Publications
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2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
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2022. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
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2021. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
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2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
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2020. Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding. Nucleic Acids Res. 48:373-389.
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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. An inter-dimer allosteric switch controls NMDA receptor activity. The EMBO journal. 38
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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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2018. Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
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2018. DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43. J Phys Chem Lett. 9:3800-3807.
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2018. From Virtual Reality to Immersive Analytics in Bioinformatics.. J Integr Bioinform. 15(2)
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2018. The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation .. Elife. 7
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2018. Meet-U: Educating through research immersion. PLOS Computational Biology. 14:1-10.
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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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2017. Molecular Visualization of Computational Biology Data: A Survey of Surveys. EuroVis 2017 - Short Papers.
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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. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J. Chem. Theory Comput.. 12:6077–6097.
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2015. Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
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2015. How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.. Proc. Natl. Acad. Sci. Usa. 112:9270–5.
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2015. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248