The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

The scope of this review is the nature and dynamics of the singlet excited electronic states
created in nucleic acids and their constituents by UV light. Interest in the UV photochemistry …

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 …

Many interesting dynamic properties of biological molecules cannot be simulated directly
using molecular dynamics because of nanosecond time scale limitations. These systems are …

Molecular dynamics simulation methods produce trajectories of atomic positions (and
optionally velocities and energies) as a function of time and provide a representation of the …

Generalized Born (GB) models provide an attractive way to include some thermodynamic
aspects of aqueous solvation into simulations that do not explicitly model the solvent …

Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the
folding and dynamics of RNA and DNA and their complexes with proteins and with each …

Molecular dynamics simulations rely on integrating the classical (Newtonian) equations of
motion for a molecular system and thus, sample a microcanonical (constant-energy) …

The structure, function and reactions of nucleic acids are central to molecular biology and
are crucial for the understanding of complex biological processes involved. Revised and …

Atomic-scale modeling of compacted nucleic acids has the ability to reveal the inner
workings of spectacular biomolecular machines, yet the outcome of such modeling efforts …