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Man VHoang, Li MSuan, Wang J, Derreumaux P, Nguyen PH.  2019.  Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion. The Journal of chemical physics. 151:024103.
Nguyen PH, Stock G.  2006.  Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
Nguyen P.H., Hamm P., Stock G..  2009.  Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment.
Nguyen PH, Park S-M, Stock G.  2010.  Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J. Chem. Phys.. 132
Nguyen PH, Stock G.  2003.  Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water. J. Chem. Phys.. 119:11350–11358.
Grznarova K, Torrent J, Munoz-Montesino C, Nasica J, Derreumaux P, Beringue V, Deslys J-P, Rezaei H.  2016.  Non-equivalent binding sites for Abeta1-40 on PrP determine the oligomerisation pathway. Prion. 10:S40.
Stirnemann G, Castrillon SRomero-Var, Hynes JT, Rossky PJ, Debenedetti PG, Laage D.  2011.  Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity: competing effects of the hydration structure and hydrogen-bond strength. Phys. Chem. Chem. Phys.. 13:19911.
Floquet N, Maréchal J-D, Badet-Denisot M-A, Robert CH, Dauchez M, Perahia D.  2006.  Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors. Febs Lett.. 580:5130–5136.
Taly A.  2013.  Novel approaches to drug design for the treatment of schizophrenia. Expert Opin. Drug Discovery. 8:1285–1296.
Woll KA, Murlidaran S, Pinch BJ, Hénin J, Wang X, Salari R, Covarrubias M, Dailey WP, Brannigan G, Garcia BA et al..  2016.  A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of gamma-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes.. J. Biol. Chem. 291:20473–86.
Prevost M., Sauguet L., Nury H., Van Renterghem C., Huon C., Poitevin F., Baaden M, Delarue M., Corringer P.-J..  2012.  A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel. Nature Structural & Molecular Biology.
Pasquali S., Nitti F., Maggs A.C..  2008.  Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.
Pasquali S., Maggs A.C..  2009.  Numerical studies of Lifshitz interactions between dielectrics. Phys. Rev. A. 79:020102(R).
Nury H., Poitevin F., Van Renterghem C., Changeux J.P, Corringer P.J, Delarue M., Baaden M.  2010.  One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
Taly A.  2007.  Opened by a twist: a gating mechanism for the nicotinic acetylcholine receptor. Eur. Biophys. J.. 36:911–918.
Lemoine D., Habermacher C., Martz A., Mery P.F, Bouquier N., Diverchy F., Taly A, Rassendren F., Specht A., Grutter T..  2013.  Optical control of an ion channel gate. Proc. Natl. Acad. Sci. U.s.a.. 110:20813–20818.
Hajjar E, Perahia D, Débat H, Nespoulous C, Robert CH.  2006.  Odorant Binding and Conformational Dynamics in the Odorant-binding Protein. J. Biol. Chem.. 281:29929–29937.
Mazur AK, Nazarova N.I, Elyakova L.A.  1985.  Oligomer distribution of depolymerase digests: Comparison of theory and experiments. Febs Lett.. 192:43–46.
Baaden M, Sansom MSP.  2004.  OmpT: Molecular dynamics simulations of an outer membrane enzyme. Biophys. J.. 87:2942–2953.
Sterpone F., Melchionna S., Tuffery P, Pasquali S., Mousseau N., Cragnolini T., Chebaro Y, St-Pierre J.-F., Kalimeri M., Barducci A. et al..  2014.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem. Soc. Rev.. 43:4871–4893.
da Silva FLuis Barro, Sterpone F, Derreumaux P.  2019.  OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. Journal of Chemical Theory and Computation. 15:3875-3888.
Colas C., Nguyen P.H., Gelly J-C., Derreumaux P..  2008.  OPERA: An OPtimized coarsed-grained Energy model for RnA. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:185–187.
Dorofeyev VE, Mazur AK.  1993.  Optimization of numerical algorithms for internal coordinate molecular dynamics. J. Comput. Phys.. 107:359–366.
Miné-Hattab J, Fleury G, Prévost C, Dutreix M, Viovy J-L.  2011.  Optimizing the design of oligonucleotides for homology directed gene targeting. Plos One. 6:e14795.