Eukaryotic genome and methylome encode DNA fragments' propensity to form nucleosome
particles. Although the mechanical properties of DNA possibly orchestrate such encoding …

We investigate the effects of topological constraints in catenanes composed of interlinked
ring polymers on their size in a good solvent as well as on the location of their θ-point when …

It is well established that many physical properties of DNA at sufficiently long length scales
can be understood by means of simple polymer models. One of the most widely used …

Cytosine methylation affects mechanical properties of DNA and potentially alters the
hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not …

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 …

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending.
While the wormlike chain model provides a good description of small to moderate bending …

For short DNA molecules in crowded environments, we evaluate macroscopic parameters
such as the average end-to-end distance and the twist conformation by tuning the strength of …

I present a computational method to evaluate the end-to-end and the contour length
distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The …

DNA bending is critical for DNA packaging, recognition, and repair, and occurs toward either
the major or the minor groove. The anisotropy of B-DNA groove bending was quantified for …

The propensity of short DNA sequences to convert to the circular form is studied by a
mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis …