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    Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates
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    DNA double helix, a tiny electromotor
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    Unidirectional single-file transport of full-length proteins through a nanopore
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    Toward a physical model of a replisome
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    Percolation controls passive transport through nuclear pores
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    Resolving isomeric posttranslational modifications using a biological nanopore as a sensor of molecular shape
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    Multiple rereads of single protein sequence
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    Self-folding water filter
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    Infinite-depth sequencing of single nucleic acid molecules
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    Mrdna: Multi-resolution DNA modeling package blends speed and accuracy for structure determination
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    Nanopore recognition of the twenty amino acids
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    Predicting energy production of entire photosynthetic organelle from atomic simulations
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    Artificial water channels enable rapid and selective water transport
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    Guiding the capture of DNA molecules and proteins
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    Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates
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    Under Pressure: repellant nanopores
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    Simulations capture diffusive substeps of a protein moving along ssDNA
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    MD simulations link DNA flexibility to base modifications
  • #3366cc
    Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA
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    DNA origami: Deformable material with programmable electrical properties

Recent publications

Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates

Kumar Sarthak, David Winogradoff, Yingda Ge, Sua Myong, and Aleksei Aksimentiev
Journal of Chemical Theory and Computation (2023)
DOI:10.1021/acs.jctc.3c00148  BibTex

Multi-resolution simulation of DNA transport through large synthetic nanostructures.

Adnan Choudhary, Christopher Maffeo, and Aleksei Aksimentiev
Phys Chem Chem Phys 24(5) 2706-2716 (2022)
DOI:10.1039/d1cp04589j  PMID:35050282  BibTex

Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport.

Jie Shen, Arundhati Roy, Himanshu Joshi, Laxmicharan Samineni, Ruijuan Ye, Yu-Ming Tu, Woochul Song, Matthew Skiles, Manish Kumar, Aleksei Aksimentiev, and Huaqiang Zeng
Nano Lett 22(12) 4831-4838 (2022)
DOI:10.1021/acs.nanolett.2c01137  PMID:35674810  BibTex

Trapping of protein cargo molecules inside DNA origami nanocages

Merle Scherf, Florian Scheffler, Christopher Maffeo, Ulrich Kemper, Jingjing Ye, Aleksei Aksimentiev, Ralf Seidel, and Uta Reibetanz
Nanoscale 14 18041-18050 (2022)
DOI:10.1039/d2nr05356j  BibTex

Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex.

David Winogradoff, Han-Yi Chou, Christopher Maffeo, and Aleksei Aksimentiev
Nat Commun 13(1) 5138 (2022)
DOI:10.1038/s41467-022-32857-1  PMID:36050301  BibTex

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Yi Li, Christopher Maffeo, Himanshu Joshi, Aleksei Aksimentiev, Brice Ménard, and Rebecca Schulman
Science Advances 8(36) (2022)
DOI:10.1126/sciadv.abq4834  BibTex

Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape

Tobias Ennslen, Kumar Sarthak, Aleksei Aksimentiev, and Jan C. Behrends
Journal of the American Chemical Society 144(35) 16060-16068 (2022)
DOI:10.1021/jacs.2c06211  BibTex

Discrimination of RNA fiber structures using solid-state nanopores

Prabhat Tripathi, Morgan Chandler, Christopher Michael Maffeo, Ali Fallahi, Amr Makhamreh, Justin Halman, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu
Nanoscale 14(18) 6866-6875 (2022)
DOI:10.1039/D1NR08002D  BibTex

Single-molecule biophysics experiments in silico: Toward a physical model of a replisome

Christopher Maffeo, Han-Yi Chou, and Aleksei Aksimentiev
iScience 25(5) 104264 (2022)
DOI:10.1016/j.isci.2022.104264  BibTex

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing

Kasra S Tabatabaei, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, Aleksei Aksimentiev, Min Chen, Charles M. Schroeder, and Olgica Milenkovic
Nano Letters (2022)
DOI:10.1021/acs.nanolett.1c04203  BibTex