Condensed Matter Theory

Abstract:

We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore, the model reproduces the temperature dependence of the overstretching force well. The mechanism of overstretching is always force-induced melting by unpeeling from the free ends. That we never see S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that S-DNA is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.

Abstract:

Synchronization induced by long-range hydrodynamic interactions is attracting attention as a candidate mechanism behind coordinated beating of cilia and flagella. Here we consider a minimal model of hydrodynamic synchronization in the low Reynolds number limit. The model consists of rotors, each of which assumed to be a rigid bead making a fixed trajectory under periodically varying driving force. By a linear analysis, we derive the necessary and sufficient conditions for a pair of rotors to synchronize in phase. We also derive a non-linear evolution equation for their phase difference, which is reduced to minimization of an effective potential. The effective potential is calculated for a variety of trajectory shapes and geometries (either bulk or substrated), for which the stable and metastable states of the system are identified. Finite size of the trajectory induces asymmetry of the potential, which also depends sensitively on the tilt of the trajectory. Our results show that flexibility of cilia or flagella is {\it not} a requisite for their synchronized motion, in contrast to previous expectations. We discuss the possibility to directly implement the model and verify our results by optically driven colloids.

Abstract:

We study the nematic phase of rodlike f d-virus particles confined to channels with wedge-structured walls. Using laser scanning confocal microscopy we observe a splay-to-bend transition at the single particle level as a function of the wedge opening angle. Lattice Boltzmann simulations reveal the underlying origin of the transition and its dependence on nematic elasticity and wedge geometry. Our combined work provides a simple method to estimate the splay-to-bend elasticity ratios of the virus and offers a way to control the position of defects through the confining boundary conditions.