Publications
"The structure and physical properties of a packaged bacteriophage particle." Nature 627:905-914 (2024).
"A DNA turbine powered by a transmembrane potential across a nanopore." Nature Nanotechnology 19:338-344 (2024).
"Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore." ACS Nanosci. Au 4:21-29 (2024).
"Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein." Biochemistry (2024).
"Electro-Osmotic Flow Generation via a Sticky Ion Action." ACS nano 18:17521-17533 (2024).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces 16:20865-20877 (2024).
"DNA double helix, a tiny electromotor." Nature Nanotechnology 18:238-242 (2023).
"A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein." The Journal of Physical Chemistry Letters 14:10719-10726 (2023).
"Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
"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) "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) "Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology 41:1130-1139 (2023).
"Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
"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) "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) "Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport." Nano Lett 22:4831-4838 (2022).
"Trapping of protein cargo molecules inside DNA origami nanocages." Nanoscale 14:18041-18050 (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) "Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
"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) "Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"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) "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) "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
"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) "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 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) "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) "Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons." Nature Nanotechnology 16:911-917 (2021). si.pdf (2.73 MB)
si.pdf (2.73 MB) "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) "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) "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) "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) "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) "Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures." ACS Nano 15:5109-5117 (2021). si_published.pdf (1.28 MB)
si_published.pdf (1.28 MB) "Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). yang2021si.pdf (1.2 MB)
yang2021si.pdf (1.2 MB) "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
"Netting proteins, one at a time." Nature Nanotechnology 16:1178-1179 (2021).
"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) "Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (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) "Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate." J. Phys. Chem. Lett. 11:4923-4929 (2020). supporting_information.pdf (481.68 KB)
supporting_information.pdf (481.68 KB) "Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme." Nano Letters 20:4306-4311 (2020). si.pdf (2.57 MB)
si.pdf (2.57 MB) "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) "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) "Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels." Angewandte Chemie International Edition 12:4806-4813 (2020). si-final.pdf (3.1 MB)
si-final.pdf (3.1 MB) "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) "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) "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) "Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
"Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019). si.pdf (1.74 MB)
si.pdf (1.74 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) "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).
"Step-defect guided delivery of DNA to a graphene nanopore." Nature Nanotechnology (2019). gs_si.pdf (3.95 MB)
gs_si.pdf (3.95 MB) "The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
"Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes." ACS Applied Polymer Materials 1:722-736 (2019). si-aba_sans_revised.pdf (2.84 MB)
si-aba_sans_revised.pdf (2.84 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) "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) "Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
"Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes." Langmuir 34:15084-15092 (2018). supplementary_information.pdf (2.54 MB)
supplementary_information.pdf (2.54 MB) "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) "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) "Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore." The Journal of Physical Chemistry Letters 9:4686-4694 (2018). supporting_information.pdf (1.77 MB)
supporting_information.pdf (1.77 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) "Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). Supporting Information (7.41 MB)
Supporting Information (7.41 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).
"New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions." Physical Chemistry Chemical Physics 20:8432-8449 (2018). si_nbfixperspec.pdf (3.85 MB)
si_nbfixperspec.pdf (3.85 MB) "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) "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) "Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
"Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
"Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"Nanoscale Ion Pump Derived from a Biological Water Channel." The Journal of Physical Chemistry B 121:7899-7906 (2017). supporting_information.pdf (8.9 MB)
supporting_information.pdf (8.9 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) "Nanopore Sensing of Protein Folding." ACS Nano 11, 7091-7100 (2017). nn7b02718_si_001.pdf (12.07 MB)
nn7b02718_si_001.pdf (12.07 MB) "SDS-assisted protein transport through solid-state nanopores." Nanoscale 9:11685-11693 (2017). Supporting Information (1.24 MB)
Supporting Information (1.24 MB) "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (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) "Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis." ACS Nano 11:1204-1213 (2017). Supporting Information (pdf) (8.47 MB)
Supporting Information (pdf) (8.47 MB)"A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems." In Protocols in DNA Nanotechology. 2nd ed. Methods in Molecular Biology. Humana Press), 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) "Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones." J Am Chem Soc 138:13207-13218 (2016).
"Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations." Journal of Physical Chemistry Letters 7:3812-3818 (2016). jz6b01747_si_001.pdf (6.89 MB)
jz6b01747_si_001.pdf (6.89 MB) "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) "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) "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).
"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) "DNA sequence-dependent ionic currents in ultra-small solid-state nanopores." Nanoscale 18:9600-9613 (2016). supp_triplet.pdf (98.62 KB)
supp_triplet.pdf (98.62 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) "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
"Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nature Communications 7:11045 (2016). ncomms11045-s1.pdf (1.81 MB)
ncomms11045-s1.pdf (1.81 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) "The structure and intermolecular forces of DNA condensates." Nucleic Acids Research 44:2036-2046 (2016). dnapack_supp.pdf (9.65 MB)
dnapack_supp.pdf (9.65 MB) "Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability." Nature Communications 7:10813 (2016). ncomms10813-s1.pdf (529.11 KB)
ncomms10813-s1.pdf (529.11 KB) "Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields." Journal of Chemical Theory and Computation 12:430-443 (2016). ct5b00967_si_001.pdf (2.12 MB)
ct5b00967_si_001.pdf (2.12 MB) "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) "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).
"Mapping fast protein folding with multiple-site fluorescent probes." Proc Natl Acad Sci U S A 112:7966-71 (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) "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015). Supporting Information (8.81 MB)
Supporting Information (8.81 MB) "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
"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).
"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) "Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (2014).
"Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding." J Phys Chem B (2014).
"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).
"Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene." Nature Communications 5:5171 (2014).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
"Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling." The Journal of Physical Chemistry C 118:9809-9819 (2014).
"Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
"In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci U S A 110:20099-104 (2013). Supporting Information (4.15 MB)
Supporting Information (4.15 MB) "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
"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) "Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations." J Phys Chem B 116:12946-54 (2012). jp306598y_si_001.pdf (343.44 KB)
jp306598y_si_001.pdf (343.44 KB) "DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
"End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). Supporting Information (2.95 MB)
Supporting Information (2.95 MB) "Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
"Slowing down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
"Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (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).
"Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems." The Journal of Physical Chemistry Letters 3:45-50 (2012). jz201501a_si_001.pdf (1.69 MB)
jz201501a_si_001.pdf (1.69 MB) "Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (2011).
"Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).
"Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (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).
"Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (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).
"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.
"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.
"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).
"DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
"Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
"Dehydration and ionic conductance quantization in nanopores." J Phys Condens Matter 22:454126 (2010).
"Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
"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) "Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (2010).
"The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
"Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
"Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
"Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
"Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
"Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
"Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
"Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
"DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
"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) "Stretching and unzipping nucleic acid hairpins using a synthetic nanopore." Nucleic Acids Res 36:1532-41 (2008).
"Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).
"Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
"In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
"Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).
"Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
"Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
"Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
"Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).
"The role of molecular modeling in bionanotechnology." Phys Biol 3:S40-53 (2006).
"The electromechanics of DNA in a synthetic nanopore." Biophys J 90:1098-106 (2006).
"Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor." Nanotechnology 17:622-633 (2006).
"Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor." 17:3160-3165 (2006).
"Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
"Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map." Biophys J 88:3745-61 (2005).
"Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).
"Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
"Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).
"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.
"Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
"Sizing DNA using a nanometer-diameter pore." Biophys J 87:2905-11 (2004).
"Extending molecular modeling methodology to study insertion of membrane nanopores." Proc Natl Acad Sci U S A 101:4337-8 (2004).
"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).
"Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements." Advances in Chemical Physics 121:141-239 (2002).
"Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems." Phys Rev Lett 86:240-3 (2001).
"Application of the Euler characteristic to the study of homopolymer blends and copolymer melts." Polimery 46:309-322 (2001).
"Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62:6821-30 (2000).
"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).
"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).
"Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
"Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (1999).
"Single chain conformations in the system of symmetric and asymmetric diblock copolymers." Macromolecular Theory and Simulations 8:328-342 (1999).
"Single-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
"Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).