• #003366
    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

Recent publications

Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate

Han-Yi Chou, and Aleksei Aksimentiev
J. Phys. Chem. Lett. 11 4923-4929 (2020)  BibTex

Molecular Transport across the Ionic Liquid−Aqueous Electrolyte Interface in a MoS2 Nanopore

Manish Shankla, and Aleksei Aksimentiev
ACS Appl. Mater. Interfaces 12 26624-26634 (2020)
DOI:10.1021/acsami.0c04523  BibTex

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé et al.
J. Chem. Phys. 153 (2020)
DOI:10.1063/5.0014475  BibTex

Molecular dynamics simulations of DNA--DNA and DNA--protein interactions

Jejoong Yoo, David Winogradoff, and Aleksei Aksimentiev
Current Opinion in Structural Biology 64 88-96 (2020)
DOI:https://doi.org/10.1016/j.sbi.2020.06.007  BibTex

Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme

Diana Sobota, Himanshu Joshi, Alexander Ohmann, Aleksei Aksimentiev, and Ulrich F. Keyser
Nano Letters (2020)  BibTex