Publications

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A    
Woochul Song, Himanshu Joshi, Ratul Chowdhury, Joseph S. Najem, Yue-xiao Shen, Chao Lang, Codey B. Henderson, Yu-Ming Tu, Megan Farell, Megan E. Pitz, Costas D. Maranas, Paul S. Cremer, Robert J. Hickey, Stephen A. Sarles, Jun-li Hou, Aleksei Aksimentiev, and Manish Kumar. "Artificial Water Channels Enable Fast and Selective Water Permeation Through Water-wire Networks." Nature Nanotechnology. 15,:73-79 (2020). PDF icon song2019_si.pdf (15.29 MB)
Abhishek Singharoy, Christopher Maffeo, Karelia H. Delgado-Magnero, David J. K. Swainsbury, Melih Sener, Ulrich Kleinekathöfer, John W. Vant, Jonathan Nguyen, Andrew Hitchcock, Barry Isralewitz, Ivan Teo, Danielle E. Chandler, John E. Stone, James C. Phillips, Taras V. Pogorelov, Ilaria M. Mallus, Christophe Chipot, Zaida Luthey-Schulten, Peter D. Tieleman, Neil C. Hunter et al. "Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism." Cell 179:1098-1111.e23 (2019).
C    
D Winogradoff, Pin‐Yi Li, H Joshi, L Quednau, C Maffeo, and Aleksei Aksimentiev. "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
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).
Binquan Luan, and Aleksei Aksimentiev. "Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
D    
Hyeonji Oh, Yu-Ming Tu, Laximicharan Samineni, Sophie De Respino, Behzad Mehrafrooz, Himanshu Joshi, Lynnicia Massenburg, Horacio Lopez-Marques, Nada Elessawy, Woochul Song, Harekrushna Behera, Raman Dhiman, Veda Sheersh Boorla, Kartik Kher, Yi-Chih Lin, Costas Maranas, Aleksei Aksimentiev, Benny D. Freeman, and Manish Kumar. "Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces (2024).
Hyeonji Oh, Yu-Ming Tu, Laximicharan Samineni, Sophie De Respino, Behzad Mehrafrooz, Himanshu Joshi, Lynnicia Massenburg, Horacio Lopez-Marques, Nada Elessawy, Woochul Song, Harekrushna Behera, Raman Dhiman, Veda Sheersh Boorla, Kartik Kher, Yi-Chih Lin, Costas Maranas, Aleksei Aksimentiev, Benny D. Freeman, and Manish Kumar. "Dehydrated Biomimetic Membranes with Skinlike Structure and Function." ACS Applied Materials & Interfaces (2024).
Binquan Luan, and Aleksei Aksimentiev. "DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
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)
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)
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)
E    
Binquan Luan, Rogan Carr, Martin Caffrey, and Aleksei Aksimentiev. "The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
Binquan Luan, and Aleksei Aksimentiev. "Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (2010).
Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton. "Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor." 17:3160-3165 (2006).
Binquan Luan, and Aleksei Aksimentiev. "Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
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).
Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev. "End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). PDF icon Supporting Information (2.95 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).
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).
Kasra S Tabatabaei, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, Aleksei Aksimentiev, Min Chen, Charles M. Schroeder, and Olgica Milenkovic. "Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing." Nano Letters (2022). PDF icon si.pdf (2.42 MB)
F    
Arundhati Roy, Jie Shen, Himanshu Joshi, Woochul Song, Yu-Ming Tu, Ratul Chowdhury, Ye Ruijuan, Ning Li, Changliang Ren, Manish Kumar, Aleksei Aksimentiev, and Huaqiang Zeng. "Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons." Nature Nanotechnology 16:911-917 (2021). PDF icon si.pdf (2.73 MB)
H    
Lili Sun, Marcin Tabaka, Sen Hou, Lin Li, Krzysztof Burdzy, Aleksei Aksimentiev, Christopher Maffeo, Xuzhu Zhang, and Robert Holyst. "The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study." PLoS ONE 11:e0152002 (2016). PDF icon s1file.pdf (4.91 MB)
I    
Vadim Cherezov, Wei Liu, Jeremy P. Derrick, Binquan Luan, Aleksei Aksimentiev, Vsevolod Katritch, and Martin Caffrey. "In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
Vadim Cherezov, Wei Liu, Jeremy P. Derrick, Binquan Luan, Aleksei Aksimentiev, Vsevolod Katritch, and Martin Caffrey. "In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
Christopher R. Benson, Christopher Maffeo, Elisabeth M. Fatila, Yun Liu, Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, and Amar H. Flood. "Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem." Proceedings of the National Academy of Sciences (2018).
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)
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)
L    
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)
Yi Li, Christopher Maffeo, Himanshu Joshi, Aleksei Aksimentiev, Brice Ménard, and Rebecca Schulman. "Leakless end-to-end transport of small molecules through micron-length DNA nanochannels." Science Advances 8 (2022).
Siddharth Krishnan, Aleksei Aksimentiev, Stuart Lindsay, and Dmitry Matyushov. "Long-Range Conductivity in Proteins Mediated by Aromatic Residues." ACS Physical Chemistry Au 3:444-455 (2023). PDF icon sidd2023_si.pdf (792.94 KB)
M    
Florian Leonardus Lucas, Kumar Sarthak, Erica Mariska Lenting, David Coltan, Nieck Jordy van der Heide, Roderick Corstiaan Versloot, Aleksei Aksimentiev, and Giovanni Maglia. "The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition." ACS Nano (2021). PDF icon nn0c09958_si_001.pdf (1.59 MB)
Florian Leonardus Lucas, Kumar Sarthak, Erica Mariska Lenting, David Coltan, Nieck Jordy van der Heide, Roderick Corstiaan Versloot, Aleksei Aksimentiev, and Giovanni Maglia. "The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition." ACS Nano (2021). PDF icon nn0c09958_si_001.pdf (1.59 MB)
Jingqian Liu, and Aleksei Aksimentiev. "Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore." ACS Nanosci. Au (2023).
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)
Henry Brinkerhoff, Albert S. W. Kang, Jingqian Liu, Aleksei Aksimentiev, and Cees Dekker. "Multiple rereads of single proteins at single–amino acid resolution using nanopores." Science 374:1509-1513 (2021). PDF icon si.pdf (33.12 MB)
P    
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).
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)
Q    
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).
R    
Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chú, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. "The role of molecular modeling in bionanotechnology." Phys Biol 3:S40-53 (2006).
S    
James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé et al. "Scalable molecular dynamics on CPU and GPU architectures with NAMD." J. Chem. Phys. 153 (2020).
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)
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)
Maria E. Gracheva, A. Xiong, Aleksei Aksimentiev, Klaus Schulten, Gregory Timp, and Jean-Pierre Leburton. "Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor." Nanotechnology 17:622-633 (2006).
Binquan Luan, and Aleksei Aksimentiev. "Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. "Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
Jie Shen, Deepa R, Zhongyan Li, Hyeonji Oh, Harekrushna Behera, Himanshu Joshi, Manish Kumar, Aleksei Aksimentiev, and Huaqiang Zeng. "Sulfur-Containing Foldamer-Based Artificial Lithium Channels." Angewandte Chemie International Edition 62:e202305623 (2023). PDF icon anie202305623-sup-0001-misc_information.pdf (2.67 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)
T    
Fengyu Liu, Xiaoming Liu, Qing Shi, Christopher Maffeo, Masaru Kojima, Lixin Dong, Aleksei Aksimentiev, Qiang Huang, Toshio Fukuda, and Tatsuo Arai. "A tetrahedral DNA nanorobot with conformational change in response to molecular trigger." Nanoscale (2021).
Fengyu Liu, Xiaoming Liu, Qing Shi, Christopher Maffeo, Masaru Kojima, Lixin Dong, Aleksei Aksimentiev, Qiang Huang, Toshio Fukuda, and Tatsuo Arai. "A tetrahedral DNA nanorobot with conformational change in response to molecular trigger." Nanoscale (2021).
Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang, Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony H. Ho, Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten. "Third Generation DNA Sequencing with a Nanopore." In Nanopores: Sensing fundamental biological interactions at the single molecule level, edited by Samir M. Iqbal and Rashid Bashir, 287-311. Springer US, 2011.
U    
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 (2023).