Polyampholytes are charged polymers with both positively and negatively charged groups.
The conformation of these polymers in solutions strongly depends on the distribution of …

We present a brief, and largely personal, history of computer simulations of DNA and RNA
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …

We present the first microsecond MD simulation of B-DNA. Trajectory shows good
agreement with available data and clarifies the μs dynamics of DNA. The duplex is sampling …

We describe herein a computationally intensive project aimed at carrying out molecular
dynamics (MD) simulations including water and counterions on B-DNA oligomers containing …

All atom molecular dynamics simulations have become a standard method for mapping
equilibrium protein dynamics and non-equilibrium events like folding and unfolding. Here …

Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers
containing all 136 unique tetranucleotide basepair steps are reported. The objective is to …

A reparameterization of the torsional parameters for the glycosidic dihedral angle, χ, for the
AMBER99 force field in RNA nucleosides is used to provide a modified force field …

▪ Abstract Is it by design or by default that water molecules are observed at the interfaces of
some protein-DNA complexes? Both experimental and theoretical studies on the …

The role of base motions in delocalization and propagation of charge through double helical
DNA must be established experimentally and incorporated into mechanistic descriptions of …