Different theoretical methods for the description of nucleic acid structures are reviewed.
Firstly, we introduce the concept of classical force-field in the context of nucleic acid …

Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …

Recent years have seen considerable progress in simulations of nucleic acids.
Improvements in force fields, simulation techniques and protocols, and increasing computer …

Molecular dynamics simulations have been performed to characterize the conformation of
DNA that is present when DNA links gold nanoparticles to form nanoparticle superlattice …

Deformation of DNA takes place quite often due to binding of small molecules or proteins
with DNA. Such deformation is significant due to minor groove binding and, besides …

The ability to determine the stability of non-Watson− Crick base pairs in DNA by computer
simulation is a necessary prerequisite for quantitative theoretical studies of DNA replication …

One of the common mechanisms of DNA bending by minor groove-binding proteins is the
insertion of protein side chains between basepair steps, exemplified in TBP (TATA box …

Assembly of transcription pre-initiation complexes proceeds from the initial complex formed
between" TATA" bearing promoter DNA and the TATA-binding protein (TBP). Our laboratory …

The fundamental relationship between DNA sequence/deformability and biological function
has attracted numerous experimental and theoretical studies. A classic prototype system …

We model the site-specific association of a protein molecule with DNA as a random walk
with random jumps. Results show that the simultaneous occurrence of processes such as …