Developments and further applications of ephemeral data derived potentials.

Machine-learned interatomic potentials are fast becoming an indispensable tool in computational materials science. One approach is the ephemeral data-derived potential (EDDP), which was designed to accelerate atomistic structure prediction. The EDDP is simple and cost-efficient. It relies on training data generated in small unit cells and is fit using a lightweight neural network, leading to smooth interactions which exhibit the robust transferability essential for structure prediction. Here, we present a variety of applications of EDDPs, enabled by recent developments of the open-source EDDP software. New features include interfaces to phonon and molecular dynamics codes, as well as deployment of the ensemble deviation for estimating the confidence in EDDP predictions. Through case studies ranging from elemental carbon and lead to the binary scandium hydride and the ternary zinc cyanide, we demonstrate that EDDPs can be trained to cover wide ranges of pressures and stoichiometries, and used to evaluate phonons, phase diagrams, superionicity, and thermal expansion. These developments complement continued success in accelerated structure prediction.

Pressure-Induced Synthesis and Properties of an H2S-H2Se-H2 Molecular Alloy.

The chalcogens are known to react with one another to form interchalcogens, which exhibit a diverse range of bonding and conductive behavior due to the difference in electronegativity between the group members. Through a series of high-pressure diamond anvil experiments combined with density functional theory calculations, we report the synthesis of an S-Se hydride. At pressures above 4 GPa we observe the formation of a single solid composed of both H2Se and H2S molecular units. Further compression in a hydrogen medium leads to the formation of an alloyed compound (H2SxSe1-x)2H2, after which there is a sequence of pressure-induced phase transitions associated with the arrested rotation of molecules. At pressures above 50 GPa, there is a symmetrization of hydrogen bonds concomitantly with a closing band gap and increased reflectivity of the compound, indicative of a transition to a metallic state.

Quantitative Rotational to Librational Transition in Dense H2 and D2.

Raman spectroscopy demonstrates that the rotational spectrum of solid hydrogen, and its isotope deuterium, undergoes profound transformations upon compression while still remaining in phase I. We show that these changes are associated with a loss of quantum character in the rotational modes and that the angular momentum J gradually ceases to be a good quantum rotational number. Through isotopic comparisons of the rotational Raman contributions, we reveal that hydrogen and deuterium evolve from a quantum rotor to a harmonic oscillator. We find that the mechanics behind this transformation can be well-described by a quantum-mechanical single inhibited rotor, accurately reproducing the striking spectroscopic changes observed in phase I.

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder.

We present here the hypothesis that alternative poly-adenylation (APA) is dysregulated in the brains of individuals affected by Autism Spectrum Disorder (ASD), due to disruptions in the calcium signaling networks. APA, the process of selecting different poly-adenylation sites on the same gene, yielding transcripts with different-length 3' untranslated regions (UTRs), has been documented in different tissues, stages of development and pathologic conditions. Differential use of poly-adenylation sites has been shown to regulate the function, stability, localization and translation efficiency of target RNAs. However, the role of APA remains rather unexplored in neurodevelopmental conditions. In the human brain, where transcripts have the longest 3' UTRs and are thus likely to be under more complex post-transcriptional regulation, erratic APA could be particularly detrimental. In the context of ASD, a condition that affects individuals in markedly different ways and whose symptoms exhibit a spectrum of severity, APA dysregulation could be amplified or dampened depending on the individual and the extent of the effect on specific genes would likely vary with genetic and environmental factors. If this hypothesis is correct, dysregulated APA events might be responsible for certain aspects of the phenotypes associated with ASD. Evidence supporting our hypothesis is derived from standard RNA-seq transcriptomic data but we suggest that future experiments should focus on techniques that probe the actual poly-adenylation site (3' sequencing). To address issues arising from the use of post-mortem tissue and low numbers of heterogeneous samples affected by confounding factors (such as the age, gender and health of the individuals), carefully controlled in vitro systems will be required to model the effect of calcium signaling dysregulation in the ASD brain.