In the context of molecular dynamics simulations of proteins, the term “force field” refers to
the combination of a mathematical formula and associated parameters that are used to …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Nucleic acids are polyanionic molecules that were historically considered to be solely
surrounded by a shell of water molecules and a neutralizing cloud of monovalent and …

Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report
the discovery of specific unstacking effects in certain semihydrophobic environments. Water …

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural
diversity. Some structural variations are linked to sequence and may serve as signaling units …

Recently we presented a first-generation all-atom Drude polarizable force field for DNA
based on the classical Drude oscillator model, focusing on optimization of key dihedral …

Until nowadays most infrared microspectroscopy (IRMS) experiments on biological
specimens (ie, tissues or cells) have been routinely carried out on fixed or dried samples in …

Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of
melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate …

This work investigates the effects of dielectric environment and cluster shape on electronic
excitations of fluorescent DNA-stabilized silver clusters, AgN–DNA. We first establish that the …

The right-handed DNA helix exhibits two major conformations, A-DNA and B-DNA,
depending on the environmental conditions. The B-DNA to A-DNA (B→ A) transition is …