A. Pastore, Francesco Piazza, A Temussi. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10–14 June 2012). Physical Biology, Institute of Physics: Hybrid Open Access, 2013, 10 (4), pp.040301. ⟨10.1088/1478-3975/10/4/040301⟩. ⟨hal-02071788⟩
  • F. Piazza, N Dorsaz, C. de Michele, P de Los Rios, F Foffi. Diffusion-limited reactions in crowded environments: a local density approximation. Journal of Physics: Condensed Matter, IOP Publishing, 2013, 25 (37), pp.375104. ⟨10.1088/0953-8984/25/37/375104⟩. ⟨hal-02071799⟩
  • Francesco Piazza, Giuseppe Foffi, Cristiano de Michele. Irreversible bimolecular reactions with inertia: from the trapping to the target setting at finite densities. Journal of Physics: Condensed Matter, IOP Publishing, 2013, 25 (24), pp.245101. ⟨10.1088/0953-8984/25/24/245101⟩. ⟨hal-02070906⟩
  • Pierre de Buyl, Giovanni de Ninno, Duccio Fanelli, Cesare Nardini, Aurelio Patelli, et al.. Absence of thermalization for systems with long-range interactions coupled to a thermal bath. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, American Physical Society, 2013, 87 (4), ⟨10.1103/PhysRevE.87.042110⟩. ⟨hal-02070760⟩
  • Carlo Maffi, Marco Baiesi, Lapo Casetti, Francesco Piazza, Paolo de Los Rios. First-order coil-globule transition driven by vibrational entropy.. Nature Communications, Nature Publishing Group, 2012, 3, pp.1065. ⟨10.1038/ncomms2055⟩. ⟨hal-00748173⟩
  • Peter Csermely, Kuljeet Singh Sandhu, Eszter Hazai, Zsolt Hoksza, Huba J M Kiss, et al.. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.. Current Protein and Peptide Science, Bentham Science Publishers, 2012, 13 (1), pp.19-33. ⟨hal-00721841⟩
  • Stefano Luccioli, Alberto Imparato, Stefano Lepri, Francesco Piazza, Alessandro Torcini. Discrete breathers in a realistic coarse-grained model of proteins.. Physical Biology, Institute of Physics: Hybrid Open Access, 2011, 8 (4), pp.046008. ⟨10.1088/1478-3975/8/4/046008⟩. ⟨hal-00720642⟩
  • Alessio Zaccone, Nicolas Dorsaz, Francesco Piazza, Cristiano de Michele, Massimo Morbidelli, et al.. Crowding, intermolecular interactions, and shear flow effects in the diffusion model of chemical reactions.. Journal of Physical Chemistry B, American Chemical Society, 2011, 115 (22), pp.7383-96. ⟨10.1021/jp200439a⟩. ⟨hal-00720723⟩
  • Francesco Piazza, Yves-Henri Sanejouand. Breather-mediated energy transfer in proteins. Discrete and Continuous Dynamical Systems - Series S, American Institute of Mathematical Sciences, 2011, 4 (5), pp.1247-1266. ⟨hal-00720691⟩

KNELLER Gérald

 

email : gerald.kneller@cnrs-orleans.fr

Phone : +33 2.38.25.78.42

Professor, co-coordinator of the team “theoretical and computational biophysics”  and co-coordinator of the thematic group “statistical and computational physics of biomolecular systems”

 



96 documents

Article dans une revue

  • Gérald Kneller. Reply to Doster: Franck–Condon and Van Hove formulation of quasielastic neutron scattering from complex systems. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2019, 116 (18), pp.8651-8652. ⟨10.1073/pnas.1901851116⟩. ⟨hal-02154052⟩
  • 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⟩
  • Melek Saouessi, Judith Peters, Gerald Kneller. Asymptotic analysis of quasielastic neutron scattering data from human acetylcholinesterase reveals subtle dynamical changes upon ligand binding. Journal of Chemical Physics, American Institute of Physics, 2019, 150 (16), pp.161104. ⟨10.1063/1.5094625⟩. ⟨hal-02156638⟩
  • Gerald Kneller. Franck–Condon picture of incoherent neutron scattering. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2018, 115 (38), pp.9450-9455. ⟨hal-01966151⟩
  • G. Kneller. Model-free Approach to Quasielastic Neutron Scattering from Anomalously Diffusing Quantum Particles. Acta Physica Polonica B, Jagellonian University, Cracow, 2018, 49 (5), pp.893. ⟨hal-01966150⟩
  • Rana Ashkar, Hassina Bilheux, Heliosa Bordallo, Robert Briber, David Callaway, et al.. Neutron scattering in the biological sciences: progress and prospects. Acta crystallographica. Section D, Structural biology, International Union of Crystallography, 2018, 74 (12), pp.1129-1168. ⟨10.1107/S2059798318017503⟩. ⟨hal-01990351⟩
  • Gerald Kneller. General framework for constraints in molecular dynamics simulations. Molecular Physics, Taylor & Francis, 2017, 115 (9-12), pp.1352 - 1361. ⟨10.1080/00268976.2017.1297503⟩. ⟨hal-01656448⟩
  • 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⟩
  • Gerald R. Kneller. Asymptotic neutron scattering laws for anomalously diffusing quantum particles. Journal of Chemical Physics, American Institute of Physics, 2016, 145 (4), pp.044103. ⟨10.1063/1.4959124⟩. ⟨hal-01407912⟩
  • 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⟩
  • Paolo A. Calligari, Vania Calandrini, Jacques Ollivier, Jean-Baptiste Artero, Michael Härtlein, et al.. Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6. Journal of Physical Chemistry B, American Chemical Society, 2015, 119 (25), pp.7860-7873. ⟨10.1021/acs.jpcb.5b02034⟩. ⟨hal-01170680⟩
  • Sławomir Stachura, Gerald Kneller. Communication: Probing anomalous diffusion in frequency space. Journal of Chemical Physics, American Institute of Physics, 2015, 143 (19), pp.191103. ⟨10.1063/1.4936129⟩. ⟨hal-02072308⟩
  • G. Kneller. Anomalous Diffusion in Biomolecular Systems from the Perspective of Non-equilibrium Statistical Physics. Acta Physica Polonica B, Jagellonian University, Cracow, 2015, 46 (6), pp.1167. ⟨10.5506/APhysPolB.46.1167⟩. ⟨hal-02072278⟩
  • Gerald R. Kneller. Communication: A scaling approach to anomalous diffusion. Journal of Chemical Physics, American Institute of Physics, 2014, 141 (4), pp.041105. ⟨10.1063/1.4891357⟩. ⟨hal-01179255⟩
  • Sławomir Stachura, Gerald R. Kneller. Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields. Molecular Simulation, Taylor & Francis, 2014, 40 (1-3), pp.245-250. ⟨10.1080/08927022.2013.840902⟩. ⟨hal-01180893⟩
  • 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⟩
  • Judith Peters, Gerald Kneller. Motional heterogeneity in human acetylcholinesterase revealed by a non-Gaussian model for elastic incoherent neutron scattering Motional heterogeneity in human acetylcholinesterase revealed by a non-Gaussian model for elastic incoherent neutron scattering. Journal of Chemical Physics, American Institute of Physics, 2013, 139 (16), pp.165102. ⟨10.1063/1.4825199⟩. ⟨hal-01582670⟩
  • P.A. Calligari, G.R. Kneller. ScrewFit: combining localization and description of protein secondary structure. Acta Crystallographica Section D: Biological Crystallography, International Union of Crystallography, 2012, 68, pp.1690-1693. ⟨hal-00751382⟩
  • 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⟩
  • Gerald R Kneller, Guillaume Chevrot. Impact of anisotropic atomic motions in proteins on powder-averaged incoherent neutron scattering intensities.. Journal of Chemical Physics, American Institute of Physics, 2012, 137 (22), pp.225101. ⟨10.1063/1.4769782⟩. ⟨hal-00817098⟩
  • N. Smolin, R. Biehl, G. R. Kneller, D. Richter, J. C. Smith. Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation.. Biophysical Journal, Biophysical Society, 2012, 102 (5), pp.1108-17. ⟨10.1016/j.bpj.2012.01.002⟩. ⟨hal-00726260⟩
  • 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⟩
  • Paolo Calligari, Vania Calandrini, Gerald R Kneller, Daniel Abergel. From NMR relaxation to fractional Brownian dynamics in proteins: results from a virtual experiment.. Journal of Physical Chemistry B, American Chemical Society, 2011, 115 ((43)), pp.12370-9. ⟨10.1021/jp205380f⟩. ⟨hal-00688787⟩
  • 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⟩
  • Gerald R. Kneller. Generalized Kubo relations and conditions for anomalous diffusion: Physical insights from a mathematical theorem. Journal of Chemical Physics, American Institute of Physics, 2011, 134 (22), pp.Article Number: 224106. ⟨10.1063/1.3598483⟩. ⟨hal-00614940⟩
  • G.R. Kneller, K. Baczynski, M. Pasenkiewicz-Gierula. Communication: consistent picture of lateral subdiffusion in lipid bilayers: molecular dynamics simulation and exact results. Journal of Chemical Physics, American Institute of Physics, 2011, 135 (14), pp.141105. ⟨10.1063/1.3651800⟩. ⟨hal-00720633⟩
  • Gerald R. Kneller. Comment on "Fast Determination of the Optimal Rotational Matrix for Macromolecular Superpositions" [J. Comp. Chem. 31, 1561 (2010)]. Journal of Computational Chemistry, Wiley, 2011, 32 (1), pp.183-184. ⟨10.1002/jcc.21607⟩. ⟨hal-00602439⟩
  • Vania Calandrini, Daniel Abergel, Gerald R Kneller. Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment.. Journal of Chemical Physics, American Institute of Physics, 2010, 133 (14), pp.145101. ⟨10.1063/1.3486195⟩. ⟨hal-00593171⟩
  • Gerald R. Kneller, Vania Calandrini. Self-similar dynamics of proteins under hydrostatic pressure-Computer simulations and experiments. Biochimica et Biophysica Acta Proteins and Proteomics, Elsevier, 2010, 1804 (1), pp.56-62. ⟨10.1016/j.bbapap.2009.05.007⟩. ⟨hal-00529350⟩
  • 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⟩
  • Denis Horváth, Gerald R. Kneller. A least-constraint principle for population dynamics and reaction kinetics: Modeling entropy-controlled chemical hypercycles. Journal of Chemical Physics, American Institute of Physics, 2009, 131 (17), pp.171101. ⟨10.1063/1.3253688⟩. ⟨hal-00522464⟩
  • Roger Fourme, Isabella Ascone, Gerald R. Kneller. New trends in high-pressure molecular biophysics. Synchrotron Radiation News, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2009, 22 (5), pp.39-41. ⟨10.1080/08940880903256866⟩. ⟨hal-00522408⟩
  • Paolo A. Calligari, Gerald R. Kneller, Andrea Giansanti, Paolo Ascenzi, Alessandro Porrello, et al.. Inhibition of viral group-1 and group-2 neuraminidases by oseltamivir: A comparative structural analysis by the ScrewFit algorithm. Biophysical Chemistry, Elsevier, 2009, 141 (1), pp.117. ⟨10.1016/j.bpc.2009.01.004⟩. ⟨hal-00531141⟩
  • Vania Calandrini, Godehard Sutmann, Antonio Deriu, Gerald R. Kneller. Rigid Molecule Approximation in Memory Function-based Models for Molecular Liquids: Application to Liquid Water. ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS, 2009, 223 (9), pp.957-978. ⟨10.1524/zpch.2009.6063⟩. ⟨hal-00521840⟩
  • K. Wood, S. Grudinin, B. Kessler, M. Weik, M. Johnson, et al.. Dynamical heterogeneity of specific amino acids in bacteriorhodopsin. Journal of Molecular Biology, Elsevier, 2008, 380 (3), pp.581-591. ⟨10.1016/j.jmb.2008.04.077⟩. ⟨hal-00518913⟩
  • Gerald R. Kneller. Eckart axis conditions, Gauss’ principle of least constraint, and the optimal superposition of molecular structures. Journal of Chemical Physics, American Institute of Physics, 2008, 128 (19), pp.194101. ⟨10.1063/1.2902290⟩. ⟨hal-01378837⟩
  • Vania Calandrini, Daniel Abergel, Gerald R. Kneller. Protein dynamics from a NMR perspective: networks of coupled rotators and fractional brownian dynamics. Journal of Chemical Physics, American Institute of Physics, 2008, 128 (14), pp.145102. ⟨10.1063/1.2894844⟩. ⟨hal-00283232⟩
  • 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⟩
  • Vania Calandrini, Gerald R. Kneller. Influence of pressure on the low and fast fractional relaxation dynamics in lysozyme: a simulation study. Journal of Chemical Physics, American Institute of Physics, 2008, 128 (6), pp.065102. ⟨10.1063/1.2828769⟩. ⟨hal-00283234⟩
  • 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⟩
  • V. Calandrini, V. Hamon, K. Hinsen, P. Calligari, M.-C. Bellissent-Funel, et al.. Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering. Chemical Physics, Elsevier, 2008, 345 (2-3), pp.289-297. ⟨10.1016/j.chemphys.2007.07.018⟩. ⟨hal-00408024⟩
  • Gerald Kneller. Projection formalism for constrained dynamical systems: From Newtonian to Hamiltonian mechanics. Journal of Chemical Physics, American Institute of Physics, 2007, 127, 164114 (5 p.). ⟨10.1063/1.2779326⟩. ⟨hal-00188115⟩
  • Gerald R. Kneller, Vania Calandrini. Estimating the influence of finite instrumental resolution on elastic neutron scattering intensities from proteins. Journal of Chemical Physics, American Institute of Physics, 2007, 126, 125107 (2007) (8 p.). ⟨10.1063/1.2711207⟩. ⟨hal-00159577⟩
  • G.R. Kneller, P. Calligari. Efficient characterization of protein secondary structure in terms of screw motions. Acta Crystallographica Section D: Biological Crystallography, International Union of Crystallography, 2006, 62, pp.302-311. ⟨10.1107/S0907444905042654⟩. ⟨hal-00088869⟩
  • 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⟩
  • Vania Calandrini, Godehard Sutmann, Antonio Deriu, Gerald R. Kneller. Role of effective atomic masses in memory function-based models for liquids: A simulation study of liquid water. Journal of Chemical Physics, American Institute of Physics, 2006, 125 (23), 236102 (2006) (2 p.). ⟨10.1063/1.2403877⟩. ⟨hal-00166737⟩
  • Gérald Kneller. Hamiltonian formalism for semiflexible molecules in Cartesian coordinates.. Journal of Chemical Physics, American Institute of Physics, 2006, 125, 114107 (10 p.). ⟨10.1063/1.2220037⟩. ⟨hal-00110254⟩
  • B. Brutovsky, G.R. Kneller. Linear prediction of force time series to accelerate molecular dynamics simulations. Computer Physics Communications, Elsevier, 2005, 169, pp.339-342. ⟨hal-00088530⟩
  • G.R. Kneller. Simulations moléculaires et leur analyse. Journal de Physique IV Colloque, 2005, 130, pp.155-178. ⟨hal-00088724⟩
  • G.R. Kneller. Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2005, 7, pp.2641-2655. ⟨hal-00088607⟩
  • G.R. Kneller. Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)]. Journal of Computational Chemistry, Wiley, 2005, 26, pp.1660-1662. ⟨hal-00088606⟩
  • 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⟩
  • Kneller G.R., G. Sutmann. Scaling of the memory function and Brownian motion. Journal of Chemical Physics, American Institute of Physics, 2004, 120, pp.1667-1669. ⟨hal-00113062⟩
  • 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⟩
  • B. Brutovsky, T. Mülders, G.R. Kneller. Accelerating molecular dynamics simulations by linear prediction of time series. Journal of Chemical Physics, American Institute of Physics, 2003, 118, pp.6179-6187. ⟨hal-00087705⟩
  • 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⟩
  • K. Hinsen, Petrescu A.J., S. Dellerue, Bellissent-Funel M.C., Kneller Gr.. Liquid-like and solid-like motions in proteins. Journal of Molecular Liquids, Elsevier, 2002, 98-99, pp.383-400. ⟨hal-00114769⟩
  • T. Mülders, S. Toxvaerd, G. Kneller. Reply to “Comment on ‘Efficient stress relaxation in molecular dynamics simulations of semiflexible n -alkanes’ ”. Physical Review E , American Physical Society (APS), 2001, 63 (2), ⟨10.1103/PhysRevE.63.028702⟩. ⟨hal-02155426⟩
  • 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⟩
  • 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⟩
  • M. Jardat, S. Durand-Vidal, P. Turq, G.R. Kneller. Brownian dynamics simulations of electrolyte mixtures: computation of transport coefficients and comparison with an analytical transport theory. Journal of Molecular Liquids, Elsevier, 2000, 85 (1-2), pp.45-55. ⟨10.1016/S0167-7322(99)00163-4⟩. ⟨hal-02155493⟩
  • M. Jardat, O. Bernard, C. Treiner, G. Kneller, P. Turq. Dynamical properties of electrolyte solutions from Brownian dynamics simulations. Journal de Physique 4, EDP Sciences, 2000, 10 (PR5), pp.Pr5-113-Pr5-116. ⟨10.1051/jp4:2000514⟩. ⟨hal-02155486⟩
  • 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⟩
  • Gérald Kneller. Inelastic neutron scattering from damped collective vibrations of macromolecules. Chemical Physics, Elsevier, 2000, 261 (1-2), pp.1-24. ⟨10.1016/S0301-0104(00)00223-8⟩. ⟨hal-02155466⟩
  • 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⟩
  • 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⟩
  • Marie Jardat, Olivier Bernard, Pierre Turq, Gerald R. Kneller. Transport coefficients of electrolyte solutions from smart brownian dynamics simulations.. Journal of Chemical Physics, American Institute of Physics, 1999, 110, pp.7993-7999. ⟨hal-00164882⟩
  • T. Mülders, S. Toxvaerd, G. Kneller. Efficient stress relaxation in molecular dynamics simulations of semiflexible n -alkanes. Physical Review E , American Physical Society (APS), 1998, 58 (5), pp.6766-6780. ⟨10.1103/PhysRevE.58.6766⟩. ⟨hal-02155551⟩
  • Nhan-Duc Morelon, Gérald Kneller, Michel Ferrand, André Grand, Jeremy Smith, et al.. Dynamics of alkane chains included in an organic matrix: Molecular dynamics simulation and comparison with neutron scattering experiment. Journal of Chemical Physics, American Institute of Physics, 1998, 109 (7), pp.2883-2894. ⟨10.1063/1.476879⟩. ⟨hal-02155566⟩
  • G. Kneller, T. Mülders. Comment on “Atomic stress isobaric scaling for systems subjected to holonomic constraints” [J. Chem. Phys. 106 , 195 (1997)]. Journal of Chemical Physics, American Institute of Physics, 1998, 109 (15), pp.6508-6509. ⟨10.1063/1.477189⟩. ⟨hal-02155576⟩
  • G. Kneller, T. Mülders. Nosé-Andersen dynamics of partially rigid molecules: Coupling all degrees of freedom to heat and pressure baths. Physical Review E , American Physical Society (APS), 1997, 54 (6), pp.6825-6837. ⟨10.1103/PhysRevE.54.6825⟩. ⟨hal-02155694⟩
  • 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, Volker Keiner, Meinhard Kneller, Matthias Schiller. nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations. Computer Physics Communications, Elsevier, 1995, 91 (1-3), pp.191-214. ⟨10.1016/0010-4655(95)00048-K⟩. ⟨hal-02155711⟩
  • Gérald Kneller, Jeremy Smith. Liquid-like Side-chain Dynamics in Myoglobin. Journal of Molecular Biology, Elsevier, 1994, 242 (3), pp.181-185. ⟨10.1006/jmbi.1994.1570⟩. ⟨hal-02156653⟩
  • 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⟩
  • A. Dianoux, G. Kneller, J. Sauvajol, J. Smith. Dynamics of sodium‐doped polyacetylene. Journal of Chemical Physics, American Institute of Physics, 1994, 101 (1), pp.634-644. ⟨10.1063/1.468119⟩. ⟨hal-02155946⟩
  • G.R. Kneller. Inelastic neutron scattering from classical systems. Molecular Physics, Taylor & Francis, 1994, 83 (1), pp.63-87. ⟨10.1080/00268979400101081⟩. ⟨hal-02155937⟩
  • A. Dianoux, G. Kneller, J. Sauvajol, J. Smith. The polarized density of states of crystalline polyacetylene. Molecular dynamics analysis and comparison with neutron scattering results. Journal of Chemical Physics, American Institute of Physics, 1993, 99 (7), pp.5586-5596. ⟨10.1063/1.465951⟩. ⟨hal-02156035⟩
  • Sylvie Furois-Corbin, Jeremy Smith, Gerald Kneller. Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin. Proteins: Structure, Function, and Genetics, Wiley, 1993, 16 (2), pp.141-154. ⟨10.1002/prot.340160203⟩. ⟨hal-02156032⟩
  • J. Smith, G. Kneller. Combination of Neutron Scattering and Molecular Dynamics to Determine Internal Motions in Biomolecules. Molecular Simulation, Taylor & Francis, 1993, 10 (2-6), pp.363-375. ⟨10.1080/08927029308022173⟩. ⟨hal-02155958⟩
  • G. Kneller, W. Doster, M. Settles, S. Cusack, J. Smith. Methyl group dynamics in the crystalline alanine dipeptide: A combined computer simulation and inelastic neutron scattering analysis. Journal of Chemical Physics, American Institute of Physics, 1992, 97 (12), pp.8864-8879. ⟨10.1063/1.463361⟩. ⟨hal-02156042⟩
  • Gr Kneller, Gérald Kneller. Quaternions as a tool for the analysis of molecular systems. Journal de Chimie Physique et de Physico-Chimie Biologique, EDP Sciences, 1991, 88, pp.2709-2715. ⟨10.1051/jcp/1991882709⟩. ⟨hal-02156142⟩
  • J Garen, M.J Field, G. Kneller, M. Karplus, J Smith. Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations. Journal de Chimie Physique et de Physico-Chimie Biologique, EDP Sciences, 1991, 88, pp.2587-2596. ⟨10.1051/jcp/1991882587⟩. ⟨hal-02156196⟩
  • U. Niesar, G. Corongiu, E. Clementi, G. Kneller, D. Bhattacharya. Molecular dynamics simulations of liquid water using the NCC ab initio potential. The Journal of physical chemistry, American Chemical Society (ACS), 1990, 94 (20), pp.7949-7956. ⟨10.1021/j100383a037⟩. ⟨hal-02156207⟩
  • Gerald Kneller. Superposition of Molecular Structures using Quaternions. Molecular Simulation, Taylor & Francis, 1990, 7 (1-2), pp.113-119. ⟨10.1080/08927029108022453⟩. ⟨hal-02156153⟩
  • Gerald Kneller, Alfons Geiger. Molecular-dynamics studies and neutron-scattering experiments on methylene chloride. II. Dynamics. Molecular Physics, Taylor & Francis, 1990, 70 (3), pp.465-483. ⟨10.1080/00268979000101131⟩. ⟨hal-02156214⟩
  • Gerald Kneller, Alfons Geiger. Molecular dynamics studies and neutron scattering experiments on methylene chloride. I. Structure. Molecular Physics, Taylor & Francis, 1989, 68 (2), pp.487-498. ⟨10.1080/00268978900102311⟩. ⟨hal-02156230⟩
  • Gerald Kneller, Alfons Geiger. A Method to Calculate the g-Coefficients of the Molecular Pair Correlation Function from Molecular Dynamics Simulations. Molecular Simulation, Taylor & Francis, 1989, 3 (5-6), pp.283-300. ⟨10.1080/08927028908031381⟩. ⟨hal-02156222⟩
  • Gerald Kneller, U.M. Titulaer. Boundary layer effects on the rate of diffusion-controlled reactions. Physica A: Statistical Mechanics and its Applications, Elsevier, 1985, 129 (3), pp.514-534. ⟨10.1016/0378-4371(85)90183-9⟩. ⟨hal-02156241⟩
  • Gerald Kneller, U.M. Titulaer. The covariant form of the Klein-Kramers equation and the associated moment equations. Physica A: Statistical Mechanics and its Applications, Elsevier, 1984, 129 (1), pp.81-94. ⟨10.1016/0378-4371(84)90022-0⟩. ⟨hal-02156257⟩
  • D.F. Anderson, R. Bouclier, G. Charpak, S. Majewski, G. Kneller. Coupling of a BaF2 scintillator to a TMAE photocathode and a low-pressure wire chamber. Nuclear Instruments and Methods in Physics Research, Elsevier, 1983, 217 (1-2), pp.217-223. ⟨10.1016/0167-5087(83)90137-0⟩. ⟨hal-02156250⟩

Chapitre d'ouvrage

  • Gerald Kneller. Dynamics of biological macromolecules. Salvatore Magazù, Federica Migliardo. Dynamics of Biological Macromolecules by Neutron Scattering, BENTHAM SCIENCE PUBLISHERS, 2012, 978-1608053346. ⟨hal-02071825⟩

 

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”

 



98 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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. 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⟩
  • 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⟩
  • 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. Commentary: Scientific communication in the digital age. Physics today, American Institute of Physics, 2016, 69 (6), pp.10-11. ⟨10.1063/PT.3.3181⟩. ⟨hal-02159751⟩
  • 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⟩
  • 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. 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. 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, 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⟩
  • 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⟩
  • 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⟩
  • 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. 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. 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⟩
  • 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. Managing State. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2012, 14 (1), pp.80-86. ⟨10.1109/MCSE.2012.11⟩. ⟨hal-00726599⟩
  • 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⟩
  • Konrad Hinsen. Caring for Your Data. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2012, 14 (6), pp.70-74. ⟨10.1109/MCSE.2012.108⟩. ⟨hal-00817362⟩
  • 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⟩
  • 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, 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⟩
  • 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. 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. Economic growth: indicators not targets.. Nature, Nature Publishing Group, 2010, 468, pp.897. ⟨10.1038/468897a⟩. ⟨hal-00726312⟩
  • Konrad Hinsen. Computer code: incentives needed. Nature, Nature Publishing Group, 2010, 468, pp.370. ⟨10.1038/468037b⟩. ⟨hal-00726320⟩
  • 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, Konstantin Laeufer, K. Thiruvathukal George. Essential tools: version control systems. COMPUTING IN SCIENCE & ENGINEERING, IEEE, 2009, 11 (6), pp.84-90. ⟨hal-00522455⟩
  • 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⟩
  • 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, 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⟩
  • V. Calandrini, V. Hamon, K. Hinsen, P. Calligari, M.-C. Bellissent-Funel, et al.. Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering. Chemical Physics, Elsevier, 2008, 345 (2-3), pp.289-297. ⟨10.1016/j.chemphys.2007.07.018⟩. ⟨hal-00408024⟩
  • 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⟩
  • K. Hinsen, H.P. Langtangen, O. Skavhaug, A. Odegard. Using BSP and Python to simplify parallel programming. Future Generation Computer Systems, Elsevier, 2006, 22, pp.123-157. ⟨10.1016/j.future.2003.09.003⟩. ⟨hal-00088866⟩
  • 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. Comment on: “Energy landscape of a small peptide revealed by dihedral angle principal component analysis”. Proteins: Structure, Function, and Bioinformatics, 2006, 64 (3), pp.795-797. ⟨10.1002/prot.20900⟩. ⟨hal-02159753⟩
  • 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⟩
  • Nathalie Reuter, Konrad Hinsen, Jean-Jacques Lacapere. Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study. Biophysical Journal, Biophysical Society, 2003, 85 (4), pp.2186-2197. ⟨10.1016/S0006-3495(03)74644-X⟩. ⟨hal-02159756⟩
  • 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⟩
  • K. Hinsen, Petrescu A.J., S. Dellerue, Bellissent-Funel M.C., Kneller Gr.. Liquid-like and solid-like motions in proteins. Journal of Molecular Liquids, Elsevier, 2002, 98-99, pp.383-400. ⟨hal-00114769⟩
  • 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⟩
  • 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. The molecular modeling toolkit: A new approach to molecular simulations. Journal of Computational Chemistry, Wiley, 2000, 21 (2), pp.79-85. 3.0.CO;2-B">⟨10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B⟩. ⟨hal-02159757⟩
  • 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⟩
  • Konrad Hinsen, Aline Thomas, Martin Field. Analysis of domain motions in large proteins. Proteins: Structure, Function, and Genetics, Wiley, 1999, 34 (3), pp.369-382. 3.0.CO;2-F">⟨10.1002/(SICI)1097-0134(19990215)34:3<369::AID-PROT9>3.0.CO;2-F⟩. ⟨hal-02159761⟩
  • Olivier Roche, Konrad Hinsen, Martin Field. Theoretical study of the conformation of the H-protein lipoamide arm as a function of its terminal group. Proteins: Structure, Function, and Genetics, Wiley, 1999, 36 (2), pp.228-237. 3.0.CO;2-Q">⟨10.1002/(SICI)1097-0134(19990801)36:2<228::AID-PROT8>3.0.CO;2-Q⟩. ⟨hal-02159759⟩
  • D. Thomas, Konrad Hinsen, Martin Field, David Perahia, Aline Thomas. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins: Structure, Function, and Genetics, Wiley, 1999, 34 (1), pp.96-112. 3.0.CO;2-0">⟨10.1002/(SICI)1097-0134(19990101)34:1<96::AID-PROT8>3.0.CO;2-0⟩. ⟨hal-02159763⟩
  • 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. Analysis of domain motions by approximate normal mode calculations. Proteins: Structure, Function, and Genetics, Wiley, 1998, 33 (3), pp.417-429. 3.0.CO;2-8">⟨10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8⟩. ⟨hal-02159766⟩
  • Konrad Hinsen, Benoît Roux. Potential of mean force and reaction rates for proton transfer in acetylacetone. Journal of Chemical Physics, American Institute of Physics, 1997, 106 (9), pp.3567-3577. ⟨10.1063/1.473439⟩. ⟨hal-02159771⟩
  • Omar Sharafeddin, Konrad Hinsen, Tucker Carrington, Benoît Roux. Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone. Journal of Computational Chemistry, Wiley, 1997, 18 (14), pp.1760-1772. 3.0.CO;2-I">⟨10.1002/(SICI)1096-987X(19971115)18:14<1760::AID-JCC5>3.0.CO;2-I⟩. ⟨hal-02159768⟩
  • Konrad Hinsen, Benoît Roux. A potential function for computer simulation studies of proton transfer in acetylacetone. Journal of Computational Chemistry, Wiley, 1997, 18 (3), pp.368-380. 3.0.CO;2-S">⟨10.1002/(SICI)1096-987X(199702)18:3<368::AID-JCC7>3.0.CO;2-S⟩. ⟨hal-02159788⟩
  • Paul Dubois, Konrad Hinsen, James Hugunin. Numerical Python. Computers in Physics, American Institute of Physics (AIP), 1996, 10 (3), pp.262. ⟨10.1063/1.4822400⟩. ⟨hal-02159793⟩
  • 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⟩
  • K. Hinsen. HYDROLIB: a library for the evaluation of hydrodynamic interactions in colloidal suspensions. Computer Physics Communications, Elsevier, 1995, 88 (2-3), pp.327-340. ⟨10.1016/0010-4655(95)00029-F⟩. ⟨hal-02159867⟩
  • B. Cichocki, K. Hinsen. Stokes drag on conglomerates of spheres. Physics of Fluids, American Institute of Physics, 1995, 7 (2), pp.285-291. ⟨10.1063/1.868626⟩. ⟨hal-02159864⟩
  • 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⟩
  • B. Cichocki, B. Felderhof, K. Hinsen, E. Wajnryb, J. Bl/awzdziewicz. Friction and mobility of many spheres in Stokes flow. Journal of Chemical Physics, American Institute of Physics, 1994, 100 (5), pp.3780-3790. ⟨10.1063/1.466366⟩. ⟨hal-02159862⟩
  • K. Hinsen, B. Felderhof. Reduced description of electric multipole potential in Cartesian coordinates. Journal of Mathematical Physics, American Institute of Physics (AIP), 1992, 33 (11), pp.3731-3735. ⟨10.1063/1.529869⟩. ⟨hal-02159851⟩
  • K. Hinsen, A. Bratz, B. Felderhof. Nonlinear dielectric constant of nonpolar fluids. Journal of Chemical Physics, American Institute of Physics, 1992, 97 (12), pp.9299-9302. ⟨10.1063/1.463305⟩. ⟨hal-02159857⟩
  • K. Hinsen, B. Felderhof. Dielectric constant of a suspension of uniform spheres. Physical Review B : Condensed matter and materials physics, American Physical Society, 1992, 46 (20), pp.12955-12963. ⟨10.1103/physrevb.46.12955⟩. ⟨hal-02159854⟩
  • B. Cichocki, K. Hinsen. Dynamic computer simulation of concentrated hard sphere suspensions II. Re-analysis of mean square displacement data. Physica A: Statistical Mechanics and its Applications, Elsevier, 1992, 187 (1-2), pp.133-144. ⟨10.1016/0378-4371(92)90414-L⟩. ⟨hal-02159834⟩
  • K. Hinsen, A. Bratz, B. Felderhof. Anisotropic dielectric tensor and the Hall effect in a suspension of spheres. Physical Review B : Condensed matter and materials physics, American Physical Society, 1992, 46 (23), pp.14995-15003. ⟨10.1103/physrevb.46.14995⟩. ⟨hal-02159856⟩
  • K. Hinsen, B. Felderhof. Dielectric constant of a hard‐sphere fluid with induced dipoles and quadrupoles. Journal of Chemical Physics, American Institute of Physics, 1991, 94 (8), pp.5655-5662. ⟨10.1063/1.460476⟩. ⟨hal-02159835⟩
  • B. Cichocki, K. Hinsen. Dynamic computer simulation of concentrated hard sphere suspensions I. Simulation technique and mean square displacement data. Physica A: Statistical Mechanics and its Applications, Elsevier, 1990, 166 (3), pp.473-491. ⟨10.1016/0378-4371(90)90068-4⟩. ⟨hal-02159842⟩
  • B. Cichocki, B.U. Felderhof, Konrad Hinsen. Electrostatic interactions in periodic Coulomb and dipolar systems.. Physical Review A (General Physics), 1989, 39 (10), pp.5350-5358. ⟨10.1103/PhysRevA.39.5350⟩. ⟨hal-02159845⟩

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⟩

Ouvrage (y compris édition critique et traduction)


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⟩
  • Konrad Hinsen. Normal Mode Theory and Harmonic Potential Approximations. Normal Mode Analysis : Theory and Applications to Biological and Chemical Systems, pp.1-16, 2006, ⟨https://pdfs.semanticscholar.org/0e3a/52148c10dae8d8c5edfdbaf32e9ffdbd4ce1.pdf⟩. ⟨hal-02159881⟩