1,296 research outputs found
Experimental compaction of anisotropic granular media
We report on experiments to measure the temporal and spatial evolution of
packing arrangements of anisotropic and weakly confined granular material,
using high-resolution -ray adsorption. In these experiments, the
particle configurations start from an initially disordered,
low-packing-fraction state and under vertical solicitations evolve to a dense
state. We find that the packing fraction evolution is slowed by the grain
anisotropy but, as for spherically shaped grains, can be well fitted by a
stretched exponential. For a given type of grains, the characteristic times of
relaxation and of convection are found to be of the same order of magnitude. On
the contrary compaction mechanisms in the media strongly depend on the grain
anisotropy.Comment: to appear in the european physical journal E (EPJE
Molecular Dating, Evolutionary Rates, and the Age of the Grasses
Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae ∼51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important group
Steady State Behavior of Mechanically Perturbed Spin Glasses and Ferromagnets
A zero temperature dynamics of Ising spin glasses and ferromagnets on random
graphs of finite connectivity is considered, like granular media these systems
have an extensive entropy of metastable states. We consider the problem of what
energy a randomly prepared spin system falls to before becoming stuck in a
metastable state. We then introduce a tapping mechanism, analogous to that of
real experiments on granular media, this tapping, corresponding to flipping
simultaneously any spin with probability , leads to stationary regime with a
steady state energy . We explicitly solve this problem for the one
dimensional ferromagnet and spin glass and carry out extensive
numerical simulations for spin systems of higher connectivity. The link with
the density of metastable states at fixed energy and the idea of Edwards that
one may construct a thermodynamics with a flat measure over metastable states
is discussed. In addition our simulations on the ferromagnetic systems reveal a
novel first order transition, whereas the usual thermodynamic transition on
these graphs is second order.Comment: 11 pages, 7 figure
Why Effective Medium Theory Fails in Granular Materials
Experimentally it is known that the bulk modulus, K, and shear modulus, \mu,
of a granular assembly of elastic spheres increase with pressure, p, faster
than the p^1/3 law predicted by effective medium theory (EMT) based on
Hertz-Mindlin contact forces. To understand the origin of these discrepancies,
we perform numerical simulations of granular aggregates under compression. We
show that EMT can describe the moduli pressure dependence if one includes the
increasing number of grain-grain contacts with p. Most important, the affine
assumption (which underlies EMT), is found to be valid for K(p) but breakdown
seriously for \mu(p). This explains why the experimental and numerical values
of \mu(p) are much smaller than the EMT predictions.Comment: 4 pages, 5 figures, http://polymer.bu.edu/~hmaks
Random close packing of granular matter
We propose an interpretation of the random close packing of granular
materials as a phase transition, and discuss the possibility of experimental
verification.Comment: 6 page
A microscopic 2D lattice model of dimer granular compaction with friction
We study by Monte Carlo simulation the compaction dynamics of hard dimers in
2D under the action of gravity, subjected to vertical and horizontal shaking,
considering also the case in which a friction force acts for horizontal
displacements of the dimers. These forces are modeled by introducing effective
probabilities for all kinds of moves of the particles. We analyze the dynamics
for different values of the time during which the shaking is applied to
the system and for different intensities of the forces. It turns out that the
density evolution in time follows a stretched exponential behavior if is
not very large, while a power law tail develops for larger values of .
Moreover, in the absence of friction, a critical value exists which
signals the crossover between two different regimes: for the
asymptotic density scales with a power law of , while for
it reaches logarithmically a maximal saturation value. Such behavior smears out
when a finite friction force is present. In this situation the dynamics is
slower and lower asymptotic densities are attained. In particular, for
significant friction forces, the final density decreases linearly with the
friction coefficient. We also compare the frictionless single tap dynamics to
the sequential tapping dynamics, observing in the latter case an inverse
logarithmic behavior of the density evolution, as found in the experiments.Comment: 10 pages, 15 figures, to be published in Phys. Rev.
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Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects.
Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development
Social Interactions vs Revisions, What is important for Promotion in Wikipedia?
In epistemic community, people are said to be selected on their knowledge
contribution to the project (articles, codes, etc.) However, the socialization
process is an important factor for inclusion, sustainability as a contributor,
and promotion. Finally, what does matter to be promoted? being a good
contributor? being a good animator? knowing the boss? We explore this question
looking at the process of election for administrator in the English Wikipedia
community. We modeled the candidates according to their revisions and/or social
attributes. These attributes are used to construct a predictive model of
promotion success, based on the candidates's past behavior, computed thanks to
a random forest algorithm.
Our model combining knowledge contribution variables and social networking
variables successfully explain 78% of the results which is better than the
former models. It also helps to refine the criterion for election. If the
number of knowledge contributions is the most important element, social
interactions come close second to explain the election. But being connected
with the future peers (the admins) can make the difference between success and
failure, making this epistemic community a very social community too
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