Publications
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Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology (2023).
"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)
"The structure and intermolecular forces of DNA condensates." Nucleic Acids Research 44:2036-2046 (2016). dnapack_supp.pdf (9.65 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)
"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)
"Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nature Communications 7:11045 (2016). 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)
"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)
"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)
"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)
"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)
"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)
"Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
"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)
"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)
"Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). yang2021si.pdf (1.2 MB)
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