Publications

Export 196 results:
2024    
Kush Coshic, Christopher Maffeo, David Winogradoff, and Aleksei Aksimentiev. "The structure and physical properties of a packaged bacteriophage particle." Nature (2024).
2023    
Christopher Maffeo, Lauren Quednau, James Wilson, and Aleksei Aksimentiev. "DNA double helix, a tiny electromotor." Nature Nanotechnology 18:238-242 (2023).
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).
Prabhat Tripathi, Behzad Mehrafrooz, Aleksei Aksimentiev, Sophie E. Jackson, Martin Gruebele, and Meni Wanunu. "A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein." The Journal of Physical Chemistry Letters:10719-10726 (2023).
Jingqian Liu, and Aleksei Aksimentiev. "Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore." ACS Nanosci. Au (2023).
Siddharth Krishnan, Aleksei Aksimentiev, Stuart Lindsay, and Dmitry Matyushov. "Long-Range Conductivity in Proteins Mediated by Aromatic Residues." ACS Physical Chemistry Au 3:444-455 (2023). PDF icon sidd2023_si.pdf (792.94 KB)
Xiaojun Wei, Tadas Penkauskas, Joseph E. Reiner, Celeste Kennard, Mark J. Uline, Qian Wang, Sheng Li, Aleksei Aksimentiev, Joseph W. F. Robertson, and Chang Liu. "Engineering Biological Nanopore Approaches toward Protein Sequencing." ACS Nano 17:16369-16395 (2023).
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). PDF icon Supporting Information (2.98 MB)
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, and Meni Wanunu. "Unidirectional single-file transport of full-length proteins through a nanopore." Nature Biotechnology (2023).
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).
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). PDF icon anie202305623-sup-0001-misc_information.pdf (2.67 MB)
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)
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).
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).
David Winogradoff, Han-Yi Chou, Christopher Maffeo, and Aleksei Aksimentiev. "Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex." Nature Communications 13:5138 (2022). PDF icon Supplementary Information (20.83 MB)
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).
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). PDF icon supplementary_information.pdf (4.85 MB)
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).
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)
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).
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)
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)
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)
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). PDF icon si.pdf (2.41 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)
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). PDF icon si.pdf (2.73 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).
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)
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)
Diana Morzy, Roger Rubio-Sánchez, Himanshu Joshi, Aleksei Aksimentiev, Lorenzo Di Michele, and Ulrich F. Keyser. "Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures." Journal of the American Chemical Society 143:7358-7367 (2021). PDF icon si.pdf (2.68 MB)
Prabhat Tripathi, Abdelkrim Benabbas, Behzad Mehrafrooz, Hirohito Yamazaki, Aleksei Aksimentiev, Paul M. Champion, and Meni Wanunu. "Electrical unfolding of cytochrome during translocation through a nanopore constriction." Proceedings of the National Academy of Sciences 118 (2021). PDF icon si_published.pdf (5.09 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)
Wayne Yang, Boya Radha, Adnan Choudhary, Yi You, Gangaiah Mettela, Andre K. Geim, Aleksei Aksimentiev, Ashok Keerthi, and Cees Dekker. "Translocation of DNA through Ultrathin Nanoslits." Advanced Materials 33:2007682 (2021). PDF icon yang2021si.pdf (1.2 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).
D Winogradoff, Pin‐Yi Li, H Joshi, L Quednau, C Maffeo, and Aleksei Aksimentiev. "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
Aleksei Aksimentiev. "Netting proteins, one at a time." Nature Nanotechnology 16:1178-1179 (2021).
2020    
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)
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).
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).
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). PDF icon si.pdf (2.57 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). PDF icon supportinginformation_final.pdf (4.48 MB)
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)
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). PDF icon si-final.pdf (3.1 MB)
David Winogradoff, Shalini John, and Aleksei Aksimentiev. "Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly." Nanoscale 12:5422-5434 (2020). PDF icon supplement.pdf (6.71 MB)
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). PDF icon Supplementary Information (15.98 MB)
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). PDF icon si.pdf (2.47 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)
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    
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). PDF icon si.pdf (1.74 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).
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)
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)
Haiqing Zhao, David Winogradoff, Yamini Dalal, and Garegin A. Papoian. "The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
Yiming Yang, Aaron Alford, Veronika Kozlovskaya, Shidi Zhao, Himanshu Joshi, Eunjung Kim, Shuo Qian, Volker Urban, Donald Cropek, Aleksei Aksimentiev, and Eugenia Kharlampieva. "Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes." ACS Applied Polymer Materials 1:722-736 (2019). PDF icon si-aba_sans_revised.pdf (2.84 MB)
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).
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). PDF icon sem_si.pdf (4.02 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).
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). PDF icon supplementary_material.pdf (8.62 MB)
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)
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)
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)
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). PDF icon supporting_information.pdf (1.77 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)
James Wilson, and Aleksei Aksimentiev. "Water-compression gating of nanopore transport." Physical Review Letters 120:268101 (2018). PDF icon Supporting Information (7.41 MB)
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).
Jejoong Yoo, and Aleksei Aksimentiev. "New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions." Physical Chemistry Chemical Physics 20:8432-8449 (2018). PDF icon si_nbfixperspec.pdf (3.85 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)
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.Binary Data origamitutorial.tar.gz (103.69 MB)
2017    
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).
Christopher Maffeo, and Aleksei Aksimentiev. "Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (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).
Karl Decker, Martin Page, and Aleksei Aksimentiev. "Nanoscale Ion Pump Derived from a Biological Water Channel." The Journal of Physical Chemistry B 121:7899-7906 (2017). PDF icon supporting_information.pdf (8.9 MB)
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)
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)
Wei Si, and Aleksei Aksimentiev. "Nanopore Sensing of Protein Folding." ACS Nano 11, 7091-7100 (2017). PDF icon nn7b02718_si_001.pdf (12.07 MB)
Manish Shankla, and Aleksei Aksimentiev. "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
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)
Kai Tian, Karl Decker, Aleksei Aksimentiev, and Li-Qun Gu. "Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis." ACS Nano 11:1204-1213 (2017). PDF icon Supporting Information (pdf) (8.47 MB)
"A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems." In Protocols in DNA Nanotechology. 2nd ed. Methods in Molecular Biology. Humana Press), 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)
Haiqing Zhao*, David Winogradoff*, Minh Bui, Yamini Dalal, and Garegin A. Papoian. "Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones." J Am Chem Soc 138:13207-13218 (2016).
Jejoong Yoo, and Aleksei Aksimentiev. "Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations." Journal of Physical Chemistry Letters 7:3812-3818 (2016). PDF icon jz6b01747_si_001.pdf (6.89 MB)
Kerstin Göpfrich*, Chen-Yu Li*, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. "Large-Conductance Transmembrane Porin Made from DNA Origami." ACS Nano 10:8207-8214 (2016). PDF icon supporting_information.pdf (3.19 MB)
Jejoong Yoo, James Wilson, and Aleksei Aksimentiev. "Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields." Biopolymers 105:752-763 (2016). PDF icon bip22868-sup-0001-suppinfo01.pdf (921.41 KB)
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). PDF icon supporting_information.pdf (1.32 MB)
James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev. "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
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)
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)
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)
Swati Bhattacharya, Jejoong Yoo, and Aleksei Aksimentiev. "Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore." ACS Nano 10:4644-4651 (2016). PDF icon supporting_mspa.pdf (3.61 MB)
Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev. "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
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).
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)
Haiqing Zhao*, David Winogradoff*, Minh Bui, Yamini Dalal, and Garegin Papoian. "Promiscuous histone mis-assembly is actively prevented by chaperones." Journal of the American Chemical Society 138:13207-13218 (2016). PDF icon The cover image on JACS (2.25 MB)PDF icon SI for the paper (33.5 MB)
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)
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)
Jejoong Yoo, and Aleksei Aksimentiev. "Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields." Journal of Chemical Theory and Computation 12:430-443 (2016). PDF icon ct5b00967_si_001.pdf (2.12 MB)
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)
Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev. "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA." ACS Nano 9:10598-10611 (2015). PDF icon nn5b04173_si_001.pdf (681.52 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).
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).
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)
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)
David Winogradoff, Ignacia Echeverria, Davit A. Potoyan, and Garegin A. Papoian. "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." J Am Chem Soc 137:6245-6253 (2015).
David Winogradoff, Haiqing Zhao, Yamini Dalal, and Garegin A. Papoian. "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
2014    
Christopher Maffeo, J Yoo, Jeffrey Comer, D B. Wells, B Luan, and Aleksei Aksimentiev. "Close encounters with DNA." J Phys Condens Matter 26:413101 (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)
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).
J S. Goodman, Shu-Han Chao, T V. Pogorelov, and Martin Gruebele. "Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding." J Phys Chem B (2014).
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).
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).
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).
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).
Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu. "Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
2013    
Jejoong Yoo, and Aleksei Aksimentiev. "In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci U S A 110:20099-104 (2013). PDF icon Supporting Information (4.15 MB)
James Wilson, and Massimiliano Di Ventra. "Single-base DNA discrimination via transverse ionic transport." Nanotechnology 24:415101 (2013).
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)
2012    
Jejoong Yoo, and Aleksei Aksimentiev. "Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations." J Phys Chem B 116:12946-54 (2012). PDF icon jp306598y_si_001.pdf (343.44 KB)
Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev. "DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev. "End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). PDF icon Supporting Information (2.95 MB)
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).
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).
Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (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, Maxim Belkin, Jeffrey Comer, and Aleksei Aksimentiev. "Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (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)
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).
Jejoong Yoo, and Aleksei Aksimentiev. "Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems." The Journal of Physical Chemistry Letters 3:45-50 (2012). PDF icon jz201501a_si_001.pdf (1.69 MB)
2011    
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).
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).
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).
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, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
Swati Bhattacharya, L Muzard, Linda Payet, Jérôme Mathé, Ulrich Bockelmann, Aleksei Aksimentiev, and Virgile Viasnoff. "Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments." The Journal of Physical Chemistry C 115:4255-4264 (2011).
Meni Wanunu, Swati Bhattacharya, Yun Xie, Yitzhak Tor, Aleksei Aksimentiev, and Marija Drndic. "Nanopore analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (2011).
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).
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.
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.
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.
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.
2010    
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).
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).
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).
Binquan Luan, and Aleksei Aksimentiev. "Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
Michael Zwolak, James Wilson, and Massimiliano Di Ventra. "Dehydration and ionic conductance quantization in nanopores." J Phys Condens Matter 22:454126 (2010).
Winston Timp, Utkur M. Mirsaidov, Deqiang Wang, Jeffrey Comer, Aleksei Aksimentiev, and Gregory Timp. "Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
David B. Wells, and Aleksei Aksimentiev. "Mechanical properties of a complete microtubule revealed through molecular dynamics simulation." Biophys J 99:629-37 (2010). PDF icon Supporting Information (pdf) (2.75 MB)File Atomic coordinates of the equilibrated "N" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated "S" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated complete microtubule (pdb) (13.16 MB)
Binquan Luan, and Aleksei Aksimentiev. "Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (2010).
Aleksei Aksimentiev. "Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
Binquan Luan, Rogan Carr, Martin Caffrey, and Aleksei Aksimentiev. "The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
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).
Christopher Maffeo, and Aleksei Aksimentiev. "Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
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).
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).
Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
2008    
Binquan Luan, and Aleksei Aksimentiev. "Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
Binquan Luan, and Aleksei Aksimentiev. "DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (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).
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).
Binquan Luan, and Aleksei Aksimentiev. "Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
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).
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).
2007    
David B. Wells, Volha Abramkina, and Aleksei Aksimentiev. "Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. "Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
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).
2006    
Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).
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).
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).
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).
Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton. "Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor." 17:3160-3165 (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).
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).
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).
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).
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).
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.
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).
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).
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).
2003    
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).
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).