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At least 1,063 records · Page 59

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Design and performance of a variable gap system for thermal conductivity measurements of high temperature, corrosive, and reactive fluids

We report high-temperature fluids such as molten salts, liquid metals, and gasses are being proposed for many advanced energy systems including thermal energy storage devices, concentrating solar plants, and advanced nuclear reactor designs. However, the chemical behavior and thermophysical properties of many of these fluids have not been well characterized, which hinders the design, modeling, safety analysis, and deployment of these systems. Thermal conductivity is a property that is especially limited by existing measurement capabilities, which are subject to errors caused by convection, material interaction, radiative heat transfer, and instrument degradation. Therefore, there is a lack of standard, systematic measurement techniques for high-temperature, reactive, and corrosive fluids. In this work, the development of a variable gap thermal conductivity measurement system is detailed. The system is designed to measure the thermal conductivity of highly corrosive and reactive fluids, and survive operation between 100 °C and 800 °C. The effects of convection are minimized by limiting the thickness of the specimen to thin sizes (<0.3 mm). Corrections for radiative heat transfer were included in the working equations to consider specimens with varying optical properties. The design, construction, instrumentation, operating principles, and data analysis techniques are discussed in detail. The system was tested up to 500 °C using helium gas and molten KNO 3 -NaNO 3 to verify the measurement technique and determine the sources of error. At 300 and 400 °C KNO 3 -NaNO 3 , results showed maximum relative error of 6% when compared to results in the literature. The helium results were within 13% of those in the literature at 300 and 400 °C. Higher errors were observed at 500 °C for both fluids, and the sources of these errors are discussed.

42 ENGINEERING↗

Bulk Transfer Coefficients Estimated From Eddy-Covariance Measurements Over Lakes and Reservoirs

The drag coefficient, Stanton number and Dalton number are of particular importance for estimating the surface turbulent fluxes of momentum, heat and water vapor using bulk parameterization. Although these bulk transfer coefficients have been extensively studied over the past several decades in marine and large-lake environments, there are no studies analyzing their variability for smaller lakes. Here, we evaluated these coefficients through directly measured surface fluxes using the eddy-covariance technique over more than 30 lakes and reservoirs of different sizes and depths. Our analysis showed that the transfer coefficients (adjusted to neutral atmospheric stability) were generally within the range reported in previous studies for large lakes and oceans. All transfer coefficients exhibit a substantial increase at low wind speeds (<3 m s -1 ), which was found to be associated with the presence of gusts and capillary waves (except Dalton number). Stanton number was found to be on average a factor of 1.3 higher than Dalton number, likely affecting the Bowen ratio method. At high wind speeds, the transfer coefficients remained relatively constant at values of 1.6·10 -3 , 1.4·10 -3 , 1.0·10 -3 , respectively. We found that the variability of the transfer coefficients among the lakes could be associated with lake surface area. In flux parameterizations at lake surfaces, it is recommended to consider variations in the drag coefficient and Stanton number due to wind gustiness and capillary wave roughness while Dalton number could be considered as constant at all wind speeds.

54 ENVIRONMENTAL SCIENCES↗

Equatorial Origin of the Observed Tropical Pacific Quasi-Decadal Variability From ENSO Nonlinearity

Quasi-decadal (QD) climate variability is detected in the tropical Pacific based on the recent 70 years of observations. This QD variability is identified in equatorial sea surface temperatures (SSTs), the pattern of which resembles the Central Pacific (CP) El Niño-Southern Oscillation (ENSO) but extends further meridionally to the northeastern subtropical Pacific. Whereas equatorial upper-ocean heat content and SSTs are in quadrature for ENSO, these two quantities are almost in phase on the QD timescale. Further analysis shows that nonlinear dynamical heating, primarily originating from strong El Niño events, tends to lead QD SSTs by a quarter of its dominant period (approximately 30 months) and shapes the dominant QD periodicity in observations. Here, our results suggest that the observed QD variability largely originates from ENSO nonlinearity and thus is fundamentally different from ENSO's oscillatory nature.

54 ENVIRONMENTAL SCIENCES↗

Techno-Economic Analysis for a Potential Geothermal District Heating System in Tuttle, Oklahoma: Preprint

Geothermal deep direct use (DDU) has potential across a wide swath of the United States but is underutilized due to challenging project economics associated with developing a deep geothermal resource for a large-scale and variable heat demand. The National Renewable Energy Laboratory (NREL) and University of Oklahoma evaluated the feasibility of a geothermal district heating (GDH) and cooling system in two schools and 250 houses by utilizing existing oil and gas (O&G) wells in Tuttle, Oklahoma. Heating and cooling demand in the two schools and a typical single-family house were modeled using EnergyPlus building energy simulation software. The modeling results indicated that annual heating demand in two schools and 250 houses is approximately 2.61 GWhth, and cooling demand in the two schools is approximately 2.65 GWhth. In this scope, the techno-economic analysis (TEA) was conducted using the GEOPHIRES tool combined with the TOUGH2 reservoir simulator. The reservoir performance, including geothermal heat production capacity, was modeled by the reservoir simulator TOUGH2. Then, levelized cost of heat (LCOH) was calculated using GEOPHIRES version 3.0, which includes new features such as hourly heat load optimization and peak performance evaluation. Geothermal reservoir temperature was estimated as 90.5 degrees C at a total depth of 3.3 km by the regional average temperature gradient of 22.8 degrees C/km and validated by cation geothermometer calculations. Four production scenarios with two different well configurations and two different heat load profiles have been developed for well flow rates ranging between 3.1 kg/s and 9.3 kg/s. The LCOH of the district heating and cooling system was calculated between $95 and $210/MWh ($28/MMBtu to $62/MMBtu) for four different production scenarios. Typical natural gas prices for residential customers in Oklahoma have ranged from 9 to 19 $/MMBtu over the past decade, which indicates a challenge for deployment of such a GDH system.

deep direct-use↗

Techno-Economic Analysis for Co-Processing Fast Pyrolysis Liquid in Fossil Refineries

Recent work at the National Renewable Energy Laboratory (NREL) and throughout the bioenergy community has highlighted incentives associated with co-processing bio-intermediates in existing refineries to reduce capital costs associated with renewable fuels and chemicals production and reduce overall risk for emerging biomass conversion technologies. This presentation summarizes the techno-economic analysis results from the NREL-Petrobras collaboration that focused on refinery integration of fast pyrolysis oil through co-processing in the fluid catalytic cracking (FCC) process. The NREL-Petrobras work highlights the economic opportunity for refiners to engage in co-processing for low-carbon products and introduces the risks for refiners based on variability in crude and fossil-product markets. The NREL-Petrobras results also serve as a basis to inform policy design that reduces economic risk for refinery co-processing and repurposing opportunities. The final topics in the presentation highlight experimental capabilities and emerging analysis approaches at NREL and partner laboratories that support the development and commercial deployment of refinery utilization strategies.

bio-fuels↗

Application of FARM to an IES scenario within the FORCE ecosystem

The FARM (Feasible Actuator Range Modifier) software module is a component of the RAVEN-based FORCE framework for analysis of Integrated Energy Systems (IES). FARM supports the HERON software module in the evaluation of the optimal dispatch by evaluating feasible set-points for the different IES unit components. Set-points are required to satisfy limits on both production variables (i.e., the variables to be optimized such as the electrical power, the hydrogen production rate, etc.) and process variables tied to the service life of equipment (e.g., steam flowrate, vessel pressure, turbine firing temperature, etc.). This problem is addressed by adopting a two-stage approach. First, the HERON power dispatcher determines set-points that meet the constraints on the former variables (e.g., power levels and power ramp rate limits). These constraints are called explicit constraints. Then, FARM adjusts these set-points to ensure the respect of the limits on the latter variables given the knowledge of the system physics acquired through machine learning algorithms. These constraints are called implicit constraints. From this standpoint, FARM constitutes a bridge between the HERON power dispatcher that adopts a simplified description of the IES unit (low-resolution physics) and the HYBRID high-fidelity models (high-resolution physics). The original version of the FARM software module (FARM-Alpha) was released by Argonne National Laboratory in January 2021. In the latest version of the code released in July 2022 (FARM-Delta), the Reference Governor (RG) algorithm was upgraded to a Multi-Input Multi-Output version from its original Single-Input Single-Output form. The RG algorithm acts to enforce constraints. With this improvement an IES unit is now treated as a single dynamic system from the standpoint of control. The crosstalk among components in an IES unit is now fully considered thereby ensuring a true optimization is obtained for those units that have multiple set-points. In this report, the capabilities of FARM-Delta operating within the FORCE ecosystem are demonstrated for an IES test case. The specific configuration of IES unit for this case was selected by the IES team with consultation from the Advanced Reactor IES Expert Group. A full TEA analysis that invoked HERON, HYBRID, FARM, and RAVEN was performed and serves to demonstrate how the latest modification to FARM algorithms (i.e., state variable selection, state-space matrices derivation, set-point verification) can shape setpoints that might otherwise compromise the health of equipment through accelerated wear and tear. In this specific test case, it was demonstrated that these algorithms ensure a more efficient utilization of steam resources to be shared by two different subsystems, namely Balance of Plant (BOP) and High-Temperature Steam Electrolysis (HTSE). Finally, some code improvements that can further enhance the user-friendliness are suggested.

97 MATHEMATICS AND COMPUTING↗

Reliability-Informed Life Cycle Warranty Cost and Life Cycle Analysis of Newly Manufactured and Remanufactured Units

Standard life cycle techniques such as life cycle warranty cost (LCWC) analysis and life cycle analysis (LCA) are used to respectively quantify the relative economical and environmental advantages of remanufactured goods while simultaneously identifying avenues for improvement. In this paper, we contribute to the literature on life cycle studies by incorporating reliability into LCWC analysis and LCA with the goal of improving long-term/multiple life cycle decision making. We develop a branched power-law model to incorporate the physical degradation mechanisms leading to reduced reuse rates of system parts over multiple life cycles. We then follow a standard LCA protocol to quantify the difference between a new unit and its remanufactured version in terms of environmental impact items such as abiotic depletion potential, global warming potential, and energy consumption. We then devise four practical warranty policies that vary in the choice of replacement and/or provision for extended warranty. All possible replacement scenarios for multiple life cycles are explored for each policy and a mathematically rigorous framework is provided, where the reliability information is used to calculate probabilistic LCWC and life cycle impact items. This reliability-informed LCWC analysis and LCA framework enables design engineers to compare design options and warranty policies by quantifying both economical and environmental impacts to aid in decision making. Although the framework is presented in a general form applicable to any engineered system, we demonstrate the utility of this framework by using a case study of an infinitely variable transmission used in agricultural equipment.

42 ENGINEERING↗

Advanced Method Optimization with Categorical and Constrained Continuous Parameters

Traditional approaches to analytical method optimization (e.g., univariate and “guess-and-check”) can be time-consuming, costly, and often fail to identify true optima within the parameter space. Previous work defined and implemented a generalized technique for method optimization for continuous method parameters, but a knowledge gap remains for the incorporation of categorical variables into these advanced method optimization schemes. This work presents and validates a generalized optimization approach that incorporates both continuous and categorical variables while also utilizing a multivariate, multiobjective optimization scheme with Karush–Kuhn–Tucker conditions to bound the optimization space to solutions within the physical limitations of the parameter space. Method optimization from a case study using GC–MS for the analysis of 11 analytical standards with objectives to minimize peak width and maximize peak height resulted in a 3 orders of magnitude improvement in the average peak height and a 2 orders of magnitude improvement in the average peak width compared to the least optimal (but reasonable) instrumental parameters utilized in this study. This approach to optimization allows for a customizable method optimization in which users can include both continuous and categorical variables to achieve objectives specific to their analytical goals. This approach significantly reduces the labor and cost associated with traditional method development approaches and can be applied in a variety of scientific fields across a range of laboratory techniques (e.g., instrument method development, sample preparation, and extraction techniques).

Amorphous materials↗

Dimuon production in the MicroBooNE detector

This analysis studies the production of the rare signal with two muons (dimuon) in the finalstate at µB using the Booster Neutrino Beam (BNB) as source of neutrino interactions. Themain background source for the dimuon signal are pions. Differentiating muons and pions hasbeen challenging at µB because the tracks left by these particles are almost identical. Thisanalysis faces this problem using a supervised classifier algorithm called boosted decisiontree (BDT). A Monte Carlo simulation (MC) enhanced dimuon signal sample was producedto train a BDT capable of recognizing this signal. A set of variables that show somediscrimination characteristics was used to perform the training. A MC neutrino interactionsimulation sample was used to estimate the background. Estimations of dimuon productionin real data samples were made for different cases. Additionally, an analysis of the systematicuncertainties, fake data studies, and BDT performance checks were obtained.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulation and analysis of slip flow of water at hydrophobic silica surfaces of nanometer slit pores

Water flow in nanopores is controlled fundamentally by pore wettability and interfacial water features. In the research herein reported, Molecular dynamics (MD) was used to simulate water flow in nanometer slit pores of silica surfaces with variable wetting characteristics. Compared to Couette flow, the simulated slit-pores of the talc (001) and octadecyltrichlorosilane (OTS) monolayer surfaces exhibited water flow enhancement and a positive slip length at the interface, whereas water flow velocity at the quartz (001) and amorphous silica surfaces was zero, adhering to the no slip condition. More intensive interactions between the interfacial water and hydrophilic silica surfaces were confirmed by MD simulation and sum-frequency vibrational spectroscopy (SFVS) results. A water exclusion zone of approximately 3 Å was found at the hydrophobic silica surfaces by quantitative MD interfacial water analysis and validated by SFVS. This exclusion zone dimension was similar in magnitude to the slip length (4–5 Å) as determined from simulated water flow in hydrophobic silica slit pores. The simulated slip lengths at the hydrophobic surfaces (0.2–1 nm) were significantly less than the experimental slip lengths (>40 nm) reported in the literature. In the case of the experimental results, this difference appears to be due to nanobubbles expected to be present at hydrophobic surfaces.

42 ENGINEERING↗

Performance and Commissioning of the BigBite Timing Hodoscope for Nucleon Form Factor Measurements at Jefferson Lab

The BigBite Timing Hodoscope detector is the primary subject of this thesis. The Super BigBite Spectrometer is a Jefferson Lab Hall A Collaboration project that has and will continue to measure nucleon electromagnetic form factors. This spectrometer includes the Timing Hodoscope which provides high resolution particle timing data for scattered electrons in the electron arm of BigBite. The Timing Hodoscope utilizes 90, 25 × 25 × 600 mm3 scintillator bars stacked on top of each other to form a single detector plane, and these bars are connected to 180 photo-multiplier tubes via light guides. Particles collide with the scintillating material creating a shower of optical photons and these particle events in the bars are collected to generate signals that are readout by the data acquisition (DAQ) electronics. NINO ASIC amplifier-discriminator cards output signals from the photo-multiplier tubes into analogue and logic signals, which are sent to analogue-to-digital (ADC) and time-to-digital (TDC) converter data acquisition readout modules. This data is then used for analysis of the detector. The focus of this thesis is the construction, commissioning, calibration, and performance of the BigBite Timing Hodoscope before and during the first of five nucleon electromagnetic form factor experiments at Jefferson Lab Hall A. Before the neutron magnetic form factor, G n M, experiment, cosmic ray data was collected during commissioning to confirm proper operation of the Timing Hodoscope electronics by observing the ADC and TDC data. Commissioning studies for charge normalization, gain matching, and other ADC and TDC detector data variables were performed before moving the detector into Hall A. Following installation in Hall A, several calibration studies were implemented to fine-tune the detector in preparation for use in the experiment. The calibration studies included analysis of timing cuts, TDC alignment, the time-walk effect, time difference offsets, and scintillator velocity corrections. Once the Timing Hodoscope was well-calibrated, data-taking during the experiment commenced and the beam-on-target data was used to characterize the Timing Hodoscope performance during the G n M experiment run-time. The performance analysis included studies observing energy deposit, cluster size, rates, accidentals, pile-up, tracking efficiency, position resolution, and time resolution. After application of physics cuts to ensure a data set comprised of particle tracks corresponding to elastic electrons, which is the main data of interest for measurement of G n M, the Timing Hodoscope is shown on average across all kinematic settings to have a >98% tracking efficiency, a position resolution of 4-6 cm in the non-dispersive plane and 1.5-2 cm in the dispersive plane, and a time resolution of 500-750 ps. These performance results are compared to a GEANT4 based performance simulation of the BigBite Timing Hodoscope for reference, showing to what degree the measured performance values match those taken from the simulation.

Marinaro, Ralph↗

Fault Detection via Occupation Kernel Principal Component Analysis

Reliable operation of automatic systems is heavily dependent on the ability to detect faults in the underlying dynamics. While traditional model-based methods have been widely used for fault detection, data-driven approaches have garnered increasing attention due to their ease of deployment and minimal need for expert knowledge. In this letter, we present a novel principal component analysis (PCA) method that uses occupation kernels. Occupation kernels result in feature maps that are tailored to the measured data, have inherent noise-robustness due to the use of integration, and can utilize irregularly sampled system trajectories of variable lengths for PCA. The occupation kernel PCA method is used to develop a reconstruction error approach to fault detection and its efficacy is validated using numerical simulations.

42 ENGINEERING↗

Seasonal forecasting skill for the High Mountain Asia region in the Goddard Earth Observing System

Seasonal variability of the global hydrologic cycle directly impacts human activities, including hazard assessment and mitigation, agricultural decisions, and water resources management. This is particularly true across the High Mountain Asia (HMA) region, where availability of water resources can change depending on local seasonality of the hydrologic cycle. Forecasting the atmospheric states and surface conditions, including hydrometeorologically relevant variables, at subseasonal-to-seasonal (S2S) lead times of weeks to months is an area of active research and development. NASA's Goddard Earth Observing System (GEOS) S2S prediction system has been developed with this research goal in mind. Here, we benchmark the forecast skill of GEOS-S2S (version 2) hydrometeorological forecasts at 1–3-month lead times in the HMA region, including a portion of the Indian subcontinent, during the retrospective forecast period, 1981–2016. To assess forecast skill, we evaluate 2 m air temperature, total precipitation, fractional snow cover, snow water equivalent, surface soil moisture, and terrestrial water storage forecasts against the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) and independent reanalysis data, satellite observations, and data fusion products. Anomaly correlation is highest when the forecasts are evaluated against MERRA-2 and particularly in variables with long memory in the climate system, likely due to the similar initial conditions and model architecture used in GEOS-S2S and MERRA-2. When compared to MERRA-2, results for the 1-month forecast skill range from an anomaly correlation of R anom =0.18 for precipitation to R anom =0.62 for soil moisture. Anomaly correlations are consistently lower when forecasts are evaluated against independent observations; results for the 1-month forecast skill range from R anom =0.13 for snow water equivalent to R anom =0.24 for fractional snow cover. We find that, generally, hydrometeorological forecast skill is dependent on the forecast lead time, the memory of the variable within the physical system, and the validation dataset used. Overall, these results benchmark the GEOS-S2S system's ability to forecast HMA hydrometeorology.

54 ENVIRONMENTAL SCIENCES↗

Effects of input gradient regularization on neural networks time-series forecasting of thermal power systems

This study proposes using neural networks, specifically gated recurrent unit (GRU), long-short-term memory (LSTM), and transformer networks, to improve control strategies in a 450 MW coal-fired power plant. However, neural networks face issues of becoming overly dependent on just a few variables to make predictions, which negatively impacts control decisions that rely on the model to determine the value of all manipulated variables. The paper introduces regularization techniques, including noise injection and input gradient regularization, during the training phase. Here, the work presents novel contributions in adapting neural networks to control industrial systems and applying regularization techniques from computer vision to industrial process control. Results demonstrate the effectiveness of input gradient regularization in reducing model dependence on subsets of variables, emphasizing the balance between fidelity and controllability. Further exploration is recommended, including the development of recurrent transformers, closed-loop control testing, and a sensitivity analysis on computer models to provide further insight.

20 FOSSIL-FUELED POWER PLANTS↗

Ensemble cure kinetics network (ECK-Net): A method to derive cure kinetics of thermosetting resin

This paper introduces an Ensemble Cure Kinetics Network (ECK-Net), a neural network (NN)–based framework for modeling the cure kinetics of thermosetting resins within a phenomenological context. ECK-Net replaces traditional analytic models, which require extensive chemical insight and multiple isothermal/non-isothermal experiments, with a data-driven surrogate that maps nonlinear relationships between temperature, degree of cure, and reaction rate from differential scanning calorimetry data. The proposed approach predicts input-dependent kinetic coefficients of a generalized nth-order reaction equation rather than reaction rates directly, enabling a single unified model to represent various epoxy systems without relying on iso-conversional analysis or predefined functional forms. To ensure robustness, multiple independently trained networks under different random initializations are blended through an ensemble strategy, effectively mitigating the stochastic variability inherent to neural networks. The framework is validated using experimental datasets from multiple resin systems, including aerospace-grade materials (Toray 3900-2, Cycom 5320-1, and Hexcel 8552) and a windmill-grade resin (RIMR 035c). The model accurately reproduces the temporal evolution of the degree of cure under manufacturers’ recommended cure cycles across all tested resins systems, yielding Pearson’s correlation coefficients of 0.992, 0.994, 0.993, 0.997, respectively. To demonstrate process-level applicability, the trained network was implemented within the Abaqus environment to simulate out-of-autoclave (OOA) curing process of the CFRP panel composed of Toray T830H-6K/3900-2D prepreg. The simulation results showed excellent agreement with experimental temperature response (maximum peak temperature, simulation: 189.6 °C, experiment: 188.5 °C) and the final degree of cure (simulation: 0.948, experiment: 0.960 ± 0.013), confirming ECK-Net’s capability as a reliable alternative to conventional cure kinetics modeling methods.

Composite curing↗

Thermoelectric air conditioning undergarment for personal thermal management and HVAC energy saving

Personal thermal management systems (PTMS) are highly desirable for improving individual thermal comfort and reducing indoor HVAC energy consumption. Although there have been many attempts in developing PTMS, existing PTMS are generally bulky, heavy or immobile. Besides, previous analysis on additional personal cooling and heating power required for maintaining thermal comfort in changing environments did not consider the individual difference in metabolism and the variability of comfort skin temperature with environmental conditions. In this paper, we report on the development of a novel lightweight (<1 kg) thermoelectric air conditioning undergarment system with a preferred design of branching tubing network (branching angle of 60° and diameter ratio of 0.782) for air distribution. Through thermal manikin and human subject tests, we demonstrated that the novel system is capable of providing a maximum of 15.5 W of personal cooling and 18.1 W personal heating with a coefficient of performance (COP) greater than 0.4, which is sufficient to the expansion of the indoor set-points by at least 2.2 °C (4 °F) on both sides without compromising thermal comfort and the potential saving of about 15% HVAC energy. Furthermore, our study improved the understanding of the required additional personal cooling and heating power for changing environmental conditions, which are essential guidelines for the further development of PTMS.

42 ENGINEERING↗