Directory

Aleksei Aksimentiev's directory photo.

Aleksei Aksimentiev

Professor

Primary Affiliation

Theoretical and Computational Biophysics

Affiliations

Status Part-time Faculty

Home Department of Physics

Phone 333-6495

Email aksiment@illinois.edu

Address 3065 Beckman Institute, 405 North Mathews Avenue

  • Biography

    Professor Aksimentiev is a professor in the Department of Physics and an affiliate faculty member of Carl R. Woese Institute for Genomic Biology. He received postdoctoral training at the Materials Science Laboratory R&D Center of Mitsui Chemicals, Tokyo, Japan, from 1999 to 2001, when he joined the Theoretical and Computational Biophysics Group at the University of Illinois as a postdoctoral research associate. He accepted the position of assistant professor of physics at Illinois in 2005.

    Education

    • M.S., particle physics, Franko Lviv State University, 1996
    • Ph.D., chemistry, Institute of Physical Chemistry Polish Academy of Sciences, 1999
  • Honors
    • 2015-2016: National Center for Supercomputing Applications (NCSA)
    • 2015: Dean's Award for Excellence in Research 
    • 2014: Blue Waters Professorship 
    • 2010: NSF CAREER Award 
    • 2009-2010: Beckman Fellow, Center for Advanced Studies 
    • 2008: IBM Faculty Fellow Award 
  • Research

    Research areas:

    • Nanopore systems for single molecule detection and manipulation

    • Molecular mechanics of DNA processing machinery

    • The physics of DNA assemblies

    • Synthetic molecular systems

    Research interests:

    • Silicon-based synthetic membranes

    • Biomolecules

    • Biosynthetic complexes

    Imagine assembling a few thousand marbles into a machine capable of transforming the energy of an electric field into mechanical torque at nearly 100% efficiency and lasting ten million cycles. Although marbles are not atoms, Nature has done exactly that, assembling carbon, oxygen, nitrogen, and hydrogen atoms into remarkable nanomachines. And while Nature took billions of years to transform primordial dirt into the molecular motors that power living cells, the atoms comprising present-day bio machines are no different from those found in common inorganic compounds, and they obey the same laws of physics that enable the machines' amazing properties. Understanding how the remarkable functionality of biological nanomachines comes about from the spatial arrangement of their atoms and using this knowledge to design synthetic systems that exceed in the performance of their biological counterparts is the focus of this group's research program.

  • 2024

    • A DNA turbine powered by a transmembrane potential across a nanopore Shi, X., Pumm, A.-K., Maffeo, C., Kohler, F., Feigl, E., Zhao, W., Verschueren, D., Golestanian, R., Aksimentiev, A., Dietz, H. and Dekker, C., Mar 2024, In: Nature Nanotechnology. 19, 3, p. 338-344 7 p.
    • Dehydrated Biomimetic Membranes with Skinlike Structure and Function Oh, H., Tu, Y. M., Samineni, L., De Respino, S., Mehrafrooz, B., Joshi, H., Massenburg, L., Lopez-Marques, H., Elessawy, N., Song, W., Behera, H., Dhiman, R., Boorla, V. S., Kher, K., Lin, Y. C., Maranas, C., Aksimentiev, A., D. Freeman, B. and Kumar, M., 2024, (Accepted/In press) In: ACS Applied Materials and Interfaces.
    • Electro-osmotic Flow Generation via a Sticky Ion Action Mehrafrooz, B., Yu, L., Pandey, L., Siwy, Z. S., Wanunu, M. and Aksimentiev, A., Jul 9 2024, In: ACS Nano. 18, 27, p. 17521-17533 13 p.
    • Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore Liu, J. and Aksimentiev, A., Feb 21 2024, In: ACS Nanoscience Au. 4, 1, p. 21-29 9 p.
    • Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix Boškovic, F., Maffeo, C., Patiño-Guillén, G., Tivony, R., Aksimentiev, A. and Keyser, U. F., Jun 11 2024, In: ACS Nano. 18, 23, p. 15013-15024 12 p.
    • Single molecule delivery into living cells Chau, C. C., Maffeo, C. M., Aksimentiev, A., Radford, S. E., Hewitt, E. W. and Actis, P., Dec 2024, In: Nature communications. 15, 1, 4403.
    • The structure and physical properties of a packaged bacteriophage particle Coshic, K., Maffeo, C., Winogradoff, D. and Aksimentiev, A., Mar 28 2024, In: Nature. 627, 8005, p. 905-914 10 p.

    2023

    • A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein Tripathi, P., Mehrafrooz, B., Aksimentiev, A., Jackson, S. E., Gruebele, M. and Wanunu, M., Nov 30 2023, In: Journal of Physical Chemistry Letters. 14, 47, p. 10719-10726 8 p.
    • All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores Joshi, H., Li, C. Y. and Aksimentiev, A., 2023, Methods in Molecular Biology. Humana Press Inc., p. 113-128 16 p. (Methods in Molecular Biology; vol. 2639).
    • Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates Sarthak, K., Winogradoff, D., Ge, Y., Myong, S. and Aksimentiev, A., Jun 27 2023, In: Journal of Chemical Theory and Computation. 19, 12, p. 3721-3740 20 p.
    • DNA double helix, a tiny electromotor Maffeo, C., Quednau, L., Wilson, J. and Aksimentiev, A., Mar 2023, In: Nature Nanotechnology. 18, 3, p. 238-242 5 p.
    • Engineering Biological Nanopore Approaches toward Protein Sequencing Wei, X., Penkauskas, T., Reiner, J. E., Kennard, C., Uline, M. J., Wang, Q., Li, S., Aksimentiev, A., Robertson, J. W. F. and Liu, C., Sep 12 2023, In: ACS Nano. 17, 17, p. 16369-16395 27 p.
    • Long-Range Conductivity in Proteins Mediated by Aromatic Residues Krishnan, S., Aksimentiev, A., Lindsay, S. and Matyushov, D., Sep 27 2023, In: ACS Physical Chemistry Au. 3, 5, p. 444-455 12 p.
    • Sulfur-Containing Foldamer-Based Artificial Lithium Channels Shen, J., Deepa, R., Li, Z., Oh, H., Behera, H., Joshi, H., Kumar, M., Aksimentiev, A. and Zeng, H., Sep 25 2023, In: Angewandte Chemie - International Edition. 62, 39, e202305623.
    • Super-Resolution Detection of DNA Nanostructures Using a Nanopore Chen, K., Choudhary, A., Sandler, S. E., Maffeo, C., Ducati, C., Aksimentiev, A. and Keyser, U. F., Mar 23 2023, In: Advanced Materials. 35, 12, 2207434.
    • Unidirectional single-file transport of full-length proteins through a nanopore Yu, L., Kang, X., Li, F., Mehrafrooz, B., Makhamreh, A., Fallahi, A., Foster, J. C., Aksimentiev, A., Chen, M. and Wanunu, M., Aug 2023, In: Nature Biotechnology. 41, 8, p. 1130–1139 10 p.

    2022

    • Discrimination of RNA fiber structures using solid-state nanopores Tripathi, P., Chandler, M., Maffeo, C. M., Fallahi, A., Makhamreh, A., Halman, J., Aksimentiev, A., Afonin, K. A. and Wanunu, M., May 14 2022, In: Nanoscale. 14, 18, p. 6866-6875
    • Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M. and Milenkovic, O., Mar 9 2022, In: Nano letters. 22, 5, p. 1905-1914 10 p.
    • Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport Shen, J., Roy, A., Joshi, H., Samineni, L., Ye, R., Tu, Y. M., Song, W., Skiles, M., Kumar, M., Aksimentiev, A. and Zeng, H., Jun 22 2022, In: Nano letters. 22, 12, p. 4831-4838 8 p.
    • Leakless end-to-end transport of small molecules through micron-length DNA nanochannels Li, Y., Maffeo, C., Joshi, H., Aksimentiev, A., Ménard, B. and Schulman, R., Sep 2022, In: Science Advances. 8, 36, eabq4834.
    • Multi-resolution simulation of DNA transport through large synthetic nanostructures Choudhary, A., Maffeo, C. and Aksimentiev, A., Feb 7 2022, In: Physical Chemistry Chemical Physics. 24, 5, p. 2706-2716 11 p.
    • Nanopore-based system for trapping, controlled displacement, and sequencing of (bio)macromolecules Aksimentiev, A. (Inventor) and Dekker, C. (Inventor), May 17 2022, U.S. Patent No. 11333655, Sep 6 2017
    • Nucleic Acid Compositions And Methods For Modulation Of Cell Membranes Aksimentiev, A. (Inventor), Keyser, U. F. (Inventor) and Wilkinson, M. (Inventor), Sep 13 2022, U.S. Patent No. 11441118
    • Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex Winogradoff, D., Chou, H. Y., Maffeo, C. and Aksimentiev, A., Dec 2022, In: Nature communications. 13, 1, 5138.
    • Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape Ensslen, T., Sarthak, K., Aksimentiev, A. and Behrends, J. C., Sep 7 2022, In: Journal of the American Chemical Society. 144, 35, p. 16060-16068 9 p.
    • Single-molecule biophysics experiments in silico: Toward a physical model of a replisome Maffeo, C., Chou, H. Y. and Aksimentiev, A., May 20 2022, In: iScience. 25, 5, 104264.
    • Trapping of protein cargo molecules inside DNA origami nanocages Scherf, M., Scheffler, F., Maffeo, C., Kemper, U., Ye, J., Aksimentiev, A., Seidel, R. and Reibetanz, U., Nov 22 2022, In: Nanoscale. 14, 48, p. 18041-18050 10 p.

    2021

    • A nanoscale reciprocating rotary mechanism with coordinated mobility control Bertosin, E., Maffeo, C. M., Drexler, T., Honemann, M. N., Aksimentiev, A. and Dietz, H., Dec 2021, In: Nature communications. 12, 1, 7138.
    • A tetrahedral DNA nanorobot with conformational change in response to molecular trigger Liu, F., Liu, X., Shi, Q., Maffeo, C., Kojima, M., Dong, L., Aksimentiev, A., Huang, Q., Fukuda, T. and Arai, T., Oct 7 2021, In: Nanoscale. 13, 37, p. 15552-15559 8 p.
    • Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures Morzy, D., Rubio-Sánchez, R., Joshi, H., Aksimentiev, A., Di Michele, L. and Keyser, U. F., May 19 2021, In: Journal of the American Chemical Society. 143, 19, p. 7358-7367 10 p.
    • Chiral Systems Made from DNA Winogradoff, D., Li, P. Y., Joshi, H., Quednau, L., Maffeo, C. and Aksimentiev, A., Mar 3 2021, In: Advanced Science. 8, 5, 2003113.
    • Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures Hübner, K., Joshi, H., Aksimentiev, A., Stefani, F. D., Tinnefeld, P. and Acuna, G. P., Mar 23 2021, In: ACS Nano. 15, 3, p. 5109-5117 9 p.
    • DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity Ochmann, S. E., Joshi, H., Büber, E., Franquelim, H. G., Stegemann, P., Saccà, B., Keyser, U. F., Aksimentiev, A. and Tinnefeld, P., Oct 27 2021, In: Nano letters. 21, 20, p. 8634-8641 8 p.
    • DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity Ochmann, S. E., Joshi, H., Büber, E., Franquelim, H. G., Stegemann, P., Saccà, B., Keyser, U. F., Aksimentiev, A. and Tinnefeld, P., Oct 27 2021, In: Nano letters. 21, 20, p. 8634-8641 8 p.
    • Electrical unfolding of cytochrome c during translocation through a nanopore constriction Tripathi, P., Benabbas, A., Mehrafrooz, B., Yamazaki, H., Aksimentiev, A., Champion, P. M. and Wanunu, M., Apr 27 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 17, e2016262118.
    • Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons Roy, A., Shen, J., Joshi, H., Song, W., Tu, Y. M., Chowdhury, R., Ye, R., Li, N., Ren, C., Kumar, M., Aksimentiev, A. and Zeng, H., Aug 2021, In: Nature Nanotechnology. 16, 8, p. 911-917 7 p.
    • Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes Jones, S. F., Joshi, H., Terry, S. J., Burns, J. R., Aksimentiev, A., Eggert, U. S. and Howorka, S., Jun 9 2021, In: Journal of the American Chemical Society. 143, 22, p. 8305-8313 9 p.
    • Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure Morzy, D., Joshi, H., Sandler, S. E., Aksimentiev, A. and Keyser, U. F., Nov 24 2021, In: Nano letters. 21, 22, p. 9789-9796 8 p.
    • Multiple rereads of single proteins at single-amino acid resolution using nanopores Brinkerhoff, H., Kang, A. S. W., Liu, J., Aksimentiev, A. and Dekker, C., Dec 17 2021, In: Science. 374, 6574, p. 1509-1513 5 p.
    • Netting proteins, one at a time Aksimentiev, A., Nov 2021, In: Nature Nanotechnology. 16, 11, p. 1178-1179 2 p.
    • Nucleic acid nanoparticles for analyte detection Aksimentiev, A. (Inventor), Afonin, K. A. (Inventor) and Wanunu, M. (Inventor), Jan 26 2021, U.S. Patent No. 10900067
    • Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport Qiao, D., Joshi, H., Zhu, H., Wang, F., Xu, Y., Gao, J., Huang, F., Aksimentiev, A. and Feng, J., Oct 6 2021, In: Journal of the American Chemical Society. 143, 39, p. 15975-15983 9 p.
    • The emerging landscape of single-molecule protein sequencing technologies Alfaro, J. A., Bohländer, P., Dai, M., Filius, M., Howard, C. J., van Kooten, X. F., Ohayon, S., Pomorski, A., Schmid, S., Aksimentiev, A., Anslyn, E. V., Bedran, G., Cao, C., Chinappi, M., Coyaud, E., Dekker, C., Dittmar, G., Drachman, N., Eelkema, R. and Goodlett, D. and 23 others, , Jun 2021, In: Nature Methods. 18, 6, p. 604-617 14 p.
    • The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition Lucas, F. L. R., Sarthak, K., Lenting, E. M., Coltan, D., Van Der Heide, N. J., Versloot, R. C. A., Aksimentiev, A. and Maglia, G., Jun 22 2021, In: ACS Nano. 15, 6, p. 9600-9613 14 p.
    • Translocation of DNA through Ultrathin Nanoslits Yang, W., Radha, B., Choudhary, A., You, Y., Mettela, G., Geim, A. K., Aksimentiev, A., Keerthi, A. and Dekker, C., Mar 18 2021, In: Advanced Materials. 33, 11, 2007682.

    2020

    • Artificial water channels enable fast and selective water permeation through water-wire networks Song, W., Joshi, H., Chowdhury, R., Najem, J. S., Shen, Y. X., Lang, C., Henderson, C. B., Tu, Y. M., Farell, M., Pitz, M. E., Maranas, C. D., Cremer, P. S., Hickey, R. J., Sarles, S. A., Hou, J. L., Aksimentiev, A. and Kumar, M., Jan 1 2020, In: Nature Nanotechnology. 15, 1, p. 73-79 7 p.
    • Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore Ouldali, H., Sarthak, K., Ensslen, T., Piguet, F., Manivet, P., Pelta, J., Behrends, J. C., Aksimentiev, A. and Oukhaled, A., Feb 1 2020, In: Nature Biotechnology. 38, 2, p. 176-181 6 p.
    • High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System Choudhary, A., Joshi, H., Chou, H.-Y., Sarthak, K., Wilson, J., Maffeo, C. and Aksimentiev, A., Nov 24 2020, In: ACS Nano. 14, 11, p. 15566-15576 11 p.
    • Molecular dynamics simulations of DNA–DNA and DNA–protein interactions Yoo, J., Winogradoff, D. and Aksimentiev, A., Oct 2020, In: Current Opinion in Structural Biology. 64, p. 88-96 9 p.
    • Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2Nanopore Shankla, M. and Aksimentiev, A., Jun 10 2020, In: ACS Applied Materials and Interfaces. 12, 23, p. 26624-26634 11 p.
    • MrDNA: A multi-resolution model for predicting the structure and dynamics of DNA systems Maffeo, C. and Aksimentiev, A., May 21 2020, In: Nucleic acids research. 48, 9, p. 5135-5146 12 p.
    • Polyhydrazide-Based Organic Nanotubes as Efficient and Selective Artificial Iodide Channels Roy, A., Joshi, H., Ye, R., Shen, J., Chen, F., Aksimentiev, A. and Zeng, H., Mar 16 2020, In: Angewandte Chemie - International Edition. 59, 12, p. 4806-4813 8 p.
    • Protein unfolding by SDS: The microscopic mechanisms and the properties of the SDS-protein assembly Winogradoff, D., John, S. and Aksimentiev, A., Mar 7 2020, In: Nanoscale. 12, 9, p. 5422-5434 13 p.
    • Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors Tripathi, P., Shuai, L., Joshi, H., Yamazaki, H., Fowle, W. H., Aksimentiev, A., Fenniri, H. and Wanunu, M., Jan 29 2020, In: Journal of the American Chemical Society. 142, 4, p. 1680-1685 6 p.
    • Scalable molecular dynamics on CPU and GPU architectures with NAMD Phillips, J. C., Hardy, D. J., Maia, J. D. C., Stone, J. E., Ribeiro, J. V., Bernardi, R. C., Buch, R., Fiorin, G., Hénin, J., Jiang, W., McGreevy, R., Melo, M. C. R., Radak, B. K., Skeel, R. D., Singharoy, A., Wang, Y., Roux, B., Aksimentiev, A., Luthey-Schulten, Z. and Kalé, L. V. and 3 others, , Jul 28 2020, In: Journal of Chemical Physics. 153, 4, 044130.
    • Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate Chou, H. Y. and Aksimentiev, A., Jun 18 2020, In: Journal of Physical Chemistry Letters. 11, 12, p. 4923-4929 7 p.
    • Tailoring Interleaflet Lipid Transfer with a DNA-based Synthetic Enzyme Sobota, D., Joshi, H., Ohmann, A., Aksimentiev, A., Aksimentiev, A., Keyser, U. F. and Keyser, U. F., Jun 10 2020, In: Nano letters. 20, 6, p. 4306-4311 6 p.

    2019

    • Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P. and Hunter, C. N. and 3 others, , Nov 14 2019, In: Cell. 179, 5, p. 1098-1111.e23
    • Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features Farell, M., Wetherington, M., Shankla, M., Chae, I., Subramanian, S., Kim, S. H., Aksimentiev, A., Robinson, J. and Kumar, M., Apr 2 2019, In: Langmuir. 35, 13, p. 4726-4735 10 p.
    • Controlling aggregation of cholesterol-modified DNA nanostructures Ohmann, A., Göpfrich, K., Joshi, H., Thompson, R. F., Sobota, D., Ranson, N. A., Aksimentiev, A. and Keyser, U. F., Dec 2 2019, In: Nucleic acids research. 47, 21, p. 11441-11451 11 p.
    • 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 Yang, Y., Alford, A., Kozlovskaya, V., Zhao, S., Joshi, H., Kim, E., Qian, S., Urban, V., Cropek, D., Aksimentiev, A. and Kharlampieva, E., Apr 12 2019, In: ACS Applied Polymer Materials. 1, 4, p. 722-736 15 p.
    • Electro-mechanical conductance modulation of a nanopore using a removable gate Zhao, S., Restrepo-Pérez, L., Soskine, M., Maglia, G., Joo, C., Dekker, C. and Aksimentiev, A., Feb 26 2019, In: ACS Nano. 13, 2, p. 2398-2409 12 p.
    • Molecular Mechanism of Spontaneous Nucleosome Unraveling Winogradoff, D. and Aksimentiev, A., Jan 18 2019, In: Journal of Molecular Biology. 431, 2, p. 323-335 13 p.
    • Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations Maffeo, C., Chou, H. Y. and Aksimentiev, A., May 1 2019, In: Advanced Theory and Simulations. 2, 5, 1800191.
    • Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model Wilson, J., Sarthak, K., Si, W., Gao, L. and Aksimentiev, A., Mar 22 2019, In: ACS Sensors. 4, 3, p. 634-644 11 p.
    • Single molecule analysis of structural fluctuations in DNA nanostructures Jepsen, M. D. E., Sørensen, R. S., Maffeo, C., Aksimentiev, A., Kjems, J. and Birkedal, V., Oct 21 2019, In: Nanoscale. 11, 39, p. 18475-18482 8 p.
    • Step-defect guided delivery of DNA to a graphene nanopore Shankla, M. and Aksimentiev, A., Sep 1 2019, In: Nature Nanotechnology. 14, 9, p. 858-865 8 p.

    2018

    • A practical guide to molecular dynamics simulations of DNA origami systems Yoo, J., Li, C. Y., Slone, S. M., Maffeo, C. and Aksimentiev, A., 2018, Methods in Molecular Biology. Humana Press Inc., p. 209-229 21 p. (Methods in Molecular Biology; vol. 1811).
    • A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes Ohmann, A., Li, C. Y., Maffeo, C., Al Nahas, K., Baumann, K. N., Göpfrich, K., Yoo, J., Keyser, U. F. and Aksimentiev, A., Dec 1 2018, In: Nature communications. 9, 1, 2426.
    • Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes Arnott, P. M., Joshi, H., Aksimentiev, A. and Howorka, S., Dec 11 2018, In: Langmuir. 34, 49, p. 15084-15092 9 p.
    • Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore Shi, X., Li, Q., Gao, R., Si, W., Liu, S. C., Aksimentiev, A. and Long, Y. T., Aug 16 2018, In: Journal of Physical Chemistry Letters. 9, 16, p. 4686-4694 9 p.
    • Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem Benson, C. R., Maffeo, C., Fatila, E. M., Liu, Y., Sheetz, E. G., Aksimentiev, A., Singharoy, A. and Flood, A. H., Sep 18 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 38, p. 9391-9396 6 p.
    • New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions Yoo, J. and Aksimentiev, A., 2018, In: Physical Chemistry Chemical Physics. 20, 13, p. 8432-8449 18 p.
    • Optical Voltage Sensing Using DNA Origami Hemmig, E. A., Fitzgerald, C., Maffeo, C., Hecker, L., Ochmann, S. E., Aksimentiev, A., Tinnefeld, P. and Keyser, U. F., Mar 14 2018, In: Nano letters. 18, 3, p. 1962-1971 10 p.
    • PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore Chowdhury, R., Ren, T., Shankla, M., Decker, K., Grisewood, M., Prabhakar, J., Baker, C., Golbeck, J. H., Aksimentiev, A., Kumar, M. and Maranas, C. D., Dec 1 2018, In: Nature communications. 9, 1, 3661.
    • Sequence-dependent DNA condensation as a driving force of DNA phase separation Kang, H., Yoo, J., Sohn, B. K., Lee, S. W., Lee, H. S., Ma, W., Kee, J. M., Aksimentiev, A. and Kim, H., Oct 12 2018, In: Nucleic acids research. 46, 18, p. 9401-9413 13 p.
    • Water-Compression Gating of Nanopore Transport Wilson, J. and Aksimentiev, A., Jun 26 2018, In: Physical review letters. 120, 26, 268101.

    2017

    • Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis Tian, K., Decker, K., Aksimentiev, A. and Gu, L. Q., Feb 28 2017, In: ACS Nano. 11, 2, p. 1204-1213 10 p.
    • Method and apparatus for controlling a flow of particles by way of a through-hole Aksimentiev, A. (Inventor), May 2 2017, U.S. Patent No. 9638661
    • Modulation of Molecular Flux Using a Graphene Nanopore Capacitor Shankla, M. and Aksimentiev, A., Apr 20 2017, In: Journal of Physical Chemistry B. 121, 15, p. 3724-3733 10 p.
    • Molecular mechanism of DNA association with single-stranded DNA binding protein Maffeo, C. and Aksimentiev, A., Dec 1 2017, In: Nucleic acids research. 45, 21, p. 12125-12139 15 p.
    • Nanopore Sensing of Protein Folding Si, W. and Aksimentiev, A., Jul 25 2017, In: ACS Nano. 11, 7, p. 7091-7100 10 p.
    • Nanoscale Ion Pump Derived from a Biological Water Channel Decker, K., Page, M. and Aksimentiev, A., Aug 24 2017, In: Journal of Physical Chemistry B. 121, 33, p. 7899-7906 8 p.
    • Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores Alibakhshi, M. A., Halman, J. R., Wilson, J., Aksimentiev, A., Afonin, K. A. and Wanunu, M., Oct 24 2017, In: ACS Nano. 11, 10, p. 9701-9710 10 p.
    • Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization Cressiot, B., Greive, S. J., Si, W., Pascoa, T. C., Mojtabavi, M., Chechik, M., Jenkins, H. T., Lu, X., Zhang, K., Aksimentiev, A., Antson, A. A. and Wanunu, M., Dec 26 2017, In: ACS Nano. 11, 12, p. 11931-11945 15 p.
    • Quantification of Membrane Protein-Detergent Complex Interactions Wolfe, A. J., Si, W., Zhang, Z., Blanden, A. R., Hsueh, Y. C., Gugel, J. F., Pham, B., Chen, M., Loh, S. N., Rozovsky, S., Aksimentiev, A. and Movileanu, L., Nov 9 2017, In: Journal of Physical Chemistry B. 121, 44, p. 10228-10241 14 p.
    • SDS-assisted protein transport through solid-state nanopores Restrepo-Pérez, L., John, S., Aksimentiev, A., Joo, C. and Dekker, C., Aug 28 2017, In: Nanoscale. 9, 32, p. 11685-11693 9 p.
    • Selective Permeability of Truncated Aquaporin 1 in Silico Decker, K., Page, M., Boyd, A., Macallister, I., Ginsberg, M. and Aksimentiev, A., Mar 13 2017, In: ACS Biomaterials Science and Engineering. 3, 3, p. 342-348 7 p.

    2016

    • De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation Maffeo, C., Yoo, J. and Aksimentiev, A., Mar 14 2016, In: Nucleic acids research. 44, 7, p. 3013-3019 7 p.
    • Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation Yoo, J., Kim, H., Aksimentiev, A. and Ha, T., Mar 22 2016, In: Nature communications. 7, 11045.
    • DNA sequence-dependent ionic currents in ultra-small solid-state nanopores Comer, J. and Aksimentiev, A., May 14 2016, In: Nanoscale. 8, 18, p. 9600-9613 14 p.
    • Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability Ngo, T. T. M., Yoo, J., Dai, Q., Zhang, Q., He, C., Aksimentiev, A. and Ha, T., Feb 24 2016, In: Nature communications. 7, 10813.
    • Graphene Nanopores for Protein Sequencing Wilson, J., Sloman, L., He, Z. and Aksimentiev, A., Jul 19 2016, In: Advanced Functional Materials. 26, 27, p. 4830-4838 9 p.
    • Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields Yoo, J., Wilson, J. and Aksimentiev, A., Oct 1 2016, In: Biopolymers. p. 752-763 12 p.
    • Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields Yoo, J. and Aksimentiev, A., Jan 12 2016, In: Journal of Chemical Theory and Computation. 12, 1, p. 430-443 14 p.
    • Ion channels made from a single membrane-spanning DNA duplex Göpfrich, K., Li, C. Y., Mames, I., Bhamidimarri, S. P., Ricci, M., Yoo, J., Mames, A., Ohmann, A., Winterhalter, M., Stulz, E., Aksimentiev, A. and Keyser, U. F., Jul 13 2016, In: Nano letters. 16, 7, p. 4665-4669 5 p.
    • Large-Conductance Transmembrane Porin Made from DNA Origami Göpfrich, K., Li, C. Y., Ricci, M., Bhamidimarri, S. P., Yoo, J., Gyenes, B., Ohmann, A., Winterhalter, M., Aksimentiev, A. and Keyser, U. F., Sep 27 2016, In: ACS Nano. 10, 9, p. 8207-8214 8 p.
    • Mechanical Trapping of DNA in a Double-Nanopore System Pud, S., Chao, S. H., Belkin, M., Verschueren, D., Huijben, T., Van Engelenburg, C., Dekker, C. and Aksimentiev, A., Dec 14 2016, In: Nano letters. 16, 12, p. 8021-8028 8 p.
    • Method and apparatus for controlling materials through a through-hole Aksimentiev, A. (Inventor), Aug 2 2016, U.S. Patent No. 9404909
    • Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores Belkin, M. and Aksimentiev, A., May 25 2016, In: ACS Applied Materials and Interfaces. 8, 20, p. 12599-12608 10 p.
    • Molecular mechanics of DNA bricks: In situ structure, mechanical properties and ionic conductivity Slone, S. M., Li, C. Y., Yoo, J. and Aksimentiev, A., May 1 2016, In: New Journal of Physics. 18, 5, 055012.
    • Nanopore Sequencing: Graphene Nanopores for Protein Sequencing (Adv. Funct. Mater. 27/2016) Wilson, J., Sloman, L., He, Z. and Aksimentiev, A., Jul 19 2016, In: Advanced Functional Materials. 26, 27, p. 4829 1 p.
    • Nanopore Sequencing: Graphene Nanopores for Protein Sequencing (Adv. Funct. Mater. 27/2016) Wilson, J., Sloman, L., He, Z. and Aksimentiev, A., Jul 19 2016, In: Advanced Functional Materials. 26, 27, p. 4829 1 p.
    • Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations Yoo, J. and Aksimentiev, A., Oct 6 2016, In: Journal of Physical Chemistry Letters. 7, 19, p. 3812-3818 7 p.
    • The hinge region strengthens the nonspecific interaction between lac-repressor and DNA: A computer simulation study Sun, L., Tabaka, M., Hou, S., Li, L., Burdzy, K., Aksimentiev, A., Maffeo, C., Zhang, X. and Holyst, R., Mar 2016, In: PloS one. 11, 3, e0152002.
    • The structure and intermolecular forces of DNA condensates Yoo, J. and Aksimentiev, A., Feb 15 2016, In: Nucleic acids research. 44, 5, p. 2036-2046 11 p.
    • Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore Bhattacharya, S., Yoo, J. and Aksimentiev, A., Apr 26 2016, In: ACS Nano. 10, 4, p. 4644-4651 8 p.

    2015

    • Highly permeable artificial water channels that can self-assemble into two-dimensional arrays Shen, Y. X., Si, W., Erbakan, M., Decker, K., De Zorzi, R., Saboe, P. O., Kang, Y. J., Majd, S., Butler, P. J., Walz, T., Aksimentiev, A., Hou, J. L., Kumar, M. and Weitz, D. A., Aug 11 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 32, p. 9810-9815 6 p.
    • Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA Carson, S., Wilson, J., Aksimentiev, A., Weigele, P. R. and Wanunu, M., Nov 17 2015, In: Nucleic acids research. 44, 5, p. 2085-2092 8 p.
    • Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field Li, C. Y., Hemmig, E. A., Kong, J., Yoo, J., Hernández-Ainsa, S., Keyser, U. F. and Aksimentiev, A., Feb 24 2015, In: ACS Nano. 9, 2, p. 1420-1433 14 p.
    • Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating Yoo, J. and Aksimentiev, A., Dec 3 2015, In: Journal of Physical Chemistry Letters. 6, 23, p. 4680-4687 8 p.
    • Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA Belkin, M., Chao, S. H., Jonsson, M. P., Dekker, C. and Aksimentiev, A., Nov 24 2015, In: ACS Nano. 9, 11, p. 10598-10611 14 p.
    • Slowing DNA transport using graphene-DNA interactions Banerjee, S., Wilson, J., Shim, J., Shankla, M., Corbin, E. A., Aksimentiev, A. and Bashir, R., Feb 11 2015, In: Advanced Functional Materials. 25, 6, p. 936-946 11 p.

    2014

    • A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment Maffeo, C., Ngo, T. T. M., Ha, T. and Aksimentiev, A., Aug 12 2014, In: Journal of Chemical Theory and Computation. 10, 8, p. 2891-2896 6 p.
    • A stabilized finite element method for modified Poisson-Nernst-Planck equations to determine ion flow through a nanopore Chaudhry, J. H., Comer, J., Aksimentiev, A. and Olson, L. N., Jan 2014, In: Communications in Computational Physics. 15, 1, p. 93-125 33 p.
    • Characterizing stretched polynucleotides in a synthetic nanopassage Timp, G. (Inventor), Timp, W. (Inventor), Mirsaidov, U. M. (Inventor), Aksimentiev, A. (Inventor) and Comer, J. R. (Inventor), Jun 10 2014, U.S. Patent No. 8748091
    • Close encounters with DNA Maffeo, C., Yoo, J., Comer, J., Wells, D. B., Luan, B. and Aksimentiev, A., Oct 15 2014, In: Journal of Physics Condensed Matter. 26, 41, 413101.
    • Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene Shankla, M. and Aksimentiev, A., 2014, In: Nature communications. 5, 5171.
    • Modeling thermophoretic effects in solid-state nanopores Belkin, M., Chao, S. H., Giannetti, G. and Aksimentiev, A., Dec 1 2014, In: Journal of Computational Electronics. 13, 4, p. 826-838 13 p.
    • Rectification of ion current in nanopores depends on the type of monovalent cations: Experiments and modeling Gamble, T., Decker, K., Plett, T. S., Pevarnik, M., Pietschmann, J. F., Vlassiouk, I., Aksimentiev, A. and Siwy, Z. S., May 8 2014, In: Journal of Physical Chemistry C. 118, 18, p. 9809-9819 11 p.
    • Smooth DNA transport through a narrowed pore geometry Carson, S., Wilson, J., Aksimentiev, A. and Wanunu, M., Nov 18 2014, In: Biophysical journal. 107, 10, p. 2381-2393 13 p.
    • Two structural scenarios for protein stabilization by PEG Chao, S. H., Matthews, S. S., Paxman, R., Aksimentiev, A., Gruebele, M. and Price, J. L., Jul 17 2014, In: Journal of Physical Chemistry B. 118, 28, p. 8388-8395 8 p.

    2013

    • In situ structure and dynamics of DNA origami determined through molecular dynamics simulations Yoo, J. and Aksimentiev, A., Dec 10 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 50, p. 20099-20104 6 p.
    • Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores Belkin, M., Maffeo, C., Wells, D. B. and Aksimentiev, A., Aug 27 2013, In: ACS Nano. 7, 8, p. 6816-6824 9 p.

    2012

    • Assessing graphene nanopores for sequencing DNA Wells, D. B., Belkin, M., Comer, J. and Aksimentiev, A., Aug 8 2012, In: Nano letters. 12, 8, p. 4117-4123 7 p.
    • Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations Yoo, J. and Aksimentiev, A., Nov 1 2012, In: Journal of Physical Chemistry B. 116, 43, p. 12946-12954 9 p.
    • DNA base-calling from a nanopore using a viterbi algorithm Timp, W., Comer, J. and Aksimentiev, A., May 16 2012, In: Biophysical journal. 102, 10, p. L37-L39
    • End-to-end attraction of duplex DNA Maffeo, C., Luan, B. and Aksimentiev, A., May 2012, In: Nucleic acids research. 40, 9, p. 3812-3821 10 p.
    • Improved parametrization of Li +, Na +, K +, and Mg 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems Yoo, J. and Aksimentiev, A., Jan 5 2012, In: Journal of Physical Chemistry Letters. 3, 1, p. 45-50 6 p.
    • Modeling and simulation of ion channels Maffeo, C., Bhattacharya, S., Yoo, J., Wells, D. and Aksimentiev, A., Dec 12 2012, In: Chemical reviews. 112, 12, p. 6250-6284 35 p.
    • Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence Bhattacharya, S., Derrington, I. M., Pavlenok, M., Niederweis, M., Gundlach, J. H. and Aksimentiev, A., Aug 28 2012, In: ACS Nano. 6, 8, p. 6960-6968 9 p.
    • Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores Wells, D. B., Bhattacharya, S., Carr, R., Maffeo, C., Ho, A., Comer, J. and Aksimentiev, A., 2012, Nanopore-Based Technology. Gracheva, M. E. (ed.). p. 165-186 22 p. (Methods in Molecular Biology; vol. 870).
    • Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution brownian dynamics Comer, J. and Aksimentiev, A., Feb 9 2012, In: Journal of Physical Chemistry C. 116, 5, p. 3376-3393 18 p.
    • Slowing down DNA translocation through a nanopore in lithium chloride Kowalczyk, S. W., Wells, D. B., Aksimentiev, A. and Dekker, C., Feb 8 2012, In: Nano letters. 12, 2, p. 1038-1044 7 p.
    • Toward detection of DNA-bound proteins using solid-state nanopores: Insights from computer simulations Comer, J., Ho, A. and Aksimentiev, A., Dec 2012, In: Electrophoresis. 33, 23, p. 3466-3479 14 p.

    2011

    • Atoms-to-microns model for small solute transport through sticky nanochannels Carr, R., Comer, J., Ginsberg, M. D. and Aksimentiev, A., Nov 21 2011, In: Lab on a chip. 11, 22, p. 3766-3773 8 p.
    • Control of nanoscale environment to improve stability of immobilized proteins on diamond surfaces Radadia, A. D., Stavis, C. J., Carr, R., Zeng, H., King, W. P., Carlisle, J. A., Aksimentiev, A., Hamers, R. J. and Bashir, R., Mar 22 2011, In: Advanced Functional Materials. 21, 6, p. 1040-1050 11 p.
    • Lipid bilayer coated Al2O3 nanopore sensors: Towards a hybrid biological solid-state nanopore Venkatesan, B. M., Polans, J., Comer, J., Sridhar, S., Wendell, D., Aksimentiev, A. and Bashir, R., Aug 2011, In: Biomedical microdevices. 13, 4, p. 671-682 12 p.
    • Microscopic perspective on the adsorption isotherm of a heterogeneous surface Carr, R., Comer, J., Ginsberg, M. D. and Aksimentiev, A., Jul 21 2011, In: Journal of Physical Chemistry Letters. 2, 14, p. 1804-1807 4 p.
    • Modeling Nanopores for Sequencing DNA Comer, J. R., Wells, D. B. and Aksimentiev, A., 2011, Methods in Molecular Biology. Humana Press Inc., p. 317-358 42 p. (Methods in Molecular Biology; vol. 749).
    • Modeling pressure-driven transport of proteins through a nanochannel Carr, R., Comer, J., Ginsberg, M. D. and Aksimentiev, A., Jan 2011, In: IEEE Transactions on Nanotechnology. 10, 1, p. 75-82 8 p., 5535187.
    • Nanopore analysis of individual RNA/antibiotic complexes Wanunu, M., Bhattacharya, S., Xie, Y., Tor, Y., Aksimentiev, A. and Drndic, M., Dec 27 2011, In: ACS Nano. 5, 12, p. 9345-9353 9 p.
    • Rectification of the current in a-hemolysin pore depends on the cation type: The alkali series probed by molecular dynamics simulations and experiments Bhattacharya, S., Muzard, J., Payet, L., Mathé, J., Bockelmann, U., Aksimentiev, A. and Viasnoff, V., Mar 17 2011, In: Journal of Physical Chemistry C. 115, 10, p. 4255-4264 10 p.
    • Surface functionalization of thin-film diamond for highly stable and selective biological interfaces Stavis, C., Clare, T. L., Butler, J. E., Radadia, A. D., Carr, R., Zeng, H., King, W. P., Carlisle, J. A., Aksimentiev, A., Bashir, R. and Hamers, R. J., Jan 18 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 3, p. 983-988 6 p.

    2010

    • Control and reversal of the electrophoretic force on DNA in a charged nanopore Luan, B. and Aksimentiev, A., Nov 17 2010, In: Journal of Physics Condensed Matter. 22, 45, 454123.
    • Deciphering ionic current signatures of DNA transport through a nanopore Aksimentiev, A., 2010, In: Nanoscale. 2, 4, p. 468-483 16 p.
    • DNA-DNA interactions in tight supercoils are described by a small effective charge density Maffeo, C., Schöpflin, R., Brutzer, H., Stehr, R., Aksimentiev, A., Wedemann, G. and Seidel, R., Oct 4 2010, In: Physical review letters. 105, 15, 158101.
    • Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes Luan, B. and Aksimentiev, A., 2010, In: Soft Matter. 6, 2, p. 243-246 4 p.
    • Mechanical properties of a complete microtubule revealed through molecular dynamics simulation Wells, D. B. and Aksimentiev, A., Jul 21 2010, In: Biophysical journal. 99, 2, p. 629-637 9 p.
    • Nanopore sequencing: Electrical measurements of the code of life Timp, W., Mirsaidov, U. M., Wang, D., Comer, J., Aksimentiev, A. and Timp, G., May 2010, In: IEEE Transactions on Nanotechnology. 9, 3, p. 281-294 14 p., 5422648.
    • 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. Maffeo, C. and Aksimentiev, A., Sep 2010, In: Physics of Life Reviews. 7, 3, p. 353-354 2 p.
    • Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix Mirsaidov, U., Comer, J., Dimitrov, V., Aksimentiev, A. and Timp, G., Oct 1 2010, In: Nanotechnology. 21, 39, 395501.
    • The effect of calciumi on the confomation of cobalamin transporter BtuB Luan, B., Carr, R., Caffrey, M. and Aksimentiev, A., 2010, In: Proteins: Structure, Function and Bioinformatics. 78, 5, p. 1153-1162 10 p.

    2009

    • Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore Dorvel, B., Sigalov, G., Zhao, Q., Comer, J., Dimitrov, V., Mirsaidov, U., Aksimentiev, A. and Timp, G., 2009, In: Nucleic acids research. 37, 12, p. 4170-4179 10 p.
    • Ionic cürrent rectification through silica nanopores Cruz-Chu, E. R., Aksimentiev, A. and Schulten, K., Feb 5 2009, In: Journal of Physical Chemistry C. 113, 5, p. 1850-1862 13 p.
    • Microscopic mechanics of hairpin DNA translocation through synthetic nanopores Comer, J., Dimitrov, V., Zhao, Q., Timp, G. and Aksimentiev, A., Jan 21 2009, In: Biophysical journal. 96, 2, p. 593-608 16 p.
    • Modeling transport through synthetic nanopores: Simulating biomolecules in synthetic nanopores presents various challenges Aksimentiev, A., Brunner, R. K., Cruz-Chú, E., Comer, J. and Schulten, K. J., May 26 2009, IEEE Nanotechnology Magazine. 1 ed. Vol. 3. p. 20-28 9 p.
    • Structure, dynamics, and ion conductance of the phospholamban pentamer Maffeo, C. and Aksimentiev, A., 2009, In: Biophysical journal. 96, 12, p. 4853-4865 13 p.

    2008

    • Computer modeling in biotechnology: A partner in development Aksimentiev, A., Brunner, R. K., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., Rajan, A., Shih, A., Sigalov, G., Yin, Y. and Schulten, K., 2008, In: Methods in Molecular Biology. 474, p. 181-234 54 p.
    • Detection of DNA sequences using an alternating electric field in a nanopore capacitor Sigalov, G., Comer, J., Timp, G. and Aksimentiev, A., Jan 2008, In: Nano letters. 8, 1, p. 56-63 8 p.
    • DNA attraction in monovalent and divalent electrolytes Luan, B. and Aksimentiev, A., Nov 26 2008, In: Journal of the American Chemical Society. 130, 47, p. 15754-15755 2 p.
    • Electro-osmotic screening of the DNA charge in a nanopore Luan, B. and Aksimentiev, A., Aug 26 2008, In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 78, 2, 021912.
    • In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin Cherezov, V., Liu, W., Derrick, J. P., Luan, B., Aksimentiev, A., Katritch, V. and Caffrey, M., Apr 2008, In: Proteins: Structure, Function and Genetics. 71, 1, p. 24-34 11 p.
    • Strain softening in stretched DNA Luan, B. and Aksimentiev, A., Sep 10 2008, In: Physical review letters. 101, 11, 118101.
    • Stretching and unzipping nucleic acid hairpins using a synthetic nanopore Zhao, Q., Comer, J., Dimitrov, V., Yemenicioglu, S., Aksimentiev, A. and Timp, G., Mar 2008, In: Nucleic acids research. 36, 5, p. 1532-1541 10 p.
    • Synthetic ion channels via self-assembly: A route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes Carr, R., Weinstock, I. A., Sivaprasadarao, A., Müller, A. and Aksimentiev, A., Nov 2008, In: Nano letters. 8, 11, p. 3916-3921 6 p.

    2007

    • Detecting SNPs using a synthetic nanopore Zhao, Q., Sigalov, G., Dimitrov, V., Dorvel, B., Mirsaidov, U., Sligar, S., Aksimentiev, A. and Timp, G., Jun 2007, In: Nano letters. 7, 6, p. 1680-1685 6 p.
    • Exploring transmembrane transport through a -hemolysin with grid-steered molecular dynamics Wells, D. B., Abramkina, V. and Aksimentiev, A., 2007, In: Journal of Chemical Physics. 127, 12, 125101.
    • Structure refinement of the OpcA adhesin using molecular dynamics Luan, B., Caffrey, M. and Aksimentiev, A., Nov 2007, In: Biophysical journal. 93, 9, p. 3058-3069 12 p.

    2006

    • Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor Gracheva, M. E., Aksimentiev, A. and Leburton, J. P., Jul 14 2006, In: Nanotechnology. 17, 13, p. 3160-3165 6 p., 014.
    • Exploring the prospects for a nanometer-scale gene chip Dimitrov, V., Aksimentiev, A., Schulten, K., Heng, J., Sorsch, T., Mansfield, W., Miner, J., Watson, G. P., Cirelli, R., Klemens, F., Bower, J., Ferry, E., Taylor, A., Kornblit, A., Dorvel, B., Zhao, Q. and Timp, G., 2006, 2006 International Electron Devices Meeting Technical Digest, IEDM. 4154422. (Technical Digest - International Electron Devices Meeting, IEDM).
    • The electromechanics of DNA in a synthetic nanopore Heng, J. B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y. V., Sligar, S., Schulten, K. and Timp, G., Feb 2006, In: Biophysical journal. 90, 3, p. 1098-1106 9 p.
    • The role of molecular modeling in bionanotechnology Lu, D., Aksimentiev, A., Shih, A. Y., Cruz-Chu, E., Freddolino, P. L., Arkhipov, A. and Schulten, K., Mar 1 2006, In: Physical Biology. 3, 1, p. S40-S53
    • Water-silica force field for simulating nanodevices Cruz-Chu, E. R., Aksimentiev, A. and Schulten, K., Nov 2 2006, In: Journal of Physical Chemistry B. 110, 43, p. 21497-21508 12 p.

    2005

    • Beyond the gene chip Heng, J. B., Aksimentiev, A., Ho, C., Dimitrov, V., Sorsch, T. W., Miner, J. F., Mansfield, W. M., Schulten, K. and Timp, G., 2005, In: Bell System Technical Journal. 10, 3, p. 5-22 18 p.
    • Imaging a-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map Aksimentiev, A. and Schulten, K., Jun 2005, In: Biophysical journal. 88, 6, p. 3745-3761 17 p.
    • Molecular dynamics simulations of proteins in lipid bilayers Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E. and Schulten, K., Aug 2005, In: Current Opinion in Structural Biology. 15, 4, p. 423-431 9 p.
    • Orientation discrimination of single-stranded DNA inside the a-hemolysin membrane channel Mathé, J., Aksimentiev, A., Nelson, D. R., Schulten, K. and Meller, A., Aug 30 2005, In: Proceedings of the National Academy of Sciences of the United States of America. 102, 35, p. 12377-12382 6 p.
    • Stretching DNA using the electric field in a synthetic nanopore Heng, J. B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y. V., Sligar, S., Schulten, K. and Timp, G., Oct 2005, In: Nano letters. 5, 10, p. 1883-1888 6 p.

    2004

    • Extending molecular modeling methodology to study insertion of membrane nanopores Aksimentiev, A. and Schulten, K., Mar 30 2004, In: Proceedings of the National Academy of Sciences of the United States of America. 101, 13, p. 4337-4338 2 p.
    • Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase Aksimentiev, A., Balabin, I. A., Fillingame, R. H. and Schulten, K., Mar 2004, In: Biophysical journal. 86, 3, p. 1332-1344 13 p.
    • Microscopic kinetics of DNA translocation through synthetic nanopores Aksimentiev, A., Heng, J. B., Timp, G. and Schulten, K., Sep 2004, In: Biophysical journal. 87, 3, p. 2086-2097 12 p.
    • Sizing DNA using a nanometer-diameter pore. Heng, J. B., Ho, C., Kim, T., Timp, R., Aksimentiev, A., Grinkova, Y. V., Sligar, S., Schulten, K. and Timp, G., Oct 2004, In: Biophysical journal. 87, 4, p. 2905-2911 7 p.

    2003

    • Large scale simulation of protein mechanics and function Tajkhorshid, E., Aksimentiev, A., Balabin, I., Gao, M., Isralewitz, B., Phillips, J. C., Zhu, F. and Schulten, K. J., 2003, In: Advances in Protein Chemistry. 66, p. 195-247 53 p.

    2002

    • Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulations, and measurements Aksimentiev, A., Fialkowski, M. and Holyst, R., 2002, In: Advances in Chemical Physics. 121, p. 141-239 99 p.

    2001

    • Application of the Euler characteristic to the study of homopolymer blends and copolymer melts Aksimentiev, A. and Holyst, R., 2001, In: Polimery/Polymers. 46, 5, p. 307-322 16 p.
    • Morphological transformations during phase-separation/ordering phenomena Aksimentiev, A., 2001, In: Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals. 366, p. 893-900 8 p.
    • Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems Fialkowski, M., Aksimentiev, A. and Holyst, R., Jan 8 2001, In: Physical review letters. 86, 2, p. 240-243 4 p.

    2000

    • Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends Aksimentiev, A. and Holyst, R., 2000, In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 62, 5, p. 6821-6830 10 p.
    • Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends Aksimentiev, A., Holyst, R. and Moorthi, K., 2000, In: Macromolecular Theory and Simulations. 9, 8, p. 661-674 14 p.
    • Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends Aksimentiev, A., Moorthi, K. and Holyst, R., Apr 1 2000, In: Journal of Chemical Physics. 112, 13, p. 6049-6062 14 p.
    • Spinodal decomposition of homopolymer blends: Geometrical properties of the interface Aksimentiev, A., Moorthi, K. and Holyst, R., 2000, In: Progress of Theoretical Physics Supplement. 138, p. 398-399 2 p.

    1999

    • Diffusion on curved, periodic surfaces Holyst, R., Plewczynski, D., Aksimentiev, A. and Burdzy, K., 1999, In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60, 1, p. 302-307 6 p.
    • Phase behavior of gradient copolymers Aksimentiev, A. and Holyst, R., Aug 1 1999, In: Journal of Chemical Physics. 111, 5, p. 2329-2339 11 p.
    • Single chain conformations in the system of symmetric and asymmetric diblock copolymers Aksimentiev, A. and Holyst, R., Jul 1999, In: Macromolecular Theory and Simulations. 8, 4, p. 328-342 15 p.
    • Single-chain statistics in polymer systems Aksimentiev, A. and Holyst, R., Sep 1999, In: Progress in Polymer Science (Oxford). 24, 7, p. 1045-1093 49 p.

    1998

    • Swelling and shrinking of polymer chains in homopolymer blends Aksimentiev, A. and Holyst, R., Sep 1998, In: Macromolecular Theory and Simulations. 7, 5, p. 447-456 10 p.