427 research outputs found
Robustness of force and stress inference in an epithelial tissue
During morphogenesis, the shape of a tissue emerges from collective cellular
behaviors, which are in part regulated by mechanical and biochemical
interactions between cells. Quantification of force and stress is therefore
necessary to analyze the mechanisms controlling tissue morphogenesis. Recently,
a mechanical measurement method based on force inference from cell shapes and
connectivity has been developed. It is non-invasive, and can provide space-time
maps of force and stress within an epithelial tissue, up to prefactors. We
previously performed a comparative study of three force-inference methods,
which differ in their approach of treating indefiniteness in an inverse problem
between cell shapes and forces. In the present study, to further validate and
compare the three force inference methods, we tested their robustness by
measuring temporal fluctuation of estimated forces. Quantitative data of
cell-level dynamics in a developing tissue suggests that variation of forces
and stress will remain small within a short period of time (minutes).
Here, we showed that cell-junction tensions and global stress inferred by the
Bayesian force inference method varied less with time than those inferred by
the method that estimates only tension. In contrast, the amplitude of temporal
fluctuations of estimated cell pressures differs less between different
methods. Altogether, the present study strengthens the validity and robustness
of the Bayesian force-inference method.Comment: 4 pages, 4 figure
Simulations of viscous shape relaxation in shuffled foam clusters
We simulate the shape relaxation of foam clusters and compare them with the
time exponential expected for Newtonian fluid. Using two-dimensional Potts
Model simulations, we artificially create holes in a foam cluster and shuffle
it by applying shear strain cycles. We reproduce the experimentally observed
time exponential relaxation of cavity shapes in the foam as a function of the
number of strain steps. The cavity rounding up results from local rearrangement
of bubbles, due to the conjunction of both a large applied strain and local
bubble wall fluctuations
Effect of the number of shells on the pressure and energy of two-dimensional free bubble clusters
We have performed Surface Evolver simulations of two-dimensional hexagonal bubble clusters consisting of a central bubble of area lambda surrounded by s shells or layers of bubbles of unit area. Clusters of up to twenty layers have been simulated, with lambda varying between 0.01 and 100. In monodisperse clusters (i.e., for lambda = 1) [M.A. Fortes, F Morgan, M. Fatima Vaz, Philos. Mag. Lett. 87 (2007) 561] both the average pressure of the entire Cluster and the pressure in the central bubble are decreasing functions of s and approach 0.9306 for very large s, which is the pressure in a bubble of an infinite monodisperse honeycomb foam. Here we address the effect of changing the central bubble area lambda. For small lambda the pressure in the central bubble and the average pressure were both found to decrease with s, as in monodisperse clusters. However, for large,, the pressure in the central bubble and the average pressure increase with s. The average pressure of large clusters was found to be independent of lambda and to approach 0.9306 asymptotically.
We have also determined the cluster surface energies given by the equation of equilibrium for the total energy in terms of the area and the pressure in each bubble. When the pressures in the bubbles are not available, an approximate equation derived by Vaz et al. [M. Fatima Vaz, M.A. Fortes, F. Graner, Philos. Mag. Lett. 82 (2002) 575] was shown to provide good estimations for the cluster energy provided the bubble area distribution is narrow. This approach does not take cluster topology into account. Using this approximate equation, we find a good correlation between Surface Evolver Simulations and the estimated Values of energies and pressures. (C) 2008 Elsevier B.V. All rights reserved
Deformation of grain boundaries in polar ice
The ice microstructure (grain boundaries) is a key feature used to study ice
evolution and to investigate past climatic changes. We studied a deep ice core,
in Dome Concordia, Antarctica, which records past mechanical deformations. We
measured a "texture tensor" which characterizes the pattern geometry and
reveals local heterogeneities of deformation along the core. These results
question key assumptions of the current models used for dating
An elastic, plastic, viscous model for slow shear of a liquid foam
We suggest a scalar model for deformation and flow of an amorphous material
such as a foam or an emulsion. To describe elastic, plastic and viscous
behaviours, we use three scalar variables: elastic deformation, plastic
deformation rate and total deformation rate; and three material specific
parameters: shear modulus, yield deformation and viscosity. We obtain equations
valid for different types of deformations and flows slower than the relaxation
rate towards mechanical equilibrium. In particular, they are valid both in
transient or steady flow regimes, even at large elastic deformation. We discuss
why viscosity can be relevant even in this slow shear (often called
"quasi-static") limit. Predictions of the storage and loss moduli agree with
the experimental literature, and explain with simple arguments the non-linear
large amplitude trends
Dynamical derivation of Bode's law
In a planetary or satellite system, idealized as n small bodies in initially
coplanar, concentric orbits around a large central body, obeying Newtonian
point-particle mechanics, resonant perturbations will cause dynamical evolution
of the orbital radii except under highly specific mutual relationships, here
derived analytically apparently for the first time. In particular, the most
stable situation is achieved (in this idealized model) only when each planetary
orbit is roughly twice as far from the Sun as the preceding one, as observed
empirically already by Titius (1766) and Bode (1778) and used in both the
discoveries of Uranus (1781) and the Asteroid Belt (1801). ETC.Comment: 27 page
A quantum-like description of the planetary systems
The Titius-Bode law for planetary distances is reviewed. A model describing
the basic features of this rule in the "quantum-like" language of a wave
equation is proposed. Some considerations about the 't Hooft idea on the
quantum behaviour of deterministic systems with dissipation are discussed.Comment: LaTex file, 17 pages, no figures. Version published in Foundations of
Physics, August 200
Colloquium: Mechanical formalisms for tissue dynamics
The understanding of morphogenesis in living organisms has been renewed by
tremendous progressin experimental techniques that provide access to
cell-scale, quantitative information both on theshapes of cells within tissues
and on the genes being expressed. This information suggests that
ourunderstanding of the respective contributions of gene expression and
mechanics, and of their crucialentanglement, will soon leap forward.
Biomechanics increasingly benefits from models, which assistthe design and
interpretation of experiments, point out the main ingredients and assumptions,
andultimately lead to predictions. The newly accessible local information thus
calls for a reflectionon how to select suitable classes of mechanical models.
We review both mechanical ingredientssuggested by the current knowledge of
tissue behaviour, and modelling methods that can helpgenerate a rheological
diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and
tissue scale ("inter-cell") contributions. We recall the mathematical framework
developpedfor continuum materials and explain how to transform a constitutive
equation into a set of partialdifferential equations amenable to numerical
resolution. We show that when plastic behaviour isrelevant, the dissipation
function formalism appears appropriate to generate constitutive equations;its
variational nature facilitates numerical implementation, and we discuss
adaptations needed in thecase of large deformations. The present article
gathers theoretical methods that can readily enhancethe significance of the
data to be extracted from recent or future high throughput
biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few
corrections to the published version, all in Appendix D.2 devoted to large
deformation
Screening of DUB activity and specificity by MALDI-TOF mass spectrometry
Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analyzing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAMM DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs
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