Molecular mechanics force fields that explicitly account for induced polarization represent
the next generation of physical models for molecular dynamics simulations. Several …

Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is
determined by complementarity to a 20-nucleotide segment in its guide RNA. However …

Z-DNA duplexes are a particularly complicated test case for current force fields. We
performed a set of explicit solvent molecular dynamics (MD) simulations with various …

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 …

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 …

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 …

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …

The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …

Molecular simulation is a powerful computational tool for a broad range of applications
including the examination of materials properties and accelerating drug discovery. At the …