Non-equilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studie
d high-aspect-ratio self-propelled rods over a wide range of packing fraction and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluid-like behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition which, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped microorganisms.
Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size.
Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells.
Many soft-matter and biophysical systems are composed of monomers which reversibly assemble into rod-like aggregates. The aggregates can then order into liquid-crystal phases if the density is high enough, and liquid-crystal ordering promotes increas
ed growth of aggregates. Systems that display coupled aggregation and liquid-crystal ordering include wormlike micelles, chromonic liquid crystals, DNA and RNA, and protein polymers and fibrils. Coarse-grained molecular models that capture key features of coupled aggregation and liquid-crystal ordering common to many different systems are lacking; in particular, the role of monomer aspect ratio and aggregate flexibility in controlling the phase behavior are not well understood. Here we study a minimal system of sticky cylinders using Monte Carlo simulations and analytic theory. Cylindrical monomers interact primarily by hard-core interactions but can stack and bind end to end. We present results for several different cylinder aspect ratios and a range of end-to-end binding energies. The phase diagrams are qualitatively similar to those of chromonic liquid crystals, with an isotropic-nematic-columnar triple point. The location of the triple point is sensitive to the monomer aspect ratio.We find that the aggregate persistence length varies with temperature in a way that is controlled by the interaction potential; this suggests that the form of the interaction potential affects the phase behavior of the system. Our analytic theory shows improvement compared to previous theory in quantitatively predicting the I-N transition for relatively stiff aggregates, but requires a better treatment of aggregate flexibility.
Proteins from the kinesin-8 family promote microtubule (MT) depolymerization, a process thought to be important for the control of microtubule length in living cells. In addition to this MT shortening activity, kinesin 8s are motors that show plus-en
d directed motility on MTs. Here we describe a simple model that incorporates directional motion and destabilization of the MT plus end by kinesin 8. Our model quantitatively reproduces the key features of length-vs-time traces for stabilized MTs in the presence of purified kinesin 8, including length-dependent depolymerization. Comparison of model predictions with experiments suggests that kinesin 8 depolymerizes processively, i.e., one motor can remove multiple tubulin dimers from a stabilized MT. Fluctuations in MT length as a function of time are related to depolymerization processivity. We have also determined the parameter regime in which the rate of MT depolymerization is length dependent: length-dependent depolymerization occurs only when MTs are sufficiently short; this crossover is sensitive to the bulk motor concentration.
