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Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev. "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
Aleksei Aksimentiev. "Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
Q Zhao, G Sigalov, Valentin Dimitrov, B Dorvel, U Mirsaidov, S Sligar, Aleksei Aksimentiev, and Gregory Timp. "Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
G Sigalov, Jeffrey Comer, Gregory Timp, and Aleksei Aksimentiev. "Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).
Kristina Hübner, Himanshu Joshi, Aleksei Aksimentiev, Fernando D. Stefani, Philip Tinnefeld, and Guillermo P. Acuna. "Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures." ACS Nano 15:5109-5117 (2021). PDF icon si_published.pdf (1.28 MB)
Robert Hołyst, D Plewczyński, Aleksei Aksimentiev, and K Burdzy. "Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha. "Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nature Communications 7:11045 (2016). PDF icon ncomms11045-s1.pdf (1.81 MB)
Prabhat Tripathi, Morgan Chandler, Christopher Michael Maffeo, Ali Fallahi, Amr Makhamreh, Justin Halman, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu. "Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
Binquan Luan, and Aleksei Aksimentiev. "DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev. "DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
Christopher Maffeo, Lauren Quednau, James Wilson, and Aleksei Aksimentiev. "DNA double helix, a tiny electromotor." Nature Nanotechnology (2022).
Sarah E. Ochmann, Himanshu Joshi, Ece Büber, Henri G. Franquelim, Pierre Stegemann, Barbara Saccà, Ulrich F. Keyser, Aleksei Aksimentiev, and Philip Tinnefeld. "DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity." Nano Letters 21:8634-8641 (2021). PDF icon si.pdf (2.41 MB)
Jejoong Yoo, Sangwoo Park, Christopher Maffeo, Taekjip Ha, and Aleksei Aksimentiev. "DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles." Nucleic Acids Res 49:11459-11475 (2021). PDF icon supporting_information.pdf (17.16 MB)
Jeffrey Comer, and Aleksei Aksimentiev. "DNA sequence-dependent ionic currents in ultra-small solid-state nanopores." Nanoscale 18:9600-9613 (2016). PDF icon supp_triplet.pdf (98.62 KB)
Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel. "DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
Patrick M. Arnott, Himanshu Joshi, Aleksei Aksimentiev, and Stefan Howorka. "Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes." Langmuir 34:15084-15092 (2018). PDF icon supplementary_information.pdf (2.54 MB)
Xin Shi, Qiao Li, Rui Gao, Wei Si, Shao-Chuang Liu, Aleksei Aksimentiev, and Yi-Tao Long. "Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore." The Journal of Physical Chemistry Letters 9:4686-4694 (2018). PDF icon supporting_information.pdf (1.77 MB)