DNA is stored in vivo in a highly compact, so-called condensed phase, where gene
regulatory processes are governed by the intricate interplay between different states of DNA …

Ligand-and protein-DNA equilibria are extremely sensitive to solution conditions (eg, salt,
temperature, and pH), and, in general, the effects of different solution variables are …

Some problems of describing biological systems with the use of entropy as a measure of the
complexity of these systems are considered. Entropy is studied both for the organism as a …

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule
passes from the region of high viscosity values to the region of low values, open states …

Statistical–mechanical lattice models for protein–DNA binding are well established as a
method to describe complex ligand binding equilibria measured in vitro with purified DNA …

The transfer matrix methodology is proposed as a systematic tool for the statistical–
mechanical description of DNA–protein–drug binding involved in gene regulation. We show …

Ligands change the chemical and mechanical properties of polymers. In particular, single
strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA) …

Correlation functions and spectral density of the number of molecules of ligand bound to
DNA are calculated theoretically. Kinetics of rates of formation and decomposition of the …

Nucleosomes, the basic repeating unit of chromatin, consist of 147 basepairs of DNA that
are wrapped in almost two turns around a histone protein octamer core. Because∼ 3/4 of …

A method using binding site “neighbor-effect” parameters (NEPs) is introduced to evaluate
the effects of interaction between adjacent ligands on their binding to an infinite linear lattice …