Publications

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Aaron John Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack Fredrick Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei Aksimentiev, and Liviu Movileanu. "Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
D Winogradoff, Pin‐Yi Li, H Joshi, L Quednau, C Maffeo, and Aleksei Aksimentiev. "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
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)
David Winogradoff, Haiqing Zhao, Yamini Dalal, and Garegin A. Papoian. "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
David Winogradoff, and Aleksei Aksimentiev. "Molecular Mechanism of Spontaneous Nucleosome Unraveling." Journal of Molecular Biology 431:323-335 (2019). PDF icon supplementary_information.pdf (28.94 MB)
David Winogradoff, Ignacia Echeverria, Davit A. Potoyan, and Garegin A. Papoian. "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." J Am Chem Soc 137:6245-6253 (2015).
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)
James Wilson, and Aleksei Aksimentiev. "Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). PDF icon Supporting Information (7.41 MB)
James Wilson, and Massimiliano Di Ventra. "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev. "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
James Wilson, Kumar Sarthak, Wei Si, Luyu Gao, and Aleksei Aksimentiev. "Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model." ACS sensors 4:634-644 (2019). PDF icon sem_si.pdf (4.02 MB)
David B. Wells, Swati Bhattacharya, Rogan Carr, Christopher Maffeo, Anthony H. Ho, Jeffrey Comer, and Aleksei Aksimentiev. "Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
David B. Wells, Maxim Belkin, Jeffrey Comer, and Aleksei Aksimentiev. "Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
David B. Wells, Volha Abramkina, and Aleksei Aksimentiev. "Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
David B. Wells, and Aleksei Aksimentiev. "Mechanical properties of a complete microtubule revealed through molecular dynamics simulation." Biophys J 99:629-37 (2010). PDF icon Supporting Information (pdf) (2.75 MB)File Atomic coordinates of the equilibrated "N" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated "S" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated complete microtubule (pdb) (13.16 MB)
Xiaojun Wei, Tadas Penkauskas, Joseph E. Reiner, Celeste Kennard, Mark J. Uline, Qian Wang, Sheng Li, Aleksei Aksimentiev, Joseph W. F. Robertson, and Chang Liu. "Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
Meni Wanunu, Swati Bhattacharya, Yun Xie, Yitzhak Tor, Aleksei Aksimentiev, and Marija Drndic. "Nanopore analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (2011).