Influence of Crowder Geometry and Flexibility on Polymer Translocation Dynamics

Area of Science:

• Polymer physics
• Biophysics
• Soft matter physics

Background:

• Polymer dynamics and molecular crowding are vital in biological and synthetic systems.
• Understanding polymer translocation through nanopores is key for biological processes and nanotechnology.

Purpose of the Study:

• To investigate polymer translocation through nanopores under varying molecular crowding conditions.
• To analyze the influence of crowder geometry (length, rigidity) and density on translocation dynamics.

Main Methods:

• Coarse-grained molecular dynamics simulations were used.
• Polymer translocation through a nanopore was simulated.
• Crowders were modeled as rigid rods with varying lengths and bending rigidities.

Main Results:

• Increased crowder area fraction (ϕ) significantly reduced translocation probability.
• Longer and more rigid crowders amplified steric hindrance and the entropic barrier.
• Translocation time exhibited a non-monotonic trend, indicating competing effects of crowder compression and pushing.

Conclusions:

• Crowding geometry and rigidity critically influence polymer transport through nanopores.
• Findings have implications for DNA translocation and synthetic nanopore applications.
• Limitations include the absence of explicit hydrodynamic interactions and idealized crowder-polymer interactions.