Publications
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"Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
"Artificial Water Channels Enable Fast and Selective Water Permeation Through Water-wire Networks." Nature Nanotechnology. 15,:73-79 (2020). 
song2019_si.pdf (15.29 MB)
song2019_si.pdf (15.29 MB) "Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
"Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
"Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates." Journal of Chemical Theory and Computation (2023). Supporting Information (2.98 MB)
Supporting Information (2.98 MB) "Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).
"Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).
"Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures." Journal of the American Chemical Society 143:7358-7367 (2021). si.pdf (2.68 MB)
si.pdf (2.68 MB) "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
"Close encounters with DNA." J Phys Condens Matter 26:413101 (2014).
"A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment." Journal of Chemical Theory and Computation 10:2891-2896 (2014). Supporting information (3.38 MB)
Supporting information (3.38 MB) "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces (2024).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces (2024).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces (2024).
"Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
"Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"DNA double helix, a tiny electromotor." Nature Nanotechnology 18:238-242 (2023).
"DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles." Nucleic Acids Res 49:11459-11475 (2021). supporting_information.pdf (17.16 MB)
supporting_information.pdf (17.16 MB) "A DNA turbine powered by a transmembrane potential across a nanopore." Nature Nanotechnology (2023).
"DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"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) "Electrical unfolding of cytochrome during translocation through a nanopore constriction." Proceedings of the National Academy of Sciences 118 (2021). si_published.pdf (5.09 MB)
si_published.pdf (5.09 MB) "Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate." ACS Nano 13:2398-2409 (2019). supplementary_material.pdf (8.62 MB)
supplementary_material.pdf (8.62 MB) "The electromechanics of DNA in a synthetic nanopore." Biophys J 90:1098-106 (2006).
"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).
"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).
"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).
"End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). Supporting Information (2.95 MB)
Supporting Information (2.95 MB) "Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing." Nano Letters (2022). si.pdf (2.42 MB)
si.pdf (2.42 MB) "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) "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
"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) "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).
"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) "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) "Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends." Macromolecular Theory and Simulations 9:661-674 (2000).
"Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
"Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
"Long-Range Conductivity in Proteins Mediated by Aromatic Residues." ACS Physical Chemistry Au 3:444-455 (2023). sidd2023_si.pdf (792.94 KB)
sidd2023_si.pdf (792.94 KB) "The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition." ACS Nano (2021). nn0c09958_si_001.pdf (1.59 MB)
nn0c09958_si_001.pdf (1.59 MB) "A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein." The Journal of Physical Chemistry Letters:10719-10726 (2023).
"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) "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
"Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
"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) "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) "Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
"A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
"Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018). nl7b05354_si_001.pdf (2.72 MB)
nl7b05354_si_001.pdf (2.72 MB) "Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
"Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).
"Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).
"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) "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) "Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
"A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems." In DNA Nanotechology: Methods and Protocols, edited by Giampaolo Zuccheri, 209-229. 2nd ed. Vol. 1811. Methods in Molecular Biology 1811. New York: Humana Press, 2018.
origamitutorial.tar.gz (103.69 MB)
origamitutorial.tar.gz (103.69 MB) "Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"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).
"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).
"Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends." The Journal of Chemical Physics 112:6049-6062 (2000).
"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) "Sequence-Dependent DNA Condensation as a Driving Force of DNA Phase Separation." Nucleic Acids Research 46:9401-9413 (2018). supplementary_material.pdf (11.56 MB)
supplementary_material.pdf (11.56 MB) "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).
"Single molecule force measurements: insights from molecular simulations. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al." Phys Life Rev 7:353-4; discussion 358-61 (2010).
"Single-molecule biophysics experiments in silico: Toward a physical model of a replisome." iScience 25:104264 (2022). maff2022_si.pdf (1.35 MB)
maff2022_si.pdf (1.35 MB) "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
"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) "Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
"The structure and physical properties of a packaged bacteriophage particle." Nature 627:905-914 (2024).
"Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
"Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
"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) "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) "A tetrahedral DNA nanorobot with conformational change in response to molecular trigger." Nanoscale (2021).
"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.
"Toward understanding membrane channels." In Bacterial ion channels and their eukaryotic homologues, edited by Boris Martinac and Andrzej Kubalski, 153-190. Washington, DC: ASM Press, 2005.
"Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). yang2021si.pdf (1.2 MB)
yang2021si.pdf (1.2 MB) "Trapping of protein cargo molecules inside DNA origami nanocages." Nanoscale 14:18041-18050 (2022).
"Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (2014).
"Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology (2023).
"Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology (2023).