We present a brief, and largely personal, history of computer simulations of DNA and RNA
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …

Structure and dynamics are both critical to RNA's vital functions in biology. Numerous
techniques can elucidate the structural dynamics of RNA, but computational approaches …

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …

Refinement of empirical force fields for nucleic acids requires their extensive testing using as
wide range of systems as possible. However, finding unambiguous reference data is not …

Background The structure and dynamics of DNA are critically related to its function.
Molecular dynamics simulations augment experiment by providing detailed information …

Presented is a first generation atomistic force field (FF) for DNA in which electronic
polarization is modeled based on the classical Drude oscillator formalism. The DNA model …

Cells are responsive to the mechanical environment, but the methods to detect
simultaneously how different organelles react in mechanobiological processes remain …

We have created a benchmark set of quantum chemical structure–energy data denoted as
UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA …

We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two
DNA quadruplex (G-DNA) molecules, namely the antiparallel d (G4T4G4) 2 dimeric …

Knowledge of geometrical and physico-chemical properties of the sugar–phosphate
backbone substantially contributes to the comprehension of the structural dynamics, function …