• #262cc9
    Infinite-depth sequencing of single nucleic acid molecules
  • #003366
    Mrdna: Multi-resolution DNA modeling package blends speed and accuracy for structure determination
  • #0000cc
    Nanopore recognition of the twenty amino acids
  • #009999
    Predicting energy production of entire photosynthetic organelle from atomic simulations
  • #ff9933
    Artificial water channels enable rapid and selective water transport
  • #00ccff
    Guiding the capture of DNA molecules and proteins
  • #333366
    Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates
  • #ff9900
    Under Pressure: repellant nanopores
  • #000099
    Simulations capture diffusive substeps of a protein moving along ssDNA
  • #999999
    MD simulations link DNA flexibility to base modifications

Recent publications

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System

Adnan Choudhary, Himanshu Joshi, Han-Yi Chou, Kumar Sarthak, James Wilson, Christopher Maffeo, and Aleksei Aksimentiev
ACS Nano null (2020)
DOI:10.1021/acsnano.0c06191  BibTex

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