Publications
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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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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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1995. A NEW SPECTROSCOPIC MOLECULAR MECHANICS FORCE-FIELD - PARAMETERS FOR PROTEINS. J. Chem. Phys.. 102:8586–8605.
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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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2017. Multi-scale simulations of biological systems using the OPEP coarse-grained model.. Biochem Biophys Res Commun.
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2016. Multiscale simulation of molecular processes in cellular environments. Philosophical Transactions of the Royal Society A-mathematical Physical and Engineering Sciences. 374
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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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2019. Multiscale Aggregation of the Amyloid Aβ16–22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils. The Journal of Physical Chemistry Letters. 10:1594-1599.
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2017. Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.. J Chem Phys. 147(15):152715.
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2016. MP2 and DFT studies of beta-D-neocarrabiose and beta-D-neocarrabiose monohydrate. Comput. Theor. Chem.. 1091:24–30.
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2015. Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer. Eur. J. Med. Chem.. 91:43–50.
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2013. Molecular Mechanism of the Inhibition of EGCG on the Alzheimer A beta(1-42) Dimer. J. Phys. Chem. B. 117:3993–4002.
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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. Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study.. J Phys Chem B. 122(5):1573-1579.
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2019. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports. 9:16450.
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2019. Mesoscale biosimulations within a unified framework: from proteins to plasmids. Molecular Simulation. :1-12.
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2010. Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J. Chem. Phys.. 132:165103.
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1998. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J.. 74:72–81.
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1995. LONG TIMESTEP DYNAMICS OF PEPTIDES BY THE DYNAMICS DRIVER APPROACH. Proteins-structure Function and Genetics. 21:282–302.
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2011. Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies. Plos One. 6:e24329.
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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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2002. Insight into protein topology from Monte Carlo simulations. J. Chem. Phys.. 117:3499–3503.
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2015. Inhibition of protein aggregation and amyloid formation by small molecules. Curr. Opin. Struct. Biol.. 30:50–56.
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1993. INFLUENCE OF THE SPECTROSCOPIC POTENTIAL-ENERGY FUNCTION SPASIBA ON MOLECULAR-DYNAMICS OF PROTEINS - COMPARISON WITH THE AMBER POTENTIAL. Theochem-journal of Molecular Structure. 105:55–64.