Recherche - Archive ouverte HAL Accéder directement au contenu

Filtrer vos résultats

83 résultats

Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation

M. Chiricotto , T. T. Tran , P. H. Nguyen , S. Melchionna , Fabio Sterpone , et al.
Isr. J. Chem., 2017, DOI: 10.1002/ijch.201600048., ⟨10.1002/ijch.201600048⟩
Article dans une revue hal-01497997v1

Stability Effect of Quinary Interactions Reversed by Single Point Mutations

David Gnutt , Stepan Timr , Jonas Ahlers , Benedikt König , Emily Manderfeld , et al.
Journal of the American Chemical Society, 2019, 141 (11), pp.4660-4669. ⟨10.1021/jacs.8b13025⟩
Article dans une revue hal-02360012v1
Image document

MOLECULAR MODELLING AND SIMULATION: FROM BIOLOGICAL SYSTEMS TO MATERIALS

Fabio Sterpone
Theoretical and/or physical chemistry. Université Denis Diderot 2012
HDR tel-01541650v1

Multiscale simulation of molecular processes in cellular environments

Mara Chiricotto , Fabio Sterpone , Philippe Derreumaux , Simone Melchionna
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2016, 374 (2080), ⟨10.1098/rsta.2016.0225⟩
Article dans une revue hal-01497978v1

Hydrodynamic effects on beta-amyloid (16-22) peptide aggregation

Mara Chiricotto , Simone Melchionna , Philippe Derreumaux , Fabio Sterpone
Journal of Chemical Physics, 2016, 145 (3), ⟨10.1063/1.4958323⟩
Article dans une revue hal-01497984v1
Image document

Binding site plasticity regulation of the FimH catch-bond mechanism

Olivier Languin-Cattoën , Fabio Sterpone , Guillaume Stirnemann
Biophysical Journal, 2023, 122 (13), pp.2744-2756. ⟨10.1016/j.bpj.2023.05.029⟩
Article dans une revue hal-04234999v1
Image document

Explicit Models of Motion to Understand Protein Side-Chain Dynamics

Nicolas Bolik-Coulon , Olivier Languin-Cattoën , Diego Carnevale , Milan Zachrdla , Damien Laage , et al.
Physical Review Letters, 2022, 129 (20), pp.203001. ⟨10.1103/PhysRevLett.129.203001⟩
Article dans une revue hal-03861436v1

How protein Surfaces Induce nomalous Dynamics of Hydration Water

Francesso Pizzitutti , Massimo Marchi , Fabio Sterpone , Peter Rossky
Journal of Physical Chemistry B, 2007, pp.7584-7590
Article dans une revue hal-00264535v1

OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field

Fernando Luís Barroso da Silva , Fabio Sterpone , Philippe Derreumaux
Journal of Chemical Theory and Computation, 2019, 15 (6), pp.3875-3888. ⟨10.1021/acs.jctc.9b00202⟩
Article dans une revue hal-02360037v1
Image document

Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs

Arthur Hardiagon , Samuel Murail , Li-Bo Huang , Arie van Der Lee , Fabio Sterpone , et al.
Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩
Article dans une revue hal-03410227v1
Image document

Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation

Li-Bo Huang , Arthur Hardiagon , Istvan Kocsis , Cristina-Alexandra Jegu , Mihai Deleanu , et al.
Journal of the American Chemical Society, 2021, 143 (11), pp.4224-4233. ⟨10.1021/jacs.0c11952⟩
Article dans une revue hal-03364954v2
Image document

Thermal activation of 'allosteric- like' large-scale motions in a eukaryotic Lactate Dehydrogenase

Marina Katava , Marco Maccarini , Guillaume Villain , Alessandro Paciaroni , Michael Sztucki , et al.
Scientific Reports, 2017, 7, pp.41092. ⟨10.1038/srep41092⟩
Article dans une revue hal-01473622v1

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

Fabio Sterpone , Simone Melchionna , Pierre Tuffery , Samuela Pasquali , Normand Mousseau , et al.
Chemical Society Reviews, 2014, 43 (13), pp.4871-4893. ⟨10.1039/c4cs00048j⟩
Article dans une revue hal-04193590v1

Structures of the Alzheimer\textquoterights Wild-Type A beta 1-40 Dimer from Atomistic Simulations

Bogdan Tarus , Thanh T. Tran , Jessica Nasica-Labouze , Fabio Sterpone , Phuong H. Nguyen , et al.
Journal of Physical Chemistry B, 2015, 119 (33), pp.10478--10487. ⟨10.1021/acs.jpcb.5b05593⟩
Article dans une revue hal-01498010v1
Image document

Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases

Quentin Bertrand , Sandrine Coquille , Antonio Iorio , Fabio Sterpone , Dominique Madern
Journal of Structural Biology, 2023, 215 (4), pp.108039. ⟨10.1016/j.jsb.2023.108039⟩
Article dans une revue hal-04264065v1

Inquiring Protein Thermostability: Is Resistance to Temperature Stress a Rigidity/Flexibility Trade-off?

Maria Kalimeri , Simone Melchionna , Fabio Sterpone
Proceedings of the European Conference on Complex Systems 2012, Springer International Publishing, 2013
Chapitre d'ouvrage hal-01498090v1
Image document

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Xavier Martinez , Arthur Hardiagon , Hubert Santuz , Samuel Murail , Mihail Barboiu , et al.
Lecture Notes in Bioengineering / Advances in Bionanomaterials II Selected Papers from the 3rd International Conference on Bio and Nanomaterials, BIONAM 2019, September 29 – October 3, 2019, pp.78-99, 2020, ⟨10.1007/978-3-030-47705-9_8⟩
Chapitre d'ouvrage hal-02944941v1
Image document

Aggregation of disease-related peptides

Phuong H. Nguyen , Fabio Sterpone , Philippe Derreumaux
Progress in Molecular Biology and Translational Science, 170, Elsevier, pp.435-460, 2020, Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, ⟨10.1016/bs.pmbts.2019.12.002⟩
Chapitre d'ouvrage hal-03087681v1

Reorientation and Allied Dynamics in Water and Aqueous Solutions

Damien Laage , Guillaume Stirnemann , Fabio Sterpone , Rey Rossend , James T Hynes
Annual Review of Physical Chemistry, 2011, 62, pp.395--416
Article dans une revue hal-01498125v1

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

Fabio Sterpone , Phuong H. Nguyen , Maria Kalimeri , Philippe Derreumaux
Journal of Chemical Theory and Computation, 2013, 9 (10), pp.4574--4584. ⟨10.1021/ct4003493⟩
Article dans une revue hal-01498059v1
Image document

Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

Astrid F. Brandner , Stepan Timr , Simone Melchionna , Philippe Derreumaux , Marc Baaden , et al.
Scientific Reports, 2019, 9, pp.16450. ⟨10.1038/s41598-019-52760-y⟩
Article dans une revue hal-02370975v1
Image document

Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability

Nirnay Samanta , Sara Ribeiro , Mailin Becker , Emeline Laborie , Roland Pollak , et al.
Journal of the American Chemical Society, 2021, 143 (47), pp.19909-19918. ⟨10.1021/jacs.1c09589⟩
Article dans une revue hal-03827043v1

Multilevel Lattice Boltzmann-Particle Dynamics simulations at the Physics-Biology interface

Fabio Sterpone , Massimo Bernaschi , Simone Melchionna , Philippe Derreumaux , Sauro Succi
XXIXth IUPAP Conference on Computational Physics CCP2017 9–13 July 2017, Paris, France, Jul 2017, Paris, France
Communication dans un congrès hal-02359987v1
Image document

Stabilizing or Destabilizing: Simulations of Chymotrypsin Inhibitor 2 under Crowding Reveal Existence of a Crossover Temperature

Stepan Timr , Fabio Sterpone
Journal of Physical Chemistry Letters, 2021, 12, pp.1741-1746. ⟨10.1021/acs.jpclett.0c03626⟩
Article dans une revue hal-03139158v1

Early Stage of the Dehydrogenation of NaAlH4 by Ab Initio Rare Event Simulations

Fabio Sterpone , Sara Bonella , Simone Meloni
Journal of Physical Chemistry C, 2012, 116 (37), pp.19636--19643. ⟨10.1021/jp3019588⟩
Article dans une revue hal-01498114v1

Thermophilic proteins: insight and perspective from in silico experiments

Fabio Sterpone , Simone Melchionna
Chemical Society Reviews, 2012, 41 (5), pp.1665-1676. ⟨10.1039/c1cs15199a⟩
Article dans une revue hal-01498109v1
Image document

Optimized OPEP Force Field for Simulation of Crowded Protein Solutions

Stepan Timr , Simone Melchionna , Philippe Derreumaux , Fabio Sterpone
Journal of Physical Chemistry B, 2023, 127 (16), pp.3616-3623. ⟨10.1021/acs.jpcb.3c00253⟩
Article dans une revue hal-04234930v1
Image document

Dynamics and Structures of Amyloid Aggregates under Fluid Flows

Antonio Iorio , Simone Melchionna , Philippe Derreumaux , Fabio Sterpone
Journal of Physical Chemistry Letters, 2024, 15 (7), pp.1943-1949. ⟨10.1021/acs.jpclett.3c03084⟩
Article dans une revue pasteur-04534373v1

Magnitude and Molecular Origin of Water Slowdown Next to a Protein

Fabio Sterpone , Guillaume Stirnemann , Damien Laage
Journal of the American Chemical Society, 2012, 134 (9), pp.4116--4119. ⟨10.1021/ja3007897⟩
Article dans une revue hal-01498111v1

Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue

Marina Katava , Maria Kalimeri , Guillaume Stirnemann , Fabio Sterpone
Journal of Physical Chemistry B, 2016, 120, pp.2721--2730. ⟨10.1021/acs.jpcb.6b00306⟩
Article dans une revue hal-01497992v1