Condensed Matter Theory

Abstract:

We use the stochastic rotation dynamics algorithm to investigate the packaging of flexible and semiflexible polymers into a capsid that is permeable to solvent molecules. The model takes into account hydrodynamic interactions arising due to local flow. The flexible chain maintains a random configuration as it is being fed into the capsid, in contrast to the semiflexible chain, whose configuration is initially spool-like, becoming more random at high packing. We measure the packing rate, which is found to decrease with the percentage of the chain packed and highlight the difference between the flexible and semiflexible chains. Reflecting experiments, we find pauses in the packing process for individual chains as the motor loses grip of the fluctuating beads. We also find that hydrodynamics is important, in that the packaging rate is faster when flow is included.

Abstract:

In a fluctuating medium, whether of quantum, thermal, or non-thermal origins, an interaction is induced between external objects that modify the fluctuations. These interactions can appear in a vast variety of systems, leading to a plethora of interesting phenomena. Notable examples of these include: 1. like-charge attraction in the presence of multivalent counterions; 2. Ludwig-Soret effect in charged colloids; 3. mass renormalization of moving defects in a phononic background and moving metallic objects in electromagnetic quantum vacuum; 4. dissipation due to motion-induced radiation. Another related class of problems corresponds to stirring the media by dynamic deformations of the embedded bodies and benefiting from the back-reaction of the stirred media for force generation, such as force generation in swimming. The fluctuation-induced forces are statistical in nature, and this could make their measurements very difficult, because the actual value of the force might deviate most of the time from the predicted average value.