Publications
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Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).
"Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
"Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
"The structure and physical properties of a packaged bacteriophage particle." Nature 627:905-914 (2024).
"Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations." In Nanopores: Sensing and Fundamental Biological Interactions, edited by Rashid Bashir and Samir Iqbal, 335-356. New York: Springer Science and Business Media, LLC, 2011.
"Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (2012).
"Modeling nanopores for sequencing DNA." In DNA Nanotechnology: Methods and Protocols, edited by Giampaolo Zuccheri and Bruno Samori, 317-358. Vol. 749. Methods Mol. Biol. 749., 2011.
"Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
"DNA sequence-dependent ionic currents in ultra-small solid-state nanopores." Nanoscale 18:9600-9613 (2016). supp_triplet.pdf (98.62 KB)
"Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
"PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore." Nature Communications 9:3661 (2018). supporting_information.pdf (1.34 MB)
"Multi-resolution simulation of DNA transport through large synthetic nanostructures." Phys Chem Chem Phys 24:2706-2716 (2022). Supplementary Information and Hand-on Guide (239.4 KB)
"High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System." ACS Nano 14:15566-15576 (2020). nn0c06191_si_001.pdf (547.55 KB)
"Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate." J. Phys. Chem. Lett. 11:4923-4929 (2020). supporting_information.pdf (481.68 KB)
"In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
"Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
"A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore." Commun Comput Phys 15:93-125 (2014).
"Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (2014).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
"Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
"Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes." Nano Lett 8:3916-21 (2008). Supporting Information (pdf) (8.8 MB)
"Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (2011).
"Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems." In Simulations in Nanobiotechnology, edited by Kilho Eom, 43-60. CRC Press, 2011.
"Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (2011).
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