Publications
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2019. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. Journal of Chemical Theory and Computation. 15:3875-3888.
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2019. Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
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2019. The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res. 47:1836-1846.
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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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2019. Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics. J. Phys. Chem. Lett.. 10
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2019. QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces. Workshop on Molecular Graphics and Visual Analysis of Molecular Data.
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2019. Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. J Biol Chem. 294:7588-7600.
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2019. Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem. 294:8606-8616.
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2019. Stability Effect of Quinary Interactions Reversed by Single Point Mutations. Journal of the American Chemical Society. 141:4660-4669.
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2019. Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.. Data Brief. 26:104460.
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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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2019. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.. J Phys Chem B. 123(17):3643-3648.
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2019. Visualizing Biological Membrane Organization and Dynamics.. J Mol Biol. 431(10):1889-1919.
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2019. Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res. 47:7798-7808.
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2020. Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
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2020. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
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2020. Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.. Phys Chem Chem Phys. 22(3):1611-1623.
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2020. Computer Simulations Provide Guidance for Molecular Medicine Through Insights on Dynamics and Mechanisms at the Atomic Scale. 7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7).
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2020. Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why? J Mol Biol. 432(3):737-744.
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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. Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ Peptide.. J Chem Inf Model. 60(3):1399-1408.
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2020. Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation. J Phys Chem B. 124:8516–8523.
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2020. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.. J Chem Phys. 153(5):050901.
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2020. Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.. J Mol Biol. 432(4):1183-1198.
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2020. Protein thermal stability. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly.