Publications

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2022    
Prabhat Tripathi, Morgan Chandler, Christopher Michael Maffeo, Ali Fallahi, Amr Makhamreh, Justin Halman, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu. "Discrimination of RNA fiber structures using solid-state nanopores." Nanoscale 14:6866-6875 (2022).
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). PDF icon si.pdf (2.42 MB)
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).
Jejoong Yoo, Sangwoo Park, Christopher Maffeo, Taekjip Ha, and Aleksei Aksimentiev. "DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles." Nucleic Acids Res 49:11459-11475 (2021). PDF icon supporting_information.pdf (17.16 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)
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).
Sioned F. Jones, Himanshu Joshi, Stephen J. Terry, Jonathan R. Burns, Aleksei Aksimentiev, Ulrike S. Eggert, and Stefan Howorka. "Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes." Journal of the American Chemical Society 143:8305-8313 (2021). PDF icon si.pdf (20.33 MB)
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). PDF icon si_published.pdf (1.28 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).
2020    
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).
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).
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). PDF icon 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). PDF icon 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). PDF icon song2019_si.pdf (15.29 MB)
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).
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).
2018    
Patrick M. Arnott, Himanshu Joshi, Aleksei Aksimentiev, and Stefan Howorka. "Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes." Langmuir 34:15084-15092 (2018). PDF icon supplementary_information.pdf (2.54 MB)
Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, and Ulrich F. Keyser. "Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018). PDF icon nl7b05354_si_001.pdf (2.72 MB)
Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, and Ulrich F. Keyser. "Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018). PDF icon nl7b05354_si_001.pdf (2.72 MB)
2017    
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).
Mohammad Amin Alibakhshi, Justin R. Halman, James Wilson, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu. "Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores." ACS Nano 11:9701-9710 (2017). PDF icon Supporting Information (12.11 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)
James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev. "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha. "Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nature Communications 7:11045 (2016). PDF icon ncomms11045-s1.pdf (1.81 MB)
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). PDF icon s1file.pdf (4.91 MB)
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). PDF icon s1file.pdf (4.91 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)
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    
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).
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015). PDF icon Supporting Information (8.81 MB)
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015). PDF icon Supporting Information (8.81 MB)
2014    
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev. "A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment." Journal of Chemical Theory and Computation 10:2891-2896 (2014). PDF icon Supporting information (3.38 MB)
2012    
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).
David B. Wells, Swati Bhattacharya, Rogan Carr, Christopher Maffeo, Anthony H. Ho, Jeffrey Comer, and Aleksei Aksimentiev. "Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
2011    
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).
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).
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.
2008    
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).
2006    
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).
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).
2005    
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, 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, 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).
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).
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).
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).
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).
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).
2001    
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, and Robert Hołyst. "Application of the Euler characteristic to the study of homopolymer blends and copolymer melts." Polimery 46:309-322 (2001).
2000    
Aleksei Aksimentiev, and Robert Hołyst. "Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62:6821-30 (2000).
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, Robert Hołyst, and Krzysztof Moorthi. "Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends." Macromolecular Theory and Simulations 9:661-674 (2000).
1999    
Robert Hołyst, D Plewczyński, Aleksei Aksimentiev, and K Burdzy. "Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
Aleksei Aksimentiev, and Robert Hołyst. "Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (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. "Single-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
1998    
Aleksei Aksimentiev, and Robert Hołyst. "Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).