Stochastic thermodynamics as reviewed here systematically provides a framework for
extending the notions of classical thermodynamics such as work, heat and entropy …

I review single-molecule experiments (SMEs) in biological physics. Recent technological
developments have provided the tools to design and build scientific instruments of high …

Recent developments on fluorescent proteins and microscopy techniques have allowed the
probing of single molecules in a living bacterial cell with high specificity, millisecond time …

The mathematical theory of nonequilibrium steady state (NESS) has a natural application in
open biochemical systems which have sustained source (s) and sink (s) in terms of a …

For chemical reaction networks in a dilute solution described by a master equation, the
authors define energy and entropy on a stochastic trajectory and develop a consistent …

For a single enzyme or molecular motor operating in an aqueous solution of non-
equilibrated solute concentrations, a thermodynamic description is developed on the level of …

In the last decade, the thermostatted kinetic theory has been proposed as a general
paradigm for the modeling of complex systems of the active matter and, in particular, in …

Statistical mechanics is a powerful method for understanding equilibrium thermodynamics.
An equivalent theoretical framework for nonequilibrium systems has remained elusive. The …

Transition state or Kramers' rate theory has been used to quantify the kinetic speed of many
chemical, physical and biological equilibrium processes successfully. For non-equilibrium …

DNA methylation is an epigenetic mechanism that plays important roles in various biological
processes including transcriptional and post-transcriptional regulation, genomic imprinting …