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Conformational ensembles and sampled landscapes: analysis and comparison

Frédéric Cazals , Christine--Andrea Roth , Tom Dreyfus , Dorian Mazauric , Charles H. Robert
Journal of Computational Chemistry, 2015, 36, pp.1213--31. ⟨10.1002/jcc.23913⟩
Journal articles hal-01498027v1

Introduction : le réseau Plasmas froids et la Mission des Ressources et Compétences Technologiques du CNRS

Gérard Lelièvre , Françoise F. Massines , Elodie Girard
Massines, Françoise. Plasmas froids. Génération, caractérisation et technologies, 3, PUSE-MRCT-CNRS, pp.11-16, 2004, Intégrations [des savoirs et savoir-faire], 2862723398
Book sections hal-01481540v1

TAPO: A combined method for the identification of tandem repeats in protein structures

Phuong Do Viet , Daniel Barry Roche , Andrey V. Kajava
FEBS Letters, 2015, 589 (19PartA), pp.2611--2619. ⟨10.1016/j.febslet.2015.08.025⟩
Journal articles hal-01883461v1

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

Matthieu Chavent , Antoine Vanel , Alex Tek , Bruno Levy , Sophie Robert , et al.
Journal of Computational Chemistry, 2011, 32 (13), pp.2924-35. ⟨10.1002/jcc.21861⟩
Journal articles hal-00645162v1

The Role of Dynamical Synapses in Retinal Surprise Coding

Simone Ebert , Thomas Buffet , Semichan Sermet , Olivier Marre , Bruno Cessac
AREADNE 2022 Conference : Research in Encoding And Decoding of Neural Ensembles, Jun 2022, Fira, Greece.
Conference poster hal-03697955v1
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Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity

Antrea Pavlou , Eugenio Cinquemani , Johannes Geiselmann , Hidde de Jong
Biophysical Journal, 2022, 121 (21), pp.4179-4188. ⟨10.1016/j.bpj.2022.09.021⟩
Journal articles hal-03938428v1
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Anomalous Subdiffusion in Living Cells: Bridging the Gap Between Experiments and Realistic Models Through Collaborative Challenges

Maxime Woringer , Ignacio Izeddin , Cyril Favard , Hugues Berry
Frontiers in Physics, 2020, 8, pp.134. ⟨10.3389/fphy.2020.00134⟩
Journal articles hal-02871984v1
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Dynamical Synapses in Retinal Surprise coding

Thomas Buffet , Semihchan Sermet , Olivier Marre , Bruno Cessac , Simone Bertoli
ICMNS 2022 - 2022 International Conference on Mathematical Neuroscience, Jul 2022, online, France.
Conference poster hal-03716437v1
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Position-based modeling of lesion displacement in Ultrasound-guided breast biopsy

Eleonora Tagliabue , Diego Dall’alba , Enrico Magnabosco , Chiara Tenga , Igor Peterlík , et al.
International Journal of Computer Assisted Radiology and Surgery, 2019, 14 (8), pp.1329-1339. ⟨10.1007/s11548-019-01997-z⟩
Journal articles hal-02276090v1
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Beyond the chemical master equation: stochastic chemical kinetics coupled with auxiliary processes

Davin Lunz , Gregory Batt , Jakob Ruess , Joseph Frédéric Bonnans
PLoS Computational Biology, 2021, ⟨10.1371/journal.pcbi.1009214⟩
Journal articles hal-02991103v2
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From physics to biology by extending criticality and symmetry breakings

Giuseppe Longo , Maël Montévil
Progress in Biophysics and Molecular Biology, 2011, 106 (2), pp.340 - 347. ⟨10.1016/j.pbiomolbio.2011.03.005⟩
Journal articles hal-01192902v2
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Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

Sergei Grudinin , Maria Garkavenko , Andrei Kazennov
Acta crystallographica Section D : Structural biology [1993-..], 2017, D73, pp.449 - 464. ⟨10.1107/S2059798317005745⟩
Journal articles hal-01516719v1

Computation and Projection of Spiral Wave Trajectories During Atrial Fibrillation

Ali Pashaei , Jason Bayer , Valentin Meillet , Rémi Dubois , Edward Vigmond
Cardiac Electrophysiology Clinics, 2015, 7 (1), pp.37-47. ⟨10.1016/j.ccep.2014.11.001⟩
Journal articles hal-02886271v1
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Docking-based long timescale simulation of cell-size protein systems at atomic resolution

Ilya A Vakser , Sergei Grudinin , Nathan W Jenkins , Petras J Kundrotas , Eric J Deeds
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (41), pp.e2210249119:1-8. ⟨10.1073/pnas.2210249119⟩
Journal articles hal-03874526v1
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Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect

Anne-Sophie Coquel , Jean-Pascal Jacob , Maël Primet , Alice Demarez , Mariella Dimiccoli , et al.
PLoS Computational Biology, 2013, 9 (4), e1003038 (14 p.). ⟨10.1371/journal.pcbi.100303⟩
Journal articles hal-00798053v1

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Jorge Eduardo Fajardo , Rojan Shrestha , Nelson Gil , Adam Belsom , Silvia Crivelli , et al.
Proteins - Structure, Function and Bioinformatics, 2019, Critical Assessment of Methods of Protein Structure Prediction (CASP) Special Issue, 87 (12), pp.1283-1297. ⟨10.1002/prot.25816⟩
Journal articles hal-02315542v1
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Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations

Benjamin Bouvier , Christine Cézard , Pascal Sonnet
Physical Chemistry Chemical Physics, 2015, 17 (27), pp.18022-18034. ⟨10.1039/c5cp02939b⟩
Journal articles hal-02395207v1

Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions: Binding of Ligands to Solenoid Proteins

L. Ramya , N. Gautham , Laurent Chaloin , Andrey V. Kajava
Proteins - Structure, Function and Bioinformatics, 2015, 83 (9), pp.1654--1664. ⟨10.1002/prot.24851⟩
Journal articles istex hal-01883485v1
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The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

François Inizan , Myriam Hanna , Maxim Stolyarchuk , Isaure Chauvot de Beauchêne , Luba Tchertanov
Scientific Reports, 2020, ⟨10.1038/s41598-020-62460-7⟩
Journal articles hal-03000379v1
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An efficient kinetic model for assemblies of amyloid fibrils and its application to polyglutamine aggregation.

Stephanie Prigent , Annabelle Ballesta , Frédérique Charles , Natacha Lenuzza , Pierre Gabriel , et al.
PLoS ONE, 2012, 7 (11), pp.e43273. ⟨10.1371/journal.pone.0043273⟩
Journal articles hal-00778052v1

Functional Imaging and Modeling of the Heart

Yves Coudière , Nejib Zemzemi , Edward J. Vigmond , Valéry Ozenne
FIMH 2019 - 10th International Conference on Functional Imaging and Modeling of the Heart, Jun 2019, 11504, Springer, 2019, LNCS - Lecture Notes in Computer Science, ⟨10.1007/978-3-030-21949-9⟩
Proceedings hal-02433985v1
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The retina: a fascinating object of study for a physicist

Bruno Cessac
Université Côte d'Azur Complex Days, M. Argentina; S. Barland; P. Reynaud-Bouret; F. Cauneau; K. Guillouzouic; U. Kuhl; T. Passot; F. Planchon, Jan 2018, Nice, France. pp.35-44
Conference papers hal-02006662v1
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4polar-STORM polarized super-resolution imaging of actin filament organization in cells

Caio Vaz Rimoli , Cesar Augusto Valades Cruz , Valentina Curcio , Manos Mavrakis , Sophie Brasselet
Nature Communications, 2022, 13, ⟨10.1038/s41467-022-27966-w⟩
Journal articles hal-03172831v2

Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes

Christine A. Roth , Tom Dreyfus , Charles H. Robert , Frédéric Cazals
Journal of Computational Chemistry, 2016, 37, pp.752. ⟨10.1002/jcc.24256⟩
Journal articles istex hal-01497994v1

In search of the boundary between repetitive and non-repetitive protein sequences

F. D. Richard , Andrey Kajava
Biochemical Society Transactions, 2015, 43 (5), pp.807--811. ⟨10.1042/BST20150073⟩
Journal articles hal-01883484v1
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Optimal control of bioproduction in the presence of population heterogeneity

Davin Lunz , J. Frédéric Bonnans , Jakob Ruess
Journal of Mathematical Biology, 2023, 86 (3), pp.43. ⟨10.1007/s00285-023-01876-x⟩
Journal articles hal-03445175v3
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Modelling and Efficient Characterization of Enzyme-Mediated Response to Antibiotic Treatments

Virgile Andreani
Biophysics. Ecole polytechnique, 2020. English. ⟨NNT : 2020IPPAX108⟩
Theses tel-03161857v1
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Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations

Benjamin Bouvier
Physical Chemistry Chemical Physics, 2014, 16 (1), pp.48-60. ⟨10.1039/c3cp52436a⟩
Journal articles hal-02395222v1

Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): Molecular dynamics simulations and kinetic studies of protein mutants.

Nicolas Floquet , Stéphane Mouilleron , Rasha Daher , Bernard Maigret , Bernard Badet , et al.
FEBS Letters, 2007, 581 (16), pp.2981-7. ⟨10.1016/j.febslet.2007.05.068⟩
Journal articles istex hal-00161331v1
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Quantifying membrane binding and diffusion with fluorescence correlation spectroscopy diffusion laws

Anita Mouttou , Erwan Bremaud , Julien Noero , Rayane Dibsy , Coline Arone , et al.
Biophysical Journal, 2023, 122 (11), pp.2216-2229. ⟨10.1016/j.bpj.2023.01.006⟩
Journal articles hal-04165544v1