6,437 research outputs found
Universality of the off-equilibrium response function in the kinetic Ising chain
The off-equilibrium response function and autocorrelation
function of an Ising chain with spin-exchange dynamics are studied
numerically and compared with the same quantities in the case of spin-flip
dynamics. It is found that, even though these quantities are separately
different in the two cases, the parametric plot of versus
is the same. While this result could be expected in higher
dimensionality, where is related to the equilibrium state, it is far
from trivial in the one dimensional case where this relation does not hold. The
origin of the universality of is traced back to the optimization of
domains position with respect to the perturbing external field. This mechanism
is investigated resorting to models with a single domain moving in a random
environment.Comment: 24 pages, 7 figure
Static non-reciprocity in mechanical metamaterials
Reciprocity is a fundamental principle governing various physical systems,
which ensures that the transfer function between any two points in space is
identical, regardless of geometrical or material asymmetries. Breaking this
transmission symmetry offers enhanced control over signal transport, isolation
and source protection. So far, devices that break reciprocity have been mostly
considered in dynamic systems, for electromagnetic, acoustic and mechanical
wave propagation associated with spatio-temporal variations. Here we show that
it is possible to strongly break reciprocity in static systems, realizing
mechanical metamaterials that, by combining large nonlinearities with suitable
geometrical asymmetries, and possibly topological features, exhibit vastly
different output displacements under excitation from different sides, as well
as one-way displacement amplification. In addition to extending non-reciprocity
and isolation to statics, our work sheds new light on the understanding of
energy propagation in non-linear materials with asymmetric crystalline
structures and topological properties, opening avenues for energy absorption,
conversion and harvesting, soft robotics, prosthetics and optomechanics.Comment: 19 pages, 3 figures, Supplementary information (11 pages and 5
figures
Efficient simulation of non-crossing fibers and chains in a hydrodynamic solvent
An efficient simulation method is presented for Brownian fiber suspensions,
which includes both uncrossability of the fibers and hydrodynamic interactions
between the fibers mediated by a mesoscopic solvent. To conserve hydrodynamics,
collisions between the fibers are treated such that momentum and energy are
conserved locally. The choice of simulation parameters is rationalised on the
basis of dimensionless numbers expressing the relative strength of different
physical processes. The method is applied to suspensions of semiflexible fibers
with a contour length equal to the persistence length, and a mesh size to
contour length ratio ranging from 0.055 to 0.32. For such fibers the effects of
hydrodynamic interactions are observable, but relatively small. The
non-crossing constraint, on the other hand, is very important and leads to
hindered displacements of the fibers, with an effective tube diameter in
agreement with recent theoretical predictions. The simulation technique opens
the way to study the effect of viscous effects and hydrodynamic interactions in
microrheology experiments where the response of an actively driven probe bead
in a fiber suspension is measured.Comment: 12 pages, 2 tables, 5 figure
Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks
This paper focuses on the probability that a portion of DNA closes on itself
through thermal fluctuations. We investigate the dependence of this probability
upon the size r of a protein bridge and/or the presence of a kink at half DNA
length. The DNA is modeled by the Worm-Like Chain model, and the probability of
loop formation is calculated in two ways: exact numerical evaluation of the
constrained path integral and the extension of the Shimada and Yamakawa saddle
point approximation. For example, we find that the looping free energy of a 100
base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a
protein of r = 10 nm length. It further decreases to 5 kT when the loop has a
kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures,
accepted for publication in Phys. Rev.
Unexpected crossover dynamics of single polymer in a corrugated tube
We present molecular dynamics study of a generic (coarse-grained) model for
single-polymer diffusion confined in a corrugated cylinder. For a narrow tube,
i.e., diameter of the cylinder , the axial diffusion coefficient
scales as , with chain length , up to then crosses over to Rouse scaling for the larger values. The
scaling is due to the large fluctuation of the polymer chain along
its fully stretched equilibrium conformation. The stronger scaling, namely
, is not observed for an atomistically smooth tube and/or for a
cylinder with larger diameter.Comment: 10 pages, 3 figures, LaTeX, version accepted by J. Chem. Phy
Statics and Dynamics of the Wormlike Bundle Model
Bundles of filamentous polymers are primary structural components of a broad
range of cytoskeletal structures, and their mechanical properties play key
roles in cellular functions ranging from locomotion to mechanotransduction and
fertilization. We give a detailed derivation of a wormlike bundle model as a
generic description for the statics and dynamics of polymer bundles consisting
of semiflexible polymers interconnected by crosslinking agents. The elastic
degrees of freedom include bending as well as twist deformations of the
filaments and shear deformation of the crosslinks. We show that a competition
between the elastic properties of the filaments and those of the crosslinks
leads to renormalized effective bend and twist rigidities that become
mode-number dependent. The strength and character of this dependence is found
to vary with bundle architecture, such as the arrangement of filaments in the
cross section and pretwist. We discuss two paradigmatic cases of bundle
architecture, a uniform arrangement of filaments as found in F-actin bundles
and a shell-like architecture as characteristic for microtubules. Each
architecture is found to have its own universal ratio of maximal to minimal
bending rigidity, independent of the specific type of crosslink induced
filament coupling; our predictions are in reasonable agreement with available
experimental data for microtubules. Moreover, we analyze the predictions of the
wormlike bundle model for experimental observables such as the tangent-tangent
correlation function and dynamic response and correlation functions. Finally,
we analyze the effect of pretwist (helicity) on the mechanical properties of
bundles. We predict that microtubules with different number of protofilaments
should have distinct variations in their effective bending rigidity
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