Publications
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Author Title [ Type
] Year Filters: Author is Nguyen, Phuong H. [Clear All Filters]
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2016. Alzheimer’s Disease: Insights into Amyloid Fibril Formation from Lattice Monte Carlo Simulations. Biophys. J.. 110:219A.
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2015. Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
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2014. Amyloid oligomer structure characterization from simulations: A general method. J. Chem. Phys.. 140:094105.
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2011. Coherent vibrational energy transfer along a peptide helix. J. Chem. Phys.. 134
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2015. Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry-a European Journal. 21:12657–12666.
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2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation.. The Journal of Chemical Physics. 143:021101–021101.
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2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
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2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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2006. Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis. Proteins: Struct., Funct., Bioinf.. 65:898–913.
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2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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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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2007. Conformational states and folding pathways of peptides revealed by principal-independent component analyses. Proteins: Struct., Funct., Bioinf.. 67:579–592.
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2008. Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. J. Chem. Phys.. 128
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2007. Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys.. 126
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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.
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2014. Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
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2013. Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
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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.
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2009. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
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2007. Energy transport in peptide helices. Proc. Natl. Acad. Sci. U.s.a.. 104:12749–12754.
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2008. Energy transport in peptide helices: A comparison between high- and low-energy excitations. J. Phys. Chem. B. 112:9091–9099.
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2009. Estimating configurational entropy of complex molecules: A novel variable transformation approach. Chem. Phys. Lett.. 468:90–93.
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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.
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2015. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
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2009. Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis. J. Phys. Chem. B. 113:16660–16668.