@article {287, title = {Water-compression gating of nanopore transport}, journal = {Physical Review Letters}, volume = {120}, year = {2018}, month = {06/2018}, pages = {268101}, abstract = {

Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.

}, author = {James Wilson and Aleksei Aksimentiev} } @article {247, title = {Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore}, journal = {ACS Nano}, volume = {10}, year = {2016}, month = {04/2016}, pages = {4644{\textendash}4651}, abstract = {

Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing \ via\ measurement of \ ionic current blockades \ possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. \ Unexpectedly, we \ find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout.

}, doi = {10.1021/acsnano.6b00940}, author = {Swati Bhattacharya and Jejoong Yoo and Aleksei Aksimentiev} } @article {66, title = {Water-silica force field for simulating nanodevices}, journal = {J Phys Chem B}, volume = {110}, year = {2006}, month = {2006 Nov 2}, pages = {21497-508}, abstract = {

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.

}, keywords = {Nanostructures, Silicon Dioxide, Water}, issn = {1520-6106}, doi = {10.1021/jp063896o}, author = {Eduardo Cruz-Ch{\'u} and Aleksei Aksimentiev and Klaus Schulten} }