Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …

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 …

A string of nucleotides confined within a protein capsid contains all the instructions
necessary to make a functional virus particle, a virion. Although the structure of the protein …

We present a physics-based machine learning approach to predict in vitro transcription
factor binding affinities from structural and mechanical DNA properties directly derived from …

The linear sequence of DNA provides invaluable information about genes and their
regulatory elements along chromosomes. However, to fully understand gene function and …

Diverse DNA-deforming processes are impacted by the local mechanical and structural
properties of DNA, which in turn depend on local sequence and epigenetic modifications …

Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which
assumes that the flexibility of DNA can be expressed as local harmonic movements (at the …

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

We demonstrate that nucleosomes placed in the gene body can be accurately located from
signal decay theory assuming two emitters located at the beginning and at the end of genes …

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 …