Publications
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2015. Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys. Chem. Chem. Phys.. 17:27275–27280.
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2015. Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
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2015. Structures of the Alzheimer’s Wild-Type A beta 1-40 Dimer from Atomistic Simulations. J. Phys. Chem. B. 119:10478–10487.
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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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2016. Alzheimer’s Disease: Insights into Amyloid Fibril Formation from Lattice Monte Carlo Simulations. Biophys. J.. 110:219A.
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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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2016. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr. J. Chem.. DOI: 10.1002/ijch.201600048.
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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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2016. Impact of the A2V Mutation on the Heterozygous and Homozygous A beta 1-40 Dimer Structures from Atomistic Simulations. Acs Chem. Neurosci.. 7:823–832.
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2016. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides. J. Chem. Phys.. 144
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2016. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils. J. Chem. Phys.. 145
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2016. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses. Phys. Chem. Chem. Phys.. 18:11951–11958.
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2017. Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.. J Phys Chem B. 121(11):2434-2442.
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2017. High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.. J Phys Chem B. 121(24):5977-5987.
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2017. Multi-scale simulations of biological systems using the OPEP coarse-grained model.. Biochem Biophys Res Commun.
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2017. Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer's Disease? ACS Chem Neurosci. 8(7):1435-1437.
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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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2018. Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
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2018. Molecular mechanism of the cell membrane pore formation induced by bubble stable cavitation. The Journal of Physical Chemistry B. 123:71–78.
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2018. Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study. The Journal of Chemical Physics. 148:094505.
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2019. Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
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2019. Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
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2019. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level. The Journal of chemical physics. 150:215101.
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2019. Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion. The Journal of chemical physics. 151:024103.
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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.