Aleksei Aksimentiev

This study improves molecular dynamics models to better predict nanopore blockade currents from single-stranded DNA by refining force field parameters.

This study uses DNA-origami rings to investigate FG-Nup interactions and their impact on NPC function, revealing how sequence and post-translational modifications affect protein behavior.

The paper demonstrates that rotating DNA duplexes can transport water and ions through a nanoscale pore, with cation transport driven by electrostatic interactions and potential applications in ion separation.

This study uses atomistic simulations to show how RNA bacteriophages balance genome confinement and delivery through solvent ordering and RNA-protein interactions.

This paper introduces DNA-Lipid Nanodiscs (DLNs) with a PEG interface to study membrane proteins and lipid bilayers, showing effective shielding of hydrophobic mismatch through PEG-lipid interactions.

The paper shows CTCF controls chromatin boundary permeability through a dynamic conformational ensemble, not static occupancy, influencing cohesin capture probabilities.

This study investigates DNA binding and diffusion on hBN surfaces, showing non-specific binding and confinement, and demonstrates potential for nanofluidic biomolecule manipulation.

This study develops a method to study DNA and DNA-protein interactions with high spatial and temporal resolution using graphene and energy transfer.

This study investigates how the length of poly(ADP-ribose) (PAR) affects its structural transitions in the presence of Mg2+ ions, revealing length-dependent compaction and bundle formation.

This study demonstrates a method to generate electro-osmotic flow using sticky ions, showing it works in both biological and solid-state nanopores.

The paper compares the electrophoretic translocation dynamics of RNA:DNA hybrids and DNA:DNA duplexes through nanopores, finding that RNA:DNA hybrids translocate faster despite similar contour lengths.

This paper introduces a nanoinjection platform using nanopipettes to deliver macromolecules into cells with single molecule resolution, showing phenotypic changes and enhanced detection through macromolecular crowding.

This study uses molecular dynamics simulations to show RNA increases condensate cohesiveness but affects fluidity and permeability depending on RNA length.

The paper designs DNA nanochannels that allow small molecules to diffuse through micron-length channels, demonstrating controlled transport between compartments.

This paper introduces an extended 11-letter DNA alphabet for data storage, using nanopore readout and neural networks to improve accuracy and density.

This study shows that DNA-based ion channels with continuous backbones form more stable and efficient pores in lipid membranes than those with nicks.

The paper introduces MrDNA, a multi-resolution simulation framework that predicts DNA nanostructure structures and dynamics with high accuracy, comparable to cryo-EM, in under 30 minutes.