Publications
Export 189 results:
Filters: Author is aksimentiev [Clear All Filters]
"Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
"Application of the Euler characteristic to the study of homopolymer blends and copolymer melts." Polimery 46:309-322 (2001).
"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) "Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
"Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
"Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (2011).
"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) "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) "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features." Langmuir 35:4726-4735 (2019).
"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) "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) "Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).
"Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene." Nature Communications 5:5171 (2014).
"Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein." Biochemistry (2024).
"Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
"Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).
"Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019). si.pdf (1.74 MB)
si.pdf (1.74 MB) "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
"Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
"Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces 16:20865-20877 (2024).
"Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
"Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).
"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) "Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
"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) "Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
"DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
"DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
"DNA double helix, a tiny electromotor." Nature Nanotechnology 18:238-242 (2023).
"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) "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 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) "A DNA turbine powered by a transmembrane potential across a nanopore." Nature Nanotechnology 19:338-344 (2024).
"DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
"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) "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) "The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
"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) "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) "Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (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 signatures of single-stranded DNA with single base mutations in a nanopore capacitor." 17:3160-3165 (2006).
"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) "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).
"Electro-Osmotic Flow Generation via a Sticky Ion Action." ACS nano 18:17521-17533 (2024).
"Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
"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) "Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
"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) "Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
"Extending molecular modeling methodology to study insertion of membrane nanopores." Proc Natl Acad Sci U S A 101:4337-8 (2004).
"Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport." Nano Lett 22:4831-4838 (2022).
"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) "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
"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) "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) "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
"Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map." Biophys J 88:3745-61 (2005).
"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) "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) "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) "In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
"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) "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).
"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).
"Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase." Biophys J 86:1332-44 (2004).
"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) "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) "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) "Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
"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).
"Large scale simulation of protein mechanics and function." Adv Protein Chem 66:195-247 (2003).
"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) "Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
"Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore." Biomed Microdevices 13:671-82 (2011).
"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 14:10719-10726 (2023).
"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) "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) "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) "Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
"Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
"Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (2011).
"Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
"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 Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (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.
"Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
"Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
"Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
"Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore." ACS Nanosci. Au 4:21-29 (2024).
"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) "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) "Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
"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) "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 mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
"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) "Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
"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) "Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements." Advances in Chemical Physics 121:141-239 (2002).
"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) "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) "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 analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (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.
"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) "Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
"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) "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
"Netting proteins, one at a time." Nature Nanotechnology 16:1178-1179 (2021).
"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) "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).
"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) "Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (1999).
"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) "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) "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) "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) "Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
"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) "Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
"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) "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).
"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).
"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) "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) "The role of molecular modeling in bionanotechnology." Phys Biol 3:S40-53 (2006).
"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) "Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
"Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems." Phys Rev Lett 86:240-3 (2001).
"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).
"SDS-assisted protein transport through solid-state nanopores." Nanoscale 9:11685-11693 (2017). Supporting Information (1.24 MB)
Supporting Information (1.24 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) "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) "Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor." Nanotechnology 17:622-633 (2006).
"Single chain conformations in the system of symmetric and asymmetric diblock copolymers." Macromolecular Theory and Simulations 8:328-342 (1999).
"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-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
"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) "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) "Sizing DNA using a nanometer-diameter pore." Biophys J 87:2905-11 (2004).
"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 down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
"Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
"Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (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).
"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) "Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
"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 and unzipping nucleic acid hairpins using a synthetic nanopore." Nucleic Acids Res 36:1532-41 (2008).
"Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
"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) "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).
"Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
"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) "Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
"Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
"Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).
"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) "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) "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) "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 detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (2012).
"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 41:1130-1139 (2023).
"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) "Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). Supporting Information (7.41 MB)
Supporting Information (7.41 MB) "Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).