Publications
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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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2015. Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys.. 143:155101.
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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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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. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure & Dynamics. 33:30–31.
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2000. Predicting helical hairpins from sequences by Monte Carlo simulations. J. Comput. Chem.. 21:582–589.
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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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2018. Probing the quality control mechanism of the twin-arginine translocase with folding variants of a -designed heme protein.. J Biol Chem. 293(18):6672-6681.
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2015. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J. Chem. Theory Comput.. 11:1843–1853.
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2017. Protein-RNA complexation driven by the charge regulation mechanism.. Biochem Biophys Res Commun.
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1989. RAMAN-SPECTROSCOPY, MOLECULAR-FORCE FIELDS, AND THE DYNAMICS OF BIOLOGICAL MOLECULES. Chemica Scripta. 29A:113–122.
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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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2009. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.. J. Phys. Chem. B. 113:267–274.
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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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2013. Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
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2003. Role of supersecondary structural elements in protein G folding. J. Chem. Phys.. 119:4940–4944.
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2008. Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer's peptides A beta 40 and A beta 42. Curr. Alzheimer Res.. 5:244–250.
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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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2007. Sampling small-scale and large-scale conformational changes in proteins and molecular complexes. J. Chem. Phys.. 126:105101.
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2003. Sampling the complex energy landscape of a simple beta-hairpin. J. Chem. Phys.. 119:6403–6406.
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2004. Sampling the self-assembly pathways of KFFE hexamers. Biophys. J.. 87:3648–3656.
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2008. Self-assembly of amyloid-forming peptides by molecular dynamics simulations. Front. Biosci.. 13:5681–5692.
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2008. Self-assembly of the beta 2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals beta-barrel species. J. Phys. Chem. B. 112:4410–4418.
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2008. Simulating the early steps of amyloid fibril formation and disassembly. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:7–12.
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2011. Simulation of the Oligomerization Pathway for Different Alloforms of the Amyloid Beta Protein Related to Alzheimer's Disease. Biophys. J.. 100:401.