Publications

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2024    
Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Elija Feigl, Wenxuan Zhao, Daniel Verschueren, Ramin Golestanian, Aleksei Aksimentiev, Hendrik Dietz, and Cees Dekker. "A DNA turbine powered by a transmembrane potential across a nanopore." Nature Nanotechnology 19:338-344 (2024).
Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Elija Feigl, Wenxuan Zhao, Daniel Verschueren, Ramin Golestanian, Aleksei Aksimentiev, Hendrik Dietz, and Cees Dekker. "A DNA turbine powered by a transmembrane potential across a nanopore." Nature Nanotechnology 19:338-344 (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 16:20865-20877 (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 16:20865-20877 (2024).
2023    
Kaikai Chen, Adnan Choudhary, Sarah E. Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, and Ulrich F. Keyser. "Super-Resolution Detection of DNA Nanostructures Using a Nanopore." Advanced Materials:2207434 (2023).
2021    
Eva Bertosin, Christopher M. Maffeo, Thomas Drexler, Maximilian N. Honemann, Aleksei Aksimentiev, and Hendrik Dietz. "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
Eva Bertosin, Christopher M. Maffeo, Thomas Drexler, Maximilian N. Honemann, Aleksei Aksimentiev, and Hendrik Dietz. "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
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)
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).
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).
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).
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).
Diana Morzy, Roger Rubio-Sánchez, Himanshu Joshi, Aleksei Aksimentiev, Lorenzo Di Michele, and Ulrich F. Keyser. "Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures." Journal of the American Chemical Society 143:7358-7367 (2021). PDF icon si.pdf (2.68 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)
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).
2019    
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).
Haiqing Zhao, David Winogradoff, Yamini Dalal, and Garegin A. Papoian. "The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
Shidi Zhao, Laura Restrepo-Perez, Giovanni Maglia, Misha Soskine, Chirlmin Joo, Cees Dekker, and Aleksei Aksimentiev. "Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate." ACS Nano 13:2398-2409 (2019). PDF icon supplementary_material.pdf (8.62 MB)
2018    
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)
2017    
Karl Decker, Martin Page, and Aleksei Aksimentiev. "Nanoscale Ion Pump Derived from a Biological Water Channel." The Journal of Physical Chemistry B 121:7899-7906 (2017). PDF icon supporting_information.pdf (8.9 MB)
Laura Restrepo-Perez*, Shalini John*, Aleksei Aksimentiev, Chirlmin Joo, and Cees Dekker. "SDS-assisted protein transport through solid-state nanopores." Nanoscale 9:11685-11693 (2017). PDF icon Supporting Information (1.24 MB)
Karl Decker, Martin Page, Ashley Boyd, Irene MacAllister, Mark Ginsberg, and Aleksei Aksimentiev. "Selective Permeability of Truncated Aquaporin 1 in Silico." ACS Biomaterials Science & Engineering 3:342-348 (2017). PDF icon Supporting Information (pdf) (459.46 KB)
Kai Tian, Karl Decker, Aleksei Aksimentiev, and Li-Qun Gu. "Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis." ACS Nano 11:1204-1213 (2017). PDF icon Supporting Information (pdf) (8.47 MB)
2016    
Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev. "Mechanical Trapping of DNA in a Double-Nanopore System." Nano Letters 16:8021-8028 (2016). PDF icon Supporting Information (pdf) (2.24 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).
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)
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)
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)
Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar. "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar. "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
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).
2014    
Trevor Gamble, Karl Decker, Timothy S. Plett, Matthew Pevarnik, Jan-Frederik Pietschmann, Ivan Vlassiouk, Aleksei Aksimentiev, and Zuzanna S. Siwy. "Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling." The Journal of Physical Chemistry C 118:9809-9819 (2014).
2013    
James Wilson, and Massimiliano Di Ventra. "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
2012    
Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, and Cees Dekker. "Slowing down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
Swati Bhattacharya, Ian M. Derrington, Mikhail Pavlenok, Michael Niederweis, Jens H. Gundlach, and Aleksei Aksimentiev. "Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence." ACS Nano 6:6960-8 (2012). PDF icon Supporting Information (pdf) (2.36 MB)
2011    
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).
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.
2010    
Utkur Mirsaidov, Jeffrey Comer, Valentin Dimitrov, Aleksei Aksimentiev, and Gregory Timp. "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
Michael Zwolak, James Wilson, and Massimiliano Di Ventra. "Dehydration and ionic conductance quantization in nanopores." J Phys Condens Matter 22:454126 (2010).
2009    
B Dorvel, G Sigalov, Q Zhao, Jeffrey Comer, Valentin Dimitrov, U Mirsaidov, Aleksei Aksimentiev, and Gregory Timp. "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
B Dorvel, G Sigalov, Q Zhao, Jeffrey Comer, Valentin Dimitrov, U Mirsaidov, Aleksei Aksimentiev, and Gregory Timp. "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
Jeffrey Comer, Valentin Dimitrov, Qian Zhao, Gregory Timp, and Aleksei Aksimentiev. "Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
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).
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).
2007    
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).
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).
2005    
Jiunn B. Heng, Aleksei Aksimentiev, C Ho, Valentin Dimitrov, T Sorsch, J Miner, W Mansfield, Klaus Schulten, and Gregory Timp. "Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).