Publications
"Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein." Biochemistry (2024).
"Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein." Biochemistry (2024).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces 16:20865-20877 (2024).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces 16:20865-20877 (2024).
"Sulfur-Containing Foldamer-Based Artificial Lithium Channels." Angewandte Chemie International Edition 62:e202305623 (2023). 
anie202305623-sup-0001-misc_information.pdf (2.67 MB)
anie202305623-sup-0001-misc_information.pdf (2.67 MB) "Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape." Journal of the American Chemical Society 144:16060-16068 (2022). supplementary_information.pdf (4.85 MB)
supplementary_information.pdf (4.85 MB) "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
"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) "DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity." Nano Letters 21:8634-8641 (2021). si.pdf (2.41 MB)
si.pdf (2.41 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).
"Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes." Journal of the American Chemical Society 143:8305-8313 (2021). si.pdf (20.33 MB)
si.pdf (20.33 MB) "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) "Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore." Nature Biotechnology 38:176-181 (2020). Supplementary Information (15.98 MB)
Supplementary Information (15.98 MB) "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).
"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)
supporting_information.pdf (1.34 MB) "A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes." Nature Communications 9:2426 (2018). dna-scramblase-si.pdf (5.77 MB)
dna-scramblase-si.pdf (5.77 MB) "Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem." Proceedings of the National Academy of Sciences (2018).
"Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"Selective Permeability of Truncated Aquaporin 1 in Silico." ACS Biomaterials Science & Engineering 3:342-348 (2017). Supporting Information (pdf) (459.46 KB)
Supporting Information (pdf) (459.46 KB) "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) "Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones." J Am Chem Soc 138:13207-13218 (2016).
"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) "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) "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) "Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore." ACS Nano 10:4644-4651 (2016). supporting_mspa.pdf (3.61 MB)
supporting_mspa.pdf (3.61 MB) "The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study." PLoS ONE 11:e0152002 (2016). s1file.pdf (4.91 MB)
s1file.pdf (4.91 MB) "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) "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA." ACS Nano 9:10598-10611 (2015). nn5b04173_si_001.pdf (681.52 KB)
nn5b04173_si_001.pdf (681.52 KB) "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (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) "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) "Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
"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) "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
"Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence." ACS Nano 6:6960-8 (2012). Supporting Information (pdf) (2.36 MB)
Supporting Information (pdf) (2.36 MB) "Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
"Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).
"Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
"Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
"Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments." The Journal of Physical Chemistry C 115:4255-4264 (2011).
"Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments." The Journal of Physical Chemistry C 115:4255-4264 (2011).
"Nanopore analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (2011).
"Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore." Biomed Microdevices 13:671-82 (2011).
"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.
"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.
"DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
"Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).
"Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase." Biophys J 86:1332-44 (2004).
"Large scale simulation of protein mechanics and function." Adv Protein Chem 66:195-247 (2003).
"Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).