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DOE OSTI2025

Conservative Spin-Magnitude Change in Orbital Evolution in General Relativity

We show that physical scattering observables for compact spinning objects in general relativity can depend on additional degrees of freedom in the spin tensor beyond those described by the spin vector alone. The impulse, spin kick, and leading-order waveforms exhibit such a nontrivial dependence. A signal of this additional structure is the change in the magnitude of the spin vector under conservative Hamiltonian evolution, similar to our previous studies in electrodynamics. These additional degrees of freedom describe dynamical mass multipoles of compact objects and decouple for black holes. We also show that the conservative impulse, spin kick, and change of the additional degrees of freedom are encoded in the eikonal phase.

Classical black holes↗

DOE OSTI2026

Viscous Gubser flow with conserved charges to benchmark fluid simulations

We present semi-analytical solutions for the evolution of both the temperature and chemical potentials for viscous Gubser flow with conserved charges. Such a solution can be especially useful in testing numerical codes intended to simulate relativistic fluids with large chemical potentials. The freeze-out hypersurface profiles for constant energy density are calculated, along with the corresponding normal vectors, and presented as a new unit test for numerical codes. We also compare the influence of the equation of state on the semi-analytical solutions. We benchmark the newly developed smoothed particle hydrodynamics code ccake that includes both shear viscosity and three conserved charges. Here, the numerical solutions are in excellent agreement with the semi-analytical solution and are also able to accurately reproduce the hypersurface at freeze-out.

Hydrodynamic models↗

DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗

DOE OSTI2020

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Chen, Jianhai (ORCID:0000000300932003)↗

DOE OSTI2022

Conservative and Accurate Solution Transfer Between High-Order and Low-Order Refined Finite Element Spaces

Here, in this paper, we introduce general transfer operators between high-order and low-order refined finite element spaces that can be used to couple high-order and low-order simulations. Under natural restrictions on the low-order refined space we prove that both the high-to-low-order and low-to-high-order linear mappings are conservative, constant preserving, and high-order accurate. While the proof holds for affine geometries, numerical experiments indicate that the results hold for more general curved meshes. We present several numerical results confirming our analysis and demonstrate the utility of the new mappings in the context of adaptive mesh refinement and conservative multidiscretization coupling.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

On interpretation of fluctuations of conserved charges at high T

Abstract Fluctuations of conserved charges calculated on the lattice which can be measured experimentally, are well reproduced by a hadron resonanse gas model at temperatures below$$T_{ch} \sim 155$$ T ch ∼ 155 MeV and radically deviate from the hadron resonance gas predictions above the chiral restoration crossover. This behaviour is typically interpreted as an indication of deconfinement in the quark-gluon plasma regime. We present an argument that this interpretation may be too simple. The argument is based on the scaling of quantities with the number of colors: demonstration of deconfinement and QGP requires observable that is sensitive to$$\sim N_c^2$$ ∼ N c 2 gluons while the conserved charges are sensitive only to quarks and above$$T_{ch}$$ T ch scale as$$N_c^1$$ N c 1 . The latter scaling is consistent with the existence of an intermediate regime characterized by restored chiral symmetry and by approximate chiral spin symmetry which is a symmetry of confining interaction. In this regime the energy density, pressure and entropy density scale as$$N_c^1$$ N c 1 . In the large$$N_c$$ N c limit this regime might become a distinct phase separated from the hadron gas and from QGP by phase transitions. A natural observable that associates with deconfinement and is directly sensitive to deconfined$$N_c^2-1$$ N c 2 - 1 gluons is the Polyakov loop; in the$$N_c=3$$ N c = 3 world it remains very close to 0 at temperatures well above chiral crossover, reaches the value$$\sim 0.5$$ ∼ 0.5 around$$\sim 3T_{ch}$$ ∼ 3 T ch and the value close to 1 at temperatures$$\sim 1$$ ∼ 1 GeV.

Physics↗

DOE OSTI2021

Perspective—Mass Conservation in Models for Electrodeposition/Stripping in Lithium Metal Batteries

Electrochemical models at different scales and varying levels of complexity have been used in the literature to study the evolution of the anode surface in lithium metal batteries. This includes continuum, mesoscale (phase-field approaches), and multiscale models. In this paper, using a motivating example of a moving boundary model in one dimension, we show how battery models need proper formulation for mass conservation, especially when simulated over multiple charge and discharge cycles. The article concludes with some thoughts on mass conservation and proper formulation for multiscale models.

25 ENERGY STORAGE↗

DOE OSTI2023

Strictly Enforcing Invertibility and Conservation in CNN-Based Super Resolution for Scientific Datasets

Abstract Recently, deep convolutional neural networks (CNNs) have revolutionized image “super resolution” (SR), dramatically outperforming past methods for enhancing image resolution. They could be a boon for the many scientific fields that involve imaging or any regularly gridded datasets: satellite remote sensing, radar meteorology, medical imaging, numerical modeling, and so on. Unfortunately, while SR-CNNs produce visually compelling results, they do not necessarily conserve physical quantities between their low-resolution inputs and high-resolution outputs when applied to scientific datasets. Here, a method for “downsampling enforcement” in SR-CNNs is proposed. A differentiable operator is derived that, when applied as the final transfer function of a CNN, ensures the high-resolution outputs exactly reproduce the low-resolution inputs under 2D-average downsampling while improving performance of the SR schemes. The method is demonstrated across seven modern CNN-based SR schemes on several benchmark image datasets, and applications to weather radar, satellite imager, and climate model data are shown. The approach improves training time and performance while ensuring physical consistency between the super-resolved and low-resolution data. Significance Statement Recent advancements in using deep learning to increase the resolution of images have substantial potential across the many scientific fields that use images and image-like data. Most image super-resolution research has focused on the visual quality of outputs, however, and is not necessarily well suited for use with scientific data where known physics constraints may need to be enforced. Here, we introduce a method to modify existing deep neural network architectures so that they strictly conserve physical quantities in the input field when “super resolving” scientific data and find that the method can improve performance across a wide range of datasets and neural networks. Integration of known physics and adherence to established physical constraints into deep neural networks will be a critical step before their potential can be fully realized in the physical sciences.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Conservation of Dry Air, Water, and Energy in CAM and Its Potential Impact on Tropical Rainfall

Abstract For the Community Atmosphere Model version 6 (CAM6), an adjustment is needed to conserve dry air mass. This adjustment exposes an inconsistency in how CAM6’s energy budget incorporates water—in CAM6 water in the vapor phase has energy, but condensed phases of water do not. When water vapor condenses, only its latent energy is retained in the model, while its remaining internal, potential, and kinetic energy are lost. A global fixer is used in the default CAM6 model to maintain global energy conservation, but locally the energy tendency associated with water changing phase violates the divergence theorem. This error in energy tendency is intrinsically tied to the water vapor tendency, and reaches its highest values in regions of heavy rainfall, where the error can be as high as 40 W m −2 annually averaged. Several possible changes are outlined within this manuscript that would allow CAM6 to satisfy the divergence theorem locally. These fall into one of two categories: 1) modifying the surface flux to balance the local atmospheric energy tendency and 2) modifying the local atmospheric tendency to balance the surface plus top-of-atmosphere energy fluxes. To gauge which aspects of the simulated climate are most sensitive to this error, the simplest possible change—where condensed water still does not carry energy and a local energy fixer is used in place of the global one—is implemented within CAM6. Comparing this experiment with the default configuration of CAM6 reveals precipitation, particularly its variability, to be highly sensitive to the energy budget formulation. Significance Statement This study examines and explains spurious regional sources and sinks of energy in a widely used climate model. These energy errors result from not tracking energy associated with water after it transitions from the vapor phase to either liquid or ice. Instead, the model used a global fixer to offset the energy tendency related to the energy sources and sinks associated with condensed water species. We replace this global fixer with a local one to examine the model sensitivity to the regional energy error and find a large sensitivity in the simulated hydrologic cycle. This work suggests that the underlying thermodynamic assumptions in the model should be revisited to build confidence in the model-simulated regional-scale water and energy cycles.

Harrop, Bryce E.↗

DOE OSTI2022

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws. In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability. We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Macroalgal germplasm banking for conservation, food security, and industry

Ex situ seed banking was first conceptualized and implemented in the early 20th century to maintain and protect crop lines. Today, ex situ seed banking is important for the preservation of heirloom strains, biodiversity conservation and ecosystem restoration, and diverse research applications. However, these efforts primarily target microalgae and terrestrial plants. Although some collections include macroalgae (i.e., seaweeds), they are relatively few and have yet to be connected via any international, coordinated initiative. In this piece, we provide a brief introduction to macroalgal germplasm banking and its application to conservation, industry, and mariculture. We argue that concerted effort should be made globally in germline preservation of marine algal species via germplasm banking with an overview of the technical advances for feasibility and ensured success.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans

During meiotic prophase, the essential events of homolog pairing, synapsis, and recombination are coordinated with meiotic progression to promote fidelity and prevent aneuploidy. The conserved AAA+ ATPase PCH-2 coordinates these events to guarantee crossover assurance and accurate chromosome segregation. How PCH-2 accomplishes this coordination is poorly understood. Here, we provide evidence that PCH-2 decelerates pairing, synapsis and recombination in C. elegans by remodeling meiotic HORMADs. We propose that PCH-2 converts the closed versions of these proteins, which drive these meiotic prophase events, to unbuckled conformations, destabilizing interhomolog interactions and delaying meiotic progression. Further, we find that PCH-2 distributes this regulation among three essential meiotic HORMADs in C. elegans: PCH-2 acts through HTP-3 to regulate pairing and synapsis, HIM-3 to promote crossover assurance, and HTP-1 to control meiotic progression. In addition to identifying a molecular mechanism for how PCH-2 regulates interhomolog interactions, our results provide a possible explanation for the expansion of the meiotic HORMAD family as a conserved evolutionary feature of meiosis. Taken together, our work demonstrates that PCH-2’s remodeling of meiotic HORMADs has functional consequences for the rate and fidelity of homolog pairing, synapsis, recombination and meiotic progression, ensuring accurate meiotic chromosome segregation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

AmeriFlux US-xSC NEON Smithsonian Conservation Biology Institute (SCBI)

This is the AmeriFlux version of the carbon flux data for the site US-xSC NEON Smithsonian Conservation Biology Institute (SCBI). Site Description - The Smithsonian Conservation Biology Institute (SCBI) site is a mid-continent forested eastern deciduous site, species include Oaks, Hickories, and Ash, and contains well defined ground cover and understory strata.

Network), NEON (National Ecological Observatory↗

DOE OSTI2020

Conservative Estimation of Tail Probabilities from Limited Sample Data

Several sparse-sample uncertainty quantification (UQ) methods are compared for conservative but not overly conservative estimation of small tail probabilities involving responses that lay beyond specified thresholds in the tails of probability distributions. Sixteen very differently shaped distributions (or probability density functions, PDFs) and tail probability magnitudes ranging from 10 -5 to 10 -1 are considered in order for the study to be relevant to a wide range of risk analysis and quantification of margins and uncertainty (QMU) problems. The emphasis of the study is on limited data regimes ranging from N = 2 to 20 samples, reflective of most experimental and some expensive computational situations. Relatively simple sparse-sample UQ methods tested for this regime involve statistical tolerance interval "Equivalent Normal and related "Ensemble of Normals" and "Superdistribution (SD) approaches. (The independently derived SD is effectively equivalent to the Bayesian posterior predictive distribution given the assumptions of the derivation.) The performance of the methods was generally improved for N ≥ 5 samples with a generalized Jackknife resampling technique, which determines a tail probability estimate by averaging estimates from smaller sub-samples. Several quantitative metrics for method conservatism and accuracy of tail probability estimation are used to assess and rank the methods' performance over many random trials for each test PDF and probability magnitude. A variant of Bootstrap resampling was also tried, but did not significantly improve tail probability estimates in most cases. Detailed results are presented from over 100-million tests over the above factors that provide useful granular information on which methods or combination of methods perform best in various areas of the factor space.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Resolution requirements for energy conservation in kinetic plasma simulations

The kinetic codes used to model the coupled dynamics of electromagnetic fields and charged particle transport have requirements for spatial, temporal, and charge resolution. These requirements may vary by the solution technique and scope of the problem. In this report, we investigate the resolution limits in the energy-conserving implicit particle-in-cell code CHICAGO. This report has the narrow aim of determining the maximum acceptable grid spacing for the dense plasmas generated in models of z-pinch target gases and power-flow electrode plasmas. In the 2D sample problem, the plasma drifts without external forces with velocity of 10 cm/µs. Simulations are scaled by plasma density to maintain uniform strides across the plasma and from the plasma to the boundaries. Additionally, the cloud-in-cell technique is used with 400 particles per cell and Δ t = 0.85× the Courant limit. For the linear cloud distribution, the criterion for conserving energy is Δ E/E tot < 0.01 for 50,000 time steps. The grid resolution is determined to crudely be Δx ≲ 3 l s , where l s is the electron collisionless skin depth. For the second-order cloud distribution the criterion is Δ E/E tot < 0.005 yielding Δx ≤ 15 l s . These scalings are functions of the chosen v d , Δ t , particles-per-cell, and number of steps.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗