2,548 research outputs found
Deformation of crosslinked semiflexible polymer networks
Networks of filamentous proteins play a crucial role in cell mechanics. These
cytoskeletal networks, together with various crosslinking and other associated
proteins largely determine the (visco)elastic response of cells. In this letter
we study a model system of crosslinked, stiff filaments in order to explore the
connection between the microstructure under strain and the macroscopic response
of cytoskeletal networks. We find two distinct regimes as a function primarily
of crosslink density and filament rigidity: one characterized by affine
deformation and one by non-affine deformation. We characterize the crossover
between these two.Comment: Typos fixed and some technical details clarified. To appear in Phys.
Rev. Let
Non-equilibrium mechanics and dynamics of motor activated gels
The mechanics of cells is strongly affected by molecular motors that generate
forces in the cellular cytoskeleton. We develop a model for cytoskeletal
networks driven out of equilibrium by molecular motors exerting transient
contractile stresses. Using this model we show how motor activity can
dramatically increase the network's bulk elastic moduli. We also show how motor
binding kinetics naturally leads to enhanced low-frequency stress fluctuations
that result in non-equilibrium diffusive motion within an elastic network, as
seen in recent \emph{in vitro} and \emph{in vivo} experiments.Comment: 21 pages, 8 figure
Active biopolymer networks generate scale-free but euclidean clusters
We report analytical and numerical modelling of active elastic networks,
motivated by experiments on crosslinked actin networks contracted by myosin
motors. Within a broad range of parameters, the motor-driven collapse of active
elastic networks leads to a critical state. We show that this state is
qualitatively different from that of the random percolation model.
Intriguingly, it possesses both euclidean and scale-free structure with Fisher
exponent smaller than . Remarkably, an indistinguishable Fisher exponent and
the same euclidean structure is obtained at the critical point of the random
percolation model after absorbing all enclaves into their surrounding clusters.
We propose that in the experiment the enclaves are absorbed due to steric
interactions of network elements. We model the network collapse, taking into
account the steric interactions. The model shows how the system robustly drives
itself towards the critical point of the random percolation model with absorbed
enclaves, in agreement with the experiment.Comment: 6 pages, 7 figure
Critical behaviour in the nonlinear elastic response of hydrogels
In this paper we study the elastic response of synthetic hydrogels to an
applied shear stress. The hydrogels studied here have previously been shown to
mimic the behaviour of biopolymer networks when they are sufficiently far above
the gel point. We show that near the gel point they exhibit an elastic response
that is consistent with the predicted critical behaviour of networks near or
below the isostatic point of marginal stability. This point separates rigid and
floppy states, distinguished by the presence or absence of finite linear
elastic moduli. Recent theoretical work has also focused on the response of
such networks to finite or large deformations, both near and below the
isostatic point. Despite this interest, experimental evidence for the existence
of criticality in such networks has been lacking. Using computer simulations,
we identify critical signatures in the mechanical response of sub-isostatic
networks as a function of applied shear stress. We also present experimental
evidence consistent with these predictions. Furthermore, our results show the
existence of two distinct critical regimes, one of which arises from the
nonlinear stretch response of semi-flexible polymers.
The mechanical response of semiflexible networks to localized perturbations
Previous research on semiflexible polymers including cytoskeletal networks in
cells has suggested the existence of distinct regimes of elastic response, in
which the strain field is either uniform (affine) or non-uniform (non-affine)
under external stress. Associated with these regimes, it has been further
suggested that a new fundamental length scale emerges, which characterizes the
scale for the crossover from non-affine to affine deformations. Here, we extend
these studies by probing the response to localized forces and force dipoles. We
show that the previously identified nonaffinity length [D.A. Head et al. PRE
68, 061907 (2003).] controls the mesoscopic response to point forces and the
crossover to continuum elastic behavior at large distances.Comment: 16 pages, 18 figures; substantial changes to text and figures to
clarify the crossover to continuum elasticity and the role of finite-size
effect
Nontargeted biomonitoring of halogenated organic compounds in two ecotypes of bottlenose dolphins (Tursiops truncatus) from the Southern California Bight.
Targeted environmental monitoring reveals contamination by known chemicals, but may exclude potentially pervasive but unknown compounds. Marine mammals are sentinels of persistent and bioaccumulative contaminants due to their longevity and high trophic position. Using nontargeted analysis, we constructed a mass spectral library of 327 persistent and bioaccumulative compounds identified in blubber from two ecotypes of common bottlenose dolphins (Tursiops truncatus) sampled in the Southern California Bight. This library of halogenated organic compounds (HOCs) consisted of 180 anthropogenic contaminants, 41 natural products, 4 with mixed sources, 8 with unknown sources, and 94 with partial structural characterization and unknown sources. The abundance of compounds whose structures could not be fully elucidated highlights the prevalence of undiscovered HOCs accumulating in marine food webs. Eighty-six percent of the identified compounds are not currently monitored, including 133 known anthropogenic chemicals. Compounds related to dichlorodiphenyltrichloroethane (DDT) were the most abundant. Natural products were, in some cases, detected at abundances similar to anthropogenic compounds. The profile of naturally occurring HOCs differed between ecotypes, suggesting more abundant offshore sources of these compounds. This nontargeted analytical framework provided a comprehensive list of HOCs that may be characteristic of the region, and its application within monitoring surveys may suggest new chemicals for evaluation
Magnetic anisotropy of vicinal (001) fcc Co films: role of crystal splitting and structure relaxation in step-decoration effect
The uniaxial in-plane magnetic anisotropy (UIP-MA) constant is calculated for
a single step on the (001) surface of fcc Co() films. The calculations are
done for both an undecorated step and the step decorated with one or more, up
to 7, Cu wires. Our objective is to explain the mechanisms by which the
decoration decreases the UIP-MA constant, which is the effect observed
experimentally for ultrathin Co films deposited on vicinal (001) Cu surfaces
and can lead to reorientation of magnetization within the film plane.
Theoretical calculations performed with a realistic tight-binding model show
that the step decoration changes the UIP-MA constant significantly only if the
splitting between the on-site energies of various -orbitals is included for
atoms located near the step edge. The local relaxation of atomic structure
around the step is also shown to have a significant effect on the shift of the
UIP-MA constant. The influence of these two relevant factors is analyzed
further by examining individual contributions to the UIP-MA constant from atoms
around the step. The magnitude of the obtained UIP-MA shift agrees well with
experimental data. It is also found that an additional shift due to possible
charge transfer between Cu and Co atoms is very small.Comment: 12 pages,9 figures, RevTeX, submitted to Physical Review B version 3:
additions to content version 2: minor correction
Actively Contracting Bundles of Polar Filaments
We introduce a phenomenological model to study the properties of bundles of
polar filaments which interact via active elements. The stability of the
homogeneous state, the attractors of the dynamics in the unstable regime and
the tensile stress generated in the bundle are discussed. We find that the
interaction of parallel filaments can induce unstable behavior and is
responsible for active contraction and tension in the bundle. Interaction
between antiparallel filaments leads to filament sorting. Our model could apply
to simple contractile structures in cells such as stress fibers.Comment: 4 pages, 4 figures, RevTex, to appear in Phys. Rev. Let
Simulation of associative learning with the replaced elements model
Associative learning theories can be categorised according to whether they treat the representation of stimulus compounds in an elemental or configural manner. Since it is clear that a simple elemental approach to stimulus representation is inadequate there have been several attempts to produce more elaborate elemental models. One recent approach, the Replaced Elements Model (Wagner, 2003), reproduces many results that have until recently been uniquely predicted by Pearce’s Configural Theory (Pearce, 1994). Although it is possible to simulate the Replaced Elements Model using “standard” simulation programs the generation of the correct stimulus representation is complex. The current paper describes a method for simulation of the Replaced Elements Model and presents the results of two example simulations that show differential predictions of Replaced Elements and Pearce’s Configural Theor
Velocity distributions in dissipative granular gases
Motivated by recent experiments reporting non-Gaussian velocity distributions
in driven dilute granular materials, we study by numerical simulation the
properties of 2D inelastic gases. We find theoretically that the form of the
observed velocity distribution is governed primarily by the coefficient of
restitution and , the ratio between the average number of
heatings and the average number of collisions in the gas. The differences in
distributions we find between uniform and boundary heating can then be
understood as different limits of , for and
respectively.Comment: 5 figure
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