Publications
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2014. Amyloid oligomer structure characterization from simulations: A general method. J. Chem. Phys.. 140:094105.
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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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2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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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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2016. Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study. The Journal of Physical Chemistry B. 120:7371–7379.
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2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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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. 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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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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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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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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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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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. Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.