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Christopher Maffeo, Han-Yi Chou, and Aleksei Aksimentiev. "Single-molecule biophysics experiments in silico: Toward a physical model of a replisome." iScience 25:104264 (2022). PDF icon maff2022_si.pdf (1.35 MB)
Dan Qiao, Himanshu Joshi, Huangtianzhi Zhu, Fushi Wang, Yang Xu, Jia Gao, Feihe Huang, Aleksei Aksimentiev, and Jiandong Feng. "Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport." Journal of the American Chemical Society 143:15975-15983 (2021). PDF icon si.pdf (10.35 MB)
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).
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)
Mette D. E. Jepsen, Rasmus Schøler Sørensen, Christopher Maffeo, Aleksei Aksimentiev, Jørgen Kjems, and Victoria Birkedal. "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).
Manish Shankla, and Aleksei Aksimentiev. "Step-defect guided delivery of DNA to a graphene nanopore." Nature Nanotechnology (2019). PDF icon gs_si.pdf (3.95 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)
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)
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)
Jejoong Yoo, and Aleksei Aksimentiev. "The structure and intermolecular forces of DNA condensates." Nucleic Acids Research 44:2036-2046 (2016). PDF icon dnapack_supp.pdf (9.65 MB)
Shouvik Banerjee, James Wilson, Jiwook Shim, Manish Shankla, Elise A. Corbin, Aleksei Aksimentiev, and Rashid Bashir. "Slowing DNA Transport Using Graphene–DNA Interactions." Advanced Functional Materials 25:936-946 (2015). PDF icon adfm201403719-sup-0001-s1.pdf (1.01 MB)
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).
Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu. "Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
Maxim Belkin, Christopher Maffeo, David B. Wells, and Aleksei Aksimentiev. "Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores." ACS Nano 7:6816-24 (2013). PDF icon Supporting Information (2.8 MB)
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).
Courtney J. Stavis, Tami Lasseter Clare, James E. Butler, Adarsh D. Radadia, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Rashid Bashir, and Robert J. Hamers. "Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
Christopher Maffeo, and Aleksei Aksimentiev. "Single molecule force measurements: insights from molecular simulations. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al." Phys Life Rev 7:353-4; discussion 358-61 (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).
Christopher Maffeo, and Aleksei Aksimentiev. "Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
Binquan Luan, and Aleksei Aksimentiev. "Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
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)
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).
Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. "Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
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).
Jiunn B. Heng, Aleksei Aksimentiev, Chuen Ho, Patrick Marks, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
Jiunn B. Heng, Chuen Ho, Taekyung Kim, Rolf Timp, Aleksei Aksimentiev, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "Sizing DNA using a nanometer-diameter pore." Biophys J 87:2905-11 (2004).
Marcin Fialkowski, Aleksei Aksimentiev, and Robert Hołyst. "Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems." Phys Rev Lett 86:240-3 (2001).
Aleksei Aksimentiev, Krzysztof Moorthi, and Robert Hołyst. "Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends." The Journal of Chemical Physics 112:6049-6062 (2000).
Aleksei Aksimentiev, and Robert Hołyst. "Single-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
Aleksei Aksimentiev, and Robert Hołyst. "Single chain conformations in the system of symmetric and asymmetric diblock copolymers." Macromolecular Theory and Simulations 8:328-342 (1999).
Aleksei Aksimentiev, and Robert Hołyst. "Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).