1,721,144 research outputs found
Inferring the diameter of a biopolymer from its stretching response
Full text linkWe investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides, and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with those obtained from standard entropic models, the approach allows us to extract viable estimates for the polymers diameter and granularity. This shows that the basic structural polymer features have such a profound impact on the elastic behavior that they can be recovered with the sole input of stretching measurements
Topological and entropic repulsion in biopolymers
No full textWe estimate numerically the entropic repulsion felt by two or more
approaching polymers with fixed topology. Our results complement field
theory estimates valid for infinitely long chains. For two loops, the
steric contributions to repulsion outweigh the topological one. When
many loops come together, the entropy loss scales nonlinearly with their
number. This could set a thermodynamic size for a 'rosette', a putative
organizing motif of interphase chromosomes
Hydrodynamics of non-homogeneous active gels
No full textWe present lattice Boltzmann simulations to study the hydrodynamics of
active fluids with spatially inhomogeneous activity. By patterning the
system so that there are stripes of active fluids intercalated by
passive regions, we show that it is possible to control the shape of the
resulting spontaneous flow. Even with one single active stripe, the
phenomenology is significantly richer than for uniform systems, and we
observe a transition between a shear-like and a Poiseuille like
spontaneous flow, corresponding to a switch between apparently free and
no slip hydrodynamic boundaries on the edge of the active stripe. With a
2-dimensional patterning, in which activity is confined to spherical
patches, we find that extensile gels tend to form rotating vortices
which can synchronise, whereas contractile ones show a more complicated
behaviour with spontaneous defect nucleation. We discuss possible
experimental realisations of the system and geometries we are interested
in, via, for instance, cytoskeletal fibers interacting with
micropatterned surfaces with immobilised molecular motors, or via
microfluidic devices containing bacterial colonies or suspensions
Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers
No full textWe study a spherically confined mixture of polymers and colloidal rings. Unlike in standard colloidpolymer mixtures, the polymers interact topologically with the rings by threading them. We find that, above a critical value of the ring radius, threading yields a topological transition from a fluid to a gel-like phase characterized by a space-spanning network of interlocked polymers and rings, which we refer to as a bicomponent gel, or bigel. By exploiting the mixture dual character (rings and polymers), we predict analytically the value of the critical radius. We also show that the mobility of entanglements in the mixture slows down upon entering the gel phase, due to topological hindrance arising from threadings, while the transition rates between topological states of the colloidal probes provide another strong dynamical signature of the gel phase
Permeative flows in cholesteric liquid crystals.
No full textWe use lattice Boltzmann simulations to solve the Beris-Edwards equations of motion for a cholesteric liquid crystal subjected to Poiseuille flow along the direction of the helical axis (permeative flow). The results allow us to clarify and extend the approximate analytic treatments currently available. We find that if the cholesteric helix is pinned at the boundaries there is an enormous viscosity increase. If, instead, the helix is free the velocity profile is flattened, but the viscosity is essentially unchanged. We highlight the importance of secondary flows, and, for higher flow velocities, we identify a flow-induced double twist structure in the director field--reminiscent of the texture characteristic of blue phases
Shear dynamics in cholesterics
No full textWe study shear dynamic in cholesteric liquid crystal using a lattice Boltzmann scheme that solves the full, three-dimensional Beris-Edwards equations of hydrodynamics. We show that the coupling between shear and the natural elastic deformation of cholesterics can induce twist in an initially isotropic phase. (c) 2005 Elsevier B.V. All rights reserved
Viscoelastic flows of cholesteric liquid crystals
No full textWe numerically solve the hydrodynamic equations of motion for a cholesteric liquid crystal under an imposed Poiseuille flow, by means of lattice Boltzmann simulations. The elasticity of the cholesteric helix couples to the external flow to give rise to a highly viscoelastic flow. This is a technically difficult problem for standard flow solvers due to its fully two-dimensional nature. We consider a helix with axis parallel to the boundaries, and at the same time to either the primary flow or the vorticity direction (we identify these two flow modes as permeation and vorticity mode respectively). We quantify the large difference found in the steady state director and velocity profiles, and in the apparent viscosities obtained in the two cases
Force-induced unfolding of a homopolymer on a fractal lattice: exact results versus mean-field predictions
No full textWe study the force-induced unfolding of a homopolymer on the three-dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest-neighbour sites not consecutive along the chain and to a stretching force. The hierarchical nature of the lattice we consider allows for an exact treatment which yields the phase diagram and the critical behaviour. We show that for this model mean-field predictions are not correct; in particular, in the exact phase diagram there is no low-temperature re-entrance, and we find that the force-induced unfolding transition below the theta temperature is of second order
Hydrodynamics and rheology of active liquid crystals: A numerical investigation
Full text linkWe report numerical studies of the hydrodynamics and rheology of an
active liquid crystal. We confirm the existence of a transition between
a passive and an active phase, with spontaneous flow in steady state. We
explore how the velocity profile changes with activity, and we point out
the difference in behavior for flow-aligning and tumbling materials. We
find that an active material can thicken or thin under a flow, or even
exhibit both behaviors as the forcing changes
Entropic approach curves of a polymer of fixed topology
No full textWe determine how the force needed to place a polymer close to a solid
wall varies with the positioning of the chain origin, which is kept
pinned. This force is purely entropic in origin as it arises from the
loss of available structures close to the wall. We show that with
present-day micromanipulation experiments it should be possible to
determine whether an initially linear chain forms a loop, e.g. when its
ends are rendered sticky, by measuring this entropic force. We discuss
the possibility to characterise knot topology via the same procedure
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