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, ${\varphi }^{*}$, which scales as ${\varphi }^{*}\sim {\left(a_c/L_p\right)}^{1/3}$ for $a_c\gg a_m$ and ${\varphi }^{*}\sim {\left(a_c/L_p\right)}^{1/3}{\left(a_c/a_m\right)}^{1/2}$ for $a_c\ll a_m$, where $a_c$ is the crowder diameter, $a_m$ is the monomer diameter, and $L_p$ is the polymer persistence length. For DNA, ${\varphi }^{*}$ is estimated to be around 0.25 for crowders with $a_c=2\mathrm{nm}$. We find that ${\varphi }^{*}$ also strongly depends on the shape of the channel cross section, and ${\varphi }^{*}$ 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.

Close

PrevNext

View figure in article

• Depletion interactions
• Single polymer chains
• Wormlike chain
• Molecular dynamics
• Polymer scaling theory