3,780 research outputs found
Mechanics and force transmission in soft composites of rods in elastic gels
We report detailed theoretical investigations of the micro-mechanics and bulk
elastic properties of composites consisting of randomly distributed stiff
fibers embedded in an elastic matrix in two and three dimensions. Recent
experiments published in Physical Review Letters [102, 188303 (2009)] have
suggested that the inclusion of stiff microtubules in a softer, nearly
incompressible biopolymer matrix can lead to emergent compressibility. This can
be understood in terms of the enhancement of the compressibility of the
composite relative to its shear compliance as a result of the addition of stiff
rod-like inclusions. We show that the Poisson's ratio of such a composite
evolves with increasing rod density towards a particular value, or {\em fixed
point}, independent of the material properties of the matrix, so long as it has
a finite initial compressibility. This fixed point is in three
dimensions and in two dimensions. Our results suggest an important
role for stiff filaments such as microtubules and stress fibers in cell
mechanics. At the same time, our work has a wider elasticity context, with
potential applications to composite elastic media with a wide separation of
scales in stiffness of its constituents such as carbon nanotube-polymer
composites, which have been shown to have highly tunable mechanics.Comment: 10 pages, 8 figure
Effect of dipolar moments in domain sizes of lipid bilayers and monolayers
Lipid domains are found in systems such as multi-component bilayer membranes
and single component monolayers at the air-water interface. It was shown by
Andelman et al. (Comptes Rendus 301, 675 (1985)) and McConnell et al. (Phys.
Chem. {\bf 91}, 6417 (1987)) that in monolayers, the size of the domains
results from balancing the line tension, which favors the formation of a large
single circular domain, against the electrostatic cost of assembling the
dipolar moments of the lipids. In this paper, we present an exact analytical
expression for the electric potential, ion distribution and electrostatic free
energy for different problems consisting of three different slabs with
different dielectric constants and Debye lengths, with a circular homogeneous
dipolar density in the middle slab. From these solutions, we extend the
calculation of domain sizes for monolayers to include the effects of finite
ionic strength, dielectric discontinuities (or image charges) and the
polarizability of the dipoles and further generalize the calculations to
account for domains in lipid bilayers. In monolayers, the size of the domains
is dependent on the different dielectric constants but independent of ionic
strength. In asymmetric bilayers, where the inner and outer leaflets have
different dipolar densities, domains show a strong size dependence with ionic
strength, with molecular-sized domains that grow to macroscopic phase
separation with increasing ionic strength. We discuss the implications of the
results for experiments and briefly consider their relation to other two
dimensional systems such as Wigner crystals or heteroepitaxial growth.Comment: 13 pages, 5 figues in eps Replaced with new version, one citation
added and a few statements corrected. The results of the paper are unchange
Non-local fluctuation correlations in active gels
Many active materials and biological systems are driven far from equilibrium
by embedded agents that spontaneously generate forces and distort the
surrounding material. Probing and characterizing these athermal fluctuations is
essential for understanding the properties and behaviors of such systems. Here
we present a mathematical procedure to estimate the local action of
force-generating agents from the observed fluctuating displacement fields. The
active agents are modeled as oriented force dipoles or isotropic compression
foci, and the matrix on which they act is assumed to be either a compressible
elastic continuum or a coupled network-solvent system. Correlations at a single
point and between points separated by an arbitrary distance are obtained,
giving a total of three independent fluctuation modes that can be tested with
microrheology experiments. Since oriented dipoles and isotropic compression
foci give different contributions to these fluctuation modes, ratiometric
analysis allows us characterize the force generators. We also predict and
experimentally find a high-frequency ballistic regime, arising from individual
force generating events in the form of the slow build-up of stress followed by
rapid but finite decay. Finally, we provide a quantitative statistical model to
estimate the mean filament tension from these athermal fluctuations, which
leads to stiffening of active networks.Comment: 12 pages, 7 figures; some clarifications and ammended figure
notation
A core genetic module : the Mixed Feedback Loop
The so-called Mixed Feedback Loop (MFL) is a small two-gene network where
protein A regulates the transcription of protein B and the two proteins form a
heterodimer. It has been found to be statistically over-represented in
statistical analyses of gene and protein interaction databases and to lie at
the core of several computer-generated genetic networks. Here, we propose and
mathematically study a model of the MFL and show that, by itself, it can serve
both as a bistable switch and as a clock (an oscillator) depending on kinetic
parameters. The MFL phase diagram as well as a detailed description of the
nonlinear oscillation regime are presented and some biological examples are
discussed. The results emphasize the role of protein interactions in the
function of genetic modules and the usefulness of modelling RNA dynamics
explicitly.Comment: To be published in Physical Review
Filamin cross-linked semiflexible networks: Fragility under strain
The semiflexible F-actin network of the cytoskeleton is cross-linked by a
variety of proteins including filamin, which contain Ig-domains that unfold
under applied tension. We examine a simple semiflexible network model
cross-linked by such unfolding linkers that captures the main mechanical
features of F-actin networks cross-linked by filamin proteins and show that
under sufficiently high strain the network spontaneously self-organizes so that
an appreciable fraction of the filamin cross-linkers are at the threshold of
domain unfolding. We propose an explanation of this organization based on a
mean-field model and suggest a qualitative experimental signature of this type
of network reorganization under applied strain that may be observable in
intracellular microrheology experiments of Crocker et al.Comment: 4 Pages, 3 figures, Revtex4, submitted to PR
Testing Tensile and Shear Epoxy Strength at Cryogenic Temperatures
This paper covers cryogenic, tensile testing and research completed on a number of epoxies used in cryogenic applications. Epoxies are used in many different applications; however, this research focused on the use of epoxy used to bond MLI standoffs to cryogenic storage tanks and the loads imparted to the tank through the MLI. To conduct testing, samples were made from bare stainless steel, aluminum and primed aluminum. Testing involved slowly cooling test samples with liquid nitrogen then applying gradually increasing tensile loads to the epoxy. The testing evaluated the strength and durability of epoxies at cryogenic temperatures and serves as a base for future testing. The results of the tests showed that some epoxies withstood the harsh conditions while others failed. The two epoxies yielding the best results were Masterbond EP29LPSP and Scotch Weld 2216. For all metal surfaces tested, both epoxies had zero failures for up to 11.81 kg of mass
A two-state model for helicase translocation and unwinding of nucleic acids
Helicases are molecular motors that unwind double-stranded nucleic acids
(dsNA), such as DNA and RNA). Typically a helicase translocates along one of
the NA single strands while unwinding and uses adenosine triphosphate (ATP)
hydrolysis as an energy source. Here we model of a helicase motor that can
switch between two states, which could represent two different points in the
ATP hydrolysis cycle. Our model is an extension of the earlier
Betterton-J\"ulicher model of helicases to incorporate switching between two
states. The main predictions of the model are the speed of unwinding of the
dsNA and fluctuations around the average unwinding velocity. Motivated by a
recent claim that the NS3 helicase of Hepatitis C virus follows a flashing
ratchet mechanism, we have compared the experimental results for the NS3
helicase with a special limit of our model which corresponds to the flashing
ratchet scenario. Our model accounts for one key feature of the experimental
data on NS3 helicase. However, contradictory observations in experiments
carried out under different conditions limit the ability to compare the model
to experiments.Comment: minor modification
Probing molecular free energy landscapes by periodic loading
Single molecule pulling experiments provide information about interactions in
biomolecules that cannot be obtained by any other method. However, the
reconstruction of the molecule's free energy profile from the experimental data
is still a challenge, in particular for the unstable barrier regions. We
propose a new method for obtaining the full profile by introducing a periodic
ramp and using Jarzynski's identity for obtaining equilibrium quantities from
non-equilibrium data. Our simulated experiments show that this method delivers
significant more accurate data than previous methods, under the constraint of
equal experimental effort.Comment: 4 pages, 3 figure
Proton transport and torque generation in rotary biomotors
We analyze the dynamics of rotary biomotors within a simple
nano-electromechanical model, consisting of a stator part and a ring-shaped
rotor having twelve proton-binding sites. This model is closely related to the
membrane-embedded F motor of adenosine triphosphate (ATP) synthase, which
converts the energy of the transmembrane electrochemical gradient of protons
into mechanical motion of the rotor. It is shown that the Coulomb coupling
between the negative charge of the empty rotor site and the positive stator
charge, located near the periplasmic proton-conducting channel (proton source),
plays a dominant role in the torque-generating process. When approaching the
source outlet, the rotor site has a proton energy level higher than the energy
level of the site, located near the cytoplasmic channel (proton drain). In the
first stage of this torque-generating process, the energy of the
electrochemical potential is converted into potential energy of the
proton-binding sites on the rotor. Afterwards, the tangential component of the
Coulomb force produces a mechanical torque. We demonstrate that, at low
temperatures, the loaded motor works in the shuttling regime where the energy
of the electrochemical potential is consumed without producing any
unidirectional rotation. The motor switches to the torque-generating regime at
high temperatures, when the Brownian ratchet mechanism turns on. In the
presence of a significant external torque, created by ATP hydrolysis, the
system operates as a proton pump, which translocates protons against the
transmembrane potential gradient. Here we focus on the F motor, even though
our analysis is applicable to the bacterial flagellar motor.Comment: 24 pages, 5 figure
Stiff Polymers, Foams and Fiber Networks
We study the elasticity of fibrous materials composed of generalized stiff
polymers. It is shown that in contrast to cellular foam-like structures affine
strain fields are generically unstable. Instead, a subtle interplay between the
architecture of the network and the elastic properties of its building blocks
leads to intriguing mechanical properties with intermediate asymptotic scaling
regimes. We present exhaustive numerical studies based on a finite element
method complemented by scaling arguments.Comment: 4 pages, 5 figure
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