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At least 721 records · Page 40

The hTERT core promoter forms three parallel G-quadruplexes

The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

59 BASIC BIOLOGICAL SCIENCES↗

A Review of Computational Models for the Flow of Milled Biomass Part II: Continuum-Mechanics Models

The design of efficient material-handling systems for milled lignocellulosic biomass is challenging due to their complex particle morphologies and frictional interactions. Computational modeling, including the discrete element method (DEM) and continuum-based finite-element/volume methods, may offer scientific insight and predictive capabilities for the flow of milled biomass in hoppers and feeders. Herein, this article (Part II) presents a review of current state-of-the-art continuum models for the flow of milled biomass, whereas DEM models are reviewed in a companion article (Part I). Advances of numerical methods to solve the global governing equations are discussed first, followed by a comprehensive review of constitutive models for granular materials, including Drucker–Prager, hypoplastic, Cambridge-type, inertial-rheology, and nonlocal granular fluidity models. Specifically, we provide in-depth discussion on the suitability of those models for milled lignocellulosic biomass materials in terms of nonlinear elasticity, dependence of flow strength on pressure, density and shear rate, and compaction (dilation) associated with hardening (softening). Furthermore, our study shows that, despite the recent advances in continuum granular flow modeling, the most suitable constitutive models still need further development to account for material parametrization, multiflow regimes, and multiscale behavior before they can be reliably used to optimize the design and operation of biomass handling systems.

09 BIOMASS FUELS↗

Formulation of a Consistent Multi‐Species Canopy Description for Hydrodynamic Models Embedded in Large‐Scale Land‐Surface Representations of Mixed‐Forests

Abstract The plant hydrodynamic approach represents a recent advancement to land surface modeling, in which stomatal conductance responds to water availability in the xylem rather than in the soil. To provide a realistic representation of tree hydrodynamics, hydrodynamic models must resolve processes at the level of a single modeled tree, and then scale the resulting fluxes to the canopy and land surface. While this tree‐to‐canopy scaling is trivial in a homogeneous canopy, mixed‐species canopies require careful representation of the species properties and a scaling approach that results in a realistic description of both the canopy and individual‐tree hydrodynamics, as well as leaf‐level fluxes from the canopy and their forcing. Here, we outline advantages and pitfalls of three commonly used approaches for representing mixed forests in land surface models and present a new framework for scaling vegetation characteristics and fluxes in mixed forests. The new formulation scales fluxes from the tree to canopy level in an energy‐ and mass‐conservative way and allows for a consistent multi‐species/multi‐type canopy description by hydrodynamic models.

Bohrer, G.↗

Development and Porting of Nuclear Reactor Computational Models for the NRIC Virtual Test Bed in FY23

The U.S. DOE’s National Reactor Innovation Center (NRIC) hosts an open-source website and associated GitHub repository called the Virtual Test Bed (VTB) on which computational models for advanced reactors are documented and shared with the reactor community. In FY23 under the NRIC program, computational models for nuclear reactor analysis were developed and contributed to the VTB Github repository during FY23 by contributors at Argonne National Laboratory. Other models developed outside of NRIC were also ported to the VTB as part of this work, serving a broader mission to make computational reactor analysis models more widely available to the reactor community. The model development activities focused on demonstration of gas-cooled microreactor models including computational fluid dynamics simulations of flow through an industry-inspired air jacket design, and simulation of multiphysics transients for a gas-cooled microreactor assembly. Additionally, development of a molten salt reactor (led at Idaho National Laboratory) was supported through Argonne’s expertise in multigroup cross sections generation. Models for these two reactor types were targeted due to their relevancy to NRIC’s Demonstration of Microreactor Experiments (DOME) and Laboratory for Operation and Testing in the U.S. (LOTUS) physical test beds, which are slated to host microreactor and molten salt reactor experiments. The model porting activities consisted of developing detailed documentation for several physics models which originate from the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. We include only contributions from Argonne National Laboratory in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Optimization and stabilization of Fermilab Booster using hybrid Bayesian/RL framework

PIPII project will raise Fermilab Booster intensity and ramp rate. Beam losses will limit average power and are hard to simulate. Presently, Booster uses operator-guided empirical tuning. This task is challenging due to high dimensionality, multiple objectives, critical safety constraints, and drifts. We developed a synergistic suite of Bayesian optimization (BO) and reinforcement learning (RL) tools to optimize and stabilize beam losses. First, active learning was used to build a rough model. Data was collected parasitically using two novel safety constraint types – nonlinear input space restrictions (based on optics model), and uncertainty constraints (to stop bad steps/beam aborts). We then applied online multi-objective BO with scalarized objectives and fitting to improve/rebalance losses, increasing safety margins by 25%. Using BO model as a safety veto, we tried several on/off-policy RL agents for long term stabilization; SAC had best performance. We found that adding contextual (state) information further improved performance, eventually integrating key knobs like linac phase and temperature into the parameter space. Long term testing is ongoing to enable operational use.

Kuklev, Nikita [Fermilab]↗

Data for Impact of Vertical and Seasonal Variation in Leaf Traits on Simulating Soybean Canopy Photosynthesis via 1D and 3D Modeling

Accurate modeling of photosynthesis is crucial for predicting crop productivity and quantifying the carbon cycle in agroecosystems. Leaf traits are essential inputs for modeling canopy photosynthesis. Yet, many existing models still use fixed plant functional type (PTF)-based values to parameterize leaf traits under a big-leaf or two-big-leaf assumption, neglecting their vertical profiles and seasonal changes. This simplification may introduce significant uncertainties in estimating gross primary productivity (GPP). In this study, we simulated soybean GPP and tested the effects of vertical and seasonal variation in three key leaf photosynthetic traits: the maximum carboxylation rate at 25 °C (Vcmax25), leaf chlorophyll content (LCC), and leaf mass per area (LMA) in the 1D-SCOPE and 3D-Helios models. Weekly field measurements were conducted during the growing season of 2024 to support the simulation. We designed ten leaf trait parameterization schemes by incorporating different combinations of vertical profiles and seasonal changes, while assuming homogeneous canopy architecture in both models. Our results revealed that Vcmax25 vertical and seasonal variation had the strongest influence on simulated GPP in both 1D and 3D models, while LCC and LMA effects were minimal. Particularly, the scheme with an empirically parameterized Vcmax25 profile achieved comparable performance to the scheme with the measured Vcmax25 profile. Both 1D-SCOPE and 3D-Helios accurately modeled GPP (SCOPE: R2 = 0.87, Bias = 0.55 µmol m⁻² s⁻¹; Helios: R2 = 0.9, Bias = 0.22 µmol m⁻² s⁻¹) under the most complex scheme, and their responses to vertical and seasonal variation in leaf traits were consistent, demonstrating the robustness of our findings. Based on our findings, we propose a scalable framework for parameterizing leaf traits to improve GPP simulations. This study contributes to improving the representation of leaf trait dynamics in canopy-level photosynthesis models, potentially enhancing our ability to predict crop productivity and understand agroecosystem carbon dynamics.

Photosynthesis↗

Are Remote Sensing Evapotranspiration Models Reliable Across South American Ecoregions?

Many remote sensing-based evapotranspiration (RSBET) algorithms have been proposed in the past decades and evaluated using flux tower data, mainly over North America and Europe. Model evaluation across South America has been done locally or using only a single algorithm at a time. Here, in this work, we provide the first evaluation of multiple RSBET models, at a daily scale, across a wide variety of biomes, climate zones, and land uses in South America. We used meteorological data from 25 flux towers to force four RSBET models: Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), Global Land Evaporation Amsterdam Model (GLEAM), Penman–Monteith Mu model (PM-MOD), and Penman–Monteith Nagler model (PM-VI). ET was predicted satisfactorily by all four models, with correlations consistently higher (R 2 > 6) for GLEAM and PT-JPL, and PM-MOD and PM-VI presenting overall better responses in terms of percent bias (-10 < PBIAS < 10%). As for PM-VI, this outcome is expected, given that the model requires calibration with local data. Model skill seems to be unrelated to land-use but instead presented some dependency on biome and climate, with the models producing the best results for wet to moderately wet environments. Our findings show the suitability of individual models for a number of combinations of land cover types, biomes, and climates. At the same time, no model outperformed the others for all conditions, which emphasizes the need for adapting individual algorithms to take into account intrinsic characteristics of climates and ecosystems in South America.

54 ENVIRONMENTAL SCIENCES↗

Forecast of Wildfire Potential Across California USA Using a Transformer

Wildfires are a major issue facing the United States, a matter further exacerbated by an ever-changing climate. In California alone, wildfires are responsible for billions of dollars in damages and take lives each year. Accurately predicting fire danger conditions allows preparation awareness before wildfires start. Transformers are a class of deep learning models designed to identify patterns in sequential datasets. In recent years, transformers have gained popularity through their impressive performance in natural language processing and other applications of signal recognition. This analysis demonstrates the ability of a transformer with a residual connection to forecast fire danger potential over the state of California. Wildland fire potential index (WFPI) maps collected from the US Geological Survey database from January 1st 2020 to December 31st 2023 were used to tune, train and evaluate the transformer. Meteorological inputs (provided by Daymet daily weather and climatological summaries), the normalized difference vegetation index (NDVI) (calculated from the Moderate Resolution Imaging Spectroradiometer (MODIS)), and outputs from the Scott and Burgman fire behavior fuel models (to characterize maps of fuel types), were used as inputs. Our results show that a transformer can effectively emulate the US Forest Service modeled WFPI maps of California USA for four week long forecasts over the month of July, 2023, with correlations ranging from 0.85 – 0.98.

Limber, Russell [ORNL]↗

From Event Data to Wind Power Plant DQ Admittance and Stability Risk Assessment

This paper presents a dynamic event data-based stability risk assessment method for power grids with high penetrations of inverter-based resources (IBRs). This method relies on obtaining the IBRs' DQ admittance through dynamic event data and computing the system's eigenvalues based on the admittance models. Two critical technologies are employed in this research, including time-domain and frequency-domain data fitting and dq-frame voltage and current signal derivation. The first technology is key to obtaining the s-domain expressions from the transient response data, and the s-domain DQ admittance model from the frequency-domain measurements. The second technology is key to obtaining the dq-frame voltage and current signals from either the three-phase instantaneous measurements or the phasor measurement unit (PMU) data. The method is illustrated using data generated from a Type-4 wind power plant modeled in PSCAD. This paper demonstrates the technical feasibility of the proposed approach.

17 WIND ENERGY↗

Critical thermonuclear reactions in classical novae and type I X-ray bursts

The goal of this project was to experimentally constrain the nuclear reaction rates whose uncertainties have the largest impact on models of classical novae and Type-I X-ray bursts. These astrophysical events occur when a white dwarf or neutron star, respectively, accretes hydrogen and helium from a companion star until a thermonuclear runaway ensues. The primary reactions of interest to this project for novae and X-ray bursts are 30 P(ρ,γ) 31 S and 15 O(α,γ) 19 Ne. The project methodology was to develop a new radiation detection system in two phases to measure the low-energy beta-delayed particle emissions of 31 Cl and 20 Mg at the National Superconducting Cyclotron Laboratory (NSCL) in order to constrain these two reaction rates. In particular, a gas-filled charged-particle detector was to be designed, constructed and operated, in concert with the SeGA array.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

An integrated coupling model for solving multiscale fluid-fluid coupling problems in SAM code

In this study, an integrated coupling method has been developed for solving multiscale fluid-fluid coupling problems in plant-scale safety analysis models in SAM (System Analysis Module) code. In this method, a higher-fidelity multi-dimensional (3D) flow module is used for reactor components of complex flow features (e.g., reactor core) and a lumped parameter one-dimensional (1D) flow module for plant-scale flow loops (e.g., primary loop pipe network), respectively. In this method, the 3D fluid equation/domain and 1D fluid equation/domain are tightly coupled at the residual level and solved simultaneously using the Newton’s method to overcome the convergence issues typically seen in existing approaches like separate domain approach, where the 3D fluid equation and 1D fluid equation are solved separately. Extensive and successful code verifications and demonstrations have been performed for this newly developed method. This new modeling approach significantly simplify the work flow in developing high-fidelity plant-scale safety analysis model, e.g. for pool-type reactors and pebble-bed reactors.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Simulating Marine Ecosystem Dynamics and Biogeochemical Cycling With Multiple Plankton Functional Types

Current representations of marine ecosystems in Earth System Models are greatly simplified, neglecting key interactions between dynamic food webs, biogeochemistry, and climate change. We use the Marine Biogeochemistry Library code base within the Community Earth System Model 2.2.2 to create an expanded ecosystem model with eight phytoplankton groups and four zooplankton size classes (MARBL-8P4Z). Incorporating more specific plankton types and size classes has the potential to capture a wider range of possible behaviors of the ecosystem, its complex interactions with biogeochemistry, and its feedback to climate change. It also permits stronger observational constraints, including in situ group-specific biomass and various observational estimates of plankton community composition. MARBL-8P4Z broadly captures observed global-scale patterns in biomass and community composition for both phytoplankton and zooplankton, with a good performance in simulating broad biogeochemistry fields. The model shows comparable spatial patterns and magnitudes to the observed picophytoplankton biomass (Prochlorococcus, Synechococcus, picoeukaryotes), and captures the seasonal cycle of mesozooplankton biomass. Picophytoplankton groups and microzooplankton dominate biomass and production in oligotrophic, subtropical regions, while nano-phytoplankton, diatoms and the larger zooplankton groups prevail at higher latitudes and within upwelling zones. The model simulates reasonable energy transfer efficiency through the food web, with tight linkages between the phytoplankton community composition, zooplankton grazing, and carbon export, with the potential to link to fisheries models. Thus, MARBL-8P4Z has the potential to account for key climate-driven ecological shifts in the plankton that will modify ocean biogeochemistry in the future.

54 ENVIRONMENTAL SCIENCES↗

A Generic and Multifunctional Electromagnetic Transient Model for Grid-Following Inverters

This article presents a generic and multi-functional electromagnetic transient (EMT) dynamic model of grid following (GFL) inverter-based resource (IBR) using the PSCAD software platform. The features of the developed model includes the flexibility in selecting various types and combinations of DC sources covering PV modules, battery modules, ideal DC source module, as well as flexibility in selecting either switched or averaged model of inverter. This model also covers exhaustive lists of controller logic covering open-loop/closed-loop PQ dispatch control, DC voltage and AC terminal voltage control along with the conventional current control designed in dq-domain, ate- domain and positive-negative sequence domain. Moreover, this model is equipped with the flexibility in selecting various types of current limiting schemes that includes saturation-based as well as latching-based current limiter, anti-windup protection. Moreover, the EMT model is agnostic to the MVA rating and is suitable for interfacing transmission systems by being complaint with the IEEE Std. 2800. The generality in the power circuits and the multi-functional options in operation and control of the developed EMT model makes it suitable for both academia and industry to study various power system aspects not limited to but such as fault behavior of GFL IBR and impacts on protection system, transient stability of a system interfaced with large number of GFL IBRs etc.

14 SOLAR ENERGY↗

A Generic and Multi-Functional Electromagnetic Transient Model for Grid-Following Inverter: Preprint

This article presents a generic and multi-functional electromagnetic transient (EMT) dynamic model of grid following (GFL) inverter-based resource (IBR) using the PSCAD TM software platform. The features of the developed model includes the flexibility in selecting various types and combinations of DC sources covering PV modules, battery modules, ideal DC source module, as well as flexibility in selecting either switched or averaged model of inverter. This model also covers exhaustive lists of controller logic covering open-loop/closed-loop PQ dispatch control, DC voltage and AC terminal voltage control along with the conventional current control designed in dq-domain, aB- domain and positive-negative sequence domain. Moreover, this model is equipped with the flexibility in selecting various types of current limiting schemes that includes saturation-based as well as latching-based current limiter, anti-windup protection. Moreover, the EMT model is agnostic to the MVA rating and is suitable for interfacing transmission systems by being complaint with the IEEE Std. 2800. The generality in the power circuits and the multi-functional options in operation and control of the developed EMT model makes it suitable for both academia and industry to study various power system aspects not limited to but such as fault behavior of GFL IBR and impacts on protection system, transient stability of a system interfaced with large number of GFL IBRs etc.

grid following inverter↗

Biaxial steel plated concrete constitutive models for composite structures: Implementation and validation

The Steel-plated Concrete (SC) technique is an alternative construction technique with faster onsite construction speed, reduced construction time, and increased structural performance. Aiming to predict the force transfer mechanism of SC elements, an innovative constitutive model package is proposed by implementing experimental-based biaxial steel plate concrete models into the nonlinear finite element (FE) model “Membrane Model of SC (MM-CS).” First, the formulation and implementation of the MM-SC is illustrated in detail, including the equilibrium and compatibility equations and the implementation of constitutive models. Next, various experimental data of SC members are selected and simulated using the proposed MM-SC model. In this research, two types of structures, SC panels and framed SC shear walls, and three types of loading conditions, including uniaxial compression, pure shear, and combined axial-flexural-shear tests, are analyzed respectively. Good agreements were obtained between the reported results and the FE simulation results in terms of yield capacity and ultimate capacity, proving the reliability of the implemented analytical constitutive material models and the biaxial membrane model formulations.

42 ENGINEERING↗

Facet Preferencing by Chemical Substitution Controls Semi-Hydrogenation Selectivity in Ternary Pyrite-Type Intermetallic Compounds

Intermetallic compounds serve as model catalysts for selective hydrogenation reactions, offering precise control over the active site composition(s), geometric and electronic structure. The addition of a third element to form a ternary intermetallic alters the exposed crystal facet(s), demonstrating a strategy to impart improved catalytic behavior in intermetallic catalysts. The site-specific substitution of a small fraction of Pd atoms with Au in pyrite-type PdSb 2 results in the preferential exposure of the (100) facet over the (111) facet. Electron back scattered diffraction and density functional theory calculations confirm the facet change upon the substitution of Pd with Au to form the ternary Pd 1−x Au x Sb 2 (0.075 ≤ x ≤ 0.25). The (100) facet demonstrates higher net alkene selectivity due to significantly weaker alkene binding compared to the (111) facet. Distinct from our prior work on chemical substitution to directly alter the active site composition, this work demonstrates the indirect modification of active sites via preferential facet exposure.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The lattice parameter – composition relationship of the body centered cubic uranium-niobium alloys

In this paper, in-situ time-of-flight neutron diffraction experiments were performed on uranium-niobium alloy with 6 wt% Nb to study the lattice parameter-composition relationship for the body centered cubic (bcc) alloys. Based on lattice-parameter measurements of Nb-supersaturated γs phase over the range of 450 – 790 °C, an improved Vegard's-type relationship was established for determination of Nb concentrations at elevated temperatures. Neutron diffraction data were also collected as a function of aging time over the 450 - 600 °C range when γs phase decomposed isothermally into the mixture of orthorhombic α-U and Nb-rich bcc phase, as well as at room-temperature on the alloys aged ex-situ at 500 °C up to five years. From these measurements, the average Nb concentrations in the bcc phase were determined based on the Rietveld refinements of weight fraction and mass conservation relations (lever rule). Over the 15at% – 78at% range of Nb concentrations that correspond to different experimental aging times, the lattice parameters at constant temperatures exhibit a nonlinear S-shaped variation with Nb concentration, and the associated excess volumes of mixing can be described by a subregular solution model of the Redlich–Kister type of polynomial. Over the full range of composition the S-shaped deviation from Vegard's law can be modeled using a combination of an elastic continuum model and a perturbation to the radii of the solute atoms in the solvent, suggesting that electronic interactions between solute and solvent atoms could play an important role in the compositional dependence of lattice parameter for the γ-phase U-Nb alloys. While Vegard's law is a straightforward and reasonably good approximation for the bcc solid solutions in the U-Nb system, the Nb concentrations determined from the weight fraction refinements of diffraction data provide internally consistent, mass-conserving estimates of solute redistribution for the monotectoid reaction.

36 MATERIALS SCIENCE↗

Potential for Transactive Energy to Improve the Provisioning of Grid Services from Batteries

This study assessed the degree to which transactive energy systems could help reduce or remove barriers to the deployment of battery energy storage, and realize the full potential of battery resources to supply needed services to the grid and fairly compensate various types of battery owners. To enable this assessment, typical battery deployments were characterized, along with energy markets, Federal Energy Regulatory Commission Order rulings and implementations, grid services, and current deployment barriers. Finally, this study analyzed the value that accrues to batteries supplying today’s grid services as a function of the participation models associated with three primary types of battery ownership: merchant-owned transmission-connected batteries; utility-owned distribution-connected batteries; and customer-owned behind-the-meter batteries. This provided both quantitative and qualitative assessments comparing opportunities for battery storage in business-as-usual and transactive energy scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗