Publications

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2024    
Behzad Mehrafrooz, Luning Yu, Laxmi Pandey, Zuzanna S. Siwy, Meni Wanunu, and Aleksei Aksimentiev. "Electro-Osmotic Flow Generation via a Sticky Ion Action." ACS nano 18:17521-17533 (2024).
2023    
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, and Meni Wanunu. "Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology 41:1130-1139 (2023).
2022    
Jie Shen, Arundhati Roy, Himanshu Joshi, Laxmicharan Samineni, Ruijuan Ye, Yu-Ming Tu, Woochul Song, Matthew Skiles, Manish Kumar, Aleksei Aksimentiev, and Huaqiang Zeng. "Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport." Nano Lett 22:4831-4838 (2022).
Merle Scherf, Florian Scheffler, Christopher Maffeo, Ulrich Kemper, Jingjing Ye, Aleksei Aksimentiev, Ralf Seidel, and Uta Reibetanz. "Trapping of protein cargo molecules inside DNA origami nanocages." Nanoscale 14:18041-18050 (2022).
2021    
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)
Javier Antonio Alfaro, Peggy Bohländer, Mingjie Dai, Mike Filius, Cecil J. Howard, Xander F. van Kooten, Shilo Ohayon, Adam Pomorski, Sonja Schmid, Aleksei Aksimentiev, Eric V. Anslyn, Georges Bedran, Chan Cao, Mauro Chinappi, Etienne Coyaud, Cees Dekker, Gunnar Dittmar, Nicholas Drachman, Rienk Eelkema, David Goodlett et al. "The emerging landscape of single-molecule protein sequencing technologies." Nature Methods 18 (2021).
Prabhat Tripathi, Abdelkrim Benabbas, Behzad Mehrafrooz, Hirohito Yamazaki, Aleksei Aksimentiev, Paul M. Champion, and Meni Wanunu. "Electrical unfolding of cytochrome during translocation through a nanopore constriction." Proceedings of the National Academy of Sciences 118:e2016262118 (2021). PDF icon si_published.pdf (5.09 MB)
Wayne Yang, Boya Radha, Adnan Choudhary, Yi You, Gangaiah Mettela, Andre K. Geim, Aleksei Aksimentiev, Ashok Keerthi, and Cees Dekker. "Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). PDF icon yang2021si.pdf (1.2 MB)
Wayne Yang, Boya Radha, Adnan Choudhary, Yi You, Gangaiah Mettela, Andre K. Geim, Aleksei Aksimentiev, Ashok Keerthi, and Cees Dekker. "Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). PDF icon yang2021si.pdf (1.2 MB)
2020    
Jejoong Yoo, David Winogradoff, and Aleksei Aksimentiev. "Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020).
Arundhati Roy, Himanshu Joshi, Ruijuan Ye, Jie Shen, Feng Chen, Aleksei Aksimentiev, and Huaqiang Zeng. "Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels." Angewandte Chemie International Edition 12:4806-4813 (2020). PDF icon si-final.pdf (3.1 MB)
Prabhat Tripathi, Liang Shuai, Himanshu Joshi, Hirohito Yamazaki, William H. Fowle, Aleksei Aksimentiev, Hicham Fenniri, and Meni Wanunu. "Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors." Journal of the American Chemical Society 142:1680-1685 (2020). PDF icon si.pdf (2.47 MB)
2019    
Yiming Yang, Aaron Alford, Veronika Kozlovskaya, Shidi Zhao, Himanshu Joshi, Eunjung Kim, Shuo Qian, Volker Urban, Donald Cropek, Aleksei Aksimentiev, and Eugenia Kharlampieva. "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). PDF icon si-aba_sans_revised.pdf (2.84 MB)
2018    
Hyunju Kang, Jejoong Yoo, Hong Soo Lee, Byeong-Kwon Sohn, Seung-Won Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev, and Hajin Kim. "Sequence-Dependent DNA Condensation as a Driving Force of DNA Phase Separation." Nucleic Acids Research 46:9401-9413 (2018). PDF icon supplementary_material.pdf (11.56 MB)
Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev. "A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes." Nature Communications 9:2426 (2018). PDF icon dna-scramblase-si.pdf (5.77 MB)
Jejoong Yoo, and Aleksei Aksimentiev. "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). PDF icon si_nbfixperspec.pdf (3.85 MB)
Jejoong Yoo, Chen-Yu Li, Scott Michael Slone, Christopher Maffeo, and Aleksei Aksimentiev. "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.Binary Data origamitutorial.tar.gz (103.69 MB)
2016    
Jejoong Yoo, and Aleksei Aksimentiev. "Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations." Journal of Physical Chemistry Letters 7:3812-3818 (2016). PDF icon jz6b01747_si_001.pdf (6.89 MB)
Kerstin Göpfrich*, Chen-Yu Li*, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. "Large-Conductance Transmembrane Porin Made from DNA Origami." ACS Nano 10:8207-8214 (2016). PDF icon supporting_information.pdf (3.19 MB)
Jejoong Yoo, James Wilson, and Aleksei Aksimentiev. "Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields." Biopolymers 105:752-763 (2016). PDF icon bip22868-sup-0001-suppinfo01.pdf (921.41 KB)
Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser. "Ion Channels Made from a Single Membrane-Spanning DNA Duplex." Nano Letters 16:4665-4669 (2016). PDF icon supporting_information.pdf (1.32 MB)
Scott Michael Slone, Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev. "Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New Journal of Physics 18:055012 (2016). PDF icon supporting_information.pdf (7.84 MB)
Swati Bhattacharya, Jejoong Yoo, and Aleksei Aksimentiev. "Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore." ACS Nano 10:4644-4651 (2016). PDF icon supporting_mspa.pdf (3.61 MB)
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).
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)
Jejoong Yoo, and Aleksei Aksimentiev. "The structure and intermolecular forces of DNA condensates." Nucleic Acids Research 44:2036-2046 (2016). PDF icon dnapack_supp.pdf (9.65 MB)
Thuy Ngo, Jejoong Yoo, Q Dai, Q Zhang, C He, Aleksei Aksimentiev, and Taekjip Ha. "Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability." Nature Communications 7:10813 (2016). PDF icon ncomms10813-s1.pdf (529.11 KB)
Jejoong Yoo, and Aleksei Aksimentiev. "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). PDF icon ct5b00967_si_001.pdf (2.12 MB)
2015    
Jejoong Yoo, and Aleksei Aksimentiev. "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). PDF icon Supporting Information (8.97 MB)
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015). PDF icon Supporting Information (8.81 MB)
2014    
Christopher Maffeo, J Yoo, Jeffrey Comer, D B. Wells, B Luan, and Aleksei Aksimentiev. "Close encounters with DNA." J Phys Condens Matter 26:413101 (2014).
2013    
Jejoong Yoo, and Aleksei Aksimentiev. "In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci U S A 110:20099-104 (2013). PDF icon Supporting Information (4.15 MB)
2012    
Jejoong Yoo, and Aleksei Aksimentiev. "Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations." J Phys Chem B 116:12946-54 (2012). PDF icon jp306598y_si_001.pdf (343.44 KB)
Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
Jejoong Yoo, and Aleksei Aksimentiev. "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). PDF icon jz201501a_si_001.pdf (1.69 MB)
2008    
Q Zhao, Jeffrey Comer, Valentin Dimitrov, S Yemenicioglu, Aleksei Aksimentiev, and Gregory Timp. "Stretching and unzipping nucleic acid hairpins using a synthetic nanopore." Nucleic Acids Res 36:1532-41 (2008).
Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chú, David Hardy, Aruna Rajan, Amy Y. Shih, G Sigalov, Ying Yin, and Klaus Schulten. "Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).