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 …

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2
Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins …

The sequence-dependent DNA deformability at the basepair step level was investigated
using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA …

The improvements of the force fields and the more accurate treatment of long-range
interactions are providing more reliable molecular dynamics simulations of nucleic acids …

We present theoretical work on the electronic states in a model DNA double helix of poly
(dA)− poly (dT)(10 base pairs) as the molecule undergoes thermal fluctuations at room …

Reversible transitions between the A-and B-forms of DNA are obtained in free molecular
dynamics simulations of a single double helix immersed in a water drop with Na+ …

The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate
the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the …

The review is focused on issues of transferability of the context-sensitive conformational
characteristics of DNA estimated from crystallographic structural data on the DNA in …

Molecular dynamics simulation of the decamer d (ATGCAGTCAG) 2 in aqueous solution,
electroneutralized by Li+ ions has been carried out. Emphasis is on the verification of the …

Biomolecules, such as proteins and nucleic acids, are heteropolymers, the repeating units of
which are chosen from a finite set of simple organic molecules that share certain …