Modeling transposable elements dynamics during polyploidization in plants.

In this work we study the proliferation of transposable elements (TEs) and the epigenetic response of plants during the process of polyploidization. Through a deterministic model, expanding on our previous work on TE proliferation under epigenetic regulation, we study the long-term TE distribution and TE stability in the subgenomes of both autopolyploids and allopolyploids. We also explore different small-interfering RNA (siRNA) action modes on the subgenomes, including a model where siRNAs are not directed to specific genomes and one where siRNAs are directed - i.

Sporulation and Dispersal of the Biological Control Agent AF36 Under Field Conditions.

Aflatoxins are carcinogens produced by the fungi and that contaminate pistachio crops. International markets reject pistachio when aflatoxins exceed permitted maximum levels. Releasing the atoxigenic strain AF36 of is the leading aflatoxin pre-harvest control method.

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.

Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21-22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation.

Localized instabilities and spinodal decomposition in driven systems in the presence of elasticity.

We study numerically and analytically the instabilities associated with phase separation in a solid layer on which an external material flux is imposed. The first instability is localized within a boundary layer at the exposed free surface by a process akin to spinodal decomposition. In the limiting static case, when there is no material flux, the coherent spinodal decomposition is recovered.

Thin-film electrodes for high-capacity lithium-ion batteries: influence of phase transformations on stress.

In this study, we revisit experiments by Sethuraman (2010 , , 5062-5066. (doi:10.1016/j.

Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome.

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes.

Phase-field modeling of two-dimensional crystal growth with anisotropic diffusion.

In the present article, we introduce a phase-field model for thin-film growth with anisotropic step energy, attachment kinetics, and diffusion, with second-order (thin-interface) corrections. We are mainly interested in the limit in which kinetic anisotropy dominates, and hence we study how the expected shape of a crystallite, which in the long-time limit is the kinetic Wulff shape, is modified by anisotropic diffusion. We present results that prove that anisotropic diffusion plays an important, counterintuitive role in the evolving crystal shape, and we add second-order corrections to the model that provide a significant increase in accuracy for small supersaturations.

Epitaxial graphene growth and shape dynamics on copper: phase-field modeling and experiments.

The epitaxial growth of graphene on copper foils is a complex process, influenced by thermodynamic, kinetic, and growth parameters, often leading to diverse island shapes including dendrites, squares, stars, hexagons, butterflies, and lobes. Here, we introduce a phase-field model that provides a unified description of these diverse growth morphologies and compare the model results with new experiments. Our model explicitly accounts for the anisotropies in the energies of growing graphene edges, kinetics of attachment of carbon at the edges, and the crystallinity of the underlying copper substrate (through anisotropy in surface diffusion).

Genome size variation in wild and cultivated maize along altitudinal gradients.

It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes.

Blue sky catastrophe in double-diffusive convection.

A global bifurcation of the blue sky catastrophe type has been found in a small Prandtl number binary mixture contained in a laterally heated cavity. The system has been studied numerically applying the tools of bifurcation theory. The catastrophe corresponds to the destruction of an orbit which, for a large range of Rayleigh numbers, is the only stable solution.