Modulation of DNA conformation in electrolytic nanodroplets.

The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, , , , and , are observed for different droplet sizes and ionic concentrations.

DNA Confined in a Nanodroplet: A Molecular Dynamics Study.

As a major genetic material, the configuration and the mechanical properties of a double-stranded DNA (dsDNA) molecule in confinement are crucial for the application of nanotechnology and biological engineering. In the present paper, molecular dynamics simulation is utilized to study the configuration of dsDNA in a nanodroplet on a graphene substrate. The results show that the semiflexible dsDNA molecule changes its configuration with radius of gyration ( R) of a few nanometers because of the confined space, that is, the R of the dsDNA molecule decreases with the reduction of the nanodroplet size.

Nanoscale cavitation in perforation of cellular membrane by shock-wave induced nanobubble collapse.

The collapse of the bubble induced by the shock wave leads to nano-jet, which is able to perforate cellular membranes. This phenomenon is investigated by Martini coarse-grained molecular dynamic (CG-MD) simulations in the present study. It is found that the occurrence of cavitation nucleation at the nanoscale can be observed during the perforation process.