Publications

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Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).
Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
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).
Kush Coshic, Christopher Maffeo, David Winogradoff, and Aleksei Aksimentiev. "The structure and physical properties of a packaged bacteriophage particle." Nature 627:905-914 (2024).
Jeffrey Comer, and Aleksei Aksimentiev. "Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations." In Nanopores: Sensing and Fundamental Biological Interactions, edited by Rashid Bashir and Samir Iqbal, 335-356. New York: Springer Science and Business Media, LLC, 2011.
Jeffrey Comer, Anthony H. Ho, and Aleksei Aksimentiev. "Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (2012).
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.
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).
Jeffrey Comer, and Aleksei Aksimentiev. "DNA sequence-dependent ionic currents in ultra-small solid-state nanopores." Nanoscale 18:9600-9613 (2016). PDF icon supp_triplet.pdf (98.62 KB)
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).
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)
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)
Adnan Choudhary, Himanshu Joshi, Han-Yi Chou, Kumar Sarthak, James Wilson, Christopher Maffeo, and Aleksei Aksimentiev. "High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System." ACS Nano 14:15566-15576 (2020). PDF icon nn0c06191_si_001.pdf (547.55 KB)
Han-Yi Chou, and Aleksei Aksimentiev. "Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate." J. Phys. Chem. Lett. 11:4923-4929 (2020). PDF icon supporting_information.pdf (481.68 KB)
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).
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).
Jehanzeb Hameed Chaudhry, Jeffrey Comer, Aleksei Aksimentiev, and Luke N. Olson. "A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore." Commun Comput Phys 15:93-125 (2014).
Shu-Han Chao, Sam S. Matthews, Ryan Paxman, Aleksei Aksimentiev, Martin Gruebele, and Joshua L. Price. "Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (2014).
Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu. "Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
Spencer Carson, James Wilson, Aleksei Aksimentiev, Peter R. Weigele, and Meni Wanunu. "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
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).
Rogan Carr, Ira A. Weinstock, Asipu Sivaprasadarao, Achim Müller, and Aleksei Aksimentiev. "Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes." Nano Lett 8:3916-21 (2008). PDF icon Supporting Information (pdf) (8.8 MB)
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (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.
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).