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Register a new userCross-link governed dynamics of biopolymer networks
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Cytoskeletal networks of biopolymers are cross-linked by a variety of proteins. Experiments have shown that dynamic cross-linking with physiological linker proteins leads to complex stress relaxation and enables network flow at long times. We present a model for the mechanical properties of transient networks. By a combination of simulations and analytical techniques we show that a single microscopic timescale for cross-linker unbinding leads to a broad spectrum of macroscopic relaxation times, resulting in a weak power-law dependence of the shear modulus on frequency. By performing rheological experiments, we demonstrate that our model quantitatively describes the frequency behavior of actin network cross-linked with $alpha$-Actinin-$4$ over four decades in frequency.
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Following recent X-ray diffraction experiments by Wong, Li, and Safinya on biopolymer gels, we apply Onsager excluded volume theory to a nematic mixture of rigid rods and strong ``$pi/2$ cross-linkers obtaining a long-ranged, highly anisotropic depletion attraction between the linkers. This attraction leads to breakdown of the percolation theory for this class of gels, to breakdown of Onsagers second-order virial method, and to formation of heterogeneities in the form of raft-like ribbons.
We suggest a simple model for reversible cross-links, binding and unbinding to/from a network of semiflexible polymers. The resulting frequency dependent response of the network to an applied shear is calculated via Brownian dynamics simulations. It is shown to be rather complex with the timescale of the linkers competing with the excitations of the network. If the lifetime of the linkers is the longest timescale, as is indeed the case in most biological networks, then a distinct low frequency peak of the loss modulus develops. The storage modulus shows a corresponding decay from its plateau value, which for irreversible cross-linkers extends all the way to the static limit. This additional relaxation mechanism can be controlled by the relative weight of reversible and irreversible linkers.
The statistical mechanics of polymers grafted on surfaces has been the subject of intense research activity because of many potential applications. In this paper, we analytically investigate the conformational changes caused by a single cross-link on two ideal (Gaussian) chains grafted on a rigid planar surface. Both the cross-link and the surface reduce the number of allowed configurations. In the absence of the hard substrate, the sole effect of the cross-link is a reduction in the effective Kuhn length of a tethered chain. The cross-link induced shrinkage (collapse) of the grafted chains (mushrooms) turns out to be a reduction in the variance of the distribution of the height of the chain rather than a reduction of the height itself.
We study the statistical mechanics of counterion Wigner crystals associated with hexagonal bundles of chiral biopolymers. We show that, due to spontaneous chiral symmetry breaking induced by frustration, these Wigner crystals would be chiral even if the biopolymers themselves were not chiral. Using a duality transformation of the model onto a spin-charge Hamiltonian, we show that melting of the Wigner crystal is due to the unbinding of screw dislocations and that the melting temperature has a singular dependence on the intrinsic chirality of the biopolymers. Finally, we report that, if electrostatic interactions are strongly screened, the counterions can condense in the form of an intermediate achiral Wigner solid phase that melts by the unbinding of fractional topological charges.
Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the dependence of the asymmetry of the ellipsoid measured by the aspect ratio on the translocation time. Compared with an isotropic confinement (sphere), an anisotropic confinement (ellipsoid) with the same volume slows down the translocation, and the translocation time increases with increasing the aspect ratio of the ellipsoid. We further find that it takes different time for polymer translocation into the same ellipsoid through major-axis and minor-axis directions, depending on the average density of the whole chain in the ellipsoid, $phi$. For $phi$ lower than a critical value $phi_c$, the translocation through minor axis is faster, and vice versa. These complicated behaviors are interpreted by the degree of the confinement and anisotropic confinement induced folding of the translocated chain.
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