Aleksei Aksimentiev - Publications

Affiliations: 
Physics University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
General Biophysics, Nanotechnology

115 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A. Correction to: A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. Methods in Molecular Biology (Clifton, N.J.). 1811: E3. PMID 30484170 DOI: 10.1007/978-1-4939-8582-1_23  1
2018 Kang H, Yoo J, Sohn BK, Lee SW, Lee HS, Ma W, Kee JM, Aksimentiev A, Kim H. Sequence-dependent DNA condensation as a driving force of DNA phase separation. Nucleic Acids Research. PMID 30032232 DOI: 10.1093/nar/gky639  1
2018 Ohmann A, Li CY, Maffeo C, Al Nahas K, Baumann KN, Göpfrich K, Yoo J, Keyser UF, Aksimentiev A. A synthetic enzyme built from DNA flips 10 lipids per second in biological membranes. Nature Communications. 9: 2426. PMID 29930243 DOI: 10.1038/s41467-018-04821-5  1
2018 Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A. A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. Methods in Molecular Biology (Clifton, N.J.). 1811: 209-229. PMID 29926456 DOI: 10.1007/978-1-4939-8582-1_15  1
2018 Benson CR, Maffeo C, Fatila EM, Liu Y, Sheetz EG, Aksimentiev A, Singharoy A, Flood AH. Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735677 DOI: 10.1073/pnas.1719539115  0.68
2018 Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Physical Chemistry Chemical Physics : Pccp. PMID 29547221 DOI: 10.1039/C7CP08185E  1
2018 Hemmig EA, Fitzgerald C, Maffeo C, Hecker L, Ochmann SE, Aksimentiev A, Tinnefeld P, Keyser UF. Optical voltage sensing using DNA origami. Nano Letters. PMID 29430924 DOI: 10.1021/acs.nanolett.7b05354  0.68
2017 Maffeo C, Aksimentiev A. Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Research. PMID 29059392 DOI: 10.1093/nar/gkx917  0.68
2017 Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Correction to Ion Channels Made from a Single Membrane-Spanning DNA Duplex. Nano Letters. PMID 28608698 DOI: 10.1021/acs.nanolett.7b02430  1
2016 Yoo J, Aksimentiev A. Refined Parameterization of Non-Bonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations. The Journal of Physical Chemistry Letters. PMID 27617340 DOI: 10.1021/acs.jpclett.6b01747  0.96
2016 Göpfrich K, Li CY, Ricci M, Bhamidimarri SP, Yoo J, Gyenes B, Ohmann A, Winterhalter M, Aksimentiev A, Keyser UF. Large-Conductance Transmembrane Porin Made from DNA Origami. Acs Nano. PMID 27504755 DOI: 10.1021/acsnano.6b03759  0.96
2016 Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Ion channels made from a single membrane-spanning DNA duplex. Nano Letters. PMID 27324157 DOI: 10.1021/acs.nanolett.6b02039  0.96
2016 Yoo J, Wilson J, Aksimentiev A. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields. Biopolymers. PMID 27144470 DOI: 10.1002/bip.22868  0.96
2016 Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. Nanoscale. PMID 27103233 DOI: 10.1039/c6nr01061j  0.96
2016 Bhattacharya S, Yoo J, Aksimentiev A. Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore. Acs Nano. PMID 27054820 DOI: 10.1021/acsnano.6b00940  0.96
2016 Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. Plos One. 11: e0152002. PMID 27008630 DOI: 10.1371/journal.pone.0152002  0.68
2016 Yoo J, Kim H, Aksimentiev A, Ha T. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Nature Communications. 7: 11045. PMID 27001929 DOI: 10.1038/ncomms11045  0.96
2016 Maffeo C, Yoo J, Aksimentiev A. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation. Nucleic Acids Research. PMID 26980283 DOI: 10.1093/nar/gkw155  0.96
2016 Belkin M, Aksimentiev A. Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. Acs Applied Materials & Interfaces. PMID 26963065 DOI: 10.1021/acsami.6b00463  0.96
2016 Ngo TT, 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. 7: 10813. PMID 26905257 DOI: 10.1038/ncomms10813  0.96
2016 Yoo J, Aksimentiev A. The structure and intermolecular forces of DNA condensates. Nucleic Acids Research. PMID 26883635 DOI: 10.1093/nar/gkw081  0.96
2016 Slone SM, Li CY, Yoo J, Aksimentiev A. Molecular mechanics of DNA bricks: In situ structure, mechanical properties and ionic conductivity New Journal of Physics. 18. DOI: 10.1088/1367-2630/18/5/055012  0.96
2016 Wilson J, Sloman L, He Z, Aksimentiev A. Nanopore Sequencing: Graphene Nanopores for Protein Sequencing (Adv. Funct. Mater. 27/2016) Advanced Functional Materials. 26: 4829. DOI: 10.1002/adfm.201670173  0.96
2016 Wilson J, Sloman L, He Z, Aksimentiev A. Graphene Nanopores for Protein Sequencing Advanced Functional Materials. 26: 4830-4838. DOI: 10.1002/adfm.201601272  0.96
2015 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. PMID 26632962 DOI: 10.1021/acs.jctc.5b00967  0.96
2015 Carson S, Wilson J, Aksimentiev A, Weigele PR, Wanunu M. Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA. Nucleic Acids Research. PMID 26578595 DOI: 10.1093/nar/gkv1199  0.96
2015 Yoo J, Aksimentiev A. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport and Mechanical Gating. The Journal of Physical Chemistry Letters. PMID 26551518 DOI: 10.1021/acs.jpclett.5b01964  0.96
2015 Belkin M, Chao SH, Jonsson MP, Dekker C, Aksimentiev A. Plasmonic Nanopores for Trapping, Controlling Displacement and Sequencing of DNA Molecules. Acs Nano. PMID 26401685 DOI: 10.1021/acsnano.5b04173  0.96
2015 Banerjee S, Wilson J, Shim J, Shankla M, Corbin EA, Aksimentiev A, Bashir R. Slowing DNA Transport Using Graphene-DNA Interactions. Advanced Functional Materials. 25: 936-946. PMID 26167144 DOI: 10.1002/adfm.201403719  0.96
2015 Li CY, Hemmig EA, Kong J, Yoo J, Hernández-Ainsa S, Keyser UF, Aksimentiev A. Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field. Acs Nano. 9: 1420-33. PMID 25623807 DOI: 10.1021/nn505825z  0.96
2015 Shen YX, Si W, Erbakan M, Decker K, De Zorzi R, Saboe PO, Kang YJ, Majd S, Butler PJ, Walz T, Aksimentiev A, Hou JL, Kumar M, Weitz DA. 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. 112: 9810-9815. DOI: 10.1073/pnas.1508575112  0.96
2014 Gamble T, Decker K, Plett TS, Pevarnik M, Pietschmann JF, Vlassiouk I, Aksimentiev A, Siwy ZS. Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 118: 9809-9819. PMID 25678940 DOI: 10.1021/jp501492g  0.96
2014 Carson S, Wilson J, Aksimentiev A, Wanunu M. Smooth DNA transport through a narrowed pore geometry. Biophysical Journal. 107: 2381-93. PMID 25418307 DOI: 10.1016/j.bpj.2014.10.017  0.96
2014 Belkin M, Chao SH, Giannetti G, Aksimentiev A. Modeling thermophoretic effects in solid-state nanopores. Journal of Computational Electronics. 13: 826-838. PMID 25395899 DOI: 10.1007/s10825-014-0594-8  0.96
2014 Shankla M, Aksimentiev A. Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene. Nature Communications. 5: 5171. PMID 25296960 DOI: 10.1038/ncomms6171  0.96
2014 Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 26: 413101. PMID 25238560 DOI: 10.1088/0953-8984/26/41/413101  0.96
2014 Maffeo C, Ngo TT, 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. 10: 2891-2896. PMID 25136266 DOI: 10.1021/ct500193u  0.96
2014 Chao SH, Matthews SS, Paxman R, Aksimentiev A, Gruebele M, Price JL. Two structural scenarios for protein stabilization by PEG. The Journal of Physical Chemistry. B. 118: 8388-95. PMID 24821319 DOI: 10.1021/jp502234s  0.96
2014 Chaudhry JH, Comer J, Aksimentiev A, Olson LN. A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore. Communications in Computational Physics. 15. PMID 24363784 DOI: 10.4208/cicp.101112.100413a  0.96
2013 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. 110: 20099-104. PMID 24277840 DOI: 10.1073/pnas.1316521110  0.96
2013 Belkin M, Maffeo C, Wells DB, Aksimentiev A. Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores. Acs Nano. 7: 6816-24. PMID 23876013 DOI: 10.1021/nn403575n  0.96
2012 Comer J, Ho A, Aksimentiev A. Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations. Electrophoresis. 33: 3466-79. PMID 23147918 DOI: 10.1002/elps.201200164  0.96
2012 Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chemical Reviews. 112: 6250-84. PMID 23035940 DOI: 10.1021/cr3002609  0.96
2012 Yoo J, Aksimentiev A. Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. The Journal of Physical Chemistry. B. 116: 12946-54. PMID 23016894 DOI: 10.1021/jp306598y  0.96
2012 Wells DB, Belkin M, Comer J, Aksimentiev A. Assessing graphene nanopores for sequencing DNA. Nano Letters. 12: 4117-23. PMID 22780094 DOI: 10.1021/nl301655d  0.96
2012 Bhattacharya S, Derrington IM, Pavlenok M, Niederweis M, Gundlach JH, Aksimentiev A. Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence. Acs Nano. 6: 6960-8. PMID 22747101 DOI: 10.1021/nn3019943  0.96
2012 Timp W, Comer J, Aksimentiev A. DNA base-calling from a nanopore using a Viterbi algorithm. Biophysical Journal. 102: L37-9. PMID 22677395 DOI: 10.1016/j.bpj.2012.04.009  0.96
2012 Comer J, Aksimentiev A. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 116: 3376-3393. PMID 22606364 DOI: 10.1021/jp210641j  0.96
2012 Wells DB, 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. Methods in Molecular Biology (Clifton, N.J.). 870: 165-86. PMID 22528264 DOI: 10.1007/978-1-61779-773-6_10  0.96
2012 Maffeo C, Luan B, Aksimentiev A. End-to-end attraction of duplex DNA. Nucleic Acids Research. 40: 3812-21. PMID 22241779 DOI: 10.1093/nar/gkr1220  0.96
2012 Kowalczyk SW, Wells DB, Aksimentiev A, Dekker C. Slowing down DNA translocation through a nanopore in lithium chloride. Nano Letters. 12: 1038-44. PMID 22229707 DOI: 10.1021/nl204273h  0.96
2012 Yoo J, Aksimentiev A. Improved parametrization of Li +, Na +, K +, and Mg 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems Journal of Physical Chemistry Letters. 3: 45-50. DOI: 10.1021/jz201501a  0.96
2011 Carr R, Comer J, Ginsberg MD, Aksimentiev A. Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface. The Journal of Physical Chemistry Letters. 2: 1804-1807. PMID 22611479 DOI: 10.1021/jz200749d  0.96
2011 Carr R, Comer J, Ginsberg MD, Aksimentiev A. Modeling Pressure-Driven Transport of Proteins through a Nanochannel. Ieee Transactions On Nanotechnology. 10: 75-82. PMID 22611338 DOI: 10.1109/TNANO.2010.2062530  0.96
2011 Wanunu M, Bhattacharya S, Xie Y, Tor Y, Aksimentiev A, Drndic M. Nanopore analysis of individual RNA/antibiotic complexes. Acs Nano. 5: 9345-53. PMID 22067050 DOI: 10.1021/nn203764j  0.96
2011 Carr R, Comer J, Ginsberg MD, Aksimentiev A. Atoms-to-microns model for small solute transport through sticky nanochannels. Lab On a Chip. 11: 3766-73. PMID 21986816 DOI: 10.1039/c1lc20697d  0.96
2011 Radadia AD, Stavis CJ, Carr R, Zeng H, King WP, Carlisle JA, Aksimentiev A, Hamers RJ, Bashir R. Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces. Advanced Functional Materials. 21: 1040-1050. PMID 21949497 DOI: 10.1002/adfm.201002251  0.96
2011 Bhattacharya S, Muzard L, Payet L, Mathé 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 MD simulations and experiments. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 115: 4255-4264. PMID 21860669 DOI: 10.1021/jp111441p  0.96
2011 Comer JR, Wells DB, Aksimentiev A. Modeling nanopores for sequencing DNA. Methods in Molecular Biology (Clifton, N.J.). 749: 317-58. PMID 21674382 DOI: 10.1007/978-1-61779-142-0_22  0.96
2011 Venkatesan BM, Polans J, Comer J, Sridhar S, Wendell D, Aksimentiev A, Bashir R. Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore. Biomedical Microdevices. 13: 671-82. PMID 21487665 DOI: 10.1007/s10544-011-9537-3  0.96
2011 Stavis C, Clare TL, Butler JE, Radadia AD, Carr R, Zeng H, King WP, Carlisle JA, Aksimentiev A, Bashir R, Hamers RJ. 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. 108: 983-8. PMID 20884854 DOI: 10.1073/pnas.1006660107  0.96
2010 Timp W, Mirsaidov UM, Wang D, Comer J, Aksimentiev A, Timp G. Nanopore Sequencing: Electrical Measurements of the Code of Life. Ieee Transactions On Nanotechnology. 9: 281-294. PMID 21572978 DOI: 10.1109/TNANO.2010.2044418  0.96
2010 Luan B, Aksimentiev A. Control and reversal of the electrophoretic force on DNA in a charged nanopore. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 454123. PMID 21339610 DOI: 10.1088/0953-8984/22/45/454123  0.96
2010 Maffeo C, Schöpflin 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. 105: 158101. PMID 21230940 DOI: 10.1103/PhysRevLett.105.158101  0.96
2010 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. 21: 395501. PMID 20808032 DOI: 10.1088/0957-4484/21/39/395501  0.96
2010 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. 7: 353-4; discussion 35. PMID 20673653 DOI: 10.1016/j.plrev.2010.07.004  0.96
2010 Aksimentiev A. Deciphering ionic current signatures of DNA transport through a nanopore. Nanoscale. 2: 468-83. PMID 20644747 DOI: 10.1039/b9nr00275h  0.96
2010 Wells DB, Aksimentiev A. Mechanical properties of a complete microtubule revealed through molecular dynamics simulation. Biophysical Journal. 99: 629-37. PMID 20643083 DOI: 10.1016/j.bpj.2010.04.038  0.96
2010 Luan B, Aksimentiev A. Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes. Soft Matter. 6: 243-246. PMID 20563230 DOI: 10.1039/b917973a  0.96
2010 Luan B, Carr R, Caffrey M, Aksimentiev A. The effect of calcium on the conformation of cobalamin transporter BtuB. Proteins. 78: 1153-62. PMID 19927326 DOI: 10.1002/prot.22635  0.96
2009 Aksimentiev A, Brunner RK, Cruz-Chú E, Comer J, Schulten K. Modeling Transport Through Synthetic Nanopores. Ieee Nanotechnology Magazine. 3: 20-28. PMID 21909347 DOI: 10.1109/MNANO.2008.931112  0.96
2009 Cruz-Chu ER, Aksimentiev A, Schulten K. Ionic Current Rectification Through Silica Nanopores. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 113: 1850. PMID 20126282 DOI: 10.1021/jp804724p  0.96
2009 Maffeo C, Aksimentiev A. Structure, dynamics, and ion conductance of the phospholamban pentamer. Biophysical Journal. 96: 4853-65. PMID 19527644 DOI: 10.1016/j.bpj.2009.03.053  0.96
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. 37: 4170-4179. PMID 19433506 DOI: 10.1093/nar/gkp317  0.96
2009 Comer J, Dimitrov V, Zhao Q, Timp G, Aksimentiev A. Microscopic mechanics of hairpin DNA translocation through synthetic nanopores. Biophysical Journal. 96: 593-608. PMID 19167307 DOI: 10.1016/j.bpj.2008.09.023  0.96
2008 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. Methods in Molecular Biology (Clifton, N.J.). 474: 181-234. PMID 19031067 DOI: 10.1007/978-1-59745-480-3_11  0.96
2008 Luan B, Aksimentiev A. DNA attraction in monovalent and divalent electrolytes. Journal of the American Chemical Society. 130: 15754-5. PMID 18975864 DOI: 10.1021/ja804802u  0.96
2008 Luan B, Aksimentiev A. Strain softening in stretched DNA. Physical Review Letters. 101: 118101. PMID 18851334 DOI: 10.1103/PhysRevLett.101.118101  0.96
2008 Luan B, Aksimentiev A. Electro-osmotic screening of the DNA charge in a nanopore. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 021912. PMID 18850870 DOI: 10.1103/PhysRevE.78.021912  0.96
2008 Carr R, Weinstock IA, Sivaprasadarao A, Müller A, Aksimentiev A. Synthetic ion channels via self-assembly: A route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes Nano Letters. 8: 3916-3921. PMID 18844424 DOI: 10.1021/nl802366k  0.96
2008 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. 36: 1532-1541. PMID 18208842 DOI: 10.1093/nar/gkm1017  0.96
2008 Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, Katritch V, Caffrey M. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. Proteins. 71: 24-34. PMID 18076035 DOI: 10.1002/prot.21841  0.96
2008 Sigalov G, Comer J, Timp G, Aksimentiev A. Detection of DNA sequences using an alternating electric field in a nanopore capacitor. Nano Letters. 8: 56-63. PMID 18069865 DOI: 10.1021/nl071890k  0.96
2007 Luan B, Caffrey M, Aksimentiev A. Structure refinement of the OpcA adhesin using molecular dynamics. Biophysical Journal. 93: 3058-69. PMID 17938421 DOI: 10.1529/biophysj.107.106724  0.96
2007 Wells DB, Abramkina V, Aksimentiev A. Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics. The Journal of Chemical Physics. 127: 125101. PMID 17902937 DOI: 10.1063/1.2770738  0.96
2007 Zhao Q, Sigalov G, Dimitrov V, Dorvel B, Mirsaidov U, Sligar S, Aksimentiev A, Timp G. Detecting SNPs using a synthetic nanopore Nano Letters. 7: 1680-1685. PMID 17500578 DOI: 10.1021/nl070668c  0.96
2006 Cruz-Chu ER, Aksimentiev A, Schulten K. Water-silica force field for simulating nanodevices. The Journal of Physical Chemistry. B. 110: 21497-508. PMID 17064100 DOI: 10.1021/jp063896o  0.96
2006 Lu D, Aksimentiev A, Shih AY, Cruz-Chu E, Freddolino PL, Arkhipov A, Schulten K. The role of molecular modeling in bionanotechnology. Physical Biology. 3: S40-53. PMID 16582464 DOI: 10.1088/1478-3975/3/1/S05  0.96
2006 Heng JB, Aksimentiev A, Ho C, Marks P, Grinkova YV, Sligar S, Schulten K, Timp G. The electromechanics of DNA in a synthetic nanopore. Biophysical Journal. 90: 1098-106. PMID 16284270 DOI: 10.1529/biophysj.105.070672  0.96
2006 Dimitrov V, Aksimentiev A, Schulten K, Heng J, Sorsch T, Mansfield W, Miner J, Watson GP, Cirelli R, Klemens F, Bower J, Ferry E, Taylor A, Kornblit A, Dorvel B, et al. Exploring the prospects for a nanometer-scale gene chip Technical Digest - International Electron Devices Meeting, Iedm. DOI: 10.1109/IEDM.2006.346987  0.96
2006 Gracheva ME, Xiong A, Aksimentiev A, Schulten K, Timp G, Leburton JP. Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor Nanotechnology. 17: 622-633. DOI: 10.1088/0957-4484/17/3/002  0.96
2006 Gracheva ME, Aksimentiev A, Leburton JP. Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor Nanotechnology. 17: 3160-3165. DOI: 10.1088/0957-4484/17/13/014  0.96
2005 Heng JB, Aksimentiev A, Ho C, Dimitrov V, Sorsch T, Miner J, Mansfield W, Schulten K, Timp G. Beyond the Gene Chip. Bell Labs Technical Journal. 10: 5-22. PMID 18815623 DOI: 10.1002/bltj.20102  0.96
2005 Heng JB, Aksimentiev A, Ho C, Marks P, Grinkova YV, Sligar S, Schulten K, Timp G. Stretching DNA using the electric field in a synthetic nanopore. Nano Letters. 5: 1883-8. PMID 16218703 DOI: 10.1021/nl0510816  0.96
2005 Mathé J, Aksimentiev A, Nelson DR, Schulten K, Meller A. Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel. Proceedings of the National Academy of Sciences of the United States of America. 102: 12377-82. PMID 16113083 DOI: 10.1073/pnas.0502947102  0.96
2005 Gumbart J, Wang Y, Aksimentiev A, Tajkhorshid E, Schulten K. Molecular dynamics simulations of proteins in lipid bilayers Current Opinion in Structural Biology. 15: 423-431. PMID 16043343 DOI: 10.1016/j.sbi.2005.07.007  0.96
2005 Aksimentiev A, Schulten K. Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map Biophysical Journal. 88: 3745-3761. PMID 15764651 DOI: 10.1529/biophysj.104.058727  0.96
2004 Aksimentiev A, Heng JB, Timp G, Schulten K. Microscopic Kinetics of DNA Translocation through synthetic nanopores. Biophysical Journal. 87: 2086-97. PMID 15345583 DOI: 10.1529/biophysj.104.042960  0.96
2004 Heng JB, Ho C, Kim T, Timp R, Aksimentiev A, Grinkova YV, Sligar S, Schulten K, Timp G. Sizing DNA using a nanometer-diameter pore. Biophysical Journal. 87: 2905-11. PMID 15326034 DOI: 10.1529/biophysj.104.041814  0.96
2004 Aksimentiev A, Schulten K. Extending molecular modeling methodology to study insertion of membrane nanopores Proceedings of the National Academy of Sciences of the United States of America. 101: 4337-4338. PMID 15070717 DOI: 10.1073/pnas.0400739101  0.96
2004 Aksimentiev A, Balabin IA, Fillingame RH, Schulten K. Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophysical Journal. 86: 1332-44. PMID 14990464 DOI: 10.1016/S0006-3495(04)74205-8  0.96
2003 Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. Large scale simulation of protein mechanics and function. Advances in Protein Chemistry. 66: 195-247. PMID 14631820 DOI: 10.1016/S0065-3233(03)66006-7  0.96
2002 Aksimentiev A, Fialkowski M, Holyst R. Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulations, and measurements Advances in Chemical Physics. 121: 141-239.  0.96
2001 Fialkowski M, Aksimentiev A, Hołyst R. Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems. Physical Review Letters. 86: 240-3. PMID 11177801 DOI: 10.1103/PhysRevLett.86.240  0.96
2001 Aksimentiev A. Morphological transformations during phase-separation/ordering phenomena Molecular Crystals and Liquid Crystals Science and Technology Section a: Molecular Crystals and Liquid Crystals. 366: 893-900.  0.96
2001 Aksimentiev A, Holyst R. Application of the Euler characteristic to the study of homopolymer blends and copolymer melts Polimery/Polymers. 46: 307-322.  0.96
2000 Aksimentiev A, Holyst R. Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 62: 6821-30. PMID 11102035  0.96
2000 Aksimentiev A, Holyst R, Moorthi K. Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends Macromolecular Theory and Simulations. 9: 661-674. DOI: 10.1002/1521-3919(20001101)9:8<661::AID-MATS661>3.0.CO;2-6  0.96
2000 Aksimentiev A, Moorthi K, Holyst R. Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends Journal of Chemical Physics. 112: 6049-6062.  0.96
2000 Aksimentiev A, Moorthi K, Hołyst R. Spinodal decomposition of homopolymer blends: Geometrical properties of the interface Progress of Theoretical Physics Supplement. 398-399.  0.96
1999 Ho?yst R, Plewczy?ski D, Aksimentiev A, Burdzy K. Diffusion on curved, periodic surfaces. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 302-7. PMID 11969764  0.96
1999 Aksimentiev A, Hołyst R. Single-chain statistics in polymer systems Progress in Polymer Science (Oxford). 24: 1045-1093. DOI: 10.1016/S0079-6700(99)00023-4  0.96
1999 Aksimentiev A, Hołyst R. Single chain conformations in the system of symmetric and asymmetric diblock copolymers Macromolecular Theory and Simulations. 8: 328-342.  0.96
1999 Aksimentiev A, Hołyst R. Phase behavior of gradient copolymers Journal of Chemical Physics. 111: 2329-2339.  0.96
1998 Aksimentiev A, Hołyst R. Swelling and shrinking of polymer chains in homopolymer blends Macromolecular Theory and Simulations. 7: 447-456.  0.96
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