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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Coupled Experimental and High-Temperature Discrete-Element Method Modeling Studies of Aluminosilicate Particle Handling in Concentrated Solar Power Environments

Chemically inert, aluminosilicate based particles have been investigated as both a thermal transport and sensible energy storage medium for concentrated solar power facilities. These particles will experience a wide range of operating temperatures (300-1000 K) and handling conditions (dense to dilute falling particle curtains, dense granular flows, or dense structures), requiring specially-designed and optimized infrastructures. The relative influence of collisional and frictional interactions between particles varies based on temperature-dependent particulate properties and greatly impacts the bulk, granular flow behavior. These underlying physics are captured using discrete element method modeling tools. However, this modeling method is computationally expensive as each particle position and interaction is tracked during the simulation. These modeling methods are further complicated by introducing temperature-dependent particle properties, high-temperature radiative exchange, and directional irradiation sources experienced by granular flows in concentrated solar power environments. Coupled experimental and numerical studies of aluminosilicate particles in rotary kilns and dense particle curtains were performed for bulk temperatures up to 1073 K. The three particle types investigated included Carbobead HSP 30 /60, Carbobead CP 30/60, and Granusil 4030. Temperature, spatial, and velocity profile data were extracted from experimental runs using embedded K-type thermocouple probes and particle image velocimetry techniques. Experimental and numerical studies were compared using spatial temperature profiles, velocity fields, and shape profiles of the bulk, granular flows. Numerical models were developed using commercially available discrete element method modeling software, Aspherix®. Existing Aspherix® functionality was expanded by introducing coupled radiative exchange modeling tools. The laboratory-scale rotary kiln was developed to investigate the steady-state heat and mass transfer performance of aluminosilicate particles based on particle type, bulk handling temperature, and wall roughness. The rotational speed of the rotary kiln was varied to control the relative impact of collisional and frictional effects upon the granular flow behavior. Heat and mass transfer performance was categorized based on the Froude number and the observed flow regimes of slipping, rolling, cascading, and centrifuging. Coupled discrete element method modeling studies were used to evaluate the effects of temperature-dependent, particulate mechanical properties upon bulk flow behavior and upon the relative effects of radiative, advective, and/or conductive heat transfer. A high-temperature (< 1073 K) falling particle curtain was similarly fabricated to investigate the heat and mass transfer performance of aluminosilicate particles in particle handling situations dominated by inter-particle collisions. The impact of particle type, flow preheat temperatures (< 1073K), and bulk mass flow rates were investigated upon the particle curtain shape, temperature, and velocity profiles. Coupled discrete element method modeling studies were performed to evaluate the varying impact of temperature-dependent, particulate mechanical properties on the bulk flow behavior and the temperature profile of the particle curtain.

14 SOLAR ENERGY↗

DOE OSTI2021

Characterizing the Non-linear Interactions Between Tide, Storm Surge, and River Flow in the Delaware Bay Estuary, United States

Low-lying coastal areas in the mid-Atlantic region are prone to compound flooding resulting from the co-occurrence of river floods and coastal storm surges. To better understand the contribution of non-linear tide-surge-river interactions to compound flooding, the unstructured-grid Finite Volume Community Ocean Model was applied to simulate coastal storm surge and flooding in the Delaware Bay Estuary in the United States. The model was validated with tide gauge data in the estuary for selected hurricane events. Non-linear interactions between tide-surge-river were investigated using a non-stationary tidal analysis method, which decomposes the interactions’ components at the frequency domain. Model results indicated that tide-river interactions damped semidiurnal tides, while the tide-surge interactions mainly influenced diurnal tides. Tide-river interactions suppressed the water level upstream while tide-surge interaction increased the water level downstream, which resulted in a transition zone of damping and enhancing effects where the tide-surge-river interaction was prominent. Evident compound flooding was observed as a result of non-linear tide-surge-river interactions. Furthermore, sensitivity analysis was carried out to evaluate the effect of river flooding on the non-linear interactions. The transition zone of damping and enhancing effects shifted downstream as the river flow rate increased.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Automating and Evaluating Large Language Models for Accurate Text Summarization Under Zero-Shot Conditions

Automated text summarization (ATS) is crucial for collecting specialized, domain-specific information. Zero-shot learning (ZSL) allows large language models (LLMs) to respond to prompts on information not included in their training, playing a vital role in this process. This study evaluates LLMs' effectiveness in generating accurate summaries under ZSL conditions and explores using retrieval augmented generation (RAG) and prompt engineering to enhance factual accuracy and understanding. We combined LLMs with summarization modeling, prompt engineering, and RAG, evaluating the summaries using the METEOR metric and keyword frequencies through word clouds. Results indicate that LLMs are generally well-suited for ATS tasks, demonstrating an ability to handle specialized information under ZSL conditions with RAG. However, web scraping limitations hinder a single generalized retrieval mechanism. While LLMs show promise for ATS under ZSL conditions with RAG, challenges like goal misgeneralization and web scraping limitations need addressing. Future research should focus on solutions to these issues.

Priebe Mendes Rocha, Maria Eduarda [ORNL]↗

DOE OSTI2020

Effect of water velocity and temperature on energy use, behaviour and mortality of pallid sturgeon Scaphirhynchus albus larvae

Abstract Natural reproduction of pallid sturgeon Scaphirhynchus albus has been limited for decades and a recruitment bottleneck is hypothesized to occur during the larval stage of development. In this study, we evaluated the effects of water velocity and temperature on the swimming activity, energy use, settling behaviour and mortality of endogenously feeding larvae. The swimming activity of drifting sturgeon larvae ( i.e. , fish exhibiting negative rheotaxis) increased at low water velocity. In subsequent experiments, we observed greater energy depletion and resultant mortality of larvae in no‐flow environments (0 cm s −1 ) compared to tanks with water velocity ranging from 3.5 to 8.3 cm s −1 . The growth rate of drifting larvae was positively related to water temperature (18.7–23.3°C), but reduced growth rate at low water temperature (18.7°C) resulted in protracted development that extended average drift duration by ~4 days compared to larvae reared at 23.3°C. This study provides evidence that cooler summer water temperatures, characteristic of present‐day conditions in the upper Missouri River, can reduce larval development and extend both the drift duration and distance requirements of S. albus . Moreover, if dispersed into low velocity environments, such as in reservoir headwaters, larvae may experience increased mortality owing to a mismatch between early life stage drift requirements and habitat conditions in the river. Manipulation of water releases to increase seasonal water temperature below dams may aid survival of S. albus larvae by shortening the time and distance spent drifting.

Mrnak, Joseph T.↗

DOE OSTI2021

Evaluating Deception Detection Model Robustness To Linguistic Variation

With the increasing use of automated, machine learning-driven tools and the downstream impact that algorithmic judgements can have, it is critical to develop models that are robust to evolving or manipulated inputs. Evaluating the reliability of multimodal models across linguistic variations to understand model susceptibility to intentional linguistic adversarial attacks as well as natural linguistic variations is essential in this pursuit. We present extensive analysis of model robustness and susceptibility to linguistic variations in the setting of deceptive news detection, a difficult classification task that is an increasingly important problem to solve with the impact of misinformation spread online. We evaluate the effectiveness of incorporating adversarial defense strategies and measure model susceptibility to state-of-the-art adversarial attacks using two types of linguistic attacks — character and word perturbations. We consider two multiclass prediction tasks — a 3-way classification of tweets as trustworthy, propaganda, or disinformation; and a 4-way classification as clickbait, hoax, satire, or conspiracy — and compare the performance of three embeddings that have been state-of-the-art for several NLP tasks — GloVe, ELMo, and BERT — to highlight consistent trends in susceptibility, high confidence misclassifications, and high impact failures. We find that character or mixed ensemble models are the most effective defense mechanisms and that character perturbations are a more effective attack than word perturbations for deception classification.

adversarial evaluation↗

DOE OSTI2023

Effects of soybean varieties on life-cycle greenhouse gas emissions of biodiesel and renewable diesel

This study presents a life-cycle analysis (LCA) of the greenhouse gas (GHG) emissions of biodiesel (BD) and renewable diesel (RD) produced from soybean varieties with altered oil profiles and meal composition. The varieties evaluated include those with high oleic oil content (78% of oil being oleic oil vs. the current content of 25%), high lipid content (25% vs. the current content of 19%) or high protein content (45% vs. the current content of 35%). The results suggest that high-oleic soybean oil could reduce GHG emissions of RD by 1 g CO 2 e/MJ by reducing hydrogen consumption in the hydro-treating stage of RD production. With the default allocation method (mass-based allocation between oil and meal), changes in lipid and protein contents have negligible impacts on GHG emissions of BD/RD pathways. Since high-protein soybean meal has a higher nutrient value, we employed the market-based allocation for sensitivity analysis. Assuming a market price of $1.17/dry kg and an average of two substitute feeds with similar protein contents (corn gluten and fish meal), the allocation factor for soybean meal increases from 63 to 81%. Compared with the results for the case with commodity soybean using mass allocation, GHG emissions could be 1.9 and 1.8 g CO 2 e/MJ lower for BD and RD, respectively. In addition to product-level LCA, we employed a land-based LCA to evaluate the effect of soybean properties on product slates with the same land area and the associated displacement of conventional products. The results suggest that high-lipid soybeans may offer more GHG savings than other varieties as the higher BD/RD yield replaces more fossil diesel. © 2023 UChicago Argonne, LLC, Operator of Argonne National Laboratory and Northrup, Ag. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons Ltd.

09 BIOMASS FUELS↗

DOE OSTI2025

Fused filament fabrication of thermoplastic polyurethane composites with microencapsulated phase-change material

Here, the present study examines the thermal energy storage (TES) effectiveness and printability of microencapsulated phase-change material (MEPCM) combined with thermoplastic polyurethane (TPU) for fused filament fabrication (FFF). Two formulations were assessed: 24D MEPCM, which changes phase at 24 ° C, compounded with TPU pellets and 43D MEPCM, which changes phase at 43 ° C, integrated with TPU powder. These combinations are designed to evaluate the effectiveness of the form of the TPU (pellets versus powder) in the FFF process. The investigation includes a comprehensive analysis of thermal characteristics, encompassing phase-change temperature, latent heat of fusion, thermal conductivity, and thermal decomposition, which are assessed through differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Additionally, mechanical properties, including stress-strain behavior, are examined to evaluate material suitability for TES applications, while microstructural visualization is used to provide deeper insights into material performance, structural integrity, and the quality of printed components. The 24D MEPCM and TPU pellets formulation experienced a significant loss of approximately 39.6% of PCM during filament extrusion and printing, resulting in a reduced effective latent heat. Therefore, further characterization of the pellet formulation was discontinued due to excessive leakage. In contrast, the 43D MEPCM and TPU powder formulation demonstrated minimal PCM loss, with the 60 wt.% composition achieving an effective latent heat of 132 J/g. This value represents the highest effective latent heat currently documented in the literature for PCM-polymer-composite materials produced using an FFF-based additive manufacturing process.

25 ENERGY STORAGE↗

DOE OSTI2021

Ventilation in Residential Care Environments

The purpose of this study was to evaluate the effect of ventilation rate, directional airflow (e.g. pressure relationships) and airflow barriers on bioaerosol concentration and movement within assisted-living and residential care environments. Included within this report is a comprehensive literature review, field data collection test plan and, an evaluation of commercially available mitigation technologies related to the transmission of COVID-19 in LTC environments. Additionally, this report includes aerosol testing in an actual LTC facility using the test plan developed herein. Nearly 1.5 million people live in 16,000 nursing homes in the U.S. As of December 20, 2020 the Centers for Medicare and Medicaid Services (CMS) identified a total of 662,549 confirmed and suspected COVID-19 cases in these and other long-term care (LTC) facilities resulting in 92,373 deaths. At this time, COVID-19 cases in LTC facilities accounted for only 3% of the U.S. total of 21M confirmed cases yet nearly a third of the 350,000 total U.S. deaths. Preliminary studies have found little correlation between the quality of care and transmission of COVID-19 in these facilities, suggesting that even the best infection control practices may not be effective in containing the spread of this potentially airborne disease. As a result, many LTC facilities have implemented quarantine procedures and other measures to isolate infectious residents from the general population. Unfortunately, most LTC facilities were not designed for airborne infection control and guidance for retrofitting existing LTC spaces for airborne isolation is limited.

42 ENGINEERING↗

DOE OSTI2021

Ventilation in Residential Care Environments

42 ENGINEERING↗

DOE OSTI2022

Effect of grain-boundary θ-Al 2 Cu precipitates on tensile and compressive creep properties of cast Al–Cu–Mn–Zr alloys

Tensile and compressive creep tests were performed at 300 °C on high-temperature Al–Cu–Mn–Zr (ACMZ) alloys with 6 wt% Cu (6Cu) and 9 wt% Cu (9Cu) to evaluate the effect on creep properties of micron-size θ-Al 2 Cu intergranular precipitates. For compressive creep, the increased volume fraction of θ-precipitates at grain boundaries (from ~0.7% in 6Cu to ~ 6% in 9Cu) does not affect deformation rates across the investigated stress range of 15–110 MPa, consistent with creep being controlled by submicron θ'-Al 2 Cu precipitates within grains, whose size and fractions are the same in both alloys. In contrast, for tensile creep, 9Cu creeps faster than 6Cu at stresses above 20 MPa, and this difference increases with the stress level. Additionally, this discrepancy between tensile and compressive creep behavior is explained by cavitation during tensile creep, which is favored by higher volume fraction and larger size of intergranular θ precipitates in 9Cu. Conversely, larger precipitates impede cavity linkage resulting in improved creep ductility of 9Cu as compared to 6Cu at 300 °C.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Seismic Signal Detection on International Monitoring System 3-Component Stations using PhaseNet

In this report we discuss training a deep learning seismic signal detection model on 3-component stations from the International Monitoring System (IMS) using the PhaseNet architecture. Using 14 years of associated signals from the International Data Centre’s (IDC) Late Event Bulletin (LEB), we auto-curated training data consisting of signal windows containing associated arrivals, and noise windows that contain no LEB-associated signals. We trained several models using different waveform window durations (30 seconds and 100 seconds), with and without bandpass filtering. We evaluated the effectiveness of our models using associated signals from the Unconstrained Global Event Bulletin (UGEB) and found that several of our models outperformed the signal detections from the IDC’s Selected Event List 3 (SEL3) arrival table. The SEL3 bulletin evaluated on the UGEB dataset with 100-second waveform windows registered a precision and recall of .15 and .48, respectively, versus .19 and .59 for our filtered-data model. For the 30-second waveform window dataset, the SEL3 bulletin achieved a precision and recall of .31 and .47, respectively, versus .32 and .60 for our filtered-data model. Finally, our models detected signals from all source-to-receiver distances, suggesting it is feasible to use a single PhaseNet model for the IMS network.

58 GEOSCIENCES↗

DOE OSTI2026

High-Temperature SiC Cladding End Plug Irradiation Design and HFIR Readiness

This report documents the design of a High Flux Isotope Reactor (HFIR) irradiation experiment intended to evaluate irradiation effects on the hermeticity of silicon carbide (SiC) end plug specimens under a radial fast neutron flux gradient at representative light-water reactor (LWR) temperatures of approximately 300 °C. The overarching goal of this work is to statistically evaluate SiC end plug hermeticity and mechanical properties following irradiation using the high-throughput irradiation capability discussed here. Each specimen consists of a short section of SiC fiber–reinforced SiC (SiC/SiC) tube with a single monolithic SiC end plug joined to one end. The experiment allows up to 66 specimens to be irradiated in six different stacks within a dry, sealed irradiation capsule derived from the previously developed high-temperature SiC/SiC cladding bowing experiment. The neutronics basis, thermal analysis, and HFIR readiness of the experiment are discussed in this report for two possible design cases. The first design case is based on existing approval documentation and components that are on hand and approved for use, so the experiment insertion would require only specimen receipt, specimen pre-irradiation characterization, experiment assembly, and final fabrication package approval. The second design case provides improved thermal robustness and the preferred end plug geometry but requires fabrication of a modified holder and revisions to the HFIR approval documentation, in addition to the other activities required for the first design case, before insertion.

Hott, Daniel [Oak Ridge National Laboratory (ORNL)↗

DOE OSTI2022

Flutter behavior of highly flexible blades for two- and three-bladed wind turbines

Abstract. With the progression of novel design, material, and manufacturing technologies, the wind energy industry has successfully produced larger and larger wind turbine rotor blades while driving down the levelized cost of energy (LCOE). Though the benefits of larger turbine blades are appealing, larger blades are prone to aeroelastic instabilities due to their long, slender, highly flexible nature, and this effect is accentuated as rotors further grow in size. In addition to the trend of larger rotors, non-traditional rotor concepts are emerging including two-bladed rotors and downwind configurations. In this work, we introduce a comprehensive evaluation of flutter behavior including classical flutter, edgewise vibration, and flutter mode characteristics for two-bladed, downwind rotors. Flutter speed trends and characteristics for a series of both two- and three-bladed rotors are analyzed and compared in order to illustrate the flutter behavior of two-bladed rotors relative to more well-known flutter characteristics of three-bladed rotors. In addition, we examine the important problem of blade design to mitigate flutter and present a solution to mitigate flutter in the structural design process. A study is carried out evaluating the effect of leading edge and trailing edge reinforcement on flutter speed and hence demonstrates the ability to increase the flutter speed and satisfy structural design requirements (such as fatigue) while maintaining or even reducing blade mass.

Chetan, Mayank (ORCID:0000000241978801)↗

DOE OSTI2025

Evaluation of normalization strategies for mass spectrometry-based multi-omics datasets

Introduction Data normalization is crucial for multi-omics integration, reducing systematic errors and maximizing the likelihood of discovering true biological variation. Most studies assess normalization for a single omics type or use datasets from separate experiments. Few address time-course data, where normalization might bias temporal differentiation. In this study, we compared common normalization methods and a machine learning approach, Systematical Error Removal using Random Forest (SERRF), using multi-omics datasets generated from the same experiment—even from the same cell lysate. Objectives To develop a straightforward process to assess normalization effects and identify the most robust methods across multi-omics datasets. Methods We analyzed metabolomics, lipidomics, and proteomics datasets from primary human cardiomyocytes and motor neurons exposed to acetylcholine-active compounds over time. Normalization effectiveness was evaluated based on improvement in QC features consistency and observing the change in treatment and time-related variance. Results Probabilistic Quotient Normalization (PQN) and Locally Estimated Scatterplot Smoothing (LOESS) QC were identified as optimal for metabolomics and lipidomics, while PQN, Median, and LOESS normalization excelled for proteomics. These methods consistently enhanced QC feature consistency in metabolomics and lipidomics, and preserved time-related variance or treatment-related variance in proteomics, demonstrating their effectiveness and robustness. SERRF normalization, applied only to metabolomics in this study, outperformed other methods in some datasets but inadvertently masked treatment-related variance in others. Conclusion Our evaluation identified PQN and LoessQC as the top methods for metabolomics and lipidomics, and PQN, Median, and Loess normalization for proteomics, in multi-omics integration in a temporal study.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Plasma-Coupled Flow Reactor Studies of Low-Temperature Plasma Assisted Kinetics of Methanol Blended with CO2

Ignition technologies based on low-temperature plasmas (LTP) have the potential to operate next generation engines at elevated pressures and increased dilution limits promoting higher efficiencies. From a practical standpoint, research on LTP igniters has shown to enhance combustion and ignition, improve flame stability, and extend the dilution limits of combustion. All of the aforementioned gains are complemented with higher ignition efficiencies. However, the biggest challenge with incorporating this technology into engines is the knowledge gap of how exactly plasma chemistry effects can enhance the basic combustion phenomena. This coupled with the lack of validated kinetic mechanisms for plasma-combustion chemistry is the biggest obstruction to recognize efficient ignition, especially for application relevant fuels and biofuels. In order to comprehensively evaluate the effects of LTP on an oxygenated fuel specific system, this present study examines the kinetics of methanol plasma-assisted pyrolysis and oxidation using a custom-built plasma flow reactor (PFR). Experimental regimes are also further extended to understand the effects of adding CO2 to the mixture and its consequence on reaction kinetics. The PFR is installed with a dielectric-barrier discharge (DBD) configuration to induce LTP into the fuel mixture. Non-equilibrium plasmas are generated by high-voltage pulses (nearing 20 KV) administered by a plasma pulser at high-pulse repetition rates (up to 10 kHz). In order to better understand and isolate plasma chemistry and its effect on neutral chemistry, the experiments were carried out by heavily diluting reactive mixtures in nitrogen at near isothermal conditions. This suppresses the effect of exothermic reactions on chemistry allowing stable intermediates and products to be detected and quantified using ex-situ GC/MS diagnostic methods. Experiments were carried out at 0.5 atm pressure and over a wide range of temperatures from 523 K to 1203 K. Experimental results depicted the enhancement in intermediates production as well as overall lower temperatures required for complete fuel consumption in the plasma specific cases as opposed to their pure thermal counterpart. Formation of oxygenated and nitrile compounds specific to plasma assisted pyrolysis cases illustrated the efficacy of LTP to introduce new reaction pathways accelerating fuel decomposition. Increase in reactivity at lower temperatures is sought to be an effect induced by plasma chemistry postulating the acceleration in intermediates production. The onset of thermal ignition in plasma assisted oxidation is seen 200 K earlier than thermal oxidation highlighting efficient fuel conversion to final byproducts. Enhanced collisional processes afforded by LTP is seen to perturb reaction pathways between oxygenated fuel radicals and N-atoms to alter overall chemical reactivity. New insights into kinetics are gained from this study highlighting governing plasma assisted combustion (PAC) pathways for oxygenated fuel reaction chemistry. The results from this study can be used to develop future mechanisms specific to plasma chemistry which can bridge the mechanistic knowledge gap for LTP ignition so that future engines can adopt LTPs in their design for efficient combustion.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Phase II Field Demonstration at Lansing Smith Generating Plant, Southport, Florida (Final Report)

The Final Technical Report: Field Test Design and Pressure Management Strategies for Phase II Field Demonstration of Optimal Pressure Control, Plume Management, and Produced Water Strategies presents the culmination of multi-year efforts under the U.S. Department of Energy’s Brine Extraction and Storage Test (BEST) program, led by EPRI in partnership with Gulf Power at the Plant Smith site near Panama City, Florida. The project was designed to evaluate and demonstrate the technical feasibility of managing subsurface pressures and fluid movement associated with large-scale CO₂ injection, using low-salinity water as a proxy fluid. Through a combination of field injection testing, reservoir modeling, and optimization studies, the research team developed and refined active and passive brine extraction strategies aimed at controlling injection-induced pressure buildup, mitigating risks of fault activation, and managing plume migration. The field demonstration incorporated a new injection well (TIW-2), a new monitoring/extraction well (TEMW-A), and an existing well (TIW-1) repurposed for passive pressure relief. Complementary geophysical monitoring was designed to track plume development and evaluate the effectiveness of pressure management strategies. The report details the integrated workflow encompassing wellfield development, regulatory permitting, model calibration, and survey design. It includes a comprehensive electromagnetic (EM) modeling and inversion study used to develop a cost-effective, time-lapse geophysical monitoring plan capable of imaging the evolving low-salinity plume within the highly saline Lower Tuscaloosa formation. Reservoir simulation results guided the design of the 17-month injection program and the timing of active extraction to maintain formation pressures below a hypothetical fault reactivation threshold. Supporting analyses evaluated potential injectivity risks related to clay fines migration and geochemical incompatibility, identifying practical mitigation measures such as salinity and pH control. The final design recommends a series of crosswell EM surveys—conducted before, during, and after injection—as the most effective and economical approach for plume imaging, supplemented by continuous downhole pressure and flow monitoring. Collectively, the study provides a field-ready framework for cost-effective pressure management and monitoring in support of future CO₂ storage projects.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2020

Herbicide, fertilization, and planting density effects on intensively managed loblolly pine early stand development

Production forestry in the southeast US has been partially transitioned to intensively managed short rotations (~10 years), in which multiple silvicultural interventions are performed during forest development. Understanding the responses to silvicultural practices and continued refinement of site-specific recommendations is critical to sustainably maximize forest production. We evaluated the effects of silvicultural practices (herbicide, fertilization, and planting density) on growth, stand homogeneity, and above- and belowground biomass accumulation and partitioning of loblolly pine (Pinus taeda) throughout early stand development (age 5 years) in the southeastern US. Five treatments with eight replications each were tested: no herbicide and no fertilization (C); herbicide only (H); herbicide and half-reduced fertilization rate (R); herbicide and full fertilization (F); and increased stand density (60+ %; 1346 vs. 2152 trees per hectare) with herbicide and full fertilization rate (D). Allometric equations generated from destructive harvests were applied to annual diameter measurements to estimate plot-level biomass and allocation. Herbicide was crucial to promote stand uniformity and increase yield (~600+ % stem biomass compared with C at age 5). Aboveground biomass was similar in R and F treatments, which was ~25% higher than in H at age 5. Increasing planting density along with multiple herbicide and fertilizer applications yielded higher biomass without compromising individual tree size (diameter and height). There was little effect of silviculture practices on allocation patterns. Our results parallel what was found for fertilization with herbicide from a number of loblolly stands under similar conditions and indicate a ~28% volume gain with fertilization during early stand development. Similarly, our results were consistent with other studies implementing similar differences in planting density and suggest a ~26% volume gain through early stand development with an initial 60% increase in planting density. Furthermore, our study helps to understand complex relationships between production and silvicultural practices during early stand development and demonstrates that silvicultural prescriptions can be optimized to increase sustainability of production forestry

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina

Abstract Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the ‘docking power’. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein‐ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.

Agarwal, Rupesh↗