Water-Mediated Proton Hopping Mechanisms at the SnO(110)/HO Interface from Ab Initio Deep Potential Molecular Dynamics.

The interfacial proton transfer (PT) reaction on the metal oxide surface is an important step in many chemical processes including photoelectrocatalytic water splitting, dehydrogenation, and hydrogen storage. The investigation of the PT process, in terms of thermodynamics and kinetics, has received considerable attention, but the individual free energy barriers and solvent effects for different PT pathways on rutile oxide are still lacking. Here, by applying a combination of ab initio and deep potential molecular dynamics methods, we have studied interfacial PT mechanisms by selecting the rutile SnO(110)/HO interface as an example of an oxide with the characteristic of frequently interfacial PT processes.

Band alignment of CoO(100)-water and CoO(111)-water interfaces accelerated by machine learning potentials.

Cobalt monoxide (CoO) nanomaterials have drawn attention for their remarkable photocatalytic water splitting without an externally applied potential or co-catalyst. The success of overall water splitting is due to the appropriate band edge positions of the catalyst, which span the redox potentials of water splitting. Typically, CoO nanomaterials possess complex morphologies, which consist of multiple active surfaces.

Molecular O Dimers and Lattice Instability in a Perovskite Electrocatalyst.

Structural degradation of oxide electrodes during the electrocatalytic oxygen evolution reaction (OER) is a major challenge in water electrolysis. Although the OER is known to induce changes in the surface layer, little is known about its effect on the bulk of the electrocatalyst and its overall phase stability. Here, we show that under OER conditions, a highly active SrCoO electrocatalyst develops bulk lattice instability, which results in the formation of molecular O dimers inside the bulk and nanoscale amorphization induced via chemo-mechanical coupling.

Step-induced double-row pattern of interfacial water on rutile TiO(110) under electrochemical conditions.

Metal oxides are promising (photo)electrocatalysts for sustainable energy technologies due to their good activity and abundant resources. Their applications such as photocatalytic water splitting predominantly involve aqueous interfaces under electrochemical conditions, but probing oxide-water interfaces is proven to be extremely challenging. Here, we present an electrochemical scanning tunneling microscopy (EC-STM) study on the rutile TiO(110)-water interface, and by tuning surface redox chemistry with careful potential control we are able to obtain high quality images of interfacial structures with atomic details.

Physical adsorption of OH causes anomalous charging at oxide-water interfaces.

This study reveals a charging mechanism at oxide-water interfaces, solving the puzzle that challenges the traditional electrical double layer (EDL) model. We found that the experimentally measured zeta potential is caused by physically adsorbed OH, instead of acidic dissociation of surface OHs and the first-layer water. This mechanism should apply for a wide range of material interfaces and could find applications in future.

A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation.

Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean.

ChecMatE: A workflow package to automatically generate machine learning potentials and phase diagrams for semiconductor alloys.

Semiconductor alloy materials are highly versatile due to their adjustable properties; however, exploring their structural space is a challenging task that affects the control of their properties. Traditional methods rely on ad hoc design based on the understanding of known chemistry and crystallography, which have limitations in computational efficiency and search space. In this work, we present ChecMatE (Chemical Material Explorer), a software package that automatically generates machine learning potentials (MLPs) and uses global search algorithms to screen semiconductor alloy materials.

Resolving the odd-even oscillation of water dissociation at rutile TiO(110)-water interface by machine learning accelerated molecular dynamics.

Aqueous rutile TiO(110) is the most widely studied water-oxide interface, and yet questions about water dissociation are still controversial. Theoretical studies have systematically investigated the influence of the slab thickness on water dissociation energy (E) at 1 monolayer coverage using static density functional theory calculation and found that E exhibits odd-even oscillation with respect to the TiO slab thickness. However, less studies have accounted for the full solvation of an aqueous phase using ab initio molecular dynamics due to high computational costs in which only three, four, and five trilayer models of rutile(110)-water interfaces have been simulated.

Expanding the gene pool for soybean improvement with its wild relatives.

Genetic diversity is a cornerstone of crop improvement, However, cultivated soybean () has undergone several genetic bottlenecks, including domestication in China, the introduction of landraces to other areas of the world and, latterly, selective breeding, leading to low genetic diversity the poses a major obstacle to soybean improvement. By contrast, there remains a relatively high level of genetic diversity in soybean's wild relatives, especially the perennial soybeans (), which could serve as potential gene pools for improving soybean cultivars. Wild soybeans are phylogenetically diversified and adapted to various habitats, harboring resistance to various biotic and abiotic stresses.

Time-series transcriptome comparison reveals the gene regulation network under salt stress in soybean (Glycine max) roots.

Background: Soil salinity is a primary factor limiting soybean (Glycine max) productivity. Breeding soybean for tolerance to high salt conditions is therefore critical for increasing yield. To explore the molecular mechanism of soybean responses to salt stress, we performed a comparative transcriptome time-series analysis of root samples collected from two soybean cultivars with contrasting salt sensitivity.

Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition.

Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes.

Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae).

Background: Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data.

Results: Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled.

Recent Progress toward Ab Initio Modeling of Electrocatalysis.

Electrode potential is the key factor for controlling electrocatalytic reactions at electrochemical interfaces, and moreover, it is also known that the pH and solutes (e.g., cations) of the solution have prominent effects on electrocatalysis.

The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae.

Miscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus.

Uncertainty estimation for molecular dynamics and sampling.

Machine-learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale, and complexity. Given the interpolative nature of these models, the reliability of predictions depends on the position in phase space, and it is crucial to obtain an estimate of the error that derives from the finite number of reference structures included during model training. When using a machine-learning potential to sample a finite-temperature ensemble, the uncertainty on individual configurations translates into an error on thermodynamic averages and leads to a loss of accuracy when the simulation enters a previously unexplored region.

WFhb1-1 plays an important role in resistance against Fusarium head blight in wheat.

Fusarium head blight (FHB) is a severe disease of wheat (Triticum aestivum L.). Qfhb1 is the most important quantitative trait locus (QTL) for FHB resistance.

The Genetics and Genome-Wide Screening of Regrowth Loci, a Key Component of Perennialism in .

Perennialism is common among the higher plants, yet little is known about its inheritance. Previous genetic studies of the perennialism in have yielded contradictory results. In this study, we take a reductionist approach by specifically focusing on one trait: regrowth (the plant's ability to restart a new life cycle after senescence on the same body).

Evolutionary and ecological drivers of plant flavonoids across a large latitudinal gradient.

Flavonoids are important secondary metabolites that play an integral role in protecting plants against UV radiation and other forms of environmental stress. Given widespread impacts of environmental effects associated with latitude on a multitude of biological systems and a well-documented increase in solar radiation towards the equator, plant flavonoid production is expected to increase as a response to factors associated with decreasing latitude. Using data from a Neotropical genus (Ruellia) that spans an exceptionally broad latitudinal gradient, we tested a hypothesis of a positive latitudinal gradient in flavonoid concentration and assessed other factors that influence flavonoid production including habitat type (xeric vs.

A Quantitative Proteomics View on the Function of , a Major QTL for Fusarium Head Blight Resistance in Wheat.

Fusarium head blight (FHB) is a highly detrimental disease of wheat. A quantitative trait locus for FHB resistance, , is the most utilized source of resistance in wheat-breeding programs, but very little is known about its resistance mechanism. In this study, we elucidated a prospective FHB resistance mechanism by investigating the proteomic signatures of in a pair of contrasting wheat near-isogenic lines (NIL) after 24 h of inoculation of wheat florets by .

Narcissistic chiral self-sorting of molecular face-rotating polyhedra.

Narcissistic chiral self-sorting prevailed in the assembly of molecular face-rotating polyhedra from a C building block 5,5,10,10,15,15-hexabutyl-truxene-2,7,12-tricarbaldehyde and racemic mixtures of 1,2-diamines. Out of 124 possible stereoisomers, a pair of racemic polyhedra dominated, wherein (1R,2R)-diamines were segregated in AAAA polyhedra and (1S,2S)-diamines in CCCC polyhedra. This chiral self-sorting process is regulated by facial non-covalent interactions in the polyhedra.

RADseq dataset with 90% missing data fully resolves recent radiation of (Acanthaceae) in the ultra-arid deserts of Namibia.

Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of representing 22 species.

Interconversion of molecular face-rotating polyhedra through turning inside out.

We report the post-synthesis interconversion of two enantiomeric organic cages through turning inside out. By scrutinizing the thermodynamics and kinetics, we are able to control the racemization rate by various reaction conditions and reveal that the turning-inside-out interconversion is realized through a partial disassembly pathway. The kinetics investigation also provides insight into the dynamic essence of imine chemistry using different solvents and catalysts.

The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).

The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.