Publications
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1994. Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc. Natl. Acad. Sci. U.s.a.. 91:11621–11625.
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2017. String method solution of the gating pathways for a pentameric ligand-gated ion channel.. Proc Natl Acad Sci U S A. 114(21):E4158-E4167.
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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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2010. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J. Phys. Chem. B. 114:1004–1009.
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2011. Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
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2007. Structure and aggregation mechanism of beta 2-microglobulin (83-99) peptides studied by molecular dynamics Simulations. Biophys. J.. 93:3353–3362.
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2008. The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys. J.. 95:510–517.
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2016. Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J. Am. Chem. Soc.. 138:5403–5409.
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2016. In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. J. Mol. Model.. 22
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2013. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. Plos Comput. Biol.. 9:e1003369.
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2012. Involvement of the cysteine-rich head domain in activation and desensitization of the P2X1 receptor. Proceedings of the National Academy of Sciences of the United States of America. 109:11396–11401.
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2011. On the characterization and selection of diverse conformational ensembles with applications to flexible docking. Ieee/acm Trans. Comput. Biol. Bioinform.. 8:487–98.
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2018. Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer.. J Chem Phys. 148(4):045105.
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2011. Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
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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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2012. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations. J. Chem. Phys.. 137:025101.
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2009. Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins: Struct., Funct., Bioinf.. 75:954–963.
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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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2017. Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).. J Chem Phys. 146(14):145101.
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2013. Game on, science - how video game technology may help biologists tackle visualization challenges. Plos One. 8:e57990.
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2018. MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.. J Integr Bioinform. 15(2)
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2019. Mesoscale biosimulations within a unified framework: from proteins to plasmids. Molecular Simulation. :1-12.
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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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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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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.