2,583 research outputs found
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
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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
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