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At least 145 records · Page 8

Expanded Diversity of Microbial Groups Capable of Anaerobic Pyrite Reduction and Assimilation of Dissolution Products

Pyrite, the most abundant iron sulfide mineral in the Earth's crust, has traditionally been considered as a sink for iron and sulfur in the absence of oxygen. Recent research, however, has shown that anaerobic methanogenic archaea can reductively dissolve pyrite and assimilate its products as sources of iron and sulfur. This study explores whether other anaerobic bacteria, including fermentative, nitrate-, iron oxide-, fumarate-, and sulfate-respiring bacteria, can also reduce pyrite and use its dissolution products as sources of iron and sulfur. Results indicate that heterotrophic bacteria respiring fumarate or sulfate, or fermenting organic carbon, can reduce pyrite and assimilate released iron and sulfur. In contrast, nitrate- or iron oxide-respiring cells did not reduce pyrite, suggesting that microbial pyrite reduction is metabolism-specific. All strains capable of reducing pyrite could also use mackinawite as an iron and sulfur source. With the exception of fermentative Bacteroides, strains did not require direct contact with pyrite to reduce the mineral, indicating extracellular electron transfer via electron shuttles. These findings expand the known diversity of microbial groups capable of pyrite reduction and highlight the mineral's lability in various anaerobic environments, with potential implications for the biogeochemical cycles of iron, sulfur, carbon, and oxygen.

58 GEOSCIENCES↗

Inside out: Measuring the effect of wood anatomy on the efflux and assimilation of xylem–transported CO 2

Carbon dioxide concentrations (including aqueous CO 2 , carbonic acid, bicarbonate, and carbonate) in woody tissues can be up to 750 times higher than atmospheric CO 2 concentrations, ranging from <1% to >26% vs atmospheric ~0.04% (Fig. 1) (Teskey et al. 2008). CO 2 formed through respiration is generally assumed to diffuse to the atmosphere from tissues adjacent to where it is produced. Here, this CO 2 buildups in the stem due to the diffusional barriers in woody and bark tissues. CO 2 in the stem has three fates: 1) it can be refixed for photosynthesis, 2) it can be used for anaplerotic reactions, or 3) it can exit the plant either adjacent to where it was produced (radial diffusion) or in an area remote from its point of origin (xylem-transported CO 2 ). Not accounting for assimilation of xylem-transported CO 2 may result in underestimating total plant photosynthesis. Alternatively, overlooking the transport of CO 2 away from its point of origin complicates the estimation of respiration in stems, branches, or even leaves. For example, CO 2 efflux from the stem may not solely represent stem respiration, but it may represent CO 2 generated through respiration in areas remote from the point of efflux (Stutz et al., 2017). Additionally, wood anatomy and branching architecture likely influence how much and how far xylem-transported CO 2 travels (Fig. 2). Few studies have combined measurements of both the efflux of xylem-transported CO 2 from trees together and the assimilation of xylem-transported CO 2 . Excitingly in this issue of Plant, Cell & Environment, Salomón et al. (pp. ) demonstrate the importance of xylem-transported CO 2 in plants with different wood anatomies by comparing the amount of xylem-transported CO 2 used for photosynthesis to the amount effluxed.

54 ENVIRONMENTAL SCIENCES↗

Data Assimilation for Robust UQ Within Agent-Based Simulation on HPC Systems

Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.

Spannaus, Adam [ORNL] (ORCID:0000000225213657)↗

Bayesian Assimilation of Multiscale Precipitation Data and Sparse Ground Gauge Observations in Mountainous Areas

Estimating the spatial distribution of precipitation is important for understanding ecohydrological processes at catchment scales. However, this estimation is difficult in mountainous areas because ground-based observation stations are often sparsely located and do not represent the spatial variability of precipitation. In this study, we develop a Bayesian assimilation method based on data collected on the Tibetan Plateau from 1980 to 2014 to estimate monthly and daily precipitation. To accomplish this, point-scale ground meteorological observations are combined with large-scale precipitation data such as satellite observations or reanalysis data. First, we remove the terrain effects from ground observations by fitting the precipitation data as functions of elevation, and then we spatially interpolate the residuals to 5-km-resolution grids to obtain monthly and daily precipitation. Additionally, we use Tropical Rainfall Measuring Mission (TRMM) satellite observations and ERA-Interim reanalysis data. Cross-validation methods are used to evaluate our method; the results show that our method not only captures the change in precipitation with terrain but also significantly reduces the associated uncertainty. The improvements are more evident in the main river source areas on the edge of the Tibetan Plateau, where elevation changes dramatically, and in high-altitude areas, where the ground gauges are sparse compared with those in low-altitude areas. Our assimilation method is applicable to other regions and is particularly useful for mountainous watersheds where ground meteorological stations are sparse and precipitation is considerably influenced by terrain.

54 ENVIRONMENTAL SCIENCES↗

Wave-by-Wave Forecasting via Assimilation of Marine Radar Data

Abstract This work describes a phase-resolving wave-forecasting algorithm that is based on the assimilation of marine radar image time series. The algorithm is tested against synthetic data and field observations. The algorithm couples X-band marine radar observations with a phase-resolving wave model that uses the linear mild slope equations for reconstruction of water surface elevations over a large domain of O (km) and a prescribed time window of O (min). The reconstruction also enables wave-by-wave forecasting through forward propagation in space and time. Marine radar image time series provide the input wave observations through a previously given relationship between backscatter intensity and the radial component of the sea surface slope. The algorithm assimilates the wave slope information into the model via a best-fit wave source function at the boundary that minimizes the slope reconstruction error over an annular region at the outer ranges of the radar images. The wave model is then able to propagate the waves across a polar domain to a location of interest at nearer ranges. The constraints on the method for achieving real-time forecasting are identified, and the algorithm is verified against synthetic data and tested using field observations.

Engineering↗

Adjoint sensitivity analysis and data assimilation for verification of dry storage cask contents

Dry cask storage is a method for interim storage of spent fuel assemblies which contain fissile isotopes of uranium and plutonium. These can present a proliferation concern and consequently there is a need for non-destructive testing methods to verify a dry cask's contents for proliferation protection. We present an application of adjoint sensitivity analysis and data assimilation to a multigroup diffusion model of dry cask storage. Adjoint sensitivity analysis allows the efficient calculation of sensitivities for use in data assimilation to calibrate imprecisely known parameter values and data consistency tests to detect diversion scenarios. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Data Assimilation - Advances and Applications

This presentation provides an overview of data assimilation (model calibration) for complex computer experiments. Calibration refers to the process of probabilistically constraining uncertain physics/engineering model inputs to be consistent with observed experimental data. An initial probability distribution for these parameters is updated using the experimental information. Utilization of surrogate models and empirical adjustment for model form error in code calibration form the basis for the statistical methodology considered. The role of probabilistic code calibration in supporting code validation is discussed. Incorporation of model form uncertainty in rigorous uncertainty quantification (UQ) analyses is also addressed. Design criteria used within a batch sequential design algorithm are introduced for efficiently achieving predictive maturity and improved code calibration. Predictive maturity refers to obtaining stable predictive inference with calibrated computer codes. These approaches allow for augmentation of initial experiment designs for collecting new physical data. A standard framework for data assimilation is presented and techniques for updating the posterior distribution of the state variables based on particle filtering and the ensemble Kalman filter are introduced.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Data Synthesis and Data Assimilation at Global Change Experiments and Fluxnet Toward Improving Land Process Models

The project was conducted during the period from 7/1/2012 to 6/30/2017 with three major tasks: (1) data synthesis and development of data assimilation (DA) techniques to constrain modeled ecosystem feedback to climate change; (2) applications of DA techniques to improve process models at different scales from ecosystem to regions and the globe; and 3) improvements of modeling soil carbon (C) dynamics by land surface models. During this period, we have synthesized published data from soil incubation experiments (e.g., Chen et al., 2016; Xu et al., 2016; Feng et al., 2016), global change experiments (e.g., Li et al., 2013; Shi et al., 2015, 2016; Liang et al., 2016) and fluxnet (e.g., Niu et al., 2012., Xia et al., 2015; Li et al., 2016). These data have been organized into multiple data products and have been used to identify general mechanisms and estimate parameters for model improvement. We used the data sets that we collected and the DA techniques to improve model performance of both ecosystem models and global land models. The objectives are: 1) to improve model simulations of litter and soil carbon storage (e.g., Schädel et al., 2013; Hararuk and Luo, 2014; Hararuk et al., 2014; Liang et al., 2015); 2) to explore the effects of CO 2 , warming and precipitation on ecosystem processes (e.g., van Groenigen et al., 2014; Shi et al., 2015, 2016; Feng et al., 2017); and 3) to estimate parameters variability in different ecosystems (e.g., Li et al., 2016). We developed a traceability framework, which was based on matrix approaches and decomposed the modeled steady-state terrestrial ecosystem carbon storage capacity into four can trace the difference in ecosystem carbon storage capacity among different biomes to four traceable components: net primary productivity (NPP), baseline C residence times, environmental scalars and climate forcing (Xia et al., 2013). With this framework, we can diagnose the differences in modeled carbon storage across ecosystems, biomes, and models. This framework has been successfully implemented by several global land models, such as CABLE (Xia et al., 2013), LPJ-GUESS (Ahlström et al., 2015), CLM (Hararuk et al., 2014; Huang et al., 2017, submitted; Shi et al., 2017, submitted), and ORCHIDEE (Huang et al., 2017, unpublished). Moreover, we have identified the theoretical foundation of the determinants of transient C storage dynamics by adding another term, C storage potential, to the steady-state traceability framework (Luo et al., 2017). The theoretical foundation of transient C storage dynamics has been applied to develop a transient traceability framework to explore the traceable components of transient C storage dynamics responded to the rising CO 2 and climate change in the two contrasting ecosystem types Duke needleleaved forest and Harvard deciduous broadleaved forest (Jiang et al., 2017, in revision). Overall, with the data synthesis, data assimilation techniques, and the steady-state and transient traceability frameworks, we have greatly improved land process models for predicting responses and feedback of terrestrial C dynamics to global change. The matrix approaches has the potential to be applied in theoretical research on nitrogen and phosphorus cycle, and therefore, the coupling of carbon-nitrogen-phosphorus.

58 GEOSCIENCES↗

Integration of AI/ML with Data Assimilation for Earth System Prediction

Focal Area(s): Development of dynamically consistent AI/ML methods that can integrate with the data assimilation cycle to improve the efficiency and effectiveness of state estimation and prediction at short to medium range forecast horizons. Science Challenge: This white paper addresses a first step toward complete integration of AI/ML and DA. Here, we address model emulation and its application to simple coupled atmosphere-ocean dynamics for use in data assimilation applications.

54 ENVIRONMENTAL SCIENCES↗

Assimilating Scanning Radar Data into High-Resolution Models

This report documents the findings of a project aiming to improve the initial conditions of km-scale simulations of deep convective storms by assimilating cloud-scale weather radar observations. More accurate numerical analyses will increase the effectiveness of research efforts using LES cloud models as tool to better understand land-atmosphere coupling, boundary layer turbulence, and cloud processes, each used for model parameterization development. Work reported on herein includes: i) assessment of radar data sets for use in data assimilation (‘DA’) experiments, ii) quality control of the radar data set and format conversion to one acceptable to DA schemes utilized by the Weather Research and Forecasting (WRF) model, and iii) examination of the sensitivity of the numerical representation of cloud-scale wind and microphysical features to a variety of tunable DA parameters.

54 ENVIRONMENTAL SCIENCES↗

Development of a Framework for Data Integration, Assimilation, and Learning for Geological Carbon Sequestration (DIAL-GCS) (Final Report)

This project aimed to develop and demonstrate a Data Integration, Assimilation, and Learning framework for geologic carbon sequestration projects (DIAL-GCS). DIAL-GCS is an intelligence monitoring system (IMS) for automating GCS closed-loop management by leveraging recent developments in machine learning technologies, complex event processing (CEP), and reduced-order modeling. The safe and efficient operation of GCS repositories requires integrated monitoring to track the injected CO¬2 as it moves within a storage reservoir. GCS projects are data intensive, as a result of proliferation of digital instrumentation and smart-sensing technologies. GCS projects are also resource intensive, often requiring multidisciplinary teams performing different monitoring, verification, accounting (MVA) tasks throughout the lifecycle of a project to ensure secure containment of injected CO2. The success of GCS thus depends in a large part on our ability to access, assimilate, and analyze heterogeneous data and information sources in a timely manner. This project included a number of meaningful and necessary tasks to transform the human domain knowledge into machine-interpretable rules for automating knowledge extraction and discovery in GCS. The specific technical objectives of the proposed DIAL-GCS project were to develop an ontology-driven GCS data management module for storing, querying, and exchanging GCS data (both historic and live sensor data) from multiple sources and in heterogeneous formats. Incorporate a CEP engine for detecting abnormal situations by seamlessly combining expert knowledge, rule-based reasoning, and machine learning. Enable uncertainty quantification and predictive analytics using a combination of coupled-process modeling, AI/ML methods, and reduced-order modeling, and integrate and demonstrate the system’s capabilities with both real and simulated data. As far as we know, this is one of the first projects aimed to develop intelligent monitoring systems (IMS) targeting the GCS. Under this project, the team had developed a large number of web applications and scientific algorithms that contribute the main theme of intelligent monitoring. The team has published more than a dozen peer reviewed papers and disseminated the research results at multiple technical meetings.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

ML-based Data Assimilation and History Matching: Application to the IBDP CCS Project

It is crucial to monitor the CO2 plume effectively throughout the life cycle of a geologic CO2 sequestration project to ensure safety and storage efficiency. However, the computational cost of existing data assimilation methods can be prohibitively expensive due to the complex physics with multi-component non-isothermal simulation and high dimensionality of large-scale reservoir models. We address this challenge by proposing an accelerated deep learning-based workflow for model calibration and prediction of CO2 plume evolution in the reservoir.The power and efficacy of our workflow is demonstrated by application to the Illinois Basin-Decatur Project (IBDP), a large-scale CO2 storage test in saline aquifer. The data assimilation process is implemented rapidly by the proposed workflow with given field measurements including distributed pressure and temperature sensing (DTS) data at an injection and a monitoring well. CO2 plume evolution is predicted by running the simulations of the calibrated reservoir models.

Nagao, Masahiro↗

WRF-Chem & Data Assimilation: Reconstructing a Historic Dispersion Event

CONCLUSIONS • For this particular case and use, 3D-VAR was the most useful data assimilation method applied for modeling this plume. • Slight downside was the plume was modeled to move too quickly. • Whether this result is generalizable may be debatable based on the circumstances. • The atmospheric state altered how effective the data assimilation algorithms performed. • Nudging and 3D-VAR are not mutually exclusive, but their errors for wind speed may compound

Thomas, Andrew M. [Savannah River National Laborat↗

Development of Biofuel and Bioenergy Processes for Photosynthetic CO 2 Assimilation (CRADA Final Report)

In order to fully exploit algae carbon assimilation for fuels, a preqrequisite is high photosynthetic efficiency and carbon conversion to fuel precursors. In the context of this collaborative project between NLR and EMRE we aim to address aspects of both the biological constraints around photosynthesis-driven carbon assimilation flux as well as elements that bridge the gap between laboratory cultivation and meaningful outdoor deployment, building on the unique capabilities of NLR and EMRE’s algae bioengineering teams. The goal of this work is to improve our understanding of key cellular biochemistry, mass cultivation, and biomass conversion constraints that presently limit the potential bio-oil yield. The proposed first phase of this work will focus on biomass growth improvements by testing hypotheses for alleviating identified metabolic and photophysiological bottlenecks. The results of this work could inform decisions by stakeholders (e.g., industry, community, investors) on the design and deployment of a sustainable biofuel supply chain from algae.

09 BIOMASS FUELS↗

Assimilating partial observation to enhance feedback control of stochastic dynamical systems

Here, in this paper, we present a novel methodology to tackle feedback optimal control problems in scenarios where the exact state of the controlled process is unknown. It integrates data assimilation techniques and optimal control solvers to manage partial observation of the state process, a common occurrence in practical scenarios. Traditional stochastic optimal control methods assume full state observation, which is often not feasible in real-world fluid dynamics control problems. Our approach underscores the significance of utilizing observational data to inform control policy design. Specifically, we introduce a kernel learning backward stochastic differential equation (SDE) filter to enhance data assimilation efficiency and propose a sample-wise stochastic optimization method within the stochastic maximum principle framework. We demonstrate the efficacy and accuracy of our method in the control of advection-diffusion-reaction flow problem and the Dubins airplane maneuvering problem with model uncertainty.

data driven↗

Data Assimilation with Machine Learning Surrogate Models: A Case Study with FourCastNet

Modern data-driven surrogate models for weather forecasting provide accurate short-term predictions but inaccurate and nonphysical long-term forecasts. This paper investigates online weather prediction using machine learning surrogates supplemented with partial and noisy observations. We empirically demonstrate and theoretically justify that, despite the long-time instability of the surrogates and the sparsity of the observations, filtering estimates can remain accurate in the long-time horizon. As a case study, we integrate FourCastNet, a weather surrogate model, within a variational data assimilation framework using partial, noisy ERA5 data. Our results show that filtering estimates remain accurate over a year-long assimilation window and provide effective initial conditions for forecasting tasks, including extreme event prediction.

Adrian, Melissa [Univ. of Chicago, IL (United Stat↗

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

The net CO2 assimilation (A) response to intercellular CO2 concentration (Ci) is a fundamental measurement in photosynthesis and plant physiology research. The conventional A/Ci protocols rely on steady-state measurements and take 15-40 minute per measurement, limiting data resolution or biological replication. Additionally, there are several CO2 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 CO2 protocols in steady-state measurements, and tested whether different CO2 protocols lead to systematic differences in estimations of the biochemical limitations to photosynthesis.

A/Ci response↗

Inverse modeling of pan-Arctic methane emissions at high spatial resolution: what can we learn from assimilating satellite retrievals and using different process-based wetland and lake biogeochemical models?

Understanding methane emissions from the Arctic, a fast-warming carbon reservoir, is important for projecting future changes in the global methane cycle. Here we optimized methane emissions from north of 60° N (pan-Arctic) regions using a nested-grid high-resolution inverse model that assimilates both high-precision surface measurements and column-average SCanning Imaging Absorption spectroMeter for Atmospheric CHartogrphY (SCIAMACHY) satellite retrievals of methane mole fraction. For the first time, methane emissions from lakes were integrated into an atmospheric transport and inversion estimate, together with prior wetland emissions estimated with six biogeochemical models. In our estimates, in 2005, global methane emissions were in the range of 496.4–511.5 Tg yr –1 , and pan-Arctic methane emissions were in the range of 11.9–28.5 Tg yr –1 . Methane emissions from pan-Arctic wetlands and lakes were 5.5–14.2 and 2.4–14.2 Tg yr –1 , respectively. Methane emissions from Siberian wetlands and lakes are the largest and also have the largest uncertainty. Our results indicate that the uncertainty introduced by different wetland models could be much larger than the uncertainty of each inversion. We also show that assimilating satellite retrievals can reduce the uncertainty of the nested-grid inversions. The significance of lake emissions cannot be identified across the pan-Arctic by high-resolution inversions, but it is possible to identify high lake emissions from some specific regions. In contrast to global inversions, high-resolution nested-grid inversions perform better in estimating near-surface methane concentrations.

58 GEOSCIENCES↗