Publications
"A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein." The Journal of Physical Chemistry Letters:10719-10726 (2023).
"Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore." ACS Nanosci. Au (2023).
"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)
Supplementary Information and Hand-on Guide (239.4 KB) "Multiple rereads of single proteins at single–amino acid resolution using nanopores." Science 374:1509-1513 (2021). si.pdf (33.12 MB)
si.pdf (33.12 MB) "Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure." Nano Letters 21:9789-9796 (2021). si.pdf (1.54 MB)
si.pdf (1.54 MB) "Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"Molecular Transport across the Ionic Liquid−Aqueous Electrolyte Interface in a MoS2 Nanopore." ACS Appl. Mater. Interfaces 12:26624-26634 (2020). supportinginformation_final.pdf (4.48 MB)
supportinginformation_final.pdf (4.48 MB) "MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems." Nucleic Acids Research (2020). supplement.pdf (3.94 MB)
supplement.pdf (3.94 MB) "Molecular Mechanism of Spontaneous Nucleosome Unraveling." Journal of Molecular Biology 431:323-335 (2019). supplementary_information.pdf (28.94 MB)
supplementary_information.pdf (28.94 MB) "Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
"Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
"Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
"Mechanical Trapping of DNA in a Double-Nanopore System." Nano Letters 16:8021-8028 (2016). Supporting Information (pdf) (2.24 MB)
Supporting Information (pdf) (2.24 MB) "Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New Journal of Physics 18:055012 (2016). supporting_information.pdf (7.84 MB)
supporting_information.pdf (7.84 MB) "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores." ACS Applied Materials and Interfaces 8:12599-12608 (2016). supporting.pdf (461.04 KB)
supporting.pdf (461.04 KB) "Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating." The Journal of Physical Chemistry Letters 6:4680-4687 (2015). Supporting Information (8.97 MB)
Supporting Information (8.97 MB) "Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
"Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (2011).
"Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
"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.
"Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems." In Simulations in Nanobiotechnology, edited by Kilho Eom, 43-60. CRC Press, 2011.
"Mechanical properties of a complete microtubule revealed through molecular dynamics simulation." Biophys J 99:629-37 (2010). Supporting Information (pdf) (2.75 MB)
Atomic coordinates of the equilibrated "N" protofilament (pdb) (2.02 MB) Atomic coordinates of the equilibrated "S" protofilament (pdb) (2.02 MB) Atomic coordinates of the equilibrated complete microtubule (pdb) (13.16 MB)
Supporting Information (pdf) (2.75 MB) Atomic coordinates of the equilibrated "N" protofilament (pdb) (2.02 MB) Atomic coordinates of the equilibrated "S" protofilament (pdb) (2.02 MB) Atomic coordinates of the equilibrated complete microtubule (pdb) (13.16 MB) "Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
"Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
"Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
"Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
"Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements." Advances in Chemical Physics 121:141-239 (2002).