Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …

The focus here is on incorporating electronic polarization into classical molecular
mechanical force fields used for macromolecular simulations. First, we briefly examine …

Molecular dynamics simulations are well established for the study of biomolecular systems.
Within these simulations, energy functions known as force fields are used to determine the …

A current emphasis in empirical force fields is on the development of potential functions that
explicitly treat electronic polarizability. In the present article, the commonly used …

It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …

Lennard-Jones (LJ) parameters for a variety of model compounds have previously been
optimized within the CHARMM Drude polarizable force field to reproduce accurately pure …

A polarizable force field for nucleic acid bases based on the classical Drude oscillator model
is presented. Parameter optimization was performed to reproduce crystallographic …

In this work, we assess several popular atomic partial charge schemes with the view of
accurately quantifying charge distribution, dipole moments and charge transfer in routinely …

It has become possible to distinguish DNA molecules of different nucleotide sequences by
measuring ion current passing through a narrow pore containing DNA. To assist …

It has been known for some time that the double-helix is not a uniform structure but rather
exhibits sequence-specific variations that, combined with base-specific intermolecular …