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Aleksei Aksimentiev

University of Illinois at Urbana-Champaign

Physics

2018

David Winogradoff, Christopher Maffeo, Wei Si, and Aleksei Aksimentiev (2018): All-Atom Structure and Ionic Conductivity of the Nuclear Pore Complex, Biophysical Journal, Elsevier BV, Vol 114, Num 3, pp630a

2017

Benjamin Cressiot, Sandra J. Greive, Wei Si, Tomas C. Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T. Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A. Antson, and Meni Wanunu (2017): Porphyrin-Assisted Docking of a Thermophage Portal Protein Into Lipid Bilayers: Nanopore Engineering and Characterization, ACS Nano, American Chemical Society (ACS), Vol 11, Num 12, pp11931-11945
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
Karl Decker, Martin Page, and Aleksei Aksimentiev (2017): Nanoscale Ion Pump Derived from a Biological Water Channel, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 33, pp7899-7906
Aaron J. Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack F. Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei Aksimentiev, and Liviu Movileanu (2017): Quantification of Membrane Protein-Detergent Complex Interactions, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 44, pp10228-10241
Laura Restrepo-Pérez, Shalini John, Aleksei Aksimentiev, Chirlmin Joo, and Cees Dekker (2017): SDS-Assisted Protein Transport Through Solid-State Nanopores, Nanoscale, Royal Society of Chemistry (RSC), Vol 9, Num 32, pp11685-11693
Kai Tian, Karl Decker, Aleksei Aksimentiev, and Li-Qun Gu (2017): Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis, ACS Nano, American Chemical Society (ACS), Vol 11, Num 2, pp1204-1213
Mohammad Amin Alibakhshi, Justin R. Halman, James Wilson, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu (2017): Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores, ACS Nano, American Chemical Society (ACS), Vol 11, Num 10, pp9701-9710
Wei Si, and Aleksei Aksimentiev (2017): Nanopore Sensing of Protein Folding, ACS Nano, American Chemical Society (ACS), Vol 11, Num 7, pp7091-7100
Manish Shankla, and Aleksei Aksimentiev (2017): Modulation of Molecular Flux Using a Graphene Nanopore Capacitor, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp3724--3733
Maffeo, Christopher and Aksimentiev, Aleksei (2017): Molecular mechanism of DNA association with single-stranded DNA binding protein, Nucleic Acids Research, Oxford University Press, Vol 45, Num 21, pp12125-12139

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
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
Thana Sutthibutpong, Agnes Noy, and Sarah Harris (2016): Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis, Springer New York, Methods in Molecular Biology, Vol 1431, pp195--219
Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser (2016): Ion Channels Made from a Single Membrane-Spanning DNA Duplex, Nano Letters, American Chemical Society (ACS), Vol 16, Num 7, pp4665-4669
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

2017

Aleksei Aksimentiev (2017): Molecular Mechanisim of Nuclear Transport, 2017 Blue Waters Annual Report, pp194-195
Aleksei Aksimentiev (2017): DNA Origami Membrane Channels, 2017 Blue Waters Annual Report, pp192-193

2016

Aleksei Aksimentiev (2016): Molecular Dynamics of Self-Assembled DNA Systems, 2016 Blue Waters Annual Report, pp187-189
Aleksei Aksimentiev (2016): Molecular Mechanism of Sequence Dependent DNA Looping, 2016 Blue Waters Annual Report, pp190-192

2015

Aleksei Aksimentiev: Molecular dynamics of DNA origami


Blue Waters Symposium 2015, May 11, 2015

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

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: 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
Aleksei Aksimentiev: Nanopore Sequencing: State of the Art and Future Directions
5th Annual Next Generation Sequencing Asia Congress; Sentosa Island, Singapore, Oct 13, 2015

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

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: DNA Ion Channels


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

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

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


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

Chen-Yu Li, J. Yoo and A. Aksimentiev: Making sense of DNA membrane channels


22nd International Conference on DNA Computing and Molecular Programming (DNA22); Munich, Germany, Sep 7, 2016

Aleksei Aksimentiev: Molecular dynamics of self-assembled DNA systems


Future Trends in DNA-based Nanotechnology International Workshop; Dresden, Germany, May 30, 2017

Aleksei Aksimentiev: DNA Ion Channels


Telluride Workshop on Biophysics of Ion Channels; Telluride, Colorado, U.S.A., Jul 24, 2017

Aleksei Aksimentiev: Computational Microscopy of Nanopore Transport


First Conference on Biomotors, Virus Assembly, and Nanobiotechnology Applications; The Ohio State University, Columbus, Ohio, U.S.A., Aug 16, 2017

Aleksei Aksimentiev: Sensing and Building with DNA


Center for NanoScience (CeNS) Workshop 2017 on Design and Control of Nano Systems; Venice International University, San Servolo, Italy, Sep 18, 2017

Aleksei Aksimentiev: Toward nanopore sequencing of proteins: a molecular dynamics perspective


Single-Molecule Protein Sequencing Conference; Delft University of Technology, The Netherlands, Dec 12, 2017

David Winogradoff and A. Aksimentiev: Unraveling nucleosomes through microscopic simulations


CECAM workshop on Multiscale Modeling and Experimental Approaches to Genome Organization; L’École de Physique des Houches, France, Apr 3, 2017

Wei Si: Nanopore Sensing of Protein Shape and Folding-Unfolding Transitions


First Conference on Biomotors, Virus Assembly, and Nanobiotechnology Applications; The Ohio State University, Columbus, Ohio, U.S.A., Aug 16, 2017

Christopher Maffeo: Multiscale simulations of DNA origami objects for fast and detailed structure prediction


Single-Molecule Protein Sequencing Conference; Delft University of Technology, The Netherlands, May 29, 2017

Lauren Quednau, S.-M. Slone, C. Maffeo, P. Ketterer, H. Dietz, and A. Aksimentiev: Rotary motors made from DNA


Center for NanoScience (CeNS) Workshop 2017 on Design and Control of Nano Systems; Venice International University, San Servolo, Italy, Sep 21, 2017

Researchers use supercomputers to design and test new tools for cancer detection


Jun 28, 2017

An important factor in fighting cancer is the speed at which the disease can be identified, diagnosed and treated. The current standard involves a patient feeling ill or a physician seeing signs of a tumor. These indicators lead to more precise diagnoses via blood tests, x-rays or MRI imaging. But once the disease is far enough along to be noticeable, the cancer has often spread. In the future, though, it may be possible to diagnose cancer much earlier using more sensitive body scans, new types of biomarker tests, and even nano-sensors working in the bloodstream

NCSA Grants $2.6M in Blue Waters Awards to Illinois Researchers


Jul 6, 2017

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign has awarded 3,697,000 node hours (NH) of time on the Blue Waters supercomputer to Illinois researchers from Spring 2017 proposal submissions. The combined value of these awards is over $2.6 million dollars, and through the life of the Blue Waters program, NCSA has awarded over 43 million node hours to UI researchers—a value of nearly $27 million. Some of the time allocated for Blue Waters will go to projects that focus on HIV research, Laser Interferometer Gravitational-Wave Observatory (LIGO) simulations, genomics and global warming research.


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Blue Waters Simulates Largest Membrane Channel Made of DNA Origami


Nov 8, 2016

What do you get when you cross an art form with something found in all living organisms? It may sound unusual, but DNA origami is something that has been explored in the scientific community for the last 10 years. DNA is a string of four nucleotide bases (A, T, G and C), each of which pairs only with one other base (A with T and G with C). In DNA origami, researchers take a long single strand of DNA (picture a ladder sawed in half vertically), and fold it into a shape using staple strands that have the corresponding bases. Everything from smiley faces to robots has been made using this method. While those are 2D, 3D shapes can also be made. Aleksei Aksimentiev’s group at the University of Illinois at Urbana-Champaign has been using this method to simulate membrane channels using the Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) on the University of Illinois campus.


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Charged graphene gives DNA a stage to perform molecular gymnastics


Oct 9, 2014

When Illinois researchers set out to investigate a method to control how DNA moves through a tiny sequencing device, they did not know they were about to witness a display of molecular gymnastics. Fast, accurate and affordable DNA sequencing is the first step toward personalized medicine. Threading a DNA molecule through a tiny hole, called a nanopore, in a sheet of graphene allows researchers to read the DNA sequence; however, they have limited control over how fast the DNA moves through the pore. In a new study published in the journal Nature Communications, University of Illinois physics professor Aleksei Aksimentiev and graduate student Manish Shankla applied an electric charge to the graphene sheet, hoping that the DNA would react to the charge in a way that would let them control its movement down to each individual link, or nucleotide, in the DNA chain.

17 campus teams to accelerate their research with Blue Waters


Jun 10, 2015

Seventeen U of I research teams from a wide range of disciplines have been awarded computational and data resources on the sustained-petascale Blue Waters supercomputer at NCSA. “These diverse projects highlight the breadth of computational research at the University of Illinois,” said Athol Kemball, associate professor of Astronomy and chair of the Illinois allocation review committee. “Illinois has a tremendous pool of talented researchers in fields from political science to chemistry to engineering who can harness the power of Blue Waters to discover and innovate.”


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2015 Blue Waters Symposium highlights successes, looks to the future of supercomputing


May 29, 2015

The 2015 Blue Waters Symposium, held May 10-13 at Oregon's beautiful Sunriver Resort, brought together leaders in petascale computational science and engineering to share successes and methods. Around 130 attendees, many of whom were Blue Waters users and the NCSA staff who support their work, enjoyed presentations on computational advances in a range of research areas—including sub-atomic physics, weather, biology, astronomy, and many others—as well as keynotes from innovative thinkers and leaders in high-performance computing. Over the three days of the symposium, 58 science teams from across the country presented on their work on Blue Waters.


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12 Illinois faculty awarded prestigious Blue Waters Professorships


Feb 4, 2014

Twelve University of Illinois faculty members from a range of fields have been selected as Blue Waters Professors, an honor that comes with substantial computing and data resources on the Blue Waters supercomputer at the university’s National Center for Supercomputing Applications (NCSA).


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DNA molecules directly interact with each other based on sequence


Mar 23, 2016

Proteins play a large role in DNA regulation, but a new study finds that DNA molecules directly interact with one another in a way that's dependent on the sequence of the DNA and epigenetic factors. This could have implications for how DNA is organized in the cell and even how genes are regulated in different cell types, the researchers say. Led by Aleksei Aksimentiev, a professor of physics at the University of Illinois, and Taekjip Ha, a professor of biophysics and biophysical chemistry at Johns Hopkins University and an adjunct at the University of Illinois Center for the Physics of Living Cells along with Aksimentiev, the researchers published their work in the journal Nature Communications.


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22 Illinois projects receive time on Blue Waters


Jun 11, 2013

The University of Illinois at Urbana-Champaign has awarded access to the Blue Waters supercomputer—which is capable of performing quadrillions of calculations every second and of working with quadrillions of bytes of data—to 22 campus research teams from a wide range of disciplines. The computing and data capabilities of Blue Waters, which is operated by the National Center for Supercomputing Applications (NCSA), will assist researchers in their work on understanding DNA, developing biofuels, simulating climate, and more.


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14 Illinois researchers selected for NCSA Fellowships


May 11, 2015

Fourteen faculty members at the University of Illinois at Urbana-Champaign have been selected to receive one-year fellowships that will enable their research teams to pursue collaborative projects with the National Center for Supercomputing Applications. NCSA's fellowship program aims to catalyze and develop long-term collaborations between the center and campus researchers, particularly in the center's six thematic areas of research: Bioinformatics and Health Sciences, Computing and Data Sciences, Culture and Society, Earth and Environment, Materials and Manufacturing, and Physics and Astronomy.


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