Publications
"Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
"Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
"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)
Supporting Information (pdf) (8.8 MB) "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) "Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
"Dehydration and ionic conductance quantization in nanopores." J Phys Condens Matter 22:454126 (2010).
"DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"Third Generation DNA Sequencing with a Nanopore." In Nanopores: Sensing fundamental biological interactions at the single molecule level, edited by Samir M. Iqbal and Rashid Bashir, 287-311. Springer US, 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.
"Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore." Biomed Microdevices 13:671-82 (2011).
"Nanopore analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (2011).
"Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
"Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
"Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"Slowing down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
"Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores." ACS Nano 7:6816-24 (2013). Supporting Information (2.8 MB)
Supporting Information (2.8 MB) "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
"Close encounters with DNA." J Phys Condens Matter 26:413101 (2014).
"The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." J Am Chem Soc 137:6245-6253 (2015).
"Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
"Slowing DNA Transport Using Graphene–DNA Interactions." Advanced Functional Materials 25:936-946 (2015). adfm201403719-sup-0001-s1.pdf (1.01 MB)
adfm201403719-sup-0001-s1.pdf (1.01 MB) "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
"Promiscuous histone mis-assembly is actively prevented by chaperones." Journal of the American Chemical Society 138:13207-13218 (2016). The cover image on JACS (2.25 MB) SI for the paper (33.5 MB)
The cover image on JACS (2.25 MB) SI for the paper (33.5 MB) "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Ion Channels Made from a Single Membrane-Spanning DNA Duplex." Nano Letters 16:4665-4669 (2016). supporting_information.pdf (1.32 MB)
supporting_information.pdf (1.32 MB) "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
"Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields." Biopolymers 105:752-763 (2016). bip22868-sup-0001-suppinfo01.pdf (921.41 KB)
bip22868-sup-0001-suppinfo01.pdf (921.41 KB) "Large-Conductance Transmembrane Porin Made from DNA Origami." ACS Nano 10:8207-8214 (2016). supporting_information.pdf (3.19 MB)
supporting_information.pdf (3.19 MB) "Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones." J Am Chem Soc 138:13207-13218 (2016).
"Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores." ACS Nano 11:9701-9710 (2017). Supporting Information (12.11 MB)
Supporting Information (12.11 MB) "Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores." ACS Nano 11:9701-9710 (2017). Supporting Information (12.11 MB)
Supporting Information (12.11 MB) "Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
"Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). Supporting Information (7.41 MB)
Supporting Information (7.41 MB) "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features." Langmuir 35:4726-4735 (2019).
"Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model." ACS sensors 4:634-644 (2019). sem_si.pdf (4.02 MB)
sem_si.pdf (4.02 MB) "The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
"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) "Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors." Journal of the American Chemical Society 142:1680-1685 (2020). si.pdf (2.47 MB)
si.pdf (2.47 MB) "Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly." Nanoscale 12:5422-5434 (2020). supplement.pdf (6.71 MB)
supplement.pdf (6.71 MB) "Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"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)
nn0c06191_si_001.pdf (547.55 KB) "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
"Electrical unfolding of cytochrome during translocation through a nanopore constriction." Proceedings of the National Academy of Sciences 118:e2016262118 (2021). si_published.pdf (5.09 MB)
si_published.pdf (5.09 MB) "The emerging landscape of single-molecule protein sequencing technologies." Nature Methods 18 (2021).
"The emerging landscape of single-molecule protein sequencing technologies." Nature Methods 18 (2021).
"Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport." Journal of the American Chemical Society 143:15975-15983 (2021). si.pdf (10.35 MB)
si.pdf (10.35 MB) "Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex." Nature Communications 13:5138 (2022). Supplementary Information (20.83 MB)
Supplementary Information (20.83 MB) "Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology 41:1130-1139 (2023).
"Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates." Journal of Chemical Theory and Computation 19:3721-3740 (2023). Supporting Information (2.98 MB)
Supporting Information (2.98 MB) "Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
"Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
"A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein." The Journal of Physical Chemistry Letters 14:10719-10726 (2023).
"DNA double helix, a tiny electromotor." Nature Nanotechnology 18:238-242 (2023).
"Electro-Osmotic Flow Generation via a Sticky Ion Action." ACS nano 18:17521-17533 (2024).
"The structure and physical properties of a packaged bacteriophage particle." Nature 627:905-914 (2024).