Efficient Computational Design of 2D van der Waals Heterostructures: Band-Alignment, Lattice-Mismatch, Web-app Generation and Machine-learning

We develop a computational database, web-apps and machine-learning (ML) models to accelerate the design and discovery of two-dimensional (2D)-heterostructures. Using density functional theory (DFT) based lattice-parameters and electronic band-energies for 674 non-metallic exfoliable 2D-materials, we generate 226779 possible heterostructures. We classify these heterostructures into type-I, II and III systems according to Anderson rule, which is based on the band-alignment with respect to the vacuum potential of non-interacting monolayers.We find that type-II is the most common and the type-III the least common heterostructure type. We subsequently analyze the chemical trends for each heterostructure type in terms of the periodic table of constituent elements. The band alignment data can be also used for identifying photocatalysts and high-work function 2D-metals for contacts.We validate our results by comparing them to experimental data as well as hybrid-functional predictions. Additionally, we carry out DFT calculations of a few selected systems (MoS2/WSe2, MoS2/h-BN, MoSe2/CrI3) to compare the band-alignment description with the predictions from Anderson rule. We develop web-apps to enable users to virtually create combinations of 2D materials and predict their properties. Additionally, we develop ML tools to predict band-alignment information for 2D materials. The web-apps, tools and associated data will be distributed through JARVIS-Heterostructure website (https://www.ctcms.nist.gov/jarvish).Our analysis, results and the developed web-apps can be applied to the screening and design applications, such as finding novel photocatalysts, photodetectors, and high-work function 2D-metal contacts

A Solanum lycopersicum polyamine oxidase contributes to the control of plant growth, xylem differentiation, and drought stress tolerance

Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth

Distinct Effects of p19 RNA Silencing Suppressor on Small RNA Mediated Pathways in Plants

RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection. We showed that ectopically expressed p19 sequesters endogenous small RNAs (sRNAs) in the absence, but not in the presence of virus infection. Our presented data question the generalized model in which the sequestration of endogenous sRNAs by the viral suppressor contributes to the viral symptom development. We further showed that p19 preferentially binds the perfectly paired ds-viral small interfering RNAs (vsiRNAs) but does not select based on their sequence or the type of the 5’ nucleotide. Finally, co-immunoprecipitation of sRNAs with AGO1 or AGO2 from virus-infected plants revealed that p19 specifically impairs vsiRNA loading into AGO1 but not AGO2. Our findings, coupled with the fact that p19-expressing wild type Cymbidium ringspot virus (CymRSV) overcomes the Nicotiana benthamiana silencing based defense killing the host, suggest that AGO1 is the main effector of antiviral silencing in this host-virus combination

Recent progress in the JARVIS infrastructure for next-generation data-driven materials design

The Joint Automated Repository for Various Integrated Simulations (JARVIS) infrastructure at the National Institute of Standards and Technology (NIST) is a large-scale collection of curated datasets and tools with more than 80000 materials and millions of properties. JARVIS uses a combination of electronic structure, artificial intelligence (AI), advanced computation and experimental methods to accelerate materials design. Here we report some of the new features that were recently included in the infrastructure such as: 1) doubling the number of materials in the database since its first release, 2) including more accurate electronic structure methods such as Quantum Monte Carlo, 3) including graph neural network-based materials design, 4) development of unified force-field, 5) development of a universal tight-binding model, 6) addition of computer-vision tools for advanced microscopy applications, 7) development of a natural language processing tool for text-generation and analysis, 8) debuting a large-scale benchmarking endeavor, 9) including quantum computing algorithms for solids, 10) integrating several experimental datasets and 11) staging several community engagement and outreach events. New classes of materials, properties, and workflows added to the database include superconductors, two-dimensional (2D) magnets, magnetic topological materials, metal-organic frameworks, defects, and interface systems. The rich and reliable datasets, tools, documentation, and tutorials make JARVIS a unique platform for modern materials design. JARVIS ensures openness of data and tools to enhance reproducibility and transparency and to promote a healthy and collaborative scientific environment

The C4 protein of tomato yellow leaf curl Sardinia virus primes drought tolerance in tomato through morphological adjustments

Viruses can interfere with the ability of plants to overcome abiotic stresses, indicating the existence of common molecular networks that regulate stress responses. A begomovirus causing the tomato yellow leaf curl disease was recently shown to enhance heat tolerance in tomato and drought tolerance in tomato and Nicotiana benthamiana and experimental evidence suggested that the virus-encoded protein C4 is the main trigger of drought responses. However, the physiological and molecular events underlying C4-induced drought tolerance need further elucidation. In this study, transgenic tomato plants expressing the tomato yellow leaf curl Sardinia virus (TYLCSV) C4 protein were subjected to severe drought stress, followed by recovery. Morphometric parameters, water potential, gas exchanges, and hormone contents in leaves were measured, in combination with molecular analysis of candidate genes involved in stress response and hormone metabolism. Collected data proved that the expression of TYLCSV C4 positively affected the ability of transgenic plants to tolerate water stress, by delaying the onset of stress-related features, improving the plant water use efficiency and facilitating a rapid post-rehydration recovery. In addition, we demonstrated that specific anatomical and hydraulic traits, rather than biochemical signals, are the keynote of the C4-associated stress resilience. Our results provide novel insights into the biology underpinning drought tolerance in TYLCSV C4-expressing tomato plants, paving the way for further deepening the mechanism through which such proteins tune the plant-virus interaction