In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, 
, which scales as 
for 
and 
for 
, where 
is the crowder diameter, 
is the monomer diameter, 
is the polymer persistence length. For DNA, is estimated to be around 0.25 for crowders with = 2 nm. We find that 
also strongly depends on the shape of the channel cross-section, and is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
Read more at Physical Review E:
https://journals.aps.org/pre/abstract/10.1103/PhysRevE.104.054502
08 Nov 2021