Publications
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2006. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
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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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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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2019. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.. J Phys Chem B. 123(12):2645-2653.
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2008. Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J.. 94:71–78.
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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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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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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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2011. From toxins targeting ligand gated ion channels to therapeutic molecules. Toxins (basel). 3:260–293.
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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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2011. Characterization of the Aggregation Pathway for a 20-mer of GNNQQNY using Coarse-Grained and All-Atom Representations. Biophys. J.. 100:BiophysSoc.
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2011. A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35. Plos Comput. Biol.. 7:e1002051.
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2015. What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers. Biophys. J.. 108:204A-204A.
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2018. Water permeation across artificial I-quartet membrane channels: from structure to disorder.. Faraday Discuss. 209:125-148.
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2005. Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Struct., Funct., Bioinf.. 58:45–52.
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2005. Exploring the early steps of amyloid peptide aggregation by computers. Acc. Chem. Res.. 38:885–891.
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2001. Sampling activated mechanisms in proteins with the activation-relaxation technique. Journal of Molecular Graphics \& Modelling. 19:78–86.
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2008. Exploring energy landscapes of protein folding and aggregation. Front. Biosci.. 13:4495–4516.
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2005. Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique. Phys. Biol.. 2:S101-S107.
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2006. PHYS 4-Applications of activated methods to proteins and materials science. Abstracts of Papers of the American Chemical Society. 232
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2002. New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations. Biophys. J.. 82:3224–3245.
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2015. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proc. Natl. Acad. Sci. U.s.a.. 112:2865–2870.
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2012. Structural and Spectroscopic Properties of Water around Small Hydrophobic Solutes. The Journal of Physical Chemistry B. 116:11695–11700.
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2013. When Does Trimethylamine N-Oxide Fold a Polymer Chain and Urea Unfold It? J. Phys. Chem. B. 117:8723–8732.