Prolonging assembly through dissociation:A self assembly paradigm in microtubules

We study a one-dimensional model of microtubule assembly/disassembly in which GTP bound to tubulins within the microtubule undergoes stochastic hydrolysis. In contrast to models that only consider a cap of GTP-bound tubulin, stochastic hydrolysis allows GTP-bound tubulin remnants to exist within the microtubule. We find that these buried GTP remnants enable an alternative mechanism of recovery from shrinkage, and enhances fluctuations of filament lengths. Under conditions for which this alternative mechanism dominates, an increasing depolymerization rate leads to a decrease in dissociation rate and thus a net increase in assembly.Comment: accepted for publication in Physical Review

Mechanisms of kinetic trapping in self-assembly and phase transformation

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions

Wave coupling from the lower to the middle thermosphere: Effects of mean winds and dissipation

Recent observational and modeling evidence has demonstrated that planetary waves can modulate atmospheric tides, and secondary waves arising from their nonlinear interactions are an important source of both temporal and longitude variability in the thermosphere. While significant progress has been made on understanding how this form of vertical coupling occurs, uncertainty still exists on how the horizontal structures of primary and secondary waves evolve with height and the processes responsible for this evolution, in part due to lack of global observations between 120ækm and 260ækm. In this work we employ a Thermosphere Ionosphere Mesosphere Electrodynamics general circulation model simulation covering all of 2009 that is forced by Modern-Era Retrospective Analysis for Research and Applications dynamical fields, to assess the relative contribution of zonal mean winds and molecular dissipation on the vertical coupling of the eastward propagating diurnal tide with zonal wave number 3 (DE3), the 3æday ultrafastæKelvin wave, and the secondary waves arising from their nonlinear interaction. By developing and applying a new analytic formulation describing the latitudinal structure of an equatorially trapped wave subject to dissipation and background winds, we show that dissipation is the primary contributor to the broadening of the latitudinal structures with height, while asymmetries in the background wind field are responsible for the distortion of the height-latitude structures. ©2017. American Geophysical Union. All Rights Reserved

Excitable Patterns in Active Nematics

We analyze a model of mutually-propelled filaments suspended in a two-dimensional solvent. The system undergoes a mean-field isotropic-nematic transition for large enough filament concentrations and the nematic order parameter is allowed to vary in space and time. We show that the interplay between non-uniform nematic order, activity and flow results in spatially modulated relaxation oscillations, similar to those seen in excitable media. In this regime the dynamics consists of nearly stationary periods separated by "bursts" of activity in which the system is elastically distorted and solvent is pumped throughout. At even higher activity the dynamics becomes chaotic.Comment: 4 pages, 4 figure

Active liquid crystals powered by force-sensing DNA-motor clusters

Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale non-equilibrium dynamics of active nematics.Comment: main text: text 19 pages, 6 figures. Supplementary information: text 9 pages, 12 figure