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DOE OSTI2019

A Deep Learning Approach for TNC Trip Demand Prediction Considering Spatial-Temporal Features: Preprint

Ride-hailing or transportation network companies (TNCs), such as Uber, Lyft, DiDi Chuxing, or RideAustin, are emerging as a new and disruptive on-demand mobility service in recent years. However, the methods for developing predictive analytics to explore the nature and dynamics of TNCs across cities in the United States are still nascent due to the lack of publicly available data. Recently available public datasets on TNCs by RideAustin offer a unique opportunity to examine spatial, temporal, environmental, and special event factors associated with TNC trip demand. This study explores the use of a deep learning approach - Long Short-Term Memory (LSTM) - to predict TNC trip demand at the ZIP Code level using data from Austin, Texas. The analysis includes key predictive factors such as time of day, day of week, precipitation, and temperature, indicating their corresponding associations with TNC trip demand. Results from initial analysis show that LSTM is able to predict the TNC trip demand for the upcoming hour accurately. LSTM, when compared to other prediction methods, such as historical average and instantaneous trip demand, reduces the mean absolute error (MAE) of the model predictions by 37% and 24%, respectively. This novel method offers significant potential for scaling up and/or replicability across cities where data are available for understanding TNC trip demand to inform emerging mobility system operators. Predicting trip demand can help TNC drivers make informed decisions on how to be more efficient by maximizing passenger pickups and minimizing wait times and deadheading.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2016

Pitfalls in Prediction Modeling for Normal Tissue Toxicity in Radiation Therapy: An Illustration With the Individual Radiation Sensitivity and Mammary Carcinoma Risk Factor Investigation Cohorts

Purpose: To identify the main causes underlying the failure of prediction models for radiation therapy toxicity to replicate. Methods and Materials: Data were used from two German cohorts, Individual Radiation Sensitivity (ISE) (n=418) and Mammary Carcinoma Risk Factor Investigation (MARIE) (n=409), of breast cancer patients with similar characteristics and radiation therapy treatments. The toxicity endpoint chosen was telangiectasia. The LASSO (least absolute shrinkage and selection operator) logistic regression method was used to build a predictive model for a dichotomized endpoint (Radiation Therapy Oncology Group/European Organization for the Research and Treatment of Cancer score 0, 1, or ≥2). Internal areas under the receiver operating characteristic curve (inAUCs) were calculated by a naïve approach whereby the training data (ISE) were also used for calculating the AUC. Cross-validation was also applied to calculate the AUC within the same cohort, a second type of inAUC. Internal AUCs from cross-validation were calculated within ISE and MARIE separately. Models trained on one dataset (ISE) were applied to a test dataset (MARIE) and AUCs calculated (exAUCs). Results: Internal AUCs from the naïve approach were generally larger than inAUCs from cross-validation owing to overfitting the training data. Internal AUCs from cross-validation were also generally larger than the exAUCs, reflecting heterogeneity in the predictors between cohorts. The best models with largest inAUCs from cross-validation within both cohorts had a number of common predictors: hypertension, normalized total boost, and presence of estrogen receptors. Surprisingly, the effect (coefficient in the prediction model) of hypertension on telangiectasia incidence was positive in ISE and negative in MARIE. Other predictors were also not common between the 2 cohorts, illustrating that overcoming overfitting does not solve the problem of replication failure of prediction models completely. Conclusions: Overfitting and cohort heterogeneity are the 2 main causes of replication failure of prediction models across cohorts. Cross-validation and similar techniques (eg, bootstrapping) cope with overfitting, but the development of validated predictive models for radiation therapy toxicity requires strategies that deal with cohort heterogeneity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2017

Iron Isotope Fractionation during Fe(II) Oxidation Mediated by the Oxygen-Producing Marine Cyanobacterium Synechococcus PCC 7002

In this study, we couple iron isotope analysis to microscopic and mineralogical investigation of iron speciation during circumneutral Fe(II) oxidation and Fe(III) precipitation with photosynthetically produced oxygen. In the presence of the cyanobacterium Synechococcus PCC 7002, aqueous Fe(II) (Fe(II) aq ) is oxidized and precipitated as amorphous Fe(III) oxyhydroxide minerals (iron precipitates, Fe ppt ), with distinct isotopic fractionation (ε 56 Fe) values determined from fitting the δ 56 Fe(II) aq (1.79‰ and 2.15‰) and the δ 56 Fe ppt (2.44‰ and 2.98‰) data trends from two replicate experiments. Additional Fe(II) and Fe(III) phases were detected using microscopy and chemical extractions and likely represent Fe(II) and Fe(III) sorbed to minerals and cells. The iron desorbed with sodium acetate (FeNaAc) yielded heavier δ 56 Fe compositions than Fe(II) aq . Modeling of the fractionation during Fe(III) sorption to cells and Fe(II) sorption to Feppt, combined with equilibration of sorbed iron and with Fe(II) aq using published fractionation factors, is consistent with our resulting δ 56 FeNaAc. The δ 56 Fe ppt data trend is inconsistent with complete equilibrium exchange with Fe(II)aq. Because of this and our detection of microbially excreted organics (e.g., exopolysaccharides) coating Feppt in our microscopic analysis, we suggest that electron and atom exchange is partially suppressed in this system by biologically produced organics. These results indicate that cyanobacteria influence the fate and composition of iron in sunlit environments via their role in Fe(II) oxidation through O 2 production, the capacity of their cell surfaces to sorb iron, and the interaction of secreted organics with Fe(III) minerals.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Sentinel-1 Input Data for PSInSAR Analysis

Files used to perform the Persistent Scatterer InSAR analysis with SARPROZ. The data is sourced from ESAs Sentinel-1 project and covers Brady Hot Springs and Desert Peak geothermal areas. The original titles are included for the Sentinel-1 data. The naming guide is included as a link in this submission. The data contains SAR (Radar) data from the Sentinel 1A satellite between July 2017 and December 2019. The data is necessary to replicate our results, and can be used for further PSInSAR, DInSAR and other modern interferometric analyses to determine line of sight, vertical and, possibly, East-West horizontal displacement. These displacement analysis show the soil deformation in time (including average displacement velocity), which can be used to indicate subsoil phenomena: temperature changes, subsidence, uplift, and inform other analyses like seismicity and porosity.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Reynolds-number scaling of wall-pressure–velocity correlations in wall-bounded turbulence

Wall-pressure fluctuations are a practically robust input for real-time control systems aimed at modifying wall-bounded turbulence. The scaling behaviour of the wall-pressure–velocity coupling requires investigation to properly design a controller with such input data so that it can actuate upon the desired turbulent structures. A comprehensive database from direct numerical simulations (DNS) of turbulent channel flow is used for this purpose, spanning a Reynolds-number range$Re_\tau \approx 550\unicode{x2013}5200$. Spectral analysis reveals that the streamwise velocity is most strongly coupled to the linear term of the wall pressure, at a Reynolds-number invariant distance-from-the-wall scaling of$\lambda _x/y \approx 14$(and$\lambda _x/y \approx 8$for the wall-normal velocity). When extending the analysis to both homogeneous directions in$x$and$y$, the peak coherence is centred at$\lambda _x/\lambda _z \approx 2$and$\lambda _x/\lambda _z \approx 1$for$p_w$and$u$, and$p_w$and$v$, respectively. A stronger coherence is retrieved when the quadratic term of the wall pressure is concerned, but there is only little evidence for a wall-attached-eddy type of scaling. An experimental dataset comprising simultaneous measurements of wall pressure and velocity complements the DNS-based findings at one value of$Re_\tau \approx 2$k, with ample evidence that the DNS-inferred correlations can be replicated with experimental pressure data subject to significant levels of (acoustic) facility noise. It is furthermore shown that velocity-state estimations can be achieved with good accuracy by including both the linear and quadratic terms of the wall pressure. An accuracy of up to 72 % in the binary state of the streamwise velocity fluctuations in the logarithmic region is achieved; this corresponds to a correlation coefficient of$\approx$0.6. This thus demonstrates that wall-pressure sensing for velocity-state estimation – e.g. for use in real-time control of wall-bounded turbulence – has merit in terms of its realization at a range of Reynolds numbers.

Mechanics↗

DOE OSTI2021

AI-Batt (Autonomous Identification of Battery Life Models) [SWR 21-36]

Autonomous Identification of Battery Life Models (AI-Batt) AI-Batt is a MATLAB code base for developing lifetime models for batteries from accelerated aging data. The code base provides many functions for processing, visualizing, and modeling battery aging data, making the data processing, exploration, and modeling workflow substantially faster. These tools are tailored for working with battery aging data sets, which usually consist of many separate time-series for each cell, with many test conditions and possible replicates at each condition, which makes it difficult to simply process or visualize the data set. Complex modeling tasks, such as cross-validation, sensitivity analysis, and uncertainty quantification have been implemented to enable thorough statistical investigation of model predictions. Additionally, several machine-learning algorithms are implemented to autonomously identify suitable models via symbolic regression. Data processing functions automatically cast data from the struct data type, which is commonly used to store experimental data, but is not an acceptable input for most algorithms, to the table data type, which can be easily used as input to any optimization algorithm. Also, the data can be separated into time-invariant and time-variant data tables, which is helpful for exploring the data set as well as developing separate models for time-variant and time-invariant aging mechanisms. For example, in aging tests with constant temperature, temperature is a time-invariant experimental condition. Visualization tools enable plotting of data, model fits, and model simulations possible with single-line function calls, empowering data exploration of complex data sets with both time-varying and time-invariant trends. Plots can be automatically generated for the whole data set, or separated by data group (groups of test replicates) or individual data series. Data points or data series can be automatically colored by the value of a variable with a variety of color maps, and model predictions can also be colored by the value of a fit statistic. Comparisons between data sets and the predictions/simulations of different models on the same data set can be easily plotted as well. Distributions of parameter values from bootstrap resampling can be plotted to visualize the reliability of parameter estimation, or determine any correlations between parameters. Modeling tools handle the complex task of creating and parsing symbolic equations for modeling battery lifetime. Equations are parsed to grab relevant data variables, parameter values, or specified sub-models for input into optimization, evaluation, or simulation functions. Models can be optimized locally (one set of parameters for each data series), bi-level (some parameters shared across the data set), or globally (single set of parameters for all data). Functions implementing symbolic regression algorithms help users to discover effective model equations, even in poorly sampled, high-dimensional data.

Smith, Kandler↗

DOE OSTI2017

Structural and Stratigraphic Controls on Methane Hydrate occurrence and distribution: Gulf of Mexico, Walker Ridge 313 and Green Canyon 955: Final Report

The goal of this project was to determine structural and stratigraphic controls on hydrate occurrence and distribution in Green Canyon (GC) 955 and Walker Ridge (WR) 313 blocks using seismic and well data. Gas hydrate was discovered in these blocks in coarse- and fine-grained sediments during the 2009 Joint Industrial project (JIP) Leg 11 drilling expedition. Although the immediate interest of the exploration community is exclusively hydrate which is present in coarse–grained sediments, factors that control hydrate and free gas distribution in the two blocks and whether coarse and fine-grained hydrate-bearing units are related in any manner, formed the core of this research. The project spanned from 10/01/2012 to 07/31/2016. In the project, in both the leased blocks, the interval spanning the gas hydrate stability zone (GHSZ) was characterized using a joint analysis of sparse Ocean Bottom Seismic (OBS) and dense, surface–towed multichannel seismic (MCS) data. The project team had the luxury of calibrating their results with two well logs. Advance processing methods such as depth migration and full-waveform inversion (FWI) were used for seismic data analysis. Hydrate quantification was achieved through interpretation of the FWI velocity field using appropriate rock physics models at both blocks. The seismic modeling/inversion methodology (common to both GC955 and WR313 blocks) was as follows. First, the MCS data were depth migrated using a P-wave velocity (VP) model constructed using inversion of reflection arrival times of a few (four in both cases) key horizons carefully picked in the OBS data to farthest possible offsets. Then, the resolution of the traveltime VP model was improved to wavelength scale by inverting OBS gathers up to the highest frequency possible (21.75 Hz for GC955 and 17.5 for WR313) using FWI. Finally, the hydrate saturation (or the volume fraction) was estimated at the well location assuming one of the other hydrate morphology (filling the primary or the secondary porosity) was extrapolated out from the wells using the FWI VP as a guide. General outcomes were as follows. First and foremost, an imaging methodology using sparse seismic data, which is easily replicable at other sites with similar datasets, has been demonstrated. The end product of this methodology at both the leased blocks is quantitative estimates of hydrate distribution. Second, at both locations there is strong evidence that the base of the GHSZ, which does not appear as a clear Bottom Simulating Reflection (BSR), manifests in the VP perturbations created by FWI, suggesting that FWI is sensitive to subtle compositional changes in shallow sediments and establishes it as a valuable tool for investigations of hydrate-bearing basins. Third, through joint interpretation of the depth migrated image and the FWI VP model, how structure and stratigraphy jointly determine hydrate and free gas distribution in both blocks could be clearly visualized. The joint interpretation also suggests that the coarse and fine grained hydrate-bearing sediments at both leased are connected. Site specific results, in addition to general results, are as follows. At GC955 the overlying fine-grained hydrate-bearing unit could have been sourced from the underlying hydrate coarse-grained channel-levee complex through a chimney feature. The channel-levee system at GC955 is compartmentalized by faults, of which only a few may be impermeable. Although compartmentalized, the channel-levee system in the GC955 as a whole might be in communication except selected zones. At WR313 the overlying fine-grained fracture-filled hydrate unit appears to be sourced from below the GHSZ. The reason that only a particular fine-grained unit has hydrate, despite having lower porosity that the bounding units, could be the presence of secondary porosity (such as those formed from clay dewatering under compaction). In conclusion, the project was a pioneering effort in in joint analysis of OBS and MCS datasets for advancing the knowledge about a hydrate and free–gas system dynamics using advanced processing methods such as FWI and depth migration. Results obtained in this project can greatly advance the tools and techniques used for delineating specific hydrate prospects. Results obtained in this project can also be seamlessly incorporated into other DOE funded project on modeling the potential productivity and commercial viability of hydrate from sand-dominated reservoirs. The OBS and MCS data in this project were acquired in 2012 (after the JIP II drilling) by the USGS and therefore the results are a posteriori. Nonetheless, the seismic inversion workflow established through this project can be used to generate various what-if quantification scenarios even in absence of logs and serve as a valuable tool for guiding drilling operations. Results from this project can augment other DOE sponsored projects on determining the commercial viability of methane production from the Gulf of Mexico.

03 NATURAL GAS↗

DOE OSTI2016

Replication cycle of duck hepatitis A virus type 1 in duck embryonic hepatocytes

Duck hepatitis A virus type 1 (DHAV-1) is an important agent of duck viral hepatitis. Until recently, the replication cycle of DHAV-1 is still unknown. Here duck embryonic hepatocytes infected with DHAV-1 were collected at different time points, and dynamic changes of the relative DHAV-1 gene expression during replication were detected by real-time PCR. And the morphology of hepatocytes infected with DHAV was evaluated by electron microscope. The result suggested that the adsorption of DHAV-1 saturated at 90 min post-infection, and the virus particles with size of about 50 nm including more than 20 nm of vacuum drying gold were observed on the infected cells surface. What's more, the replication lasted around 13 h after the early protein synthesis for about 5 h, and the release of DHAV-1 was in steady state after 32 h. The replication cycle will enrich the data for DVH control and provide the foundation for future studies. - Highlights: • This is the first description of the replication cycle of DHAV-1. • Firstly find that DHAV-1 adsorption saturated at 90 min post-infection. • The replication lasted around 13 h after early protein synthesis for about 5 h. • The release of DHAV-1 was in steady state after 32 h.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Evaluating Possible Formation Mechanisms of Criegee Intermediates during the Heterogeneous Autoxidation of Squalene

Organic molecules in the environment oxidatively degrade by a variety of free radical, microbial, and biogeochemical pathways. A significant pathway is heterogeneous autoxidation, in which degradation occurs via a network of carbon and oxygen centered free radicals. Recently, we found evidence for a new heterogeneous autoxidation mechanism of squalene that is initiated by hydroxyl (OH) radical addition to a carbon–carbon double bond and apparently propagated through pathways involving Criegee Intermediates (CI) produced from β-hydroxy peroxy radicals (β-OH-RO 2 •). It remains unclear, however, exactly how CI are formed from β-OH-RO 2 •, which could occur by a unimolecular or bimolecular pathway. Combining kinetic models and multiphase OH oxidation measurements of squalene, we evaluate the kinetic viability of three mechanistic scenarios. Scenario 1 assumes that CI are formed by the unimolecular bond scission of β-OH-RO 2 •, whereas Scenarios 2 and 3 test bimolecular pathways of β-OH-RO 2 • to yield CI. Scenario 1 best replicates the entire experimental data set, which includes effective uptake coefficients vs [OH] as well as the formation kinetics of the major products (i.e., aldehydes and secondary ozonides). Finally, although the unimolecular pathway appears to be kinetically viable, future high-level theory is needed to fully explain the mechanistic relationship between CI and β-OH-RO 2 • in the condensed phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A Collection of More than 900 Gas Mixture Adsorption Experiments in Porous Materials from Literature Meta-Analysis

Information on mixture adsorption equilibrium is vital in developing adsorption-based separation processes. Because measuring mixture adsorption is more difficult than measuring single-component adsorption, far more data of the latter kind are available. Previous efforts to compile experimental mixture adsorption data for gases have given data sets with at most a few dozen examples. Here, we report the results of systematic literature meta-analysis that produced a data set of more than 900 gas mixture adsorption experiments. This collection includes data from 125 different binary mixtures including 60 different molecular species and information from 333 different adsorbents. We refer to this data set as the Binary adsorption ISOtherm ExperimeNtal 2020 (BISON-20) Database. Because the BISON-20 data set enormously expands the number and variety of experimental results for binary gas adsorption that are readily available, it will be a useful resource for future efforts in developing new materials or processes for gas separations. As initial applications of the BISON-20 data set, we show how identifying replicate measurements can be used to assess the reliability of binary adsorption data, how the accuracy of Ideal Adsorbed Solution Theory (IAST) can be systematically tested using experimental data, and how trends in selectivity for gas separations across many materials can be examined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Extending Rucio with modern cloud storage support

Rucio is a software framework designed to facilitate scientific collaborations in efficiently organising, managing, and accessing extensive volumes of data through customizable policies. The framework enables data distribution across globally distributed locations and heterogeneous data centres, integrating various storage and network technologies into a unified federated entity. Rucio offers advanced features like distributed data recovery and adaptive replication, and it exhibits high scalability, modularity, and extensibility. Originally developed to meet the requirements of the high-energy physics experiment ATLAS, Rucio has been continuously expanded to support LHC experiments and diverse scientific communities. Recent R&D projects within these communities have evaluated the integration of both private and commercially-provided cloud storage systems, leading to the development of additional functionalities for seamless integration within Rucio. Furthermore, the underlying systems, FTS and GFAL/Davix, have been extended to cater to specific use cases. This contribution focuses on the technical aspects of this work, particularly the challenges encountered in building a generic interface for self-hosted cloud storage, such as MinIO or CEPH S3 Gateway, and established providers like Google Cloud Storage and Amazon Simple Storage Service. Additionally, the integration of decentralised clouds like SEAL is explored. Key aspects, including authentication and authorisation, direct and remote access, throughput and cost estimation, are highlighted, along with shared experiences in daily operations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Sensitivity of an integrated experiment to uncertainty in the high explosive equations of state

Traditionally, hydrodynamics simulations are performed with a single equation-of-state (EOS) to describe each material. These EOSs typically have a physics-informed functional form with adjustable parameters that are calibrated in order to replicate small-scale data. However, because the calibration data have uncertainty and there are typically inherent degeneracies in fitting the EOS, there are actually multiple EOSs that might be consistent with calibration data. In this work, we perform uncertainty quantification (UQ) for the reactant and product equations of state for the high explosive PBX 9501 to yield an ensemble of EOSs that match the uncertain small-scale calibration data. We then simulate an experiment of an explosively formed penetrator repeatedly with different EOSs to both validate the UQ analysis and determine the effects of EOS uncertainty on the prediction of quantities of interest in the experiment. In general, we find good agreement between the simulation predictions and the experimental measurements, and we identify an EOS variable that contributes most directly to the spread in the predictions as the EOSs are varied.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The Dynamic Assimilation Technique measures photosynthetic CO 2 response curves with similar fidelity to steady-state approaches in half the time

The net CO 2 assimilation (A) response to intercellular CO 2 concentration (C i ) is a fundamental measurement in photosynthesis and plant physiology research. The conventional A/C i protocols rely on steady-state measurements and take 15–40 min per measurement, limiting data resolution or biological replication. Additionally, there are several CO 2 protocols employed across the literature, without clear consensus as to the optimal protocol or systematic biases in their estimations. We compared the non-steady-state Dynamic Assimilation Technique (DAT) protocol and the three most used CO 2 protocols in steady-state measurements, and tested whether different CO 2 protocols lead to systematic differences in estimations of the biochemical limitations to photosynthesis. The DAT protocol reduced the measurement time by almost half without compromising estimation accuracy or precision. The monotonic protocol was the fastest steady-state method. Estimations of biochemical limitations to photosynthesis were very consistent across all CO 2 protocols, with slight differences in Rubisco carboxylation limitation. The A/C i curves were not affected by the direction of the change of CO 2 concentration but rather the time spent under triose phosphate utilization (TPU)-limited conditions. Our results suggest that the maximum rate of Rubisco carboxylation (V cmax ), linear electron flow for NADPH supply (J), and TPU measured using different protocols within the literature are comparable, or at least not systematically different based on the measurement protocol used.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Using In Vitro High‐Throughput Screening Data for Predicting Benzo[k]Fluoranthene Human Health Hazards

Today there are more than 80,000 chemicals in commerce and the environment. The potential human health risks are unknown for the vast majority of these chemicals as they lack human health risk assessments, toxicity reference values, and risk screening values. We aim to use computational toxicology and quantitative high‐throughput screening (qHTS) technologies to fill these data gaps, and begin to prioritize these chemicals for additional assessment. In this pilot, we demonstrate how we were able to identify that benzo[k]fluoranthene may induce DNA damage and steatosis using qHTS data and two separate adverse outcome pathways (AOPs). We also demonstrate how bootstrap natural spline‐based meta‐regression can be used to integrate data across multiple assay replicates to generate a concentration–response curve. We used this analysis to calculate an in vitro point of departure of 0.751 μM and risk‐specific in vitro concentrations of 0.29 μM and 0.28 μM for 1:1,000 and 1:10,000 risk, respectively, for DNA damage. Based on the available evidence, and considering that only a single HSD17B4 assay is available, we have low overall confidence in the steatosis hazard identification. This case study suggests that coupling qHTS assays with AOPs and ontologies will facilitate hazard identification. Combining this with quantitative evidence integration methods, such as bootstrap meta‐regression, may allow risk assessors to identify points of departure and risk‐specific internal/ in vitro concentrations. These results are sufficient to prioritize the chemicals; however, in the longer term we will need to estimate external doses for risk screening purposes, such as through margin of exposure methods.

Burgoon, Lyle D.↗

DOE OSTI2014

Models Derived from In Vitro Analyses of Spleen, Liver, and Lung Leukocyte Functions Predict Vaccine Efficacy against the Francisella tularensis Live Vaccine Strain (LVS)

Currently, there are no licensed vaccines and no correlates of protection against Francisella tularensis, which causes tularemia. We recently demonstrated that measuring in vitro control of intramacrophage bacterial growth by murine F. tularensis-immune splenocytes, as well as transcriptional analyses, discriminated Francisella vaccines of different efficacies. Further, we identified potential correlates of protection against systemic challenge. Here, we extended this approach by studying leukocytes derived from lungs and livers of mice immunized by parenteral and respiratory routes with F. tularensis vaccines. Liver and lung leukocytes derived from intradermally and intranasally vaccinated mice controlled in vitro Francisella Live Vaccine Strain (LVS) intramacrophage replication in patterns similar to those of splenocytes. Gene expression analyses of potential correlates also revealed similar patterns in liver cells and splenocytes. In some cases (e.g., tumor necrosis factor alpha [TNF-α], interleukin 22 [IL-22], and granulocyte-macrophage colony-stimulating factor [GM-CSF]), liver cells exhibited even higher relative gene expression, whereas fewer genes exhibited differential expression in lung cells. In contrast with their strong ability to control LVS replication, splenocytes from intranasally vaccinated mice expressed few genes with a hierarchy of expression similar to that of splenocytes from intradermally vaccinated mice. Thus, the relative levels of gene expression vary between cell types from different organs and by vaccination route. Most importantly, because studies comparing cell sources and routes of vaccination supported the predictive validity of this coculture and gene quantification approach, we combined in vitro LVS replication with gene expression data to develop analytical models that discriminated between vaccine groups and successfully predicted the degree of vaccine efficacy. Thus, this strategy remains a promising means of identifying and quantifying correlative T cell responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

The Coal-Seq III Consortium. Advancing the Science of CO 2 Sequestration in Coal Seam and Gas Shale Reservoirs

The Coal-Seq consortium is a government-industry collaborative that was initially launched in 2000 as a U.S. Department of Energy sponsored investigation into CO2 sequestration in deep, unmineable coal seams. The consortium’s objective aimed to advancing industry’s understanding of complex coalbed methane and gas shale reservoir behavior in the presence of multi-component gases via laboratory experiments, theoretical model development and field validation studies. Research from this collaborative effort was utilized to produce modules to enhance reservoir simulation and modeling capabilities to assess the technical and economic potential for CO2 storage and enhanced coalbed methane recovery in coal basins. Coal-Seq Phase 3 expands upon the learnings garnered from Phase 1 & 2, which has led to further investigation into refined model development related to multicomponent equations-of-state, sorption and diffusion behavior, geomechanical and permeability studies, technical and economic feasibility studies for major international coal basins the extension of the work to gas shale reservoirs, and continued global technology exchange. The first research objective assesses changes in coal and shale properties with exposure to CO2 under field replicated conditions. Results indicate that no significant weakening occurs when coal and shale were exposed to CO2, therefore, there was no need to account for mechanical weakening of coal due to the injection of CO2 for modeling. The second major research objective evaluates cleat, Cp, and matrix, Cm, swelling/shrinkage compressibility under field replicated conditions. The experimental studies found that both Cp and Cm vary due to changes in reservoir pressure during injection and depletion under field replicated conditions. Using laboratory data from this study, a compressibility model was developed to predict the pore-volume compressibility, Cp, and the matrix compressibility, Cm, of coal and shale, which was applied to modeling software to enhance model robustness. Research was also conducted to improve algorithms and generalized adsorption models to facilitate realistic simulation of CO2 sequestration in coal seams and shale gas reservoirs. The interaction among water and the adsorbed gases, carbon dioxide (CO2), methane (CH4), and nitrogen (N2) in coalbeds is examined using experimental in situ laboratory techniques to comprehensively model CBM production and CO2 sequestration in coals. An equation of state (EOS) module was developed which is capable of predicting the density of pure components and mixtures involving the wet CBM gases CH4, CO2, and N2 at typical reservoir condition, and is used to inform CO2 injection models. The final research objective examined the effects adsorbed CO2 has on coal strength and permeability. This research studied the weakening or failure of coal by the adsorption of CO2 from empirically derived gas production data to develop models for advanced modeling of permeability changes during CO2 sequestration. The results of this research effort have been used to construct a new and improved model for assessing changes in permeability of coal reservoirs due CO2 injection. The modules developed from these studies and knowledge learned are applied to field validation and basin assessment studies. These data were used to assess the flow and storage of CO2 in a shale reservoir, test newly developed code against large-scale projects, and conduct a basin-oriented review of coal storage potential in the San Juan Basin. The storage potential and flow of CO2 was modeled for shale sequestration of a proprietary Marcellus Shale horizontal gas production well using COMET3 simulation software. Simulation results from five model runs indicate that stored CO2 quantities are linked to the duration of primary production preceding injection. Matrix CO2 saturation is observed to increase in each shale zone after injection with an increase in primary production, and the size of the CO2 plume is also observed to increase in size the longer initial production is sustained. The simulation modules developed around the Coal-Seq experimental work are also incorporated into a pre-existing large-scale numerical simulation model of the Pump Canyon CO2-ECBM pilot in the San Juan Basin. The new model was applied to re-history match the data set to explore the improvements made in permeability prediction against previously published data sets and to validate this module. The assessment of the new data, however, indicates that the impact of the variable Cp is negligible on the overall behavior of the coal for CO2 storage purposes. Applying these new modules, the San Juan Basin and the Marcellus Shale are assessed for their technical ECBM/AGR and CO2 storage potential and the economic potential of these operations. The San Juan Basin was divided into 4 unique geographic zones based on production history, and the Marcellus was divided into nine. Each was assessed based upon each zone’s properties, and simulations were run to assess the potential of full Basin development. Models of a fully developed San Juan Basin suggest the potential for up to 104 Tcf of CO2 storage, and 12.3 Tcf of methane recovery. The Marcellus models suggest 1,248 Tcf of CO2 storage and 924 Tcf of AGR. The economics are deemed favorable where credits cover the cost of CO2 in the San Juan Basin, and in many cases in the Marcellus, but to maximize storage potential, credits need to extend to pay the operator to store CO2.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2024

The Dynamic Assimilation Technique measures photosynthetic CO2 response curves with similar fidelity as steady-state approaches in half the time

A/Ci response↗

DOE OSTI2020

CoREC: Scalable and Resilient In-memory Data Staging for In-situ Workflows

The dramatic increase in the scale of current and planned high-end HPC systems is leading new challenges, such as the growing costs of data movement and IO, and the reduced mean time between failures (MTBF) of system components. In-situ workflows, i.e., executing the entire application workflows on the HPC system, have emerged as an attractive approach to address data-related challenges by moving computations closer to the data, and staging-based frameworks have been effectively used to support in-situ workflows at scale. However, the resilience of these staging-based solutions has not been addressed, and they remain susceptible to expensive data failures. Furthermore, naive use of data resilience techniques such as n-way replication and erasure codes can impact latency and/or result in significant storage overheads. In this article, we present CoREC, a scalable and resilient in-memory data staging runtime for large-scale in-situ workflows. CoREC uses a novel hybrid approach that combines dynamic replication with erasure coding based on data access patterns. It also leverages multiple levels of replications and erasure coding to support diverse data resiliency requirements. Furthermore, the article presents optimizations for load balancing and conflict-avoiding encoding, and a low overhead, lazy data recovery scheme. We have implemented the CoREC runtime and have deployed with the DataSpaces staging service on leadership class computing machines and present an experimental evaluation in the article. Here, the experiments demonstrate that CoREC can tolerate in-memory data failures while maintaining low latency and sustaining high overall storage efficiency at large scales.

97 MATHEMATICS AND COMPUTING↗