Aleksei Aksimentiev's directory photo.

Aleksei Aksimentiev


Primary Affiliation

Theoretical and Computational Biophysics


Status Part-time Faculty

Home Department of Physics

Phone 333-6495


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.


    • 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

    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. Which includes four key themes:

    • Nanopore systems for single molecule detection and manipulation

    • Molecular mechanics of DNA processing machinery

    • The physics of DNA assemblies

    • Synthetic molecular systems

  • 2016

    • Belkin, M.; Aksimentiev, A., Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Applied Materials & Interfaces 2016, 8, (20), 12599-12608, DOI:10.1021/ACSami.6b00463.
    • Bhattacharya, S.; Yoo, J.; Aksimentiev, A., Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore. ACS Nano 2016, 10, (4), 4644-4651, DOI:10.1021/ACSnano.6b00940.
    • Carson, S.; Wilson, J.; Aksimentiev, A.; Weigele, P. R.; Wanunu, M., Hydroxymethyluracil Modifications Enhance the Flexibility and Hydrophilicity of Double-Stranded DNA. Nucleic Acids Research 2016, 44, (5), 2085-2092, DOI:10.1093/nar/gkv1199.
    • Comera, J.; Aksimentiev, A., DNA Sequence-Dependent Ionic Currents in Ultra-Small Solid-State Nanopores. Nanoscale 2016, 8, (18), 9600-9613, DOI:10.1039/c6nr01061j.
    • Maffeo, C.; Yoo, J.; Aksimentiev, A., De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation. Nucleic Acids Research 2016, 44, (7), 3013-3019, DOI:10.1093/nar/gkw155.
    • Ngo, T. T. M.; Yoo, J.; Dai, Q.; Zhang, Q.; He, C.; Aksimentiev, A.; Ha, T., Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability. Nature Communications 2016, 7, DOI:ARTN 10813 10.1038/ncomms10813.
    • Slone, S. M.; Li, C. Y.; Yoo, J.; Aksimentiev, A., Molecular Mechanics of DNA Bricks: In situ Structure, Mechanical Properties and Ionic Conductivity. New Journal of Physics 2016, 18, DOI:Artn 055012 10.1088/1367-2630/18/5/055012.
    • Sun, L. L.; Tabaka, M.; Hou, S.; Li, L.; Burdzy, K.; Aksimentiev, A.; Maffeo, C.; Zhang, X. Z.; Holyst, R., The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. Plos One 2016, 11, (3), DOI:10.1371/journal.pone.0152002.
    • Tian, K.; Decker, K.; Aksimentiev, A.; Gu, L. Q., Microcarrier-Guided Nanopore Dielectrophoresis for Selective Nucleic Acid Detection. Biophysical Journal 2016, 110, (3), 502a-502a.
    • Wilson, J.; Sloman, L.; He, Z. R.; Aksimentiev, A., Graphene Nanopores for Protein Sequencing. Biophysical Journal 2016, 110, (3), 326a-326a.
    • Yoo, J.; Aksimentiev, A., Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields. Biophysical Journal 2016, 110, (3), 646a-646a.
    • Yoo, J.; Aksimentiev, A., 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 2016, 12, (1), 430-443, DOI:10.1021/ACS.jctc.5b00967.
    • Yoo, J.; Aksimentiev, A., The Structure and Intermolecular Forces of DNA Condensates. Nucleic Acids Research 2016, 44, (5), 2036-2046, DOI:10.1093/nar/gkw081.
    • Yoo, J.; Kim, H.; Aksimentiev, A.; Ha, T., Direct Evidence for Sequence-Dependent Attraction between Double-Stranded DNA Controlled by Methylation. Nature Communications 2016, 7, DOI:ARTN 11045 10.1038/ncomms11045.
    • Yoo, J.; Kim, H.; Ha, T.; Aksimentiev, A., Effector-Free Molecular Mechanism of Epigenetic Regulation Revealed by Molecular Dynamics Simulations and Single-Molecule Fret Experiments. Biophysical Journal 2016, 110, (3), 561a-562a.
    • Yoo, J.; Li, C. Y.; Aksimentiev, A., Membrane-Spanning DNA Ion Channels: Conductance Mechanism, Electro-Osmotic Transport and Mechanical Gating. Biophysical Journal 2016, 110, (3), 119a-119a.


    • Banerjee, S.; Wilson, J.; Shim, J.; Shankla, M.; Corbin, E. A.; Aksimentiev, A.; Bashir, R., Slowing DNA Transport Using Graphene-DNA Interactions. Advanced Functional Materials 2015, 25, (6), 936-946, DOI: 10.1002/adfm.201403719.
    • Belkin, M.; Chao, S. H.; Jonsson, M. P.; Dekker, C.; Aksimentiev, A., Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 2015, 9, (11), 10598-10611, DOI:10.1021/ACSnano.5b04173.
    • Carson, S.; Wilson, J.; Aksimentiev, A.; Wanunu, M., Smooth DNA Transport through a Narrowed Pore Geometry. Biophysical Journal 2015, 108, (2), 331a-331a.
    • Li, C. Y.; Hemmig, E. A.; Kong, J. L.; Yoo, J.; Hernandez-Ainsa, S.; Keyser, U. F.; Aksimentiev, A., Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field. ACS Nano 2015, 9, (2), 1420-1433, DOI: 10.1021/Nn505825z.
    • 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.; Houb, J. L.; Kumar, M., Highly Permeable Artificial Water Channels That Can Self-Assemble into Two-Dimensional Arrays. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, (32), 9810-9815, DOI:10.1073/pnas.1508575112.
    • Yoo, J.; Aksimentiev, A., Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating. Journal of Physical Chemistry Letters 2015, 6, (23), 4680-4687, DOI:10.1021/ACS.jpclett.5b01964.


    • Belkin, M.; Chao, S. H.; Giannetti, G.; Aksimentiev, A., Modeling Thermophoretic Effects in Solid-State Nanopores. Journal of Computational Electronics 2014, 13, (4), 826-838, DOI: 10.1007/s10825-014-0594-8.
    • Carson, S.; Wilson, J.; Aksimentiev, A.; Wanunu, M., Smooth DNA Transport through a Narrowed Pore Geometry. Biophysical Journal 2014, 107, (10), 2381-2393, DOI: 10.1016/j.bpj.2014.10.017.
    • Chao, S. H.; Matthews, S. S.; Paxman, R.; Aksimentiev, A.; Gruebele, M.; Price, J. L., Two Structural Scenarios for Protein Stabilization by PEG. Journal of Physical Chemistry B 2014, Published Online.
    • Chaudhry, J. H.; Comer, J.; Aksimentiev, A.; Olson, L. N., A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow through a Nanopore. Communications in Computational Physics 2014, 15, (1), 93-125, DOI: 10.4208/cicp.101112.100413a.
    • Gamble, T.; Decker, K.; Plett, T. S.; Pevarnik, M.; Pietschmann, J. F.; Vlassiouk, I.; Aksimentiev, A.; Siwy, Z. S., Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling. Journal of Physical Chemistry C 2014, 118, (18), 9809-9819, DOI: 10.1021/jp501492g.
    • Maffeo, C.; Ngo, T. M.; Ha, T.; Aksimentiev, A., A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment. Journal of Chemical Theory and Computation 2014, Published Online.
    • Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A., Close Encounters with DNA. Journal of Physics-Condensed Matter 2014, 26, (41), DOI:Artn 413101 Doi 10.1088/0953-8984/26/41/413101.
    • Shankla, M.; Aksimentiev, A., Conformational Transitions and Stop-and-Go Nanopore Transport of Single-Stranded DNA on Charged Graphene. Nature Communications 2014, 5, DOI:Artn 5171 Doi 10.1038/Ncomms6171.


    • Belkin, M.; Maffeo, C.; Wells, D. B.; Aksimentiev, A., Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores. ACS Nano 2013, 7, (8), 6816-6824, DOI: 10.1021/nn403575n.
    • Yoo, J.; Aksimentiev, A., In Situ Structure and Dynamics of DNA Origami Determined through Molecular Dynamics Simulations. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (50), 20099-20104, DOI: 10.1073/pnas.1316521110.


    • Bhattacharya, S.; Derrington, I. M.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H.; Aksimentiev, A., Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence. ACS Nano 2012, 6, (8), 6960-6968.
    • Comer, J.; Ho, A.; Aksimentiev, A., Toward Detection of DNA-Bound Proteins Using Solid-State Nanopores: Insights from Computer Simulations. Electrophoresis 2012, 33, (23), 3466-3479.
    • Kowalczyk, S. W.; Wells, D. B.; Aksimentiev, A.; Dekker, C., Slowing Down DNA Translocation through a Nanopore in Lithium Chloride. Nano Letters 2012, 12, (2), 1038-1044.
    • Maffeo, C.; Bhattacharya, S.; Yoo, J.; Wells, D.; Aksimentiev, A., Modeling and Simulation of Ion Channels. Chemical Reviews 2012, 112, (12), 6250-6284.
    • Maffeo, C.; Luan, B. Q.; Aksimentiev, A., End-to-End Attraction of Duplex DNA. Nucleic Acids Research 2012, 40, (9), 3812-3821.
    • Timp, W.; Comer, J.; Aksimentiev, A., DNA Base-Calling from a Nanopore Using a Viterbi Algorithm. Biophysical Journal 2012, 102, (10), L37-L39.
    • Wells, D. B.; Belkin, M.; Comer, J.; Aksimentiev, A., Assessing Graphene Nanopores for Sequencing DNA. Nano Letters 2012, 12, (8), 4117-4123.
    • Wells, D. B.; Bhattacharya, S.; Carr, R.; Maffeo, C.; Ho, A.; Comer, J.; Aksimentiev, A., Optimization of the Molecular Dynamics Method for Simulations of DNA and Ion Transport through Biological Nanopores, In Nanopore-Based Technology: Single Molecule Characterization and DNA Sequencing; Gracheva, M. E., Ed.; Humana Press, 2012; Vol. 870, 165-186.
    • Yoo, J. J.; Aksimentiev, A., Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems. Journal of Physical Chemistry Letters 2012, 3, (1), 45-50.
    • Yoo, J.; Aksimentiev, A., Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations. Journal of Physical Chemistry B 2012, 116, (43), 12946-12954.


    • Bhattacharya, S.; Muzard, J.; Payet, L.; Mathe, J.; Bockelmann, U.; Aksimentiev, A.; Viasnoff, V., Rectification of the Current in alpha-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments. Journal of Physical Chemistry C 2011, 115, (10), 4255-4264. 
    • Carr, R.; Comer, J.; Aksimentiev, A., Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems, In Simulations in Nanobiotechnology; Eom, K., Ed.; CRC Press, 2011, Ch. 2, 43-60.
    • Carr, R.; Comer, J.; Ginsberg, M. D.; Aksimentiev, A., Atoms-to-Microns Model for Small Solute Transport through Sticky Nanochannels. Lab on a Chip 2011, 11, (22), 3766-3773.
    • Carr, R.; Comer, J.; Ginsberg, M. D.; Aksimentiev, A., Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface. Journal of Physical Chemistry Letters 2011, 2, (14), 1804-1807.
    • Carr, R.; Comer, J.; Ginsberg, M. D.; Aksimentiev, A., Modeling Pressure-Driven Transport of Proteins Through a Nanochannel. IEEE Transactions on Nanotechnology 2011, 10, (1), 75-82. 
    • Comer, J. R.; Wells, D. B.; Aksimentiev, A., Modeling Nanopores for Sequencing DNA, In DNA Nanotechnology: Methods and Protocols; Zuccheri, G., Samori, B., Eds. 2011; Vol. 749, 317-358.
    • Comer, J.; Aksimentiev, A. Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations, 2011, 335-356.
    • Radadia, A. D.; Stavis, C. J.; Carr, R.; Zeng, H. J.; King, W. P.; Carlisle, J. A.; Aksimentiev, A.; Hamers, R. J.; Bashir, R., Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces. Advanced Functional Materials 2011, 21, (6), 1040-1050. 
    • Stavis, C.; Clare, T. L.; Butler, J. E.; Radadia, A. D.; Carr, R.; Zeng, H. J.; King, W. P.; Carlisle, J. A.; Aksimentiev, A.; Bashir, R.; Hamers, R. J., Surface functionalization of thin-film diamond for highly stable and selective biological interfaces. Proceedings of the National Academy of Sciences of the United States of America 2011, 108, (3), 983-988. 
    • Timp, G.; Mirsaidov, U.; Timp, W.; Shim, J.; Wang, D. Q.; Dimitrov, V.; Scrimgeour, J.; Lin, C. C.; Comer, J.; Ho, A. H.; Zou, X. Q.; Aksimentiev, A.; Schulten, K. Third Generation DNA Sequencing with a Nanopore, 2011, 287-311.
    • Venkatesan, B. M.; Polans, J.; Comer, J.; Sridhar, S.; Wendell, D.; Aksimentiev, A.; Bashir, R., Lipid Bilayer Coated Al2O3 Nanopore Sensors: Towards a Hybrid Biological Solid-State Nanopore. Biomedical Microdevices 2011, 13, (4), 671-682.
    • Wanunu, M.; Bhattacharya, S.; Xie, Y.; Tor, Y.; Aksimentiev, A.; Drndic, M., Nanopore Analysis of Individual Rna/Antibiotic Complexes. ACS Nano 2011, 5, (12), 9345-9353.


    • Aksimentiev, A., Deciphering ionic current signatures of DNA transport through a nanopore. Nanoscale 2010, 2, (4), 468-483.
    • Luan, B. Q.; Aksimentiev, A., Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes. Soft Matter 2010, 6, (2), 243-246.
    • Luan, B. Q.; Carr, R.; Caffrey, M.; Aksimentiev, A., The effect of calcium on the conformation of cobalamin transporter BtuB. Proteins-Structure Function and Bioinformatics 2010, 78, (5), 1153-1162.
    • Timp, W.; Mirsaidov, U. M.; Wang, D. Q.; Comer, J.; Aksimentiev, A.; Timp, G., Nanopore Sequencing: Electrical Measurements of the Code of Life. IEEE Transactions on Nanotechnology 2010, 9, (3), 281-294.
    • Luan, B. Q.; Aksimentiev, A., Control and reversal of the electrophoretic force on DNA in a charged nanopore. Journal of Physics-Condensed Matter 2010, 22, (45).
    • Maffeo, C.; Aksimentiev, A., 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. Physics of Life Reviews 2010, 7, (3), 353-354.
    • Maffeo, C.; Schopflin, R.; Brutzer, H.; Stehr, R.; Aksimentiev, A.; Wedemann, G.; Seidel, R., DNA-DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density. Physical Review Letters 2010, 105, (15).
    • Mirsaidov, U.; Comer, J.; Dimitrov, V.; Aksimentiev, A.; Timp, G., Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix. Nanotechnology 2010, 21, (39).
    • Wells, D. B.; Aksimentiev, A., Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation. Biophysical Journal 2010, 99, (2), 629-637. 


    • Dorvel, B.; Sigalov, G.; Zhao, Q.; Comer, J.; Dimitrov, V.; Mirsaidov, U.; Aksimentiev, A.; Timp, G., Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore. Nucleic Acids Research 2009, 37, (12), 4170-4179.
    • Aksimentiev, A.; Brunner, R.; Cruz-Chu, E. R.; Comer, J.; Schulten, K., Modeling Transport Through Synthetic Nanopores. IEEE Nanotechnology Magazine 2009, 3, 21-28.
    • Comer, J.; Dimitrov, V.; Zhao, Q.; Timp, G.; Aksimentiev, A., Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores. Biophysical Journal 2009, 96, (2), 593-608.
    • Cruz-Chu, E. R.; Aksimentiev, A.; Schulten, K., Ionic Current Rectification through Silica Nanopores. Journal of Physical Chemistry C 2009, 113, (5), 1850-1862.
    • Maffeo, C.; Aksimentiev, A., Structure, dynamics, and ion conductance of a phospholamban pentamer. Biophysical Journal 2009, 96, 4853–4865.


    • Aksimentiev, A.; Brunner, R.; Cohen, J.; Comer, J.; Cruz-Chu, E.; Hardy, D.; Rajan, A.; Shih, A.; Sigalov, G.; Yin, Y.; Schulten, K., Computer Modeling in Biotechnology, a Partner in Development. In Protocols in Nanostructure Design, Methods in Molecular Biology, Humana Press: 2008; pp 181-234.
    • Carr, R.; Weinstock, I. A.; Sivaprasadarao, A.; Muller, A.; Aksimentiev, A., Synthetic Ion Channels via Self-Assembly: A Route for Embedding Porous Polyoxometalate Nanocapsules in Lipid Bilayer Membranes. Nano Letters 2008, 8, (11), 3916-3921.
    • Cherezov, V.; Liu, W.; Derrick, J. P.; Luan, B.; Aksimentiev, A.; Katritch, V.; Caffrey, M., In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA out membrane adhesin. Proteins-Structure Function and Bioinformatics 2008, 71, (1), 24-34.
    • Luan, B. Q.; Aksimentiev, A., Electro-osmotic screening of the DNA charge in a nanopore. Physical Review E 2008, 78, (2).
    • Luan, B.; Aksimentiev, A., DNA Attraction in Monovalent and Divalent Electrolytes. Journal of the American Chemical Society 2008, 130, (47), 15754-+.
    • Luan, B.; Aksimentiev, A., Strain softening in stretched DNA. Physical Review Letters 2008, 101, (11).
    • Sigalov, G.; Comer, J.; Timp, G.; Aksimentiev, A., Detection of DNA sequences using an alternating electric ?eld in a nanopore capacitor. Nano Letters 2008, 8, (56-63).
    • Zhao, Q.; Comer, J.; Dimitrov, V.; Yemenicioglu, S.; Aksimentiev, A.; Timp, G., Stretching and unzipping nucleic acid hairpins using a synthetic nanopore. Nucleic Acids Research 2008, 36, (5), 1532-1541.


    • Cruz, E.; Aksimentiev, A.; Schulten, K., Computational studies of ionic conduction through silica nanopores. Biophysical Journal 2007, 651A-651A.
    • Luan, B. Q.; Caffrey, M.; Aksimentiev, A., Structure refinement of the OpcA adhesin using molecular dynamics. Biophysical Journal 2007, 93, (9), 3058-3069.
    • Luan, B.; Cherezov, V.; Liu, W.; Moore, J.; Derrick, J.; Caffrey, M.; Aksimentiev, A. Refining X-ray structures of the adhesin OpcA with molecular dynamics. Biophysical Journal 2007, 5A-5A.
    • Wells, D. B.; Abramkina, V.; Aksimentiev, A., Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics. Journal of Chemical Physics 2007, 127, (12).
    • Zhao, Q.; Sigalov, G.; Dimitrov, V.; Dorvel, B.; Mirsaidov, U.; Sligar, S.; Aksimentiev, A.; Timp, G. Detecting SNPs using a synthetic nanopore. Nano Letters 2007, 6, 1680-1685.


    • Cruz-Chu, E. R.; Aksimentiev, A.; Schulten, K. (2006), "Water-silica force field for simulating nanodevices," Journal of Physical Chemistry B, 110, (43), 21497-21508.
    • Zhao, Q.; Dimitrov, V.; Dimauro, O.; Dorvel, B.; Sigalov, G.; Aksimentiev, A.; Sligar, S.; Timp, G. Force spectroscopy using an electric field in a synthetic nanopore. Biophysical Journal 2007, 162A-162A.