We investigate the distribution of bubble lifetimes and bubble lengths in DNA at
physiological temperature, by performing extensive molecular dynamics simulations with the …

We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-
Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov …

We study the role of cations on the stability of double stranded DNA (dsDNA) molecules. It is
known that the two strands of double stranded DNA (dsDNA) have negative charge due to …

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base
pairs are presented for different gene promoters and corresponding mutants that either …

Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand,
conferring greater strength on the hydrogen bonds that connect complementary strands into …

Abstract Information about molecular interactions in DNA can be obtained from experimental
melting temperature data by using mesoscopic statistical physics models. Here, we extend …

To exploit the formation of DNA duplexes, the charge repulsion between complementary
DNA strands can be reduced by adding salts or by replacing the negatively charged natural …

A mesoscopic model which allows us to identify and quantify the strength of binding sites in
DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for …

The stability of DNA molecules during viral or biotechnological encapsulation is a topic of
active current research. We studied the thermal stability of double-stranded DNA molecules …

The identification of protein binding sites in promoter sequences is a key problem to
understand and control regulation in biochemistry and biotechnological processes. We use …