The effect of echoes interference on phonon attenuation in a nanophononic membrane.

Nanophononic materials are characterized by a periodic nanostructuration, which may lead to coherent scattering of phonons, enabling interference and resulting in modified phonon dispersions. We have used the extreme ultraviolet transient grating technique to measure phonon frequencies and lifetimes in a low-roughness nanoporous phononic membrane of SiN at wavelengths between 50 and 100 nm, comparable to the nanostructure lengthscale. Surprisingly, phonon frequencies are only slightly modified upon nanostructuration, while phonon lifetime is strongly reduced. Finite element calculations indicate that this is due to coherent phonon interference, which becomes dominant for wavelengths between ~ half and twice the inter-pores distance. Despite this, vibrational energy transport is ensured through an energy flow among the coherent modes created by reflections. This interference of phonon echos from periodic interfaces is likely another aspect of the mutual coherence effects recently highlighted in amorphous and complex crystalline materials and, in this context, could be used to tailor transport properties of nanostructured materials.

Ballistic Heat Transport in Nanocomposite: The Role of the Shape and Interconnection of Nanoinclusions.

In this article, the effect on the vibrational and thermal properties of gradually interconnected nanoinclusions embedded in an amorphous silicon matrix is studied using molecular dynamics simulations. The nanoinclusion arrangement ranges from an aligned sphere array to an interconnected mesh of nanowires. Wave-packet simulations scanning different polarizations and frequencies reveal that the interconnection of the nanoinclusions at constant volume fraction induces a strong increase of the mean free path of high frequency phonons, but does not affect the energy diffusivity. The mean free path and energy diffusivity are then used to estimate the thermal conductivity, showing an enhancement of the effective thermal conductivity due to the existence of crystalline structural interconnections. This enhancement is dominated by the ballistic transport of phonons. Equilibrium molecular dynamics simulations confirm the tendency, although less markedly. This leads to the observation that coherent energy propagation with a moderate increase of the thermal conductivity is possible. These findings could be useful for energy harvesting applications, thermal management or for mechanical information processing.

Thermal Transport in a 2D Nanophononic Solid: Role of bi-Phasic Materials Properties on Acoustic Attenuation and Thermal Diffusivity.

Nanophononic materials have recently arisen as a promising way for controlling heat transport, mirroring the results in macroscopic phononic materials for sound transmission, filtering and attenuation applications. Here we present a Finite Element numerical simulation of the transient propagation of an acoustic Wave-Packet in a 2D nanophononic material, which allows to identify the effect of the nanostructuration on the acoustic attenuation length and thus on the transport regime for the vibrational energy. Assuming elastic behavior in the matrix and in the inclusions, we find that the rigidity contrast between them not only tunes the apparent attenuation length of the wave packet along its main trajectory, but gives rise to different behaviours, from weak to strong scattering, and waves pinning. As a consequence, different energy transport regimes can be identified in the three-parameter space of the excitation frequency, inclusions size and rigidity contrast, leading to the identification of a combination of parameters allowing for the shortest attenuation distance. These results could have applications both in the field of acoustic insulation, and for the control of heat transfer.

Effect of composition and pressure on the shear strength of sodium silicate glasses: An atomic scale simulation study.

The elastoplastic behavior of sodium silicate glasses is studied at different scales as a function of composition and pressure, with the help of quasistatic atomistic simulations. The samples are first compressed and then sheared at constant pressure to calculate yield strength and permanent plastic deformations. Changes occurring in the global response are then compared to the analysis of local plastic rearrangements and strain heterogeneities. It is shown that the plastic response results from the succession of well-identified localized irreversible deformations occurring in a nanometer-size area. The size and the number of these local rearrangements, as well as the amount of internal deviatoric and volumetric plastic deformation, are sensitive to the composition and to the pressure. In the early stages of the deformation, plastic rearrangements are driven by sodium mobility. Consequently, the elastic yield strength decreases when the sodium content increases, and the same when pressure increases. Finally, good correlation was found between global and local stress-strain relationships, reinforcing again the role of sodium ions as local initiators of the plastic behavior observed at larger scales.

Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids.

*The present study aims to understand regulation of gene expression in synthetic and natural wheat (Triticum aestivum) allohexaploids, that combines the AB genome of Triticum turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. *We conducted a comprehensive genome-wide analysis of gene expression that allowed characterization of the effect of variability of the D genome progenitor, the intergenerational stability as well as the comparison with natural wheat allohexaploid. We used the Affymetrix GeneChip Wheat Genome Array, on which 55 049 transcripts are represented. *Additive expression was shown to represent the majority of expression regulation in the synthetic allohexaploids, where expression for more than c. 93% of transcripts was equal to the mid-parent value measured from a mixture of parental RNA. This leaves c. 2000 (c. 7%) transcripts, in which expression was nonadditive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high intergenerational stability and low effect of the D genome progenitor variability were revealed. *Our study suggests that gene expression regulation in wheat allohexaploids is established early upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids.

Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity.

To understand key mechanisms leading to stabilized allopolyploid species, we characterized the meiotic behaviour of wheat allohexaploids in relation to structural and genetic changes. For that purpose, we analysed first generations of synthetic allohexaploids obtained through interspecific hybridization, followed by spontaneous chromosome doubling, between several genotypes of Triticum turgidum and Aegilops tauschii wheat species, donors of AB and D genomes, respectively. As expected for these Ph1 (Pairing homoeologous 1) gene-carrying allopolyploids, chromosome pairing at metaphase I of meiosis essentially occurs between homologous chromosomes. However, the different synthetic allohexaploids exhibited progenitor-dependent meiotic irregularities, such as incomplete homologous pairing, resulting in univalent formation and leading to aneuploidy in the subsequent generation. Stability of the synthetic allohexaploids was shown to depend on the considered genotypes of both AB and D genome progenitors, where few combinations compare to the natural wheat allohexaploid in terms of regularity of meiosis and euploidy. Aneuploidy represents the only structural change observed in these synthetic allohexaploids, as no apparent DNA sequence elimination or rearrangement was observed when analysing euploid plants with molecular markers, developed from expressed sequence tags (ESTs) as well as simple sequence repeat (SSR) and transposable element sequences.

Homoeologous recombination within bread wheat to develop novel combinations of HMW-GS genes: transfer of the Glu-A1 locus to chromosome 1D.

In an attempt to improve the bread-making quality within hexaploid wheat by elaborating novel high-molecular weight glutenin subunits (HMW-GS) combinations useful in wheat-breeding programmes, a 1A chromosome fragment carrying the Glu-A1 locus encoding the subunit Ax2*, was translocated to the long arm of chromosome 1D. The partially isohomoeoallelic line, designated RR239, had a meiotic behaviour as regular as cv. Courtot. It was characterised using genomic in situ hybridization and microsatellite markers as well as biochemical and proteomic approaches. The translocated 1D chromosome had an interstitial 1AL segment representing in average 30% of the recombinant arm length that was confirmed by molecular analysis. The genetic length of the removed segment in chromosome 1DL was estimated to be at least 51 cM, and that of the interstitial 1AL translocation to be at least 33 cM. Proteome analysis performed on total endosperm proteins revealed variation in amounts, 8 spots and 1 spot being up- and downregulated, respectively. Quantitative variations in HMW-GS were observed for the Glu-A1 (Ax2*) and Glu-B1 (Bx7 + By8) loci in response to duplication of the Glu-A1 locus.

Local elasticity map and plasticity in a model Lennard-Jones glass.

In this work we calculate the local elastic moduli in a weakly polydispersed two-dimensional Lennard-Jones glass undergoing a quasistatic shear deformation at zero temperature. The numerical method uses coarse-grained microscopic expressions for the strain, displacement, and stress fields. This method allows us to calculate the local elasticity tensor and to quantify the deviation from linear elasticity (local Hooke's law) at different coarse-graining scales. From the results a clear picture emerges of an amorphous material with strongly spatially heterogeneous elastic moduli that simultaneously satisfies Hooke's law at scales larger than a characteristic length scale of the order of five interatomic distances. At this scale, the glass appears as a composite material composed of a rigid scaffolding and of soft zones. Only recently calculated in nonhomogeneous materials, the local elastic structure plays a crucial role in the elastoplastic response of the amorphous material. For a small macroscopic shear strain, the structures associated with the nonaffine displacement field appear directly related to the spatial structure of the elastic moduli. Moreover, for a larger macroscopic shear strain we show that zones of low shear modulus concentrate most of the strain in the form of plastic rearrangements. The spatiotemporal evolution of this local elasticity map and its connection with long term dynamical heterogeneity as well as with the plasticity in the material is quantified. The possibility to use this local parameter as a predictor of subsequent local plastic activity is also discussed.

Assignment of Aegilops variabilis Eig chromosomes and translocations carrying resistance to nematodes in wheat.

The allotetraploid species Aegilops variabilis Eig (2n = 28, UUSvSv) belongs to the tribe Triticeae and is closely related to wheat. One accession, Ae. variabilis No. 1, was found to be resistant to the cereal cyst nematode (CCN) and the root-knot nematode (RKN). As the genetic variability for resistance to those two pests is limited within wheat, this accession was crossed to bread wheat. Previous work enabled the development of two addition lines and two translocation lines carrying resistance. Here, we demonstrate, using genomic in situ hybridization, that there is no U-Sv interchange in the parental accession of Ae. variabilis. However, there are multiple rearrangements in the Sv chromosomes. The Ae. variabilis chromosome carrying the CreX gene for resistance to CCN combined segments with homoeology to wheat groups 1, 2, 4, and 6. The CreX gene belongs to the group 1 part and it was likely to have been introduced into chromosome 1BL at a similar location as the previously found QTL QCre.srd-1B for CCN resistance. The second Ae. variabilis chromosome carrying CreY and Rkn2 combined segments with homoeology to wheat groups 2, 4, and 7 on its short arm and group 3 on its long arm. It was designated as 3Sv. The two genes for resistance are carried by its long arm and have been transferred to wheat chromosome 3BL through homoeologous and genetically balanced recombination. Different SSR markers present in the introgressed segments could be used in marker-assisted selection.

Attempts to induce homoeologous pairing between wheat and Agropyron cristatum genomes.

Agropyron cristatum (2n = 4x = 28, PPPP) possesses potentially valuable traits that could be used in wheat (Triticum aestivum) improvement through interspecific hybridization. Homoeologous pairing between wheat chromosomes and P chromosomes added to wheat in a set of wheat - A. cristatum addition lines was assessed. First, the Ph-suppressing effect of P chromosomes (except 7P) was analyzed. It was concluded that this system is polygenic with no major gene, and consequently, has no prospect in the transfer of alien genes from wild relatives. In a second step, the potential of the deletion ph1b of the Ph1 gene for inducing P-ABD pairing was evaluated. Allosyndetic associations between P and ABD genomes are very rare. This very low level of pairing is likely due to divergence in the repeated sequences between Agropyron and wheat genomes. Development of translocation lines using ionizing radiation seems to be a more suitable technique than homoeologous recombination to exploit the A. cristatum genome in wheat improvement.

Structure of Aegilops ventricosa chromosome 6Nv, the donor of wheat genes Yr17, Lr37, Sr38, and Cre5.

An Aegilops ventricosa Tausch (2n = 28, DvDvNvNv) subtelocentric chromosome added to wheat (Triticum aestivum L.) in a disomic addition line was found to carry the genes for resistance Yr17, Lr37, Sr38, and Cre5 already transferred onto chromosome 2AS of the wheat line VPM1. Previous works demonstrated that this Ae. ventricosa chromosome is translocated with respect to the standard wheat genome. The present investigations showed that this chromosome pre-existed in Ae. ventricosa and contains only chromatin specific to the N genome. Using biochemical markers and suitable cytogenetic materials including the monoisosomic addition line for the translocated long arm (6NvL-2NvS), its structure was defined as being 6NvSdel.6NvL-2NvS. It consists of a segment of the short arm 2Nv, containing the resistance genes, attached to a group 6 chromosome lacking a distal part of its short arm. The 2 re arrangements could already be present in Aegilops uniaristata Vis. (2n = 14, NN), the source of the Nv genome of Ae. ventricosa.