Publications
"Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map." Biophys J 88:3745-61 (2005).
"Single-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
"Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase." Biophys J 86:1332-44 (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).
"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).
"Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (1999).
"Extending molecular modeling methodology to study insertion of membrane nanopores." Proc Natl Acad Sci U S A 101:4337-8 (2004).
"Netting proteins, one at a time." Nature Nanotechnology 16:1178-1179 (2021).
"Application of the Euler characteristic to the study of homopolymer blends and copolymer melts." Polimery 46:309-322 (2001).
"Single chain conformations in the system of symmetric and asymmetric diblock copolymers." Macromolecular Theory and Simulations 8:328-342 (1999).
"Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
"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).
"Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
"Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).
"Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).
"Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
"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).
"The emerging landscape of single-molecule protein sequencing technologies." Nature Methods 18 (2021).
"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) "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) "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) "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) "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) "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) "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).
"A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nat Commun 12:7138 (2021).
"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).
"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) "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) "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) "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) "Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
"Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (2011).
"Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (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.
"Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
"Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (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).
"Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
"In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
"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) "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) "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) "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) "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.
"Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
"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.
"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) "Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
"Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (2012).
"Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
"Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
"Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).
"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) "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) "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
"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) "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features." Langmuir 35:4726-4735 (2019).
"Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems." Phys Rev Lett 86:240-3 (2001).
"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).
"Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding." J Phys Chem B (2014).
"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) "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) "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).
"Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
"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) "Sizing DNA using a nanometer-diameter pore." Biophys J 87:2905-11 (2004).
"Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
"Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).
"The electromechanics of DNA in a synthetic nanopore." Biophys J 90:1098-106 (2006).
"Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
"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) "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).
"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) "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) "Slowing down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
"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) "Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
"A tetrahedral DNA nanorobot with conformational change in response to molecular trigger." Nanoscale (2021).
"The role of molecular modeling in bionanotechnology." Phys Biol 3:S40-53 (2006).
"DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
"Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
"Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (2010).
"Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
"Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
"Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
"The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
"Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
"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) "End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). Supporting Information (2.95 MB)
Supporting Information (2.95 MB) "Close encounters with DNA." J Phys Condens Matter 26:413101 (2014).
"Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
"Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
"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) "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"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) "DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
"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 double helix, a tiny electromotor." Nature Nanotechnology (2022).
"Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).
"Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
"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) "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) "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) "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) "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) "Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019). si.pdf (1.74 MB)
si.pdf (1.74 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) "Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Mapping fast protein folding with multiple-site fluorescent probes." Proc Natl Acad Sci U S A 112:7966-71 (2015).
"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) "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) "Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).
"SDS-assisted protein transport through solid-state nanopores." Nanoscale 9:11685-11693 (2017). Supporting Information (1.24 MB)
Supporting Information (1.24 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) "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) "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) "Trapping of protein cargo molecules inside DNA origami nanocages." Nanoscale 14:18041-18050 (2022).
"Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
"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) "Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene." Nature Communications 5:5171 (2014).
"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) "Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport." Nano Lett 22:4831-4838 (2022).
"Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
"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) "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) "Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).
"Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
"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) "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) "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) "Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
"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) "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) "Large scale simulation of protein mechanics and function." Adv Protein Chem 66:195-247 (2003).
"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.
"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) "DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
"Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (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.
"Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"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) "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) "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).
"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) "Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
"Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
"Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). Supporting Information (7.41 MB)
Supporting Information (7.41 MB) "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) "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
"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) "Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex." Nat Commun 13:5138 (2022). Supplementary Information (20.83 MB)
Supplementary Information (20.83 MB) "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
"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) "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).
"Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
"Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). yang2021si.pdf (1.2 MB)
yang2021si.pdf (1.2 MB) "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) "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) "Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"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) "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) "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) "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) "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) "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) "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) "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) "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) "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) "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) "Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology (2023).
"The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
"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) "Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
"Stretching and unzipping nucleic acid hairpins using a synthetic nanopore." Nucleic Acids Res 36:1532-41 (2008).
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