Publications
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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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2017. Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.. J Phys Chem B. 121(22):5483-5498.
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1986. Active sites of the endo-beta-1,3-glucanases from Spisula sacchalinensis and Chlyamys albidys. Bioorg. Chem.. 12:1478–1483.
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2008. Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J.. 94:71–78.
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2019. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.. J Phys Chem B. 123(12):2645-2653.
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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.
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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.
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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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2003. Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water. J. Chem. Phys.. 119:11350–11358.
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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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2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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2019. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.. J Phys Chem B. 123(31):6750-6756.
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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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2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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2005. Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 60:485–494.
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2010. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
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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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2018. Amyloid-β/drug interactions from computer simulations and cell-based assays. Journal of Alzheimer's Disease. 64:S659–S672.
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2006. Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys. J.. 91:1224–1234.
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2006. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
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2020. Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
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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.
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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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2006. Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces. J. Chem. Phys.. 124
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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.