With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last
decades, base stacking has been extensively studied by experimental and theoretical …

The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al.
AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were …

DNA-based machines that walk by converting chemical energy into controlled motion could
be of use in applications such as next-generation sensors, drug-delivery platforms and …

To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …

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

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …

Molecular dynamics (MD) simulations for RNA tetramers r (AAAA), r (CAAU), r (GACC), and r
(UUUU) are benchmarked against 1H–1H NOESY distances and 3 J scalar couplings to test …

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 …