Publications
Export 30 results:
Filters: First Letter Of Title is M [Clear All Filters]
"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).
"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 (2023).
"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)