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 …

The interconversion between the well-characterized A-and B-forms of DNA is a structural
transition for which the intermediate states and the free energy difference between the two …

The eight nucleoside constituents of nucleic acids were simulated for 50 ns in explicit water
with molecular dynamics. This provides equilibrium populations of the torsional degrees of …

The essential dynamics of different normal and chemically modified DNA duplexes
pertaining to the B family have been extensively explored from molecular dynamics …

To gain a deeper insight into cellular processes such as transcription and translation, one
needs to uncover the mechanisms controlling the configurational changes of nucleic acids …

As a result of important methodological advances, the number of molecular dynamics (MD)
simulations related to RNA systems has become significant, and simulations on more than …

Publisher Summary This chapter discusses the molecular modeling and atomistic simulation
of nucleic acids. Molecular modeling and biomolecular simulation methods have been …

As a result of important methodological advances, the number of molecular dynamics (MD)
simulations related to RNA systems has become significant, and simulations on more than …