Aleksei Aksimentiev

University of Illinois at Urbana-Champaign

Biophysics

2017

Karl Decker, Martin Page, Ashley Boyd, Irene MacAllister, Mark Ginsberg, and Aleksei Aksimentiev (2017): Selective Permeability of Truncated Aquaporin 1 in Silico, ACS Biomaterials Science & Engineering, American Chemical Society (ACS), Vol 3, Num 3, pp342--348

2016

Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha (2016): Direct Evidence for Sequence-Dependent Attraction Between Double-Stranded DNA Controlled by Methylation, Nature Communications, Springer Nature, Vol 7, pp11045
Thuy T. M. Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev, and Taekjip Ha (2016): Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability, Nature Communications, Springer Nature, Vol 7, pp10813
Göpfrich, Kerstin; Li, Chen Yu; Mames, Iwona; Bhamidimarri, Satya Prathyusha; Ricci, Maria; Yoo, Jejoong; Mames, Adam; Ohmann, Alexander; Winterhalter, Mathias; Stulz, Eugen; Aksimentiev, Aleksei; Keyser, Ulrich F. (2016): Ion channels made from a single membrane-spanning DNA duplex, Nano Letters (submitted), American Chemical Society, Vol 16, Num 7, pp4665
Yoo, Jejoong and Aksimentiev, Aleksei (2016): The structure and intermolecular forces of DNA condensates, Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp2036
Jejoong Yoo, and Aleksei Aksimentiev (2016): 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, American Chemical Society (ACS), Vol 12, Num 1, pp430--443
Carson, Spencer and Wilson, James and Aksimentiev, Aleksei and Weigele, Peter R. and Wanunu, Meni (2016): Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA, Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp2085
Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser (2016): Large-Conductance Transmembrane Porin Made from DNA Origami, ACS Nano, American Chemical Society (ACS), Vol 10, Num 9, pp8207--8214
Jejoong Yoo, James Wilson, and Aleksei Aksimentiev (2016): Improved Model of Hydrated Calcium Ion for Molecular Dynamics Simulations Using Classical Biomolecular Force Fields, Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp752--763
Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev (2016): Mechanical Trapping of DNA in a Double-Nanopore System, Nano Letters, American Chemical Society (ACS), Vol 16, Num 12, pp8021--8028
Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev (2016): De Novo Reconstruction of DNA Origami Structures Through Atomistic Molecular Dynamics Simulation, Nucleic Acids Res, Oxford University Press (OUP), Vol 44, Num 7, pp3013--3019
Maxim Belkin, and Aleksei Aksimentiev (2016): Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores, ACS Applied Materials & Interfaces, American Chemical Society (ACS), Vol 8, Num 20, pp12599--12608
S. Slone, J. Yoo, C.-Y. Li, and A. Aksimentiev (2016): Molecular Mechanics of DNA Bricks: In Situ Structure, Mechanical Properties and Ionic Conductivity, New Journal of Physics, IOP Publishing Ltd and Deutsche Physikalische Gesellschaft, Vol 18, Num 5, pp055012

2015

Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev (2015): Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field, ACS Nano, American Chemical Society (ACS), Vol 9, Num 2, pp1420--1433
Jejoong Yoo, and Aleksei Aksimentiev (2015): Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating, J. Phys. Chem. Lett., American Chemical Society (ACS), Vol 6, Num 23, pp4680--4687
Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev (2015): Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA, ACS Nano, American Chemical Society (ACS), Vol 9, Num 11, pp10598--10611
Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar (2015): Highly Permeable Artificial Water Channels That Can Self-Assemble Into Two-Dimensional Arrays, Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 112, Num 32, pp9810--9815

2014

Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev (2014): Ion Conductivity, Structural Dynamics and the Effective Force in DNA Origami Nanopores, Biophysical Journal, Elsevier BV, Vol 106, Num 2, pp414a
C Maffeo, J Yoo, J Comer, D B Wells, B Luan, and A Aksimentiev (2014): Close Encounters with DNA, Journal of Physics: Condensed Matter, IOP Publishing, Vol 26, Num 41, pp413101
Manish Shankla, and Aleksei Aksimentiev (2014): Conformational Transitions and Stop-and-Go Nanopore Transport of Single-Stranded DNA on Charged Graphene, Nature Communications, Nature Publishing Group, Vol 5, pp5171
Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev (2014): Modeling Thermophoretic Effects in Solid-State Nanopores, J Comput Electron, Springer Science + Business Media, Vol 13, Num 4, pp826--838
Shouvik Banerjee, James Wilson, Jiwook Shim, Manish Shankla, Elise A. Corbin, Aleksei Aksimentiev, and Rashid Bashir (2014): Slowing DNA Transport Using Graphene-DNA Interactions, Adv. Funct. Mater., Wiley-Blackwell, Vol 25, Num 6, pp936--946
Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu (2014): Smooth DNA Transport Through a Narrowed Pore Geometry, Biophysical Journal, Elsevier BV, Vol 107, Num 10, pp2381--2393

Aleksei Aksimentiev: Reinventing a DNA Sequence Reader


Distinguished Lecture Series: Nanotechnologies through Materials Innovation; Boston, Massachusetts, U.S.A., Feb 1, 2014
Aleksei Aksimentiev: New Approaches to Sequencing DNA Using a Nanopore
Pioneer workshop 2014 on nanopore and nanofluidics: physics and application as Biodevices; Osaka, Japan, Feb 8, 2014

Chen-Yu Li: Ion Conductivity, Structural Dynamics and the Effective Force in DNA Origami Nanopores


58th Annual Meeting of the Biophysical Society; San Francisco, California, U.S.A., Feb 17, 2014

Aleksei Aksimentiev: Meeting Materials Challenges in Nanopore Sequencing of DNA


CECAM 2014 workshop: Simulations of biomolecular interactions with inorganic and organic surfaces as a challenge for future nanotechnologies; Toulouse, France, Mar 25, 2014

Aleksei Aksimentiev: Engineering DNA Origami Through Microscopic Simulations


Workshop on Origami Engineering; Urbana, Illinois, U.S.A., Apr 14, 2014

Aleksei Aksimentiev: Molecular Dynamics of DNA Origami


11th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO14); Snowbird, Utah, U.S.A., Apr 17, 2014

Aleksei Aksimentiev: Modeling Nanopores for Sequencing DNA


2014 Gordon Research Conference on Biointerface Science; Lucca, Italy, Jun 18, 2014

Chen-Yu Li: Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field


12th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO15); Snowbird, Utah, U.S.A., Apr 15, 2015

Aleksei Aksimentiev: Molecular dynamics of DNA origami


Blue Waters Symposium 2015, May 11, 2015

Aleksei Aksimentiev: DNA Ion Channels


Telluride Science Workshop on Ion Channel Biophysics; Telluride, Colorado, U.S.A., Jul 27, 2015

Christopher Maffeo: De Novo Prediction of DNA Origami Structure Through Atomistic Molecular Dynamics Simulation


21st International Conference on DNA Computing and Molecular Programming (DNA21); Cambridge, Massachusetts, U.S.A., Aug 19, 2015
Aleksei Aksimentiev: Nanopore Sequencing: State of the Art and Future Directions
5th Annual Next Generation Sequencing Asia Congress; Sentosa Island, Singapore, Oct 13, 2015

David Winogradoff: Structure and Ionic Conductivity of the Nuclear Pore Complex


1st Conference on Biomotors, Virus Assembly, and Nanobiotechnology Applications; The Ohio State University, Columbus, Ohio, U.S.A., Aug 18, 2017