Oleksii Aksimentiev

Publications

• 2012

  • 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.; 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.; 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.

• 2011

  • 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.

  • 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.

  • 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. 

  • 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., 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., Atoms-to-Microns Model for Small Solute Transport through Sticky Nanochannels. Lab on a Chip 2011, 11, (22), 3766-3773.

  • Comer, J.; Aksimentiev, A. Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations, 2011, 335-356.

  • 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.

  • 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.; Ginsberg, M. D.; Aksimentiev, A., Modeling Pressure-Driven Transport of Proteins Through a Nanochannel. IEEE Transactions on Nanotechnology 2011, 10, (1), 75-82. 

• 2010

  • 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).

  • 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.

  • Wells, D. B.; Aksimentiev, A., Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation. Biophysical Journal 2010, 99, (2), 629-637. 

• 2009

  • 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.

• 2008

  • 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).

  • Luan, B. Q.; Aksimentiev, A., Electro-osmotic screening of the DNA charge in a nanopore. Physical Review E 2008, 78, (2).

  • 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.

  • 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.

  • 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.

  • 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.

  • 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).

• 2007

  • 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).

  • 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.

  • 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.

  • 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.

• 2006

  • 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.