We used all-atom molecular dynamics simulation to investigate the elastic properties of
double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch …

While the behavior of double-stranded DNA at mesoscopic scales is fairly well understood,
less is known about its relation to the rich mechanical properties in the base-pair scale …

All-atom simulations have become increasingly popular to study conformational and
dynamical properties of nucleic acids as they are accurate and provide high spatial and time …

Proteins often regulate their activities via allostery—or action at a distance—in which the
binding of a ligand at one binding site influences the affinity for another ligand at a distal site …

Periodic boundary conditions are commonly applied in molecular dynamics simulations in
the microcanonical (NVE), canonical (NVT), and isothermal–isobaric (NpT) ensembles. In …

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules
while maintaining computational efficiency. These models aim at preserving interactions …

We employed all-atom molecular dynamics simulations to explore the mechanical response
of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the …

The bending and twisting deformations of biopolymers have attracted considerable interests.
In this paper, we propose a ladder-type polymer chain minimal model which describes DNA …