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 3025 Beckman Institute, 405 North Mathews Avenue

  • 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.