Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …

About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming
nucleosomes. Even though the histone proteins that make up the core of nucleosomes are …

We present the results of microsecond molecular dynamics simulations carried out by the
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …

Last generation of force-fields are raising expectations on the quality of molecular dynamics
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …

A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-
stranded DNA is used to predict a sequence-averaged persistence length of l F= 53.5 nm in …

DNA supercoiling is central to many fundamental processes of living organisms. Its average
level along the chromosome and over time reflects the dynamic equilibrium of opposite …

Abstract Structure and deformability of the DNA double helix play a key role in protein and
small ligand binding, in genome regulation via looping, or in nanotechnology applications …

The structure of B-DNA, the physiological form of the DNA molecule, has been a central
topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was …

We present a new coarse grained method for the simulation of duplex DNA. The algorithm
uses a generalized multi-harmonic model that can represent any multi-normal distribution of …

We present a multi-laboratory effort to describe the structural and dynamical properties of
duplex B-DNA under physiological conditions. By processing a large amount of atomistic …