Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics.

Area of Science:

• Biophysics
• Polymer Physics
• Computational Biology

Background:

• Polymer ejection from confined spaces, like viral capsids, is fundamental to biological processes.
• Understanding these dynamics is crucial for fields ranging from drug delivery to viral infection mechanisms.

Purpose of the Study:

• To investigate the dynamics of flexible polymer ejection from a spherical capsid using Stochastic Rotation Dynamics (SRD).
• To compare SRD results with Langevin simulations and analyze the role of hydrodynamics in the ejection process.

Main Methods:

• Stochastic Rotation Dynamics (SRD) simulations were employed to model polymer ejection.
• Langevin simulations were used for comparison.
• Analysis focused on waiting times of individual polymer beads and radius of gyration.

Main Results:

• Inclusion of hydrodynamic interactions accelerates ejection and promotes polymer expansion outside the capsid, indicated by increased radius of gyration.
• Waiting time for ejection (t_w) follows a universal functional form dependent on the number of ejected monomers (s), with a transition to slower dynamics after ~63% ejection.
• A universal scaling function h(s/N_0) describes cumulative waiting time, driven by a superexponentially decreasing force at the pore.

Conclusions:

• The observed ejection dynamics and scaling behaviors are universal, with hydrodynamics primarily affecting the magnitude of waiting times.
• The force-distance relationship at the pore dictates the ejection time scaling, explaining superlinear scaling for short polymers and predicting linear scaling for long polymers.