Rings in random environments: sensing disorder through topology.

Area of Science:

• Biophysics
• Computational Biology
• Polymer Physics

Background:

• DNA gel electrophoresis is a standard technique for separating DNA fragments.
• Understanding the microscopic structure of gels is crucial for optimizing electrophoresis.
• Topological properties of polymers can influence their behavior in complex media.

Purpose of the Study:

• To investigate the role of topology in DNA gel electrophoresis.
• To use molecular dynamics simulations to model disordered gel environments.
• To assess the utility of ring polymers as probes for microscopic gel disorder.

Main Methods:

• Molecular dynamics simulations of a 3D gel model with randomly removed obstacles.
• Measuring the electrophoretic mobility of ring and linear polymers through the simulated gel.
• Comparing simulation results with an analytical model for non-equilibrium differential mobility.

Main Results:

• Ring polymers exhibit sensitivity to microscopic gel disorder, unlike linear polymers.
• The electrophoretic mobility of ring polymers serves as a reliable indicator of gel structural changes.
• Simulations show excellent agreement with the analytical model for non-equilibrium differential mobility.

Conclusions:

• Ring polymers offer a novel, non-invasive method to probe microscopic disorder in gels using topology.
• This approach enhances the understanding of DNA gel electrophoresis and polymer behavior in complex environments.
• The findings validate the use of molecular dynamics simulations and analytical models in studying such systems.