Publications
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Author Title Type [ Year
] Filters: First Letter Of Last Name is N and Author is Nguyen, Phuong H. [Clear All Filters]
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2011. Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations.
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2011. Simulation of transient infrared spectra of a photoswitchable peptide. J. Chem. Phys.. 135
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2010. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J. Chem. Phys.. 133
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2010. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J. Chem. Phys.. 132
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2010. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
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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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2009. Estimating configurational entropy of complex molecules: A novel variable transformation approach. Chem. Phys. Lett.. 468:90–93.
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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.
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2009. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
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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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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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2008. Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description. Chem. Phys.. 347:208–217.
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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.
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2008. Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties. J. Phys. Chem. B. 112:15487–15492.
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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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2007. Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys.. 126
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2007. Energy transport in peptide helices. Proc. Natl. Acad. Sci. U.s.a.. 104:12749–12754.
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2007. How complex is the dynamics of peptide folding? Phys. Rev. Lett.. 98
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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.
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2007. Quantum-classical description of the amide I vibrational spectrum of trialanine. J. Chem. Phys.. 126
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2007. Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study. J. Am. Chem. Soc.. 129:1179–1189.
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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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2006. Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces. J. Chem. Phys.. 124
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2006. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.