Publications | The Aksimentiev Group

A

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).

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).

song2019_si.pdf (15.29 MB)

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).

song2019_si.pdf (15.29 MB)

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).

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).

B

Kumar Sarthak, David Winogradoff, Yingda Ge, Sua Myong, and Aleksei Aksimentiev. "Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates." Journal of Chemical Theory and Computation (2023).

Supporting Information (2.98 MB)

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).

C

Megan Farell, Maxwell Wetherington, Manish Shankla, Inseok Chae, Shruti Subramanian, Seong H. Kim, Aleksei Aksimentiev, Joshua Robinson, and Manish Kumar. "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features." Langmuir 35:4726-4735 (2019).

Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chú, David Hardy, Aruna Rajan, Amy Y. Shih, G Sigalov, Ying Yin, and Klaus Schulten. "Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).

Manish Shankla, and Aleksei Aksimentiev. "Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene." Nature Communications 5:5171 (2014).

Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Robert J. Hamers, and Rashid Bashir. "Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).

Alexander Ohmann, Kerstin Göpfrich, Himanshu Joshi, Rebecca F. Thompson, Diana Sobota, Neil A. Ranson, Aleksei Aksimentiev, and Ulrich F. Keyser. "Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019).

si.pdf (1.74 MB)

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).

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).

G Sigalov, Jeffrey Comer, Gregory Timp, and Aleksei Aksimentiev. "Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).

Kristina Hübner, Himanshu Joshi, Aleksei Aksimentiev, Fernando D. Stefani, Philip Tinnefeld, and Guillermo P. Acuna. "Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures." ACS Nano 15:5109-5117 (2021).

si_published.pdf (1.28 MB)

Sarah E. Ochmann, Himanshu Joshi, Ece Büber, Henri G. Franquelim, Pierre Stegemann, Barbara Saccà, Ulrich F. Keyser, Aleksei Aksimentiev, and Philip Tinnefeld. "DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity." Nano Letters 21:8634-8641 (2021).

si.pdf (2.41 MB)

Sarah E. Ochmann, Himanshu Joshi, Ece Büber, Henri G. Franquelim, Pierre Stegemann, Barbara Saccà, Ulrich F. Keyser, Aleksei Aksimentiev, and Philip Tinnefeld. "DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity." Nano Letters 21:8634-8641 (2021).

si.pdf (2.41 MB)

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 (2023).

Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel. "DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).

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).

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).

supporting_information.pdf (1.77 MB)

E

Hadjer Ouldali, Kumar Sarthak, Tobias Ensslen, Fabien Piguet, Philippe Manivet, Juan Pelta, Jan C. Behrends, Aleksei Aksimentiev, and Abdelghani Oukhaled. "Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore." Nature Biotechnology 38:176-181 (2020).

Supplementary Information (15.98 MB)

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).

supplementary_material.pdf (8.62 MB)

Jiunn B. Heng, Aleksei Aksimentiev, C Ho, Patrick Marks, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "The electromechanics of DNA in a synthetic nanopore." Biophys J 90:1098-106 (2006).

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).

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).

si.pdf (2.42 MB)

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).

si.pdf (2.42 MB)

Aleksei Aksimentiev, and Klaus Schulten. "Extending molecular modeling methodology to study insertion of membrane nanopores." Proc Natl Acad Sci U S A 101:4337-8 (2004).

F

Jie Shen, Arundhati Roy, Himanshu Joshi, Laxmicharan Samineni, Ruijuan Ye, Yu-Ming Tu, Woochul Song, Matthew Skiles, Manish Kumar, Aleksei Aksimentiev, and Huaqiang Zeng. "Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport." Nano Lett 22:4831-4838 (2022).

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).

si.pdf (2.73 MB)

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).

si.pdf (2.73 MB)

G

James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev. "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).

H

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).

nn0c06191_si_001.pdf (547.55 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).

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).

s1file.pdf (4.91 MB)

I

Aleksei Aksimentiev, and Klaus Schulten. "Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map." Biophys J 88:3745-61 (2005).

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).

Aleksei Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. "Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase." Biophys J 86:1332-44 (2004).

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).

supporting_information.pdf (1.32 MB)

Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).

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Emad Tajkhorshid, Aleksei Aksimentiev, Ilya A. Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. "Large scale simulation of protein mechanics and function." Adv Protein Chem 66:195-247 (2003).

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).

Bala Murali Venkatesan, James Polans, Jeffrey Comer, Supriya Sridhar, David Wendell, Aleksei Aksimentiev, and Rashid Bashir. "Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore." Biomed Microdevices 13:671-82 (2011).

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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).

nn0c09958_si_001.pdf (1.59 MB)

Maxim B. Prigozhin*, Shu-Han Chao*, Shahar Sukenik, Taras V. Pogorelov, and Martin Gruebele. "Mapping fast protein folding with multiple-site fluorescent probes." Proc Natl Acad Sci U S A 112:7966-71 (2015).

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).

si.pdf (1.54 MB)

Aleksei Aksimentiev, Jiunn B. Heng, Gregory Timp, and Klaus Schulten. "Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).

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.

Aleksei Aksimentiev, Robert Brunner, Eduardo Cruz-Chú, Jeffrey Comer, and Klaus Schulten. "Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).

Manish Shankla, and Aleksei Aksimentiev. "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).

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).

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).

supporting_information.pdf (7.84 MB)

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).

supportinginformation_final.pdf (4.48 MB)

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Wei Si, and Aleksei Aksimentiev. "Nanopore Sensing of Protein Folding." ACS Nano 11, 7091-7100 (2017).

nn7b02718_si_001.pdf (12.07 MB)

O

Jérôme Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. "Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).

P

Arundhati Roy, Himanshu Joshi, Ruijuan Ye, Jie Shen, Feng Chen, Aleksei Aksimentiev, and Huaqiang Zeng. "Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels." Angewandte Chemie International Edition 12:4806-4813 (2020).

si-final.pdf (3.1 MB)

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).

supporting_information.pdf (1.34 MB)

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.

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

James Wilson, Kumar Sarthak, Wei Si, Luyu Gao, and Aleksei Aksimentiev. "Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model." ACS sensors 4:634-644 (2019).

sem_si.pdf (4.02 MB)

James Wilson, Kumar Sarthak, Wei Si, Luyu Gao, and Aleksei Aksimentiev. "Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model." ACS sensors 4:634-644 (2019).

sem_si.pdf (4.02 MB)

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).

Tobias Ennslen, Kumar Sarthak, Aleksei Aksimentiev, and Jan C. Behrends. "Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape." Journal of the American Chemical Society 144:16060-16068 (2022).

supplementary_information.pdf (4.85 MB)

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).

Prabhat Tripathi, Liang Shuai, Himanshu Joshi, Hirohito Yamazaki, William H. Fowle, Aleksei Aksimentiev, Hicham Fenniri, and Meni Wanunu. "Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors." Journal of the American Chemical Society 142:1680-1685 (2020).

si.pdf (2.47 MB)

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).

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).

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).

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).

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).

adfm201403719-sup-0001-s1.pdf (1.01 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).

adfm201403719-sup-0001-s1.pdf (1.01 MB)

Manish Shankla, and Aleksei Aksimentiev. "Step-defect guided delivery of DNA to a graphene nanopore." Nature Nanotechnology (2019).

gs_si.pdf (3.95 MB)

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).

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).

anie202305623-sup-0001-misc_information.pdf (2.67 MB)

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).

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).

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).

Supporting Information (pdf) (8.8 MB)

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Diana Sobota, Himanshu Joshi, Alexander Ohmann, Aleksei Aksimentiev, and Ulrich F. Keyser. "Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme." Nano Letters 20:4306-4311 (2020).

si.pdf (2.57 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).

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.

Emad Tajkhorshid, Jordi Cohen, Aleksei Aksimentiev, Marcos Sotomayor, and Klaus Schulten. "Toward understanding membrane channels." In Bacterial ion channels and their eukaryotic homologues, edited by Boris Martinac and Andrzej Kubalski, 153-190. Washington, DC: ASM Press, 2005.

Merle Scherf, Florian Scheffler, Christopher Maffeo, Ulrich Kemper, Jingjing Ye, Aleksei Aksimentiev, Ralf Seidel, and Uta Reibetanz. "Trapping of protein cargo molecules inside DNA origami nanocages." Nanoscale 14:18041-18050 (2022).

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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).