Publications

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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.
Nury H., Van Renterghem C., Weng Y., Tran A., Baaden M., Dufresne V., Changeux J.-P., Sonner J.M, Delarue M., Corringer P.-J..  2011.  X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469:428–431.
Nissen LJ, Gelly JC, Hipskind RA.  2001.  Induction-independent recruitment of CREB-binding protein to the c-fos serum response element through interactions between the bromodomain and Elk-1. J. Biol. Chem.. 276:5213–5221.
Nishikawa N., Nguyen P., Derreumaux P., Okamoto Y..  2013.  Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
Nishikawa N, Nguyen PH, Derreumaux P, Okamoto Y.  2015.  Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
Nguyent P, Derreumaux P.  2014.  Understanding Amyloid Fibril Nucleation and A beta Oligomer/Drug Interactions from Computer Simulations. Acc. Chem. Res.. 47:603–611.
Nguyen PH, Derreumaux P.  2012.  Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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 HLinh, Thu TThi Minh, Truong PMinh, Lan PDang, Man VHoang, Nguyen PH, Tu LAnh, Chen Y-C, Li MSuan.  2016.  Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study. The Journal of Physical Chemistry B. 120:7371–7379.
Nguyen P.H., Hamm P., Stock G..  2009.  Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment.
Nguyen PH, Okamoto Y, Derreumaux P.  2013.  Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
Nguyen PH.  2009.  Estimating configurational entropy of complex molecules: A novel variable transformation approach. Chem. Phys. Lett.. 468:90–93.
Nguyen PH, Derreumaux P, Stock G.  2009.  Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
Nguyen PH, Li MSuan, Stock G, Straub JE, Thirumalai D..  2007.  Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism. Proc. Natl. Acad. Sci. U.s.a.. 104:111–116.
Nguyen PH, Li MSuan, Derreumaux P.  2011.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
Nguyen PH.  2010.  Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
Nguyen PH, Del Castillo-Frias MP, Berthoumieux O, Faller P, Doig AJ, Derreumaux P.  2018.  Amyloid-β/drug interactions from computer simulations and cell-based assays. Journal of Alzheimer's Disease. 64:S659–S672.
Nguyen PH.  2007.  Conformational states and folding pathways of peptides revealed by principal-independent component analyses. Proteins: Struct., Funct., Bioinf.. 67:579–592.
Nguyen PH, Stock G.  2006.  Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
Nguyen PH, Tarus B, Derreumaux P.  2014.  Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer. J. Phys. Chem. B. 118:501–510.
Nguyen PH, Mittag E, Torda AE, Stock G.  2006.  Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces. J. Chem. Phys.. 124
Nguyen PH, Campanera JM, Ngo STung, Loquet A, Derreumaux P.  2019.  Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.. J Phys Chem B. 123(17):3643-3648.
Nguyen PH.  2006.  Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis. Proteins: Struct., Funct., Bioinf.. 65:898–913.
Nguyen PH, Sterpone F, Derreumaux P.  2020.  Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
Nguyen PH, Derreumaux P.  2013.  Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's A beta(37-42) Amyloid Peptide Oligomers. J. Phys. Chem. B. 117:5831–5840.

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