Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study, Phys. Chem. Chem. Phys., vol.118, issue.41, p.27275, 2015. ,
DOI : 10.1021/ja953070s
URL : https://hal.archives-ouvertes.fr/hal-01498007
Communication: Multiple atomistic force fields in a single enhanced sampling simulation, The Journal of Chemical Physics, vol.24, issue.2, p.21101, 2015. ,
DOI : 10.1126/science.1208351
URL : https://hal.archives-ouvertes.fr/hal-01498016
Structures of the Alzheimer?s Wild-Type A?1-40 Dimer from Atomistic Simulations, The Journal of Physical Chemistry B, vol.119, issue.33, p.10478, 2015. ,
DOI : 10.1021/acs.jpcb.5b05593
Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering, The Journal of Physical Chemistry B, vol.119, issue.23, p.6941, 2015. ,
DOI : 10.1021/acs.jpcb.5b03381
URL : https://hal.archives-ouvertes.fr/hal-01498009
Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study, The Journal of Chemical Physics, vol.7, issue.15, p.155101, 2015. ,
DOI : 10.1002/lpor.200810063
URL : https://hal.archives-ouvertes.fr/hal-01498015
Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp, Chemistry - A European Journal, vol.140, issue.36, p.12657, 2015. ,
DOI : 10.1063/1.4866902
URL : https://hal.archives-ouvertes.fr/hal-01498029
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models, The Journal of Chemical Physics, vol.51, issue.14, p.145104, 2015. ,
DOI : 10.1002/anie.200250684
Molecular structure of the NQTrp inhibitor with the Alzheimer A?1-28 monomer, European Journal of Medicinal Chemistry, vol.91, p.43, 2015. ,
DOI : 10.1016/j.ejmech.2014.07.002
URL : https://hal.archives-ouvertes.fr/hal-01498032
Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation, Molecular Simulation, vol.41, issue.10-12, p.1041, 2015. ,
DOI : 10.1002/bip. 360221211
URL : https://hal.archives-ouvertes.fr/hal-01498003
Effect of Taiwan Mutation (D7H) on Structures of Amyloid-? Peptides: Replica Exchange Molecular Dynamics Study, The Journal of Physical Chemistry B, vol.118, issue.30, p.8972, 2014. ,
DOI : 10.1021/jp503652s
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems, Chem. Soc. Rev., vol.101, issue.13, p.4871, 2014. ,
DOI : 10.1021/jp970984n
URL : https://hal.archives-ouvertes.fr/hal-01084631
Amyloid oligomer structure characterization from simulations: A general method, The Journal of Chemical Physics, vol.7, issue.9, p.94105, 2014. ,
DOI : 10.1063/1.2746330
URL : https://hal.archives-ouvertes.fr/hal-01498036
Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A?1?28 Monomer, The Journal of Physical Chemistry B, vol.118, issue.2, p.501, 2014. ,
DOI : 10.1021/jp4115404
URL : https://hal.archives-ouvertes.fr/hal-01498045
Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation, Journal of Chemical Theory and Computation, vol.9, issue.10, p.4574, 2013. ,
DOI : 10.1021/ct4003493
URL : https://hal.archives-ouvertes.fr/hal-01498059
Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations, The Journal of Physical Chemistry B, vol.112, issue.30, p.9091, 2008. ,
DOI : 10.1021/jp711046e
Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis, The Journal of Chemical Physics, vol.703, issue.24, p.245102, 2008. ,
DOI : 10.1002/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G
Energy transport in peptide helices, Proceedings of the National Academy of Sciences, vol.323, issue.3, p.12749, 2007. ,
DOI : 10.1016/j.chemphys.2005.08.047
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1937538
Dihedral angle principal component analysis of molecular dynamics simulations, The Journal of Chemical Physics, vol.62, issue.24, p.244111, 2007. ,
DOI : 10.1063/1.475378
Conformational states and folding pathways of peptides revealed by principal-independent component analyses, Proteins: Structure, Function, and Bioinformatics, vol.65, issue.3, p.579, 2007. ,
DOI : 10.1007/s008940100045
Structure and Dynamics of the Homologous Series of Alanine Peptides:? A Joint Molecular Dynamics/NMR Study, Journal of the American Chemical Society, vol.129, issue.5, p.1179, 2007. ,
DOI : 10.1021/ja0660406
Quantum-classical description of the amide I vibrational spectrum of trialanine, The Journal of Chemical Physics, vol.57, issue.5, p.54509, 2007. ,
DOI : 10.1038/nature05352
How Complex Is the Dynamics of Peptide Folding?, Physical Review Letters, vol.621, issue.2, p.28102, 2007. ,
DOI : 10.1021/bi00483a001
Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism, Proceedings of the National Academy of Sciences, vol.121, issue.21, p.111, 2007. ,
DOI : 10.1063/1.1809588
Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces, The Journal of Chemical Physics, vol.124, issue.15, p.154107, 2006. ,
DOI : 10.1063/1.1632136
Sud). I worked closely with the student on the effects of force fields on the laser-induced disssociation of amyloid fibrils, Laboratory of Chemical Physics, 2015. ,
PhD student, Institute of Physical and Theoretical ChemistryOfficial advisor: Professor Gerhard Stock). I worked directly with the student on the simulations of energy transfer along peptides, 2005. ,
PhD student, Institute of Physical and Theoretical ChemistryOfficial advisor: Professor Gerhard Stock). I worked directly with the student on the simulations of RNA systems, 2002. ,
The Physics of Liquid Crystals, J. Chem. Phys, vol.56, issue.2, p.4213, 1975. ,
Theory of Simple Liquids, Academic J. Chem. Phys, vol.119, p.1214, 1986. ,
Hydrodynamic fluctuations, broken symmetry and correlation functions, Frontiers in Physics, 1975. ,
I. Liquid crystals. On the theory of liquid crystals, Discussions of the Faraday Society, vol.25, p.19, 1958. ,
DOI : 10.1039/df9582500019
URL : https://hal.archives-ouvertes.fr/in2p3-00011556
Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water, The Journal of Chemical Physics, vol.7, issue.21, p.11350, 2003. ,
DOI : 10.1103/PhysRevLett.4.239
Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations, The Journal of Physical Chemistry B, vol.112, issue.30, p.9091, 2008. ,
DOI : 10.1021/jp711046e
Nonequilibrium molecular dynamics simulation of a photoswitchable peptide, Chemical Physics, vol.323, issue.1, p.36, 2006. ,
DOI : 10.1016/j.chemphys.2005.08.047
Photoinduced Conformational Dynamics of a Photoswitchable Peptide: A Nonequilibrium Molecular Dynamics Simulation Study, Biophysical Journal, vol.91, issue.4, p.1224, 2006. ,
DOI : 10.1529/biophysj.106.084996
Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment, The Journal of Physical Chemistry B, vol.115, issue.44, pp.13084-13092, 2011. ,
DOI : 10.1021/jp207945p
Quantum-classical description of the amide I vibrational spectrum of trialanine, The Journal of Chemical Physics, vol.57, issue.5, p.54509, 2007. ,
DOI : 10.1038/nature05352
Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description, Chemical Physics, vol.347, issue.1-3, p.208, 2008. ,
DOI : 10.1016/j.chemphys.2007.10.034
Simulation of transient infrared spectra of a photoswitchable peptide, The Journal of Chemical Physics, vol.135, issue.22, p.225102, 2011. ,
DOI : 10.1063/1.455649
Energy landscape of a small peptide revealed by dihedral angle principal component analysis, Proteins: Structure, Function, and Bioinformatics, vol.295, issue.1, pp.45-52, 2005. ,
DOI : 10.1007/978-94-015-7658-1_21
Dihedral angle principal component analysis of molecular dynamics simulations, The Journal of Chemical Physics, vol.62, issue.24, p.244111, 2007. ,
DOI : 10.1063/1.475378
Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis, The Journal of Chemical Physics, vol.703, issue.24, p.245102, 2008. ,
DOI : 10.1002/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G
How Complex Is the Dynamics of Peptide Folding?, Physical Review Letters, vol.621, issue.2, p.28102, 2007. ,
DOI : 10.1021/bi00483a001
Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis, Proteins: Structure, Function, and Bioinformatics, vol.58, issue.4, p.898, 2006. ,
DOI : 10.1007/s008940100045
Conformational states and folding pathways of peptides revealed by principal-independent component analyses, Proteins: Structure, Function, and Bioinformatics, vol.65, issue.3, p.579, 2007. ,
DOI : 10.1007/s008940100045
Structure and Dynamics of the Homologous Series of Alanine Peptides:? A Joint Molecular Dynamics/NMR Study, Journal of the American Chemical Society, vol.129, issue.5, p.1179, 2007. ,
DOI : 10.1021/ja0660406
Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis, The Journal of Physical Chemistry B, vol.113, issue.52, p.16660, 2010. ,
DOI : 10.1021/jp9076036
Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study, The Journal of Physical Chemistry B, vol.113, issue.27, p.9340, 2009. ,
DOI : 10.1021/jp902013s
Structure of the Amide I Band of Peptides Measured by Femtosecond Nonlinear-Infrared Spectroscopy, The Journal of Physical Chemistry B, vol.102, issue.31, p.6123, 1998. ,
DOI : 10.1021/jp9813286
Subpicosecond conformational dynamics of small peptides probed by two-dimensional vibrational spectroscopy, Proceedings of the National Academy of Sciences, vol.70, issue.4, p.11254, 2001. ,
DOI : 10.1016/S0006-3495(96)79735-7
Ultrafast Vibrational Dynamics of the Myoglobin Amide I Band, The Journal of Physical Chemistry B, vol.103, issue.3, p.557, 1999. ,
DOI : 10.1021/jp982398f
Vibrational energy relaxation rate constants from linear response theory, The Journal of Chemical Physics, vol.94, issue.16, p.7562, 2003. ,
DOI : 10.1146/annurev.pc.45.100194.002511
URL : https://deepblue.lib.umich.edu/bitstream/2027.42/69779/2/JCPSA6-118-16-7562-1.pdf
GROMACS 3.0: a package for molecular simulation and trajectory analysis, Journal of Molecular Modeling, vol.7, issue.8, pp.306-317, 2001. ,
DOI : 10.1007/s008940100045
Photodissociation Dynamics, 1993. ,
DOI : 10.1063/1.2808612
The short?time dynamics of molecular liquids. Instantaneous?normal?mode theory, The Journal of Chemical Physics, vol.97, issue.11, p.8522, 1992. ,
DOI : 10.1103/PhysRevLett.65.2828
Biomolecular Simulation: The GROMOS96 Manual and User Guide. Vdf Hochschulverlag AG an der ETH, 1996. ,
Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study, Proteins: Structure, Function, and Bioinformatics, vol.119, issue.3, p.485, 2005. ,
DOI : 10.1007/s008940100045
Large-amplitude nonlinear motions in proteins, Physical Review Letters, vol.8, issue.17, pp.2696-2699, 1992. ,
DOI : 10.1016/0022-2836(79)90308-5
Independent component analysis, 2001. ,
Protein Misfolding, Functional Amyloid, and Human Disease, Annual Review of Biochemistry, vol.75, issue.1, pp.333-366, 2006. ,
DOI : 10.1146/annurev.biochem.75.101304.123901
Understanding Amyloid Fibril Nucleation and A? Oligomer/Drug Interactions from Computer Simulations, Accounts of Chemical Research, vol.47, issue.2, pp.603-611, 2014. ,
DOI : 10.1021/ar4002075
Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations, Journal of Molecular Biology, vol.421, issue.2-3, pp.390-416, 2012. ,
DOI : 10.1016/j.jmb.2012.02.004
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization, PLoS ONE, vol.14, issue.5, p.19129, 2011. ,
DOI : 10.1371/journal.pone.0019129.s011
Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail, Journal of the American Chemical Society, vol.134, issue.8, p.3886, 2012. ,
DOI : 10.1021/ja210826a
Amyloid Peptide Oligomers, The Journal of Physical Chemistry B, vol.117, issue.19, pp.5831-5840, 2013. ,
DOI : 10.1021/jp401563n
URL : https://hal.archives-ouvertes.fr/hal-01498064
Atomic structures of amyloid cross-? spines reveal varied steric zippers, Nature, vol.234, issue.7143, pp.453-457, 2005. ,
DOI : 10.1177/16.11.673
A Simple Lattice Model That Captures Protein Folding, Aggregation and Amyloid Formation, PLoS ONE, vol.90, issue.1, p.85185, 2014. ,
DOI : 10.1371/journal.pone.0085185.t001
URL : http://doi.org/10.1371/journal.pone.0085185
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems, Chem. Soc. Rev., vol.101, issue.13, p.4871, 2015. ,
DOI : 10.1021/jp970984n
URL : https://hal.archives-ouvertes.fr/hal-01084631
Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer?s peptides, The Journal of Chemical Physics, vol.144, issue.20, p.205103, 2016. ,
DOI : 10.1021/jp312573y
Structures of the Alzheimer???s Wild-Type A??1-40 Dimer from Atomistic Simulations, The Journal of Physical Chemistry B, vol.119, issue.33, pp.10478-10487, 2015. ,
DOI : 10.1021/acs.jpcb.5b05593
Molecular structure of the NQTrp inhibitor with the Alzheimer A?1-28 monomer, European Journal of Medicinal Chemistry, vol.91, pp.43-50, 2015. ,
DOI : 10.1016/j.ejmech.2014.07.002
URL : https://hal.archives-ouvertes.fr/hal-01498032
Complete Phenotypic Recovery of an Alzheimer's Disease Model by a Quinone-Tryptophan Hybrid Aggregation Inhibitor, PLoS ONE, vol.94, issue.10, p.11101, 2010. ,
DOI : 10.1371/journal.pone.0011101.s012
High-Resolution NMR Spectroscopy of the ??-Amyloid(1???28) Fibril Typical for Alzheimer's Disease, Angewandte Chemie International Edition, vol.40, issue.19, pp.3603-3605, 2001. ,
DOI : 10.1002/1521-3773(20011001)40:19<3603::AID-ANIE3603>3.0.CO;2-5
Overlapping profiles of Abeta peptides in the Alzheimer's disease and pathological aging brains, Alzheimer's Research & Therapy, vol.4, issue.3, p.18, 2012. ,
DOI : 10.1186/alzrt121
Investigation of the noncovalent interactions between anti-amyloid agents and amyloid ? peptides by ESI-MS, Journal of the American Society for Mass Spectrometry, vol.356, issue.9, pp.1506-1514, 2010. ,
DOI : 10.1056/NEJMoa065644
A mutation in APP protects against Alzheimer?s disease and age-related cognitive decline, Nature, vol.43, issue.7409, pp.96-99, 2012. ,
DOI : 10.1038/ng.781
A Recessive Mutation in the APP Gene with Dominant-Negative Effect on Amyloidogenesis, Science, vol.278, issue.16, pp.1473-1477, 2009. ,
DOI : 10.1074/jbc.M211976200
Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A??1???28 Monomer, The Journal of Physical Chemistry B, vol.118, issue.2, p.501, 2014. ,
DOI : 10.1021/jp4115404
URL : https://hal.archives-ouvertes.fr/hal-01498045
Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A??40 and A??42, ACS Chemical Neuroscience, vol.5, issue.8, p.646, 2014. ,
DOI : 10.1021/cn500007j
URL : https://hal.archives-ouvertes.fr/hal-01498050
Effect of Taiwan Mutation (D7H) on Structures of Amyloid-?? Peptides: Replica Exchange Molecular Dynamics Study, The Journal of Physical Chemistry B, vol.118, issue.30, p.8972, 2014. ,
DOI : 10.1021/jp503652s
Effect of Mid-infrared Free-Electron Laser Irradiation on Refolding of Amyloid-Like Fibrils of Lysozyme into Native Form, The Protein Journal, vol.95, issue.8, pp.710-716, 2012. ,
DOI : 10.1529/biophysj.107.122002
Mid-infrared free-electron laser tuned to the amide I band for converting insoluble amyloid-like protein fibrils into the soluble monomeric form, Lasers in Medical Science, vol.88, issue.5, pp.1701-1707, 2014. ,
DOI : 10.1038/385787a0
Use of a Mid-Infrared Free-Electron Laser (MIR-FEL) for Dissociation of the Amyloid Fibril Aggregates of a Peptide, Journal of Analytical Sciences, Methods and Instrumentation, vol.04, issue.01, pp.9-18, 2014. ,
DOI : 10.4236/jasmi.2014.41002
Synchrotron-Infrared Microscopy Analysis of Amyloid Fibrils Irradiated by Mid-Infrared Free-Electron Laser, American Journal of Analytical Chemistry, vol.05, issue.06, pp.384-394, 2014. ,
DOI : 10.4236/ajac.2014.56047
Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study, The Journal of Chemical Physics, vol.7, issue.15, p.155101, 2015. ,
DOI : 10.1002/lpor.200810063
URL : https://hal.archives-ouvertes.fr/hal-01498015
Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study, Phys. Chem. Chem. Phys., vol.118, issue.41, p.27275, 2015. ,
DOI : 10.1021/ja953070s
URL : https://hal.archives-ouvertes.fr/hal-01498007
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States, Physical Review Letters, vol.34, issue.10, p.2050, 2001. ,
DOI : 10.1103/PhysRevB.34.1841
Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces, The Journal of Chemical Physics, vol.124, issue.15, p.154107, 2006. ,
DOI : 10.1063/1.1632136
Replica exchange simulation method using temperature and solvent viscosity, The Journal of Chemical Physics, vol.132, issue.14, p.144109, 2010. ,
DOI : 10.1103/PhysRevLett.79.317
Communication: Simulated tempering with fast on-the-fly weight determination, The Journal of Chemical Physics, vol.138, issue.6, p.61102, 2013. ,
DOI : 10.1073/pnas.0607440104
URL : https://hal.archives-ouvertes.fr/hal-01498062
Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering, The Journal of Physical Chemistry B, vol.119, issue.23, p.6941, 2015. ,
DOI : 10.1021/acs.jpcb.5b03381
URL : https://hal.archives-ouvertes.fr/hal-01498009
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles, The Journal of Chemical Physics, vol.26, issue.3, pp.1776-1783, 1992. ,
DOI : 10.1080/07391102.1985.10508396
Simulated Tempering: A New Monte Carlo Scheme, Europhysics Letters (EPL), vol.19, issue.6, pp.451-458, 1992. ,
DOI : 10.1209/0295-5075/19/6/002
URL : http://arxiv.org/abs/hep-lat/9205018
Communication: Multiple atomistic force fields in a single enhanced sampling simulation, The Journal of Chemical Physics, vol.24, issue.2, p.21101, 2015. ,
DOI : 10.1126/science.1208351
URL : https://hal.archives-ouvertes.fr/hal-01498016
Amyloid oligomer structure characterization from simulations: A general method, The Journal of Chemical Physics, vol.7, issue.9, p.94105, 2014. ,
DOI : 10.1063/1.2746330
URL : https://hal.archives-ouvertes.fr/hal-01498036
Dominant forces in protein folding, Biochemistry, vol.29, issue.31, pp.7133-7155, 1990. ,
DOI : 10.1021/bi00483a001
Method for estimating the configurational entropy of macromolecules, Macromolecules, vol.14, issue.2, p.325, 1981. ,
DOI : 10.1021/ma50003a019
Estimating configurational entropy of complex molecules: A novel variable transformation approach, Chemical Physics Letters, vol.468, issue.1-3, p.90, 2009. ,
DOI : 10.1016/j.cplett.2008.11.061
Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature, Phys. Chem. Chem. Phys., vol.96, issue.2, pp.877-886, 2012. ,
DOI : 10.1002/prot.22972
URL : https://hal.archives-ouvertes.fr/hal-01498106