We develop a theory for the rapid search of specific sites on DNA, via a mechanism in which
a nonspecifically-bound protein can switch between two conformations. In the “inactive” …

Electrostatic interactions are important for understanding molecular interactions, since they
are long-range interactions and can guide binding partners to their correct binding positions …

The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a
search technique in which proteins slide, hop along the DNA contour or perform inter …

The increasing call for an overall picture of the interactions between the components of a
biological system that give rise to the observed function is often summarized by the …

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 …

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental
binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion …

Often considered the workhorse of the cellular machinery, proteins are responsible for
functions ranging from molecular motors to signaling. The broad recognition of their …

Diffusion is a ubiquitous phenomenon that impacts virtually all processes that involve
random fluctuations, and as such, the foundational work of Smoluchowski has proven to be …

The process of binding of small ligands to dihydrofolate reductase protein has been
investigated using all-atom molecular dynamics simulations. The existence of a mechanism …

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the
volume excluded by solute “obstacles” and (2) long-range interactions between those …