Publications

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2022    
Adnan Choudhary, Christopher Maffeo, and Aleksei Aksimentiev. "Multi-resolution simulation of DNA transport through large synthetic nanostructures." Phys Chem Chem Phys 24:2706-2716 (2022). PDF icon Supplementary Information and Hand-on Guide (239.4 KB)
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)
Diana Morzy, Himanshu Joshi, Sarah E. Sandler, Aleksei Aksimentiev, and Ulrich F. Keyser. "Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure." Nano Letters 21:9789-9796 (2021). PDF icon si.pdf (1.54 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)
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).
Manish Shankla, and Aleksei Aksimentiev. "Molecular Transport across the Ionic Liquid−Aqueous Electrolyte Interface in a MoS2 Nanopore." ACS Appl. Mater. Interfaces 12:26624-26634 (2020). PDF icon supportinginformation_final.pdf (4.48 MB)
Christopher Maffeo, and Aleksei Aksimentiev. "MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems." Nucleic Acids Research (2020). PDF icon supplement.pdf (3.94 MB)
2019    
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)
Christopher Maffeo, Han-Yi Chou, and Aleksei Aksimentiev. "Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
2017    
Christopher Maffeo, and Aleksei Aksimentiev. "Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
Manish Shankla, and Aleksei Aksimentiev. "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
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)
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)
Maxim Belkin, and Aleksei Aksimentiev. "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores." ACS Applied Materials and Interfaces 8:12599-12608 (2016). PDF icon supporting.pdf (461.04 KB)
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)
2014    
Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev. "Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
2012    
Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (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    
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (2011).
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
Jeffrey Comer, David B. Wells, and Aleksei Aksimentiev. "Modeling nanopores for sequencing DNA." In DNA Nanotechnology: Methods and Protocols, edited by Giampaolo Zuccheri and Bruno Samori, 317-358. Vol. 749. Methods Mol. Biol. 749., 2011.
Rogan Carr, Jeffrey Comer, and Aleksei Aksimentiev. "Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems." In Simulations in Nanobiotechnology, edited by Kilho Eom, 43-60. CRC Press, 2011.
2009    
Aleksei Aksimentiev, Robert Brunner, Eduardo Cruz-Chú, Jeffrey Comer, and Klaus Schulten. "Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (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).
2005    
James Gumbart, Yi Wang, Aleksei Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. "Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
2004    
Aleksei Aksimentiev, Jiunn B. Heng, Gregory Timp, and Klaus Schulten. "Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
2002    
Aleksei Aksimentiev, Robert Hołyst, and Marcin Fialkowski. "Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements." Advances in Chemical Physics 121:141-239 (2002).