To perform their functions, transcription factors and DNA-repair/modifying enzymes
randomly search DNA in order to locate their specific targets on DNA. Discrete-state …

ABSTRACT “Gating” is a widely observed phenomenon in biochemistry that describes the
transition between the activated (or open) and deactivated (or closed) states of an ion …

The Journal of Chemical Physics article collection on Markov Models of Molecular Kinetics
(MMMK) features recent advances in developing and using Markov State Models (MSMs) 1 …

Protein searching and binding to specific sites on DNA is a fundamentally important process
that marks the beginning of all major cellular transformations. While the dynamics of protein …

For two molecules to react they first have to meet. Yet, reaction times are rarely on par with
the first-passage times that govern such molecular encounters. A prime reason for this …

Reaction coordinates chart pathways from reactants to products of chemical reactions.
Determination of reaction coordinates from ensembles of molecular trajectories has thus …

In a process known as facilitated diffusion, DNA-binding proteins find their target sites by
combining three-dimensional diffusion and one-dimensional scanning of the DNA …

Gated first-passage processes, where completion depends on both hitting a target and
satisfying additional constraints, are prevalent across various fields. Despite their …

Gene regulation is one of the most important fundamental biological processes in living
cells. It involves multiple protein molecules that locate specific sites on DNA and assemble …

Protein–DNA interactions are important for all biological processes and involve the process
of proteins searching for and recognizing specific binding sites on the DNA. Many aspects of …