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DOE OSTI2021

Nonintuitive Surface Self-Assembly of Functionalized Molecules on Ag(111)

The fabrication of nanomaterials involves selfordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/ inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.

structure prediction↗

DOE OSTI2020

Lipid analysis of CO 2 -rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

Sediment-hosted CO 2 -rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO 2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Synthetic hybrids of six yeast species

Abstract Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Investigating property-porosity relationships for micro-architected lattice structures

Micro-architected structures are increasingly valued for their light weight and tunable mechanical properties; this class of material includes sheet structures like the Schöen gyroid and beam lattices like the octet. For design purposes, it is critical to understand how to tune the relative density (RD) to obtain desired mechanical properties. This study investigates the mechanical response of Ti-6Al-4V gyroid structures, spanning a broad range of RDs (0.03–0.90), unit cell sizes (1–4 cm), and sheet thicknesses (0.2–7.8 mm). Results demonstrate that the classical Gibson-Ashby power law scaling between RD and modulus and yield stress does not adequately capture the response over a wide range of RDs, nor does it extrapolate correctly to the fully dense solid. Analytical models, in concert with experimental results and high-fidelity finite element calculations, show that the deviation from Gibson-Ashby reflects a transition from structure-dominated to material-dominated behavior. Distinctions are drawn between scaling relationships and property-porosity models, and an analytical model is proposed to better capture the evolution of mechanical properties with RD. These observations are mirrored in other architected topologies, like the octet, and highlight the importance of understanding the relationship between mechanical properties and geometry for design purposes.

Materials science↗

DOE OSTI2020

Investigation of the effect of taurine supplementation on muscle taurine content in the mdx mouse model of Duchenne muscular dystrophy using chemically specific synchrotron imaging

Duchenne muscular dystrophy (DMD) is a lethal genetic muscle wasting disorder, which currently has no cure. Supplementation with the drug taurine has been shown to offer therapeutic benefit in the mdx model for DMD, however the mechanism by which taurine protects dystrophic muscle is not fully understood. Mdx muscle is deficient in taurine, however it is not known if this deficiency occurs in the extracellular space, in other cells present in the tissue (such as immune cells) or in the myofibre itself. Likewise, the tissue location of taurine enrichment in taurine treated mdx muscle is not known. In this study we applied X-ray absorption near edge spectroscopy (XANES) at the sulfur K-edge in an imaging format to determine taurine distribution in muscle tissue. XANES is the only technique currently capable of imaging taurine directly in muscle tissue, at a spatial resolution approaching myocyte cell size (20–50 μm). Using a multi-modal approach of XANES imaging and histology on the same tissue sections, we show that in mdx muscle, it is the myofibres that are deficient in taurine, and taurine supplementation ameliorates this deficiency. Increasing the taurine content of mdx myofibres was associated with a decrease in myofibre damage (as shown by the percentage of intact myofibres) and inflammation. These data presented here will help drive future studies to better elucidate the molecular mechanisms through which taurine protects dystrophic muscle; they also support the continued investigation of taurine as a therapeutic intervention for DMD.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Crystal structure prediction with host-guided inpainting generation and foundation potentials

Unconditional crystal structure generation with diffusion models faces challenges in identifying symmetric crystals as the unit cell size increases. Here, we present the crystal host-guided generation (CHGGen) framework to address this challenge through conditional generation using an inpainting method, which optimizes a fraction of atomic positions within a predefined and symmetrized host structure to improve the success rate for symmetric structure generation. By integrating inpainting structure generation with a foundation potential for structure optimization, we demonstrate the method on the ZnS–P 2 S 5 and Li–Si chemical systems, where the inpainting method generates a higher fraction of symmetric structures than unconditional generation. The practical significance of CHGGen extends to enabling the structural modification of crystal structures, particularly for systems with partial occupancy or intercalation chemistry. The inpainting method also allows for seamless integration with other generative models, providing a versatile framework for accelerating materials discovery.

Zhong, Peichen [University of California, Berkeley↗

DOE OSTI2020

Atomic imprinting in the absence of an intrinsic length scale

Bulk metallic glasses (BMGs) have successfully been used to replicate molds that are structured at the nano- and even atomic scale through thermoplastic forming (TPF), an ability that was speculated to be rooted in the glass’ featureless atomic structure. These previous demonstrations of atomically precise imprinting, however, were performed under conditions where mold atomic feature dimensions coincided with the unit cell size of constituents in the BMG. In order to evaluate if accurate atomic-scale replication is possible in general, i.e., independent of the accidental presence of favorable constituent size/feature size relationships, we have used Pt 57.5 Cu 14.7 Ni 5.3 P 22.5 to replicate three different crystalline facets of LaAlO 3 single crystals, each exposing distinct atomic step heights. We find that in all cases, the terraced surface termination can be copied with remarkable fidelity, corroborating that BMGs when thermoplastic formed are capable of adapting to any externally imposed confinement with sub-angstrom precision without being limited by factors related to the specifics of their internal structure. This unprecedented capability of quasi-limitless replication fidelity reveals that the deformation mechanism in the supercooled liquid state of BMGs is essentially homogeneous and suggests TPF of BMGs to be a versatile toolbox for atomic and precision nanoscale imprinting.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Effective optimization of atomic decoration in giant and superstructurally ordered crystals with machine learning

Crystals with complicated geometry are often observed with mixed chemical occupancy among Wyckoff sites, presenting a unique challenge for accurate atomic modeling. Similar systems possessing exact occupancy on all the sites can exhibit superstructural ordering, dramatically inflating the unit cell size. In this work, a crystal graph convolutional neural network (CGCNN) is used to predict optimal atomic decorations on fixed crystalline geometries. This is achieved with a site permutation search (SPS) optimization algorithm based on Monte Carlo moves combined with simulated annealing and basin-hopping techniques. Our approach relies on the evidence that, for a given chemical composition, a CGCNN estimates the correct energetic ordering of different atomic decorations, as predicted by electronic structure calculations. This provides a suitable energy landscape that can be optimized according to site occupation, allowing the prediction of chemical decoration in crystals exhibiting mixed or disordered occupancy, or superstructural ordering. Verification of the procedure is carried out on several known compounds, including the superstructurally ordered clathrate compound Rb8Ga27Sb16 and vacancy-ordered perovskite Cs2SnI6, neither of which was previously seen during the neural network training. In addition, the critical temperature of an order–disorder phase transition in solid solution CuZn is probed with our SPS routines by sampling site configuration trajectories in the canonical ensemble. This strategy provides an accurate method for determining favorable decoration in complex crystals and analyzing site occupation at unprecedented speed and scale.

Chemistry↗

DOE OSTI2023

Grid resolution requirement of chemical explosive mode analysis for large eddy simulations of premixed turbulent combustion

Full Article Figures & data References Citations Metrics Reprints & Permissions Read this article Abstract The grid resolution requirement for trustworthy Chemical Explosive Mode Analysis (CEMA) in Large Eddy Simulation (LES) of premixed turbulent combustion is proposed. Explicit filtering, to emulate the effect of the LES filter, is applied to one-dimensional laminar flame and three-dimensional planar turbulent flames across a wide range of Karlovitz numbers (5 - 239). The identification of the flame front by CEMA is found relatively insensitive to the cell size (Δ), while the combustion mode identification shows more significant sensitivity. Specifically, increasing Δ falsely enhances the auto-ignition and local extinction modes and suppresses the diffusion-assisted mode. Limited dependence of the CEMA performance on the turbulent combustion regime (Karlovitz number) is observed. A simple grid size criterion for reliable CEMA mode identification in LES is proposed as Δ ≲ δ L /2; The criterion can be relaxed to Δ ≲ δ L in the laminar flame limit. Furthermore, theoretical analysis is conducted on an idealised chemistry-diffusion system. The effects of the filtering process and turbulence on the local combustion mode are demonstrated, which is consistent with the numerical observations. Further, by incorporating turbulent combustion models in CEMA, potential improvement in identifying local combustion modes can be expected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Generalizing to new geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation

Generation of simulated detector response to collision products is crucial to data analysis in particle physics, but computationally very expensive. One subdetector, the calorimeter, dominates the computational time due to the high granularity of its cells and complexity of the interactions. Generative models can provide more rapid sample production, but currently require significant effort to optimize performance for specific detector geometries, often requiring many models to describe the varying cell sizes and arrangements, without the ability to generalize to other geometries. Here, we develop a geometry-aware autoregressive model, which learns how the calorimeter response varies with geometry, and is capable of generating simulated responses to unseen geometries without additional training. The geometry-aware model outperforms a baseline unaware model by over 50% in several metrics such as the Wasserstein distance between the generated and the true distributions of key quantities which summarize the simulated response. A single geometry-aware model could replace the hundreds of generative models currently designed for calorimeter simulation by physicists analyzing data collected at the Large Hadron Collider. This proof-of-concept study motivates the design of a foundational model that will be a crucial tool for the study of future detectors, dramatically reducing the large upfront investment usually needed to develop generative calorimeter models.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Is more better? Polyploidy in crops with diverse end uses and the potential for future applications

Increasing the number of chromosome sets can increase cell size and improve yields in some crops. Breeding polyploid crops introduces unique challenges compared to diploid species, which has deterred many from exploring the potential benefits. Despite this, recent technological advancements have alleviated some of the challenges related to complex genomes and enabled the improvement of many polyploid crops. Given these advancements, there is a need to review the use of higher ploidy crops and explore potential opportunities for increased chromosome number. Many of the leading bioenergy crops are polyploids and there may be additional opportunities to further diversify feedstocks for emerging bioenergy markets. Such diversification would help to meet the anticipated increase in renewable and sustainable energy demands. Here, in this perspective review, we review polyploid crops and the extent to which ploidy level impacts improvement and production. The advantages and disadvantages of each crop are discussed in the context of their ploidy level and end-use. Particular emphasis is given to the current role and potential of polyploidy in creating the next generation of bioenergy feedstocks. Polyploids present challenges to crop improvement due to their complex genomes, but many of these difficulties can and have been overcome with technological advancements. Approaches that facilitate the use of higher ploidy crops open a path to capturing the many benefits of polyploidy, such as increased fruit and seed size, vigour, diversity, biomass and yield quality. However, these benefits are not observed across all species. This further emphasizes the need to study higher ploidy in traditionally diploid crops.

bioenergy↗

DOE OSTI2022

Electronic structure of intrinsic defects in c -gallium nitride: Density functional theory study without the jellium approximation

Here, we report the first nonjellium, systematic, density functional theory (DFT) study of intrinsic and extrinsic defects and defect levels in zinc-blende (cubic) gallium nitride. We use the local moment counter charge (LMCC) method, the standard Perdew-Becke-Ernzerhoff (PBE) exchange-correlation potential, and two pseudopotentials, where the Ga 3$\textit{d}$ orbitals are either in the core ($d^0$) or explicitly in the valence set ($d^{10}$). We studied 64, 216, 512, and 1000 atom supercells, and demonstrated convergence to the infinite limit, crucial for delineating deep from shallow states near band edges, and for demonstrating the elimination of finite cell-size errors. Contrary to common claims, we find that exact exchange is not required to obtain defect levels across the experimental band gap. As was true in silicon, silicon carbide, and gallium arsenide, the extremal LMCC defect levels of the aggregate of defects yield an effective LMCC defect band gap that is within 10% of the experimental gap (3.3 eV) for both pseudopotentials. We demonstrate that the gallium vacancy is more complicated than previously reported. There is dramatic metastability–a nearest-neighbor nitrogen atom shifts into the gallium site, forming an antisite, nitrogen vacancy pair, which is more stable than the simple vacancy for positive charge states. Our assessment of the $d^0$ and $d^{10}$ pseudopotentials yields minimal differences in defect structures and defect levels. The better agreement of the $d^0$ lattice constant with experiment suggests that the more computationally economical $d^0$ pseudopotentials are sufficient to achieve the fidelity possible within the physical accuracy of DFT, and thereby enable calculations in larger supercells necessary to demonstrate convergence with respect to finite size supercell errors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data

Metal oxide/water interfaces play a crucial role in many electrochemical and photocatalytic processes, such as photoelectrochemical water splitting, the creation of fuel from sunlight, and electrochemical CO 2 reduction. First-principles electronic structure calculations can reveal unique insights into these processes, such as the role of the alignment of the oxide electronic energy levels with those of liquid water. An essential prerequisite for the success of such calculations is the ability to predict accurate structural models of these interfaces, which in turn requires careful experimental validation. Here we report a general, quantitative validation protocol for first-principles molecular dynamics simulations of oxide/aqueous interfaces. The approach makes direct comparisons of interfacial x-ray reflectivity (XR) signals from experimental measurements and those obtained from ab initio simulations with semilocal and van der Waals functionals. The protocol is demonstrated here for the case of the Al 2 O 3 (001)/water interface, one of the simplest oxide/water interfaces. We discuss the technical requirements needed for validation, including the choice of the density functional, the simulation cell size, and the optimal choice of the thermodynamic ensemble. Our results establish a general paradigm for the validation of structural models and interactions at solid/water interfaces derived from first-principles simulations. Furthermore, while there is qualitative agreement between the simulated structures and the experimental best-fit structure, direct comparisons of simulated and measured XR intensities show quantitative discrepancies that derive from both bulk regions (i.e., alumina and water) as well as the interfacial region, highlighting the need for accurate density functionals to properly describe interfacial interactions. Our results show that XR data are sensitive not only to the atomic structure (i.e., the atom locations) but also to the electron-density distributions in both the substrate and at the interface.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Superconductivity of Ta-Hf and Ta-Zr alloys: Potential alloys for use in superconducting devices

The electronic properties relevant to superconductivity are reported for bulk Ta-Hf and Ta-Zr body centered cubic alloys, in a large part to determine whether their properties are suitable for potential use in superconducting qbits. The body centered cubic unit cell sizes increase with increasing alloying. Here, the results of magnetic susceptibility, electrical resistivity, and heat capacity characterization are reported. While elemental Ta is a type I superconductor, the alloys are type II strong coupling superconductors. Although decreasing the electron count per atom is expected to increase the density of electronic states at the Fermi level and thus the superconducting transition temperature (T c ) in these systems, we find that this is not sufficient to explain the significant increases in the superconducting T c 's observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Accuracy of DFT computed oxygen-vacancy formation energies and high-throughput search of solar thermochemical water-splitting compounds

The enthalpy change involved in metal oxide reduction is a key quantity in various processes related to energy conversion and storage, and is of particular interest for computational prediction. Often this prediction involves the simulation of a high temperature reduction process with a 0K methodology like density functional theory (DFT), and it is not infrequent for the high temperature and 0K stable crystal structures to differ. This introduces a conundrum with regards to the choice of crystal structure to utilize in the computation, with approaches in the literature varying and experimental validation remaining scarce. In this work we address both the crystal structure conundrum and the experimental validation, and then apply the insights we gain to guide a high-throughput search for new materials for solar thermochemical water-splitting applications. By computing the DFT+U oxygen vacancy formation energy (ΔE vf ) of a selection of ABO 3 compounds and comparing different crystal structures for each composition, we highlight the issues that arise when the structure utilized in the computation is dynamically unstable at 0K, namely the presence of an artificial lowering of ΔE vf , and the lack of convergence of ΔE vf with cell size. We solve these limitations by identifying and employing a suitable surrogate dynamically stable structure. We then validate the predictive power of our calculations against appositely generated experimental measurements of reduction enthalpy for a series of Hubbard U values, finding an accuracy ranging between 0.2-0.6 eV/O. In light of such conclusions, we revise and expand a previous a high-throughput DFT study on ABO 3 perovskite oxides. As a result, we provide a list of candidate STCH materials, highlight trends with redox-active cation and structural distortion, and identify Mn 4+ , Mn 3+ and Co 3+ as the most promising redox-active cations.

08 HYDROGEN↗

DOE OSTI2025

Intraspecific Diversity in Thermal Performance Determines Phytoplankton Ecological Niche

ABSTRACT Temperature has a primary influence on phytoplankton physiology and ecology. We grew 12 strains of Gephyrocapsa huxleyi isolated from different‐temperature regions for ~45 generations (2 months) and characterised acclimated thermal response curves across a temperature range. Even with similar temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day −1 . Thermal niche widths varied from 16.7°C to 24.8°C, suggesting that strains use distinct thermal response mechanisms. We investigated the implications of this thermal intraspecific diversity using an ocean ecosystem simulation resolving phytoplankton thermal phenotypes. Model analogues of thermal ‘generalists’ and ‘specialists’ resulted in a distinctive global biogeography of thermal niche widths with a nonlinear latitudinal pattern. We leveraged model output to predict ranges of the 12 lab‐reared strains and demonstrated how this approach could broadly refine geographic range predictions. Our combination of observations and modelled biogeography highlights the capacity of diverse groups to survive temperature shifts.

Krinos, Arianna I. [Department of Biology Woods Ho↗

DOE OSTI2020

Soft crystal martensites: An in situ resonant soft x-ray scattering study of a liquid crystal martensitic transformation

Liquid crystal blue phases (BPs) are three-dimensional soft crystals with unit cell sizes orders of magnitude larger than those of classic, atomic crystals. The directed self-assembly of BPs on chemically patterned surfaces uniquely enables detailed in situ resonant soft x-ray scattering measurements of martensitic phase transformations in these systems. The formation of twin lamellae is explicitly identified during the BPII-to-BPI transformation, further corroborating the martensitic nature of this transformation and broadening the analogy between soft and atomic crystal diffusionless phase transformations to include their strain-release mechanisms.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Functional soft materials from blue phase liquid crystals

Blue phase (BP) liquid crystals are chiral fluids wherein millions of molecules self-assemble into cubic lattices that are on the order of hundred nanometers. As the unit cell sizes of BPs are comparable to the wavelength of light, they exhibit selective Bragg reflections in the visible. The exploitation of the photonic properties of BPs for technological applications is made possible through photopolymerization, a process that renders mechanical robustness and thermal stability. We review here the preparation and characterization of stimuli-responsive, polymeric photonic crystals based on BPs. We highlight recent studies that demonstrate the promise that polymerized BP photonic crystals hold for colorimetric sensing and dynamic light control. We review using Landau–de Gennes simulations for predicting the self-assembly of BPs and the potential for using theory to guide experimental design. Finally, opportunities for using BPs to synthesize new soft materials, such as highly structured polymer meshes, are discussed.

36 MATERIALS SCIENCE↗