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DOE OSTI2024

Auxiliary field Quantum Monte Carlo for dilute neutrons on the lattice

We employ constrained path Auxiliary Field Quantum Monte Carlo (AFQMC) in the pursuit of studying physical nuclear systems using a lattice formalism. Since AFQMC has been widely used in the study of condensed-matter systems such as the Hubbard model, we benchmark our method against published results for both one- and two-dimensional Hubbard model calculations. We then turn our attention to cold atomic and nuclear systems. We use an onsite contact interaction that can be tuned in order to reproduce the known scattering length and effective range of a given interaction. Developing this machinery allows us to extend our calculations to study nuclear systems within a lattice formalism. In conclusion, we perform initial calculations for a range of nuclear systems from two- to few-body neutron systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Regulating loops in de Sitter spacetime

Perturbative quantum field theory (QFT) calculations in de Sitter space are riddled with contributions that diverge over time. These contributions often arise from loop integrals, which are notoriously hard to compute in de Sitter. We discuss an approach to evaluate loop integrals that contribute to equal-time correlators of a scalar field theory in a fixed de Sitter background. Our method is based on the Mellin-Barnes representation of correlation functions, which allows us to regulate loop divergences by adjusting the masses of the fields, or by gently deforming the underlying de Sitter spacetime. The resulting expressions have a similar structure as a standard answer from dimensional regularization in flat space QFT. These features of the regulator are illustrated with two examples, worked out in detail. Along the way, we illuminate the physical origin of these divergences and their interpretation with the machinery of the dynamical renormalization group. Our approach regulates the IR divergences of massless and massive particles in the same way. For massless scalars, the loop corrections can be incorporated as systematic improvements to the stochastic inflation framework, allowing for a more precise description of the IR dynamics of such fields in de Sitter. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DOE OSTI2025

Maximally entangled gluons for any x

Individual quarks and gluons at small x inside an unpolarized hadron can be regarded as Bell states in which qubits in the spin and orbital angular momentum spaces are maximally entangled. Using the machinery of quantum information science, we generalize this observation to all values 0 < x <1 and describe gluons (but not quarks) as maximally entangled states between a qubit and a qudit. We introduce the conditional probability distribution P⁡(l z |s z ) of a gluon’s orbital angular momentum l z given its helicity s z . Restricting to the three states l z =0,±1, which constitute a qutrit, we explicitly compute P as a function of x.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Magic-Angle Twisted Bilayer Graphene as a Topological Heavy Fermion Problem

Magic-angle (θ=1.05°) twisted bilayer graphene (MATBG) has shown two seemingly contradictory characters: the localization and quantum-dot-like behavior in STM experiments, and delocalization in transport experiments. We construct a model, which naturally captures the two aspects, from the Bistritzer-MacDonald (BM) model in a first principle spirit. A set of local flat-band orbitals (f) centered at the AA-stacking regions are responsible to the localization. A set of extended topological semimetallic conduction bands (c), which are at small energetic separation from the local orbitals, are responsible to the delocalization and transport. The topological flat bands of the BM model appear as a result of the hybridization of f and c electrons. This model then provides a new perspective for the strong correlation physics, which is now described as strongly correlated f electrons coupled to nearly free c electrons—we hence name our model as the topological heavy fermion model. Using this model, we obtain the U(4) and U(4)×U(4) symmetries of Refs. [1–5] as well as the correlated insulator phases and their energies. Simple rules for the ground states and their Chern numbers are derived. Moreover, features such as the large dispersion of the charge ±1 excitations [2,6,7], and the minima of the charge gap at the Γ M point can now, for the first time, be understood both qualitatively and quantitatively in a simple physical picture. Our mapping opens the prospect of using heavy-fermion physics machinery to the superconducting physics of MATBG.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Structured Adaptive Mesh Refinement Adaptations to Retain Performance Portability With Increasing Heterogeneity

Adaptive mesh refinement (AMR) is an important method that enables many mesh-based applications to run at effectively higher resolution within limited computing resources by allowing high resolution only where really needed. This advantage comes at a cost, however: greater complexity in the mesh management machinery and challenges with load distribution. With the current trend of increasing heterogeneity in hardware architecture, AMR presents an orthogonal axis of complexity. Additionally, the usual techniques, such as asynchronous communication and hierarchy management for parallelism and memory that are necessary to obtain reasonable performance are very challenging to reason about with AMR. Different groups working with AMR are bringing different approaches to this challenge. Here, we examine the design choices of several AMR codes and also the degree to which demands placed on them by their users influence these choices.

42 ENGINEERING↗

DOE OSTI2023

Silicon Carbide Inverter for Off-Road Heavy-Duty Applications: The Importance of Thermal and Thermomechanical Design in Power Electronics Packaging

Electrification of drivetrain systems is now seen as a major opportunity by the transportation industry across the globe to reduce the greenhouse gas emissions and revolutionize the travel patterns of millions of people. The cumulative number of plug-in hybrid and battery electric vehicles (EVs) sold in the United States has now surpassed 2 million in 2021, according to the International Energy Agency. The introduction of EVs in different classes of passenger vehicles and the continued drop in prices spurred by government incentives have attracted the attention of consumers despite certain barriers, such as higher initial cost and range anxiety. In the United States, the EV market share is now growing at an exponential pace, with the domestic automakers allocating a lion's share of new and future car sales to EVs. Additionally, different market studies project decreasing cost and rising sales of medium- and heavy-duty electric trucks. Although electrification initiatives are strongly pursued in the on-road passenger vehicle market, off-highway sectors, such as construction, mining, and agriculture, are also gradually implementing electric drivetrain technologies in their machineries. As EVs grow in popularity on a global scale, innovative drivetrain technologies must meet the increasing energy demand by significantly increasing system efficiency.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2021

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Latitudinal patterns of terrestrial phosphorus limitation over the globe

Abstract Phosphorus limitation on terrestrial plant growth is being incorporated into Earth system models. The global pattern of terrestrial phosphorus limitation, however, remains unstudied. Here, we examined the global‐scale latitudinal pattern of terrestrial phosphorus limitation by analysing a total of 1068 observations of aboveground plant production response to phosphorus additions at 351 forest, grassland or tundra sites that are distributed globally. The observed phosphorus‐addition effect varied greatly (either positive or negative), depending significantly upon fertilisation regime and production measure, but did not change significantly with latitude. In contrast, phosphorus‐addition effect standardised by fertilisation regime and production measure was consistently positive and decreased significantly with latitude. Latitudinal gradient in the standardised phosphorus‐addition effect was explained by several mechanisms involving substrate age, climate, vegetation type, edaphic properties and biochemical machinery. This study suggests that latitudinal pattern of terrestrial phosphorus limitation is jointly shaped by macro‐scale driving forces and the fundamental structure of life.

Hou, Enqing↗

DOE OSTI2020

Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis

Biomass deconstruction remains integral for enabling second-generation biofuel production at scale. However, several steps necessary to achieve significant solubilization of biomass, notably harsh pretreatment conditions, impose economic barriers to commercialization. By employing hyperthermostable cellulase machinery, biomass deconstruction can be made more efficient, leading to milder pretreatment conditions and ultimately lower production costs. The hyperthermophilic bacterium Caldicellulosiruptor bescii produces extremely active hyperthermostable cellulases, including the hyperactive multifunctional cellulase CbCel9A/Cel48A. Recombinant CbCel9A/Cel48A components have been previously produced in Escherichia coli and integrated into synthetic hyperthermophilic designer cellulosome complexes. Since then, glycosylation has been shown to be vital for the high activity and stability of CbCel9A/Cel48A. Here, we studied the impact of glycosylation on a hyperthermostable designer cellulosome system in which two of the cellulosomal components, the scaffoldin and the GH9 domain of CbCel9A/Cel48A, were glycosylated as a consequence of employing Ca. bescii as an expression host. Inclusion of the glycosylated components yielded an active cellulosome system that exhibited long-term stability at 75 degrees C. The resulting glycosylated designer cellulosomes showed significantly greater synergistic activity compared to the enzymatic components alone, as well as higher thermostability than the analogous nonglycosylated designer cellulosomes. These results indicate that glycosylation can be used as an essential engineering tool to improve the properties of designer cellulosomes. Additionally, Ca. bescii was shown to be an attractive candidate for production of glycosylated designer cellulosome components, which may further promote the viability of this bacterium both as a cellulase expression host and as a potential consolidated bioprocessing platform organism.

09 BIOMASS FUELS↗

DOE OSTI2021

Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme‐binding fold

The opportunistic pathogen Pseudomonas aeruginosa can utilize polyamines (including putrescine, cadaverine, 4‐aminobutyrate, spermidine, and spermine) as its sole source of carbon and nitrogen. Spermidine dehydrogenase (SpdH) is a component of one of the two polyamine utilization pathways identified in P . aeruginosa , but little is known about its structure and function. Here, we report the first crystal structure of SpdH from P . aeruginosa to 1.85 Å resolution. The resulting core structure confirms that SpdH belongs to the polyamine oxidase (PAO) family with flavin‐binding and substrate‐binding domains. A unique N‐terminal extension wraps around the flavin‐binding domain of SpdH and is required for heme binding, placing a heme cofactor in close proximity to the FAD cofactor. Structural and mutational analysis reveals that residues in the putative active site at the re side of the FAD isoalloxazine ring form part of the catalytic machinery. PaSpdH features an unusual active site and lacks the conserved lysine that forms part of a lysine–water–flavin N5 atom interaction in other PAO enzymes characterized to date. Mutational analysis further confirms that heme is required for catalytic activity. This work provides an important starting point for understanding the role of SpdH, which occurs universally in P . aeruginosa strains, in polyamine metabolism.

Che, Shiyou↗

DOE OSTI2024

Biophysical and Structural Features of αβT ‐Cell Receptor Mechanosensing: A Paradigmatic Shift in Understanding T‐Cell Activation

ABSTRACT αβT cells protect vertebrates against many diseases, optimizing surveillance using mechanical force to distinguish between pathophysiologic cellular alterations and normal self‐constituents. The multi‐subunit αβT‐cell receptor (TCR) operates outside of thermal equilibrium, harvesting energy via physical forces generated by T‐cell motility and actin‐myosin machinery. When a peptide‐bound major histocompatibility complex molecule (pMHC) on an antigen presenting cell is ligated, the αβTCR on the T cell leverages force to form a catch bond, prolonging bond lifetime, and enhancing antigen discrimination. Under load, the αβTCR undergoes reversible structural transitions involving partial unfolding of its clonotypic immunoglobulin‐like (Ig) domains and coupled rearrangements of associated CD3 subunits and structural elements. We postulate that transitions provide critical energy to initiate the signaling cascade via induction of αβTCR quaternary structural rearrangements, associated membrane perturbations, exposure of CD3 ITAMs to phosphorylation by non‐receptor tyrosine kinases, and phase separation of signaling molecules. Understanding force‐mediated signaling by the αβTCR clarifies long‐standing questions regarding αβTCR antigen recognition, specificity and affinity, providing a basis for continued investigation. Future directions include examining atomistic mechanisms of αβTCR signal initiation, performance quality, tissue compliance adaptability, and T‐cell memory fate. The mechanotransduction paradigm will foster improved rational design of T‐cell based vaccines, CAR‐Ts, and adoptive therapies.

Immunology↗

DOE OSTI2022

Nonclassical autophagy activation pathways are essential for production of infectious Influenza A virus in vitro

Autophagy is a critical mechanism deployed by eukaryotic cells in response to stress, including viral infection, to boost the innate antimicrobial responses. However, an increasing number of pathogens hijack the autophagic machinery to facilitate their own replication. Influenza A virus (IAV), responsible for several global pandemics, has an intricate dependence on autophagy for successful replication in mammalian cells. To elucidate key chokepoints in the host stress responses facilitating IAV replication, we constructed a meta-transcriptome of IAV and host gene expression dynamics during early (1–3 hpi), mid (4–6 hpi), and late (8–12 hpi) stages of the viral replication cycle at two multiplicities of infection (MOI): 1 and 5. We supplemented the global transcriptome study with phosphoproteomic analysis of stress-activated protein kinase (SAPK/JNK) signaling in lung carcinoma (predominantly used as an in vitro model of IAV replication) and normal human bronchial epithelial cells. We report significant differences in the activation profiles of autophagy regulating genes upon IAV infection at the two MOI as well as divergent dependence on ULK1 signaling within the normal and cancer cells. Regardless of the cell model, JNK-Thr187 signaling was crucial for the production of infectious viral particles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Spray‐induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control

Abstract Spray‐induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double‐stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole‐fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii–Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis‐antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a , lipase 1 , and acetyl‐CoA oxidase in energy production ; and genes involved in manipulation of the plant host via abscisic acid metabolism ( 9‐cis‐epoxycarotenoid dioxygenase , xanthoxin dehydrogenase , and a putative abscisic acid G‐protein coupled receptor ) and secretion of the effector protein, effector candidate 2 . Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for the Erysiphe necator–Vitis vinifera system and tested six successful targets identified using the G. orontii–A. thaliana system. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in the G. orontii–A. thaliana pathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Granal thylakoid structure and function: explaining an enduring mystery of higher plants

Summary In higher plants, photosystems II and I are found in grana stacks and unstacked stroma lamellae, respectively. To connect them, electron carriers negotiate tortuous multi‐media paths and are subject to macromolecular blocking. Why does evolution select an apparently unnecessary, inefficient bipartition? Here we systematically explain this perplexing phenomenon. We propose that grana stacks, acting like bellows in accordions, increase the degree of ultrastructural control on photosynthesis through thylakoid swelling/shrinking induced by osmotic water fluxes. This control coordinates with variations in stomatal conductance and the turgor of guard cells, which act like an accordion's air button. Thylakoid ultrastructural dynamics regulate macromolecular blocking/collision probability, direct diffusional pathlengths, division of function of Cytochrome b 6 f complex between linear and cyclic electron transport, luminal pH via osmotic water fluxes, and the separation of pH dynamics between granal and lamellar lumens in response to environmental variations. With the two functionally asymmetrical photosystems located distantly from each other, the ultrastructural control, nonphotochemical quenching, and carbon‐reaction feedbacks maximally cooperate to balance electron transport with gas exchange, provide homeostasis in fluctuating light environments, and protect photosystems in drought. Grana stacks represent a dry/high irradiance adaptation of photosynthetic machinery to improve fitness in challenging land environments. Our theory unifies many well‐known but seemingly unconnected phenomena of thylakoid structure and function in higher plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

Summary Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans ‐eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem‐born roots and base‐born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38‐mediated adventitious root formation. Protein–protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38‐regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Coupled Heat Power Operation of Smart Buildings via Modular Pumped Hydro Storage

In the United States, building sector is responsible for around 40% of total energy consumption and contributes about 40% of carbon emissions since 2012. Within the past several years, various optimization models and control strategies have been studied to improve buildings’ energy efficiency and reduce operational expenses under the constraints of satisfying occupants’ comfort requirements. However, the majority of these studies consider building electricity demand and thermal load being satisfied by unidirectional electricity flow from the power grid or on-site renewable energy generation to electrical and thermal home appliances. Opportunities for leveraging low-grade heat for electricity have largely been overlooked due to impracticality at small scale. In 2016, a modular pumped hydro storage technology was invented in Oak Ridge National Laboratory, named Ground Level Integrated Diverse Energy Storage (GLIDES). In GLIDES, employing high-efficiency hydraulic machinery instead of gas compressor/turbine, liquid is pumped to compress gas inside high-pressure vessel creating head on ground level. This unique design eliminates the geographical limitation associated with the existing state-of-the-art energy storage technologies. It is easy to be scaled for building level, community level, and grid level applications. By using this novel hydro-pneumatic storage technology, opportunities for leveraging low-grade heat in building can be economical. In this research, the potential of utilizing low-grade thermal energy to augment electricity generation of GLIDES is investigated. Since GLIDES relies on gas expansion in the discharge process and the gas temperature drops during this non-isothermal process, available thermal energy, e.g., from thermal storage, combined cooling, heat and power system (CCHP), can be utilized by GLIDES to counter the cooling effect of the expansion process and elevate the gas temperature and pressure and boost the roundtrip efficiency. Here, several groups of comparison experiments have been conducted, and the experimental results show that a maximum 12.9% cost saving could be achieved with unlimited heat source for GLIDES, and a moderate 3.8% cost improvement can be expected when operated coordinately with CCHP and thermal energy storage in a smart building.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Manufacturing and Hydro Testing of a 10 MWe sCO2 Axial Turbine

Abstract Supercritical CO2 (sCO2) power cycles designed for thermodynamic efficiencies above 50% push component designs into pressure and temperature combinations that approach the limits of American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code and ASME Piping Design Codes with Turbine inlet conditions near 250 bar and 715 °C. These design conditions which limit available materials to high nickel alloys are compounded by the high fluid densities of sCO2 at these conditions which result in very compact machinery at the 10 MWe class which are currently being developed for the DOE supercritical transformational electric power (STEP) program. Design of the STEP Turbine is complete with integrated lessons learned from a previous 1 MWth subscale demonstration of a high temperature 10 MWe Turbine designed under the DOE SunShot Program. Fabrication of the STEP Turbine is nearing completion with all housings and pressure containing components in hand. This paper provides a detailed look at design intentions and limitations for the pressurized sections of the main pressure casing and the fabrication of key turbine components. Additional discussion is provided regarding postfabrication inspection and acceptance of the casing for use after issues with casing welds were identified late in the fabrication process.

Engineering↗