Gene expression has a stochastic component because of the single-molecule nature of the
gene and the small number of copies of individual DNA-binding proteins in the cell. We show …

Three-dimensional genome structure and dynamics play critical roles in regulating DNA
functions. Flexible chromatin structure and movements suggested that the genome is …

Understanding chromatin organization and dynamics is important, since they crucially affect
DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing …

In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains,
for various cellular functions. However, their physical nature in living cells remains unclear …

The actomyosin molecular motor, the motor composed of myosin II and actin filament, is
responsible for muscle contraction, converting chemical energy into mechanical work. Although …

Intermittent and chaotic motions of the hydrogen bond network are studied with the molecular
dynamics (MD) simulation. By analyzing the fluctuation in the radial distribution function, it …

Spatiotemporal fluctuations of the local structure in liquid water are studied with the
molecular-dynamics simulation. At temperatures around and above the melting point, each molecule …

Eukaryotic chromatin is a negatively charged long polymer composed of genomic DNA,
histones, and various proteins. The charged property causes the chromatin structure to be …

Although chromatin organization and dynamics play a critical role in gene transcription, how
they interplay remains unclear. To approach this issue, we investigated genome-wide …

We present a self-consistent field approximation approach to the problem of the genetic
switch composed of two mutually repressing/activating genes. The protein and DNA state …