Comparative study of polymer looping kinetics in passive and active environments

Understanding polymer behavior in complex environments remains a challenge in soft matter physics. Looping kinetics are central to biological functions like DNA replication and protein folding. Prior research has shown that passive crowding affects polymer conformation and dynamics. However, the role of active crowders in such processes remains unclear. This uncertainty drives the need for studies that distinguish passive from active effects. Current models do not fully capture the interplay of activity and crowding in polymer systems. No prior work had resolved the dual roles of active crowders in promoting or inhibiting looping. This gap motivated the use of Langevin dynamics to explore polymer looping in active environments.

The study aims to compare polymer looping kinetics in passive and active environments. It focuses on how active crowders influence looping probabilities and times. The specific problem is to identify how crowder size, activity, and density affect polymer behavior. The motivation stems from the need to understand biological processes in crowded, active systems. The researchers propose to use Langevin dynamics simulations to model these effects. They aim to clarify the transition between facilitation and inhibition in active systems. The study also seeks to explain the mechanisms behind observed looping behaviors. This work provides a framework for interpreting polymer dynamics in living cells.

The team employed Langevin dynamics simulations to model polymer looping in controlled environments. They varied parameters such as crowder size, activity levels, and volume fractions. Looping probabilities and unlooping times were calculated for each condition. The simulations tracked polymer conformations and interactions with crowders. Free-energy barriers and diffusion rates were analyzed to explain looping mechanisms. The researchers compared results from passive and active systems to identify differences. Phase diagrams were constructed to map transitions between facilitation and inhibition. This approach allowed for a detailed exploration of polymer behavior in complex environments.

The study found a facilitation-inhibition transition in active systems based on crowder size and force. Active crowders with sizes similar to polymer monomers most effectively promoted looping. Conversely, crowders of size similar to the polymer's gyration radius inhibited looping. For small active crowders, increased diffusion rates enhanced both looping and unlooping. Moderate-sized crowders caused polymer swelling, leading to inhibited looping. Large active crowders induced a non-cage effect, increasing unlooping free-energy barriers. Volume-fraction dependencies in active baths showed significant deviations from passive systems. These findings highlight the contrasting effects of activity and crowding on polymer dynamics.

The authors propose that active crowders can either facilitate or inhibit polymer looping. They clarify the two-fold role of activity depending on crowder size and force. The study demonstrates that small active crowders enhance diffusion and promote looping. Moderate-sized crowders lead to polymer swelling and inhibited looping. Large active crowders induce a non-cage effect, increasing unlooping barriers. Volume-fraction effects in active systems differ sharply from those in passive environments. These results suggest that activity and crowding have opposing effects on polymer behavior. The findings provide a framework for understanding polymer dynamics in active biological systems.