| Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems J Yoo, A Aksimentiev The Journal of Physical Chemistry Letters 3 (1), 45-50, 2012 | 349 | 2012 |
| Modeling and simulation of ion channels C Maffeo, S Bhattacharya, J Yoo, D Wells, A Aksimentiev Chemical reviews 112 (12), 6250-6284, 2012 | 253 | 2012 |
| New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions J Yoo, A Aksimentiev Physical Chemistry Chemical Physics 20 (13), 8432-8449, 2018 | 224 | 2018 |
| Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability TTM Ngo, J Yoo, Q Dai, Q Zhang, C He, A Aksimentiev, T Ha Nature communications 7 (1), 10813, 2016 | 222 | 2016 |
| Large-conductance transmembrane porin made from DNA origami K Göpfrich, CY Li, M Ricci, SP Bhamidimarri, J Yoo, B Gyenes, ... ACS nano 10 (9), 8207-8214, 2016 | 209 | 2016 |
| In situ structure and dynamics of DNA origami determined through molecular dynamics simulations J Yoo, A Aksimentiev Proceedings of the National Academy of Sciences 110 (50), 20099-20104, 2013 | 194 | 2013 |
| Improved parameterization of amine–carboxylate and amine–phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields J Yoo, A Aksimentiev Journal of chemical theory and computation 12 (1), 430-443, 2016 | 150 | 2016 |
| Ion channels made from a single membrane-spanning DNA duplex K Göpfrich, CY Li, I Mames, SP Bhamidimarri, M Ricci, J Yoo, A Mames, ... Nano letters 16 (7), 4665-4669, 2016 | 149 | 2016 |
| Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations J Yoo, Q Cui Biophysical journal 94 (8), L61-L63, 2008 | 124 | 2008 |
| A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes A Ohmann, CY Li, C Maffeo, K Al Nahas, KN Baumann, K Göpfrich, J Yoo, ... Nature communications 9 (1), 2426, 2018 | 117 | 2018 |
| Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations J Yoo, A Aksimentiev The Journal of Physical Chemistry B 116 (43), 12946-12954, 2012 | 113 | 2012 |
| Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field CY Li, EA Hemmig, J Kong, J Yoo, S Hernández-Ainsa, UF Keyser, ... ACS nano 9 (2), 1420-1433, 2015 | 96 | 2015 |
| Molecular dynamics of membrane-spanning DNA channels: conductance mechanism, electro-osmotic transport, and mechanical gating J Yoo, A Aksimentiev The journal of physical chemistry letters 6 (23), 4680-4687, 2015 | 94 | 2015 |
| A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL Y Tang, G Cao, X Chen, J Yoo, A Yethiraj, Q Cui Biophysical journal 91 (4), 1248-1263, 2006 | 94 | 2006 |
| Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations J Yoo, Q Cui Biophysical journal 97 (8), 2267-2276, 2009 | 92 | 2009 |
| De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation C Maffeo, J Yoo, A Aksimentiev Nucleic acids research 44 (7), 3013-3019, 2016 | 89 | 2016 |
| The structure and intermolecular forces of DNA condensates J Yoo, A Aksimentiev Nucleic acids research 44 (5), 2036-2046, 2016 | 82 | 2016 |
| Close encounters with DNA C Maffeo, J Yoo, J Comer, DB Wells, B Luan, A Aksimentiev Journal of Physics: Condensed Matter 26 (41), 413101, 2014 | 81 | 2014 |
| Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation J Yoo, H Kim, A Aksimentiev, T Ha Nature communications 7 (1), 11045, 2016 | 77 | 2016 |
| Molecular dynamics simulations of DNA–DNA and DNA–protein interactions J Yoo, D Winogradoff, A Aksimentiev Current Opinion in Structural Biology 64, 88-96, 2020 | 73 | 2020 |
Aleksei AksimentievUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
