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Shock experiments give a unique insight into the behavior of matter subjected to extremely high pressures and temperatures. Understanding the behavior of materials under such extreme conditions is key to modeling material failure and deformation dynamics under impact. While studies on pure silica are extensive, the shock behavior of other commercial silicates that contain additional oxides has not been systematically investigated. To better understand the role of composition in the dynamic behavior of silicates, we performed laser-driven dynamic compression experiments on soda-lime glass (SLG) up to 315 GPa. Using the accurate pulse shaping offered by the long pulse laser system at the Matter in Extreme Conditions end-station at the Linac Coherent Light Source, SLG was shock compressed along the Hugoniot to multiple pressure-temperature points. Velocity Interferometer System for Any Reflector was used to measure the velocity and determine the pressure inside the SLG. The Us–up relationship obtained agrees well with the previous parallel plate impact studies. Within the error bars, no transformation to the crystalline phase was observed up to 70 GPa, which is in contrast to the behavior of pure silica under shock compression. Our studies show that the glass composition strongly influences the shock compression behavior of the silicate glasses.

In this study, the magnetic properties of Fe39.8Co19.92Mn20.52Cr14.77Si5 multi-principal element alloy in both bulk and thin films were studied. X-ray diffraction measurements show coexisting face centered cubic (FCC) and hexagonal close packed phases in the bulk and the 500 nm thin films, while only FCC phase is observed in the 65 nm thin film. A four orders of magnitude increase in the magnetic moment is observed for 65 nm thin film compared with the bulk sample. Evolution of magnetization as a function of temperature and applied magnetic field shows multiple magnetic transitions. A paramagnetic to spin glass transition is detected at TS ∼ 390 K for all samples. Further cooling results in a spin glass to ferromagnetic (FM) transition, and the transition temperature, TF, is dependent on the film thickness. Higher saturation magnetization and transition temperature observed for the thin film samples indicate the stabilization of FM ordering due to thickness confinement.

Symmetry is a powerful concept in physics, but its applicability to far-from-equilibrium states is still being understood. Recent attention has focused on how far-from-equilibrium states lead to spontaneous symmetry breaking. Conversely, ultrafast optical pumping can be used to drastically change the energy landscape and quench the magnetic order parameter in magnetic systems. Here, we find a distinct symmetry-dependent ultrafast behaviour by use of ultrafast x-ray scattering from magnetic patterns with varying degrees of isotropic and anisotropic symmetry. After pumping with an optical laser, the scattered intensity reveals a radial shift exclusive to the isotropic component and exhibits a faster recovery time from quenching for the anisotropic component. These features arise even when both symmetry components are concurrently measured, suggesting a correspondence between the excitation and the magnetic order symmetry. Our results underline the importance of symmetry as a critical variable to manipulate the magnetic order in the ultrafast regime.

A ferroelectric BaTiO3 thin film grown on a NdScO3 substrate was studied using x-ray photon correlation spectroscopy (XPCS) to characterize thermal fluctuations near the a/b to a/c domain structure transformation present in this low-strain material, which is absent in the bulk. XPCS studies provide a direct comparison of the role of domain fluctuations in first- and second-order phase transformations. The a/b to a/c domain transformation is accompanied by a decrease in fluctuation timescales, and an increase in intensity and correlation length. Surprisingly, domain fluctuations are observed up to 25 degrees C above the transformation, concomitant with the growth of a/c domains and coexistence of both domain types. After a small window of stability, as the Curie temperature is approached, a/c domain fluctuations are observed, albeit slower, potentially due to the structural transformation associated with the ferroelectric to paraelectric transformation. The observed time evolution and reconfiguration of domain patterns highlight the role played by phase coexistence and elastic boundary conditions in altering fluctuation timescales in ferroelectric thin films.

Background In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is regulated, we focused on delineating the chromatin signature of bidirectional promoters. Results We report generation and utility of a reporter system that enables simultaneous scoring of transcriptional activity in opposite directions. Testing of putative bidirectional promoters in this system demonstrates no measurable bias towards any one direction of transcription. We analyzed the NUP26L-PIH1D3 bidirectional gene pair during Retinoic acid mediated differentiation of embryonic carcinoma cells. In their native context, we observed that the chromatin landscape at and around the transcription regulatory region between the pair of bidirectional genes is modulated in concordance with transcriptional activity of each gene in the pair. We then extended this analysis to 974 bidirectional gene pairs in two different cell lines, H1 human embryonic stem cells and CD4 positive T cells using publicly available ChIP-Seq and RNA-Seq data. Bidirectional gene pairs were classified based on the intergenic distance separating the two TSS of the transcripts analyzed as well as the relative expression of each transcript in a bidirectional gene pair. We report that for the entire range of intergenic distance separating bidirectional genes, the expression profile of such genes (symmetric or asymmetric) matches the histone modification profile of marks associated with active transcription initiation and elongation. Conclusions We demonstrate unique distribution of histone modification marks that correlate robustly with the transcription status of genes regulated by bidirectional promoters. These findings strongly imply that occurrence of these marks might signal the transcription machinery to drive maturation of antisense transcription from the bidirectional promoters. Electronic supplementary material The online version of this article (10.1186/s12864-018-4697-7) contains supplementary material, which is available to authorized users.

The ductile and fatigue behaviour of Al 2024 – T351 alloy is investigated using a local approach to damage evolution adopting continuum damage mechanics (CDM). The investigation involves uniaxial tensile test, load-unload tensile test and low cycle fatigue test at different strain amplitude. Fractographic examination of the failed surface helped to understand the involved mechanisms of fracture. Results indicate the material has good ductility and convincing fatigue life. This aluminum alloy is widely used in aircraft structure due to their high fatigue performance, easy formability, lower structural weight, higher damage tolerance and durability, much-needed quality parameters for weight specific aerospace applications. Damage mechanics based evaluations of this material are very scanty in published literature. The test results using damage parameters from experiments were tested in ABAQUS and flow behaviour is successfully reproduced to compare experimental results. Fatigue test results are compared well with Lemaitre model. The fractographic analysis clearly revealed the signature of ductile damage controlled fracture. The experiment on fatigue fractured specimen provided crack initiation, crack propagation and the final fracture zone clearly.

We have examined the formation of alpha phase at grain boundary triple junctions of parent beta in a metastable beta titanium alloy with orientation imaging microscopy based on electron backscattered diffraction (EBSD). As in the case of alpha formed at grain boundaries of parent beta grains, alpha at a triple junction also forms with the Burgers orientation relationship with one of the three neighbouring beta grains. The experimental results are analyzed in terms of the deviation of the 36 possible alpha variants that can form at a triple junction from the Burgers orientation relationship with neighbouring grains.

The development of robust tools and practical RNA labeling strategies that would facilitate the biophysical analysis of RNA in both cell-free and cellular systems will have profound implications in the discovery of new RNA diagnostic tools and therapeutic strategies. In this context, we describe the development of a new alkyne-modified UTP analog, 5-(1,7-octadinyl)uridine triphosphate (ODUTP), which serves as an efficient substrate for the introduction of a clickable alkyne label into RNA transcripts by bacteriophage T7 RNA polymerase and mammalian cellular RNA polymerases. The ODU-labeled RNA is effectively used by reverse transcriptase to produce cDNA, a property which could be utilized in expanding the chemical space of a RNA library in the aptamer selection scheme. Further, the alkyne label on RNA provides a convenient tool for the posttranscriptional chemical functionalization with a variety of biophysical tags (fluorescent, affinity, amino acid and sugar) by using alkyne-azide cycloaddition reaction. Importantly, the ability of endogenous RNA polymerases to specifically incorporate ODUTP into cellular RNA transcripts enabled the visualization of newly transcribing RNA in cells by microscopy using click reactions. In addition to a clickable alkyne group, ODU contains a Raman scattering label (internal disubstituted alkyne), which exhibits characteristic Raman shifts that fall in the Raman-silent region of cells. Our results indicate that an ODU label could potentially facilitate two-channel visualization of RNA in cells by using click chemistry and Raman spectroscopy. Taken together, ODU represents a multipurpose ribonucleoside tool, which is expected to provide new avenues to study RNA in cell-free and cellular systems.

Tlymphocyte development and differentiation is a multi-step process that begins in the thymus and completed in the periphery. Sequential development of thymocytes is dependent on T cell receptor (TCR) signaling and an array of transcription factors. In this study we show that special 00AT-rich binding protein 1 (SATB1), a T lineage-enriched chromatin organizer and regulator, is induced in response to TCR signaling during early thymocyte development. SATB1 expression profile coincides with T lineage commitment and upregulation of SATB1 correlates with positive selection of thymocytes. CD4 thymocytes exhibit a characteristic bimodal expression pattern that corresponds to immature and mature CD4 thymocytes. We also demonstrate that GATA3, the key transcriptional regulator of αβ T cells positively regulates SATB1 expression in thymocytes suggesting an important role for SATB1 during T cell development.

Background Role of epigenetic mechanisms towards regulation of the complex life cycle/pathogenesis of Plasmodium falciparum, the causative agent of malaria, has been poorly understood. To elucidate stage-specific epigenetic regulation, we performed genome-wide mapping of multiple histone modifications of P. falciparum. Further to understand the differences in transcription regulation in P. falciparum and its host, human, we compared their histone modification profiles. Results Our comprehensive comparative analysis suggests distinct mode of transcriptional regulation in malaria parasite by virtue of poised genes and differential histone modifications. Furthermore, analysis of histone modification profiles predicted 562 genes producing anti-sense RNAs and 335 genes having bidirectional promoter activity, which raises the intriguing possibility of RNA-mediated regulation of transcription in P. falciparum. Interestingly, we found that H3K36me2 acts as a global repressive mark and gene regulation is fine tuned by the ratio of activation marks to H3K36me2 in P. falciparum. This novel mechanism of gene regulation is supported by the fact that knockout of SET genes (responsible for H3K36 methylation) leads to up-regulation of genes with highest occupancy of H3K36me2 in wild-type P. falciparum. Moreover, virulence (var) genes are mostly poised and marked by a unique set of activation (H4ac) and repression (H3K9me3) marks, which are mutually exclusive to other Plasmodium housekeeping genes. Conclusions Our study reveals unique plasticity in the epigenetic regulation in P. falciparum which can influence parasite virulence and pathogenicity. The observed differences in the histone code and transcriptional regulation in P. falciparum and its host will open new avenues for epigenetic drug development against malaria parasite. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0029-1) contains supplementary material, which is available to authorized users.