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DOE OSTI2022

Subcell limiting strategies for discontinuous Galerkin spectral element methods

Here, we present a general family of subcell limiting strategies to construct robust high-order accurate nodal discontinuous Galerkin (DG) schemes. The main strategy is to construct compatible low order finite volume (FV) type discretizations that allow for convex blending with the high-order variant with the goal of guaranteeing additional properties, such as bounds on physical quantities and/or guaranteed entropy dissipation. For an implementation of this main strategy, four main ingredients are identified that may be combined in a flexible manner: (i) a nodal high-order DG method on Legendre–Gauss–Lobatto nodes, (ii) a compatible robust subcell FV scheme, (iii) a convex combination strategy for the two schemes, which can be element-wise or subcell-wise, and (iv) a strategy to compute the convex blending factors, which can be either based on heuristic troubled-cell indicators, or using ideas from flux-corrected transport methods. By carefully designing the metric terms of the subcell FV method, the resulting methods can be used on unstructured curvilinear meshes, are locally conservative, can handle strong shocks efficiently while directly guaranteeing physical bounds on quantities such as density, pressure or entropy. We further show that it is possible to choose the four ingredients to recover existing methods such as a provably entropy dissipative subcell shock-capturing approach or a sparse invariant domain preserving approach. We test the versatility of the presented strategies and mix and match the four ingredients to solve challenging simulation setups, such as the KPP problem (a hyperbolic conservation law with non-convex flux function), turbulent and hypersonic Euler simulations, and MHD problems featuring shocks and turbulence.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Multifidelity methods for uncertainty quantification of a nonlocal model for phase changes in materials

This study is devoted to the construction of a multifidelity Monte Carlo (MFMC) method for the uncertainty quantification of a nonlocal, non-mass-conserving Cahn-Hilliard model for phase transitions with an obstacle potential. Here, we are interested in estimating the expected value of an output of interest (OoI) that depends on the solution of the nonlocal Cahn-Hilliard model. As opposed to its local counterpart, the nonlocal model captures sharp interfaces without the need for significant mesh refinement. However, the computational cost of the nonlocal Cahn-Hilliard model is higher than that of its local counterpart with similar mesh refinement, inhibiting its use for outer-loop applications such as uncertainty quantification. The MFMC method augments the desired high-fidelity, high-cost OoI with a set of lower-fidelity, lower-cost OoIs to alleviate the computational burden associated with nonlocality. Most of the computational budget is allocated to sampling the cheap surrogate models to achieve speedup, whereas the high-fidelity model is sparsely sampled to maintain accuracy. For the non-mass-conserving nonlocal Cahn-Hilliard model, the use of the MFMC method results in, for a given computational budget, about an order of magnitude reduction in the mean-squared error of the expected value of the OoI relative to that of the Monte Carlo method.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Transparent window film with embedded nano-shades for thermoregulation

Every year, more than 20% of the energy consumption in the United States and more than 10% of the global consumption is used towards HVAC (Heating, Ventilating, Air-Conditioning) systems in buildings. Although continued efforts in advancing renewable energy, efficient appliances, and smart building systems are desired, the most critical factors that cause extensive indoor energy consumption are thermal leakage and thermal waste generation. We demonstrate a smart window film that allows natural lighting with a clear view while blocking oblique incident sunlight to make the building interior cooler without using electricity or generating heat. Building upon the concept of, often overlooked, traditional window shades and privacy window films, we emphasize and elevate the application and impact of using magnetically arranged nanoscale material for energy conservation purpose in buildings. By embedding vertically aligned Ni flakes (VANF) in a polymer matrix film, nanoscale mirror array serve as shades to block the high-angled incident sunlight, blocking approximately 73% of total solar irradiance and bringing down the indoor temperature by 1.92 °C during the daytime in a model house while providing nearly 90% transparency. Global application was simulated by applying the respective solar angle and intensity at selected latitudes, indicating their potential. This passively energy-conserving smart film is a low cost, maintenance free, and simple product for users and easy-to-manufacture product for the industry.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

we report a multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

An Eulerian Vlasov-Fokker–Planck algorithm for spherical implosion simulations of inertial confinement fusion capsules

Here, we present a numerical algorithm that enables a phase-space adaptive Eulerian Vlasov–Fokker–Planck (VFP) simulation of inertial confinement fusion (ICF) capsule implosions. The approach relies on extending a recent mass, momentum, and energy conserving phase-space moving-mesh adaptivity strategy to spherical geometry. In configuration space, we employ a mesh motion partial differential equation (MMPDE) strategy while, in velocity space, the mesh is expanded/contracted and shifted with the plasma’s evolving temperature and drift velocity. The mesh motion is dealt with by transforming the underlying VFP equations into a computational (logical) coordinate, with the resulting inertial terms carefully discretized to ensure conservation. To deal with the spatial and temporally varying dynamics in a spherically imploding system, we have developed a novel nonlinear stabilization strategy for MMPDE in the configuration space. The strategy relies on a nonlinear optimization procedure that optimizes between mesh quality and the volumetric rate change of the mesh to ensure both accuracy and stability of the solution. Implosions of ICF capsules are driven by several boundary conditions: (1) an elastic moving wall boundary; (2) a time-dependent Maxwellian Dirichlet boundary; and (3) a pressure-driven Lagrangian boundary. Of these, the pressure-driven Lagrangian boundary driver is new to our knowledge. The implementation of our strategy is verified through a set of test problems, including the Guderley and Van-Dyke implosion problems — the first-ever reported using a Vlasov–Fokker–Planck model.

1D2V↗

DOE OSTI2025

Comparative genomics of Aspergillus nidulans and section Nidulantes

Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.

Theobald, Sebastian [Technical University of Denma↗

DOE OSTI2020

Response to a comment on Dessert et al. “The dark matter interpretation of the 3.5 keV line is inconsistent with blank-sky observations”

The dark matter explanation of the 3.5 keV line is strongly disfavored by our work in Dessert et al. (2020). Boyarsky et al. (2004) questions that conclusion: modeling additional background lines is claimed to weaken the limit sufficiently to re-allow a dark matter interpretation. Here, we respond as follows. (1) A more conservative limit is obtained by modeling additional lines; this point appeared in its entirety in our work in Dessert et al. (2020), though we also showed that the inclusion of such lines is not necessary. (2) Despite suggestions in Boyarsky et al. (2004), even the more conservative limits strongly disfavor a decaying dark matter origin of the 3.5 keV line.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A data-driven sensor placement approach for detecting voltage violations in distribution systems

Stochastic fluctuations in power injections from distributed energy resources (DERs) combined with load variability can cause constraint violations (e.g., exceeded voltage limits) in electric distribution systems. To monitor grid operations, sensors are placed to measure important quantities such as the voltage magnitudes. Here, in this paper, we consider a sensor placement problem which seeks to identify locations for installing sensors that can capture all possible violations of voltage magnitude limits. We formulate a bilevel optimization problem that minimizes the number of sensors and avoids false sensor alarms in the upper level while ensuring detection of any voltage violations in the lower level. This problem is challenging due to the nonlinearity of the power flow equations and the presence of binary variables. Accordingly, we employ recently developed conservative linear approximations of the power flow equations that overestimate or underestimate the voltage magnitudes. By replacing the nonlinear power flow equations with conservative linear approximations, we can ensure that the resulting sensor locations and thresholds are sufficient to identify any constraint violations. Additionally, we apply various problem reformulations to significantly improve computational tractability while simultaneously ensuring an appropriate placement of sensors. Lastly, we improve the quality of the results via an approximate gradient descent method that adjusts the sensor thresholds. We demonstrate the effectiveness of our proposed method for several test cases, including a system with multiple switching configurations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Migrating Populus with climate change: Phenology, coppice management, cold spell susceptibility, leaf dynamics, and biomass production

Understanding the phenology and productivity of Populus species is crucial for effective management and conservation strategies amid climate change. We investigated leaf budbreak timing, susceptibility to cold damage, leaf dynamics, and biomass production of 168 Populus genotypes with diverse provenances in the southeastern United States. Our study revealed significant variation in budbreak timing across different taxa and years, with genotypes inheriting traits adapted to their parents’ local climates. Temperature emerged as a key factor triggering budbreak, while leaf development depended on other environmental cues such as photoperiod. Notably, budbreak occurred approximately 20 days earlier in 2023 compared to 2022 due to higher accumulated degree days (ADDs). Short-rotation-coppice (SRC) management delayed budbreak by five to ten days. Cold damage was significant in 2023, particularly for genotypes from northern provenances and those with P. maximowiczii parentage. Severe damage was also observed in eastern cottonwood ( Populus deltoides × Populus deltoides (D × D)) genotypes, despite most having southeastern US parentages. Leaf dynamics, including leaf duration and leaf area index (LAI), varied across taxa and sites, with earlier budbreak correlating with extended growing seasons and increased LAI. Biomass production was intricately linked to phenological events, with earlier budbreak leading to increased biomass production and greater susceptibility to cold damage. Our findings highlight the importance of genetics, environment, and coppicing management in understanding and managing Populus phenology and biomass production. These insights provide valuable guidance for developing effective breeding, conservation, and management strategies for Populus species in the context of climate change.

Accumulated degree days (ADDs)↗

DOE OSTI2025

Litter production and foliar nutrient resorption in fast- and slow-growing tree species in the Central Amazon

Litterfall is crucial for forest maintenance, serving as a primary mechanism for nutrient return to the nutrient-poor soils of tropical forests. Foliar nutrient resorption likewise represents an important nutrient-conservation mechanism. Yet, little is known about how these processes vary between fast- and slow-growing species in post-logging areas of the Amazon forest. Here, the objective of this study was to quantify litterfall production and the resorption of foliar nutrients in fast-growing and slow-growing tree species of the Central Amazon, in a forest that was experimentally logged in 1987. The study was conducted from May 2022 to April 2023. Litterfall was collected biweekly using four collectors that were systematically distributed beneath the canopy of each monitored tree, totaling 72 collectors. Three fast-growing and three slow-growing species were selected, each with three replicates, totaling 18 monitored individuals. Species-specific samples of fresh (green) and senesced (litter) leaves were collected and analyzed for their nutrient content and resorption efficiency. Fast-growing species had a monthly leaf litter deposition of 13.53 ± 1.6 g m −2 month −1 , compared to 2.59 ± 0.4 g m −2 month −1 for slow-growing species. The average annual litter production across both functional types was 8.6 ± 2.6 Mg ha −1 year −1 . Nutrient inputs through litterfall were higher in fast-growing species for all elements, particularly nitrogen (N), with 21.92 ± 4.9 kg ha −1 year −1 . Phosphorus (P) and potassium (K) exhibited the highest foliar resorption. P resorption efficiency was 68.3 % in fast-growing species and 57.8 % in slow-growing species. For K, efficiencies were 59.0 % and 41.7 %, respectively. These results highlight the substantial role that fast-growing species play in restoring forest productivity in managed Amazon forests, both through higher litter deposition and nutrient fluxes, and through nutrient conserving-mechanisms such as foliar nutrient resorption.

Amazon forest↗

DOE OSTI2023

Walking on the dark side: Anthropogenic factors limit suitable habitat for gray wolf ( Canis lupus ) in a large natural area covering Belarus and Ukraine

Due to successful conservation initiatives and legislations, the grey wolf (Canis lupus) is recolonising its historic range in Europe. However, wolves have never been extirpated across large areas in Eastern Europe but are often constrained to remote and inaccessible places due to centuries of persecution. This study aimed to identify the potentially suitable wolf habitats in Polesia, a massive cross-border lowland region extending over southern Belarus and northern Ukraine, which are often neglected in large carnivore studies at the continental scale. We hypothesized that anthropogenic rather than environmental factors govern wolf habitat suitability. We used a dataset of 4191 GPS locations obtained from radio-collared wolves (n = 26) and confirmed observations (n = 231) during 2014–2021 and applied maximum entropy method to estimate relative habitat suitability for wolves in Polesia. Artificial light at night (ALAN), proportion of cropland and tree cover were the most important factors affecting wolf habitat suitability. Road densities contributed poorly to predicting habitat suitability for wolves. Our models predicted a quarter of Polesia as suitable habitat and revealed priority areas connecting the important source populations in the Chornobyl Exclusion Zone in the east and the Bialowieza Forest in the west and thus essential for long-term wolf conservation. Our results provide the bases for effective, long-term wolf monitoring and management programs in both Belarus and Ukraine. However, national and transboundary wolf management in Polesia has been extremely challenging since 2022 due to the ongoing war and subsequent habitat degradation in this part of Europe.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A Performance analysis of the Claridge-Culp-Liu dehumidification process: A novel approach for drying moist air based on membrane separation, vacuum compression and sub-atmospheric condensation

This article covers a basic model for analyzing the performance of the Claridge-Culp-Liu dehumidification process. The fundamental process efficiency limit for dehumidification is close to COP Carnot , but for the eight dehumidification cases examined, the limiting or ideal energy use required is 26% to 56% that of a Carnot condensing system as shown in an earlier paper. The model presented in this paper is used to show the membrane system performance reduction caused by finite membrane area, finite water vapor permeance, non-zero air permeance, non-zero system air pressure drop, non-ideal compressors, vacuum pumps, and condensers. The performance of a “conservative” membrane system based on the use of existing components is computed for eight specific conditions along with that of a “target” system that assumes expected component performance after additional future component development. The “conservative” membrane system would use 36% to 66% as much energy as a system with a COP=7 chiller to produce the same dehumidification for the eight cases examined while the “target” system would use 15% to 40% the energy of a system with a COP=7 chiller. In addition to the significant energy reduction over conventional technology, the membrane system offers the advantages of: 1) no HFC refrigerant use; 2) direct isothermal control over humidity ratio setpoint; 3) maximum capacity occurs at design conditions; and 4) system generates pure water extracted from air as a by-product.

42 ENGINEERING↗

DOE OSTI2021

Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation

Far-red light photoacclimation (FaRLiP) exhibited by some cyanobacteria allows these organisms to use light of the far-red region of the solar spectrum (700 to 800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that are synthesized by chlorophyll f synthase and that absorb far-red light. However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl fbinding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells (FRLPSI) of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity, and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core antenna regions of PSI, and Chl f was not observed among the electron transport cofactors. This structural analysis also reveals both conserved and non-conserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FaRLiP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ

Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells

The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.

SARS-CoV-2 main protease (Mpro/3CLpro)↗

DOE OSTI2020

Iodine effective diffusion coefficients through volcanic rock: Influence of iodine speciation and rock geochemistry

Accurate prediction of the subsurface transport of iodine species is important for the assessment of long-term nuclear waste repository performance, as well as monitoring compliance with the Comprehensive Nuclear-Test-Ban Treaty, given that radioiodine decays into radioxenon. However, the transport of iodine through intact geologic media is not well understood, compromising our ability to assess risk associated with radioiodine migration. The current study's goal is to quantify the matrix diffusion of iodine species through saturated volcanic rock, with particular attention paid to the redox environment and potential speciation changes. Here, diffusion experiments were run for iodide through lithophysae-rich lava, lithophysae-poor lava, and welded tuff, whereas iodate diffusion was studied through welded tuff. Iodine transport was compared with a conservative tracer, HDO, and effective diffusion coefficients were calculated. Likely due to a combination of size and anion exclusion effects, iodine species diffused more slowly than the conservative tracer through all rock types tested. Furthermore, oxidation of iodide to iodate was observed in the lithophysae-poor lava, affecting transport. Results provide much needed data for subsurface transport models that predict radioiodine migration from underground sources, and indicate the pressing need for geochemical and redox interactions to be incorporated into these models.

58 GEOSCIENCES↗

DOE OSTI2020

Non-local model for surface tension in fluid-fluid simulations

We propose a non-local model for surface tension obtained in the form of an integral of a molecular-force-like function with support 3.5e added to the Navier-Stokes momentum conservation equation. We demonstrate analytically and numerically that with the non-local model interfaces with a radius of curvature larger than the support length behave macroscopically and microscopically, otherwise. For static droplets, the pressure difference Pe,in - Pe,out satisfies the Young-Laplace law for droplet radius greater than 3.5e and other- wise deviates from the Young-Laplace law. The latter indicates that the surface tension in the proposed model decreases with decreasing radius of curvature, which agrees with molecular dynamics and experimental studies of nanodroplets. Using the non-local model we perform numerical simulations of droplets under dynamic conditions, including a rising droplet, a droplet in shear flow, and two colliding droplets in shear flow, and compare results with a standard Navier-Stokes model subject to the Young-Laplace boundary condition at the fluid-fluid interface implemented via the Conservative Level Set (CLS) method. We find good agreement with existing numerical methods and analytical results for a rising macroscopic droplet and a droplet in a shear flow. For colliding droplets in shear flow, the non- local model converges (with respect to the grid size) to the correct behavior, including sliding, coalescence, and merging and breaking of two droplets depending on the capillary number. In contrast, we find that the results of the CLS model are highly grid-size dependent.

Howard, Amanda A.↗

DOE OSTI2021

An unsupervised machine-learning checkpoint-restart algorithm using Gaussian mixtures for particle-in-cell simulations

We propose an unsupervised machine-learning checkpoint-restart (CR) algorithm for particle-in-cell (PIC) algorithms using Gaussian mixtures (GM). The algorithm compresses the particle population per spatial cell by constructing a velocity distribution function using GM. Particles are reconstructed at restart time by local resampling of the Gaussians. To guarantee fidelity of the CR process, we ensure the exact preservation of invariants such as charge, momentum, and energy for both compression and reconstruction stages, everywhere on the mesh. We also ensure the preservation of Gauss' law after particle reconstruction by exactly matching the density profile at restart time. As a result, the GM CR algorithm is shown to provide a clean, conservative restart capability while potentially affording orders of magnitude savings in input/output requirements. Here, we demonstrate the algorithm using a recently developed exactly energy- and charge-conserving PIC algorithm using both electrostatic and electromagnetic tests. The tests demonstrate not only a high-fidelity CR capability, but also its potential for enhancing the fidelity of the PIC solution for a given particle resolution.

97 MATHEMATICS AND COMPUTING↗