Publications

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Nguyen PH, Mu YG, Stock G.  2005.  Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 60:485–494.
Nguyen PH.  2010.  Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
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.
Nguyen PH, Gorbunov RD, Stock G.  2006.  Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys. J.. 91:1224–1234.
Nguyen PH, Stock G.  2006.  Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
Nguyen PH, Okamoto Y, Derreumaux P.  2013.  Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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, Stock G, Mittag E, Hu CK, Li MS.  2005.  Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 61:795–808.
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, Sterpone F, Derreumaux P.  2020.  Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
Nguyen PH, Sterpone F, Pouplana R, Derreumaux P, Campanera JM.  2016.  Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J. Phys. Chem. B. 120:12111–12126.
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.  2007.  Conformational states and folding pathways of peptides revealed by principal-independent component analyses. Proteins: Struct., Funct., Bioinf.. 67:579–592.
Nguyen P.H., Hamm P., Stock G..  2009.  Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment.
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, Sterpone F, Campanera JM, Nasica-Labouze J, Derreumaux P.  2016.  Impact of the A2V Mutation on the Heterozygous and Homozygous A beta 1-40 Dimer Structures from Atomistic Simulations. Acs Chem. Neurosci.. 7:823–832.
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, Staudt H, Wachtveitl J, Stock G.  2011.  Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment. J. Phys. Chem. B. 115:13084–13092.
Ngo STung, Derreumaux P, Vu VV.  2019.  Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.. J Phys Chem B. 123(12):2645-2653.
Ngo STung, Nguyen PH, Derreumaux P.  2020.  Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics.. J Phys Chem B. 124(7):1175-1182.
Ngo STung, Nguyen PHoang, Derreumaux P.  2020.  Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. The Journal of Physical Chemistry B.
Neri M, Baaden M, Carnevale V, Anselmi C, Maritan A, Carloni P.  2008.  Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J.. 94:71–78.
Nazarova N.I, Mazur AK, Elyakova L.A.  1986.  Active sites of the endo-beta-1,3-glucanases from Spisula sacchalinensis and Chlyamys albidys. Bioorg. Chem.. 12:1478–1483.
Nayeem SM, Oteri F, Baaden M, Deep S.  2017.  Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.. J Phys Chem B. 121(22):5483-5498.
Nawrocki W.J, Tourasse N.J, Taly A, Rappaport F., Wollman F.A.  2015.  The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. Annu. Rev. Plant Biol.. 66:49–74.

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