Publications

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1999    
Aleksei Aksimentiev, and Robert Hołyst. "Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (1999).
2012    
Jeffrey Comer, and Aleksei Aksimentiev. "Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
2015    
Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev. "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA." ACS Nano 9:10598-10611 (2015). PDF icon nn5b04173_si_001.pdf (681.52 KB)
2016    
Haiqing Zhao*, David Winogradoff*, Minh Bui, Yamini Dalal, and Garegin Papoian. "Promiscuous histone mis-assembly is actively prevented by chaperones." Journal of the American Chemical Society 138:13207-13218 (2016). PDF icon The cover image on JACS (2.25 MB)PDF icon SI for the paper (33.5 MB)
Haiqing Zhao*, David Winogradoff*, Minh Bui, Yamini Dalal, and Garegin A. Papoian. "Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones." J Am Chem Soc 138:13207-13218 (2016).
2017    
"A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems." In Protocols in DNA Nanotechology. 2nd ed. Methods in Molecular Biology. Humana Press), 2017.
Mohammad Amin Alibakhshi, Justin R. Halman, James Wilson, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu. "Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores." ACS Nano 11:9701-9710 (2017). PDF icon Supporting Information (12.11 MB)
Benjamin Cressiot*, Sandra J. Greive*, Wei Si*, Tomas Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw Thomas Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A. Antson, and Meni Wanunu. "Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano 11:11931-11945 (2017).
2018    
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)
Ratul Chowdhury, Tingwei Ren, Manish Shankla, Karl Decker, Matthew Grisewood, Jeevan Prabhakar, Carol Baker, John H. Golbeck, Aleksei Aksimentiev, Manish Kumar, and Costas D. Maranas. "PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore." Nature Communications 9:3661 (2018). PDF icon supporting_information.pdf (1.34 MB)
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)
David Winogradoff, Shalini John, and Aleksei Aksimentiev. "Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly." Nanoscale 12:5422-5434 (2020). PDF icon supplement.pdf (6.71 MB)
2022    
David Winogradoff, Han-Yi Chou, Christopher Maffeo, and Aleksei Aksimentiev. "Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex." Nature Communications 13:5138 (2022). PDF icon Supplementary Information (20.83 MB)