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A Machine Learning Bias Correction on Large–Scale Environment of High–Impact Weather Systems in E3SM Atmosphere Model
Large–scale dynamical and thermodynamical processes are common environmental drivers of high–impact weather systems causing extreme weather events. However, such large–scale environmental conditions often display systematic biases in climate simulations, posing challenges to evaluating high–impact weather systems and extreme weather events. In this paper, a machine learning (ML) approach was employed to bias correct the large–scale wind, temperature, and humidity simulated by the atmospheric component of the Energy Exascale Earth System Model (E3SM) at ~1° resolution. The usefulness of the ML approach for extreme weather analysis was demonstrated with a focus on three high–impact weather systems, including tropical cyclones (TCs), extratropical cyclones (ETCs), and atmospheric rivers (ARs). We show that the ML model can effectively reduce climate bias in large–scale wind, temperature, and humidity while preserving their responses to imposed climate change perturbations. The bias correction is found to directly improve water vapor transport associated with ARs, and representations of thermodynamical flows associated with ETCs. When the bias–corrected large–scale winds are used to drive a synthetic TC track forecast model over the Atlantic basin, the resulting TC track density agrees better with that of the TC track model driven by observed winds. In addition, the ML model insignificantly interferes with the mean climate change signals of large–scale storm environments as well as the occurrence and intensity of three weather systems. This study suggests that the proposed ML approach can be used to improve the downscaling of extreme weather events by providing more realistic large–scale storm environments simulated by low–resolution climate models.
Towards Improved Decision Making for the Smarter Grid: Geomagnetic Disturbance Implicit Modeling Uncertainty Quantification
Geomagnetic disturbances can greatly disrupt the power grid operation. This is caused by low-frequency changes in the earth’s magnetic field, which upon interaction with the deep earth conductivity induces a changing electric field at the earth’s surface. This in turn induces quasi-direct currents which have the potential to cause protective devices to operate, widespread damage to high-voltage transformers, or voltage collapse due to induced reactive power losses. While these impacts have been known since the 1940s, only recently have standards for GMD response been implemented. Because these standards are heavily based on models, it is important to understand when it is appropriate to make certain modeling assumptions. In this work, implicit modeling uncertainty is quantified for the purpose of enhanced decision making for disturbance impact mitigation. Considering electromagnetic models, modeling assumptions of non-uniform grounding, imbalanced operation, transformer saturation, and geomagnetically induced currents, voltage estimation values are analyzed. Statistical characteristics of modeling uncertainty are obtained by analysis of synthetically generated data. Results statistically characterize geomagnetic disturbances modeling uncertainty, providing an important tool for impact mitigation.
Bioinformatic Prediction and High Throughput In Vivo Screening to Identify Cis-Regulatory Elements for the Development of Algal Synthetic Promoters
Not Available
Recovering the effects of subgrid heterogeneity in simulations of radionuclide transport through fractured media
Groundwater flow and contaminant transport through fractured media can be simulated using Discrete Fracture Network (DFN) models which provide a natural description of structural heterogeneity. However, this approach is computationally expensive, with the large number of intersecting fractures necessitated by many real-world applications requiring modeling simplifications to be made for calculations to be tractable. Upscaling methods commonly used for this purpose can result in some loss of local-scale variability in the groundwater flow velocity field, resulting in underestimation of particle travel times, transport resistance and retention in transport calculations. In this paper, a transport downscaling algorithm to recover the transport effects of heterogeneity is tested on a synthetic Brittle Fault Zone model, motivated by the problem of large safety assessment calculations for geological repositories of spent nuclear fuel. We show that the variability in the local-scale velocity field which is lost by upscaling can be recovered by sampling from a library of DFN transport paths, accurately reproducing DFN transport statistic distributions and radionuclide breakthrough curves in an upscaled model.
The Modeled Performance of the ORNL Matched Filter Detector for Seismic Signatures of Multi-Axle Tractor Trailers
The MINOS program seeks methods to passively monitor the transfer of special materials, which are reproducible and quantitatively defensible. To date, we have demonstrated that short-period seismometers deployed near vehicle tracks can detect and monitor signatures of multi-axle tractor trailers impacting small road obstacles as means to detect and identify some transfer activities. In this report, we model the seismic velocity signal output from a tractor-trailer impacting a small obstacle (a template waveform) to parameterize a matched filter that identifies signals with similar shapes buried in noise, and that indicate repeating events (target waveforms). We then use this model to perform thousands of synthetic experiments, in which we apply our detector to identify noisy waveforms output from a similarly modeled vehicle data set; we process all data in the same manner as we process real data collected from the Oak Ridge National Laboratory (ORNL) seismic network. Our experiments, while limited, reveal that the matched filter shows a high discrimination capability, and at very low SNR values (at visibility thresholds). This means that template waveforms can match target waveforms that are sourced by models that share the same vehicle speed (target vehicles), and have a low probability of mis-identification. In particular, a matched filter designed to detect a five-axle tractor-trailer will reliably identify that target vehicle down to an SNR of 11.25 dB, and within ±0.1 km/hr, while successfully screening target vehicles with three axles.
A Novel Integrated Fermentation Process with Engineered Microbial Consortia for Butanol Production from Lignocellulose Sugars without CO 2 Emission
The goal of this project was to develop a synthetic microbial consortium consisting of a lactic acid bacterium, a carboxydotrophic acetogen, and a solventogenic clostridia for the production of n butanol, an advanced biofuel and industrial chemical, from lignocellulose sugars (mainly glucose and xylose) and formate (produced from CO 2 by electrochemical reduction) in an integrated bioprocess (biorefinery), which can provide an effective solution to the technical challenges in developing energy and carbon optimized synthesis for the bioeconomy and achieve the program objectives of ARPA-E. The project focused on the design, modeling and construction of synthetic microbial consortia consisting of three bacterial species to maximize carbon conversion and butanol production with a 100% theoretical product yield from glucose and zero or negative CO 2 emission.
Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly
Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.
The pGinger Family of Expression Plasmids
Metabolic engineering and synthetic biology are predicated on the precise control of gene expression. As synthetic biology expands beyond model organisms, more tools will be required that function robustly in a wide range of bacterial hosts. The pGinger family of plasmids constitutes 43 plasmids that will enable both constitutive and inducible gene expression in a wide range of nonmodel Proteobacteria .
Geometrical defect detection for additive manufacturing with machine learning models
This study proposed a scheme based on Machine Learning (ML) models to detect geometric defects of additively manufactured objects. The ML models are trained with synthetic 3D point clouds with defects and then applied to detect defects in actual production. Using synthetic 3D point clouds rather than experimental data could save a huge amount of training time and costs associated with many prints for each design. Besides distance differences of individual points between source and target point clouds, this scheme uses a new concept called “patch” to capture macro-level information about nearby points for ML training and implementation. Numerical comparisons of prediction results on experimental data with different shapes showed that the proposed scheme outperformed the existing Z-difference method in the literature. Five ML methods (Bagging of Trees, Gradient Boosting, Random Forest, K-nearest Neighbors and Linear Supported Vector Machine) were compared under various conditions, such as different point cloud densities and defect sizes. Bagging and Random Forest were found the two best models regarding predictability; and the right patch size was found to be at 20. The proposed ML-based scheme is applicable to in-situ defect detection during additive manufacturing with the aid of a proper 3D data acquisition system.
Quantification of manganese for ChemCam Mars and laboratory spectra using a multivariate model
In this work, we report a new calibration model for manganese using the laser-induced breakdown spectroscopy instrument that is part of the ChemCam instrument suite onboard the NASA Curiosity rover. The model has been trained using an expanded set of 523 manganese-bearing rock, mineral, metal ore, and synthetic standards. The optimal calibration model uses the Partial Least Squares (PLS) and Least Absolute Shrinkage and Selection Operator (LASSO) multivariate techniques, with a novel “double blending” technique. We determined the detection limit for manganese is 82 ppm using a method blank procedure and is possibly as low as 27 ppm based on visual inspection of the spectra. Based on a representative test set consisting of measurements on 93 standards, the double blended multivariate model shows a Root Mean Squared Error of Prediction (RMSEP) accuracy of 1.39 wt% MnO for the full blended model. Employing a local RMSEP estimate where the model performance is evaluated based on nearby test samples, the accuracy is 0.03 wt% at the quantification limit (0.05 wt% MnO), 0.4 wt% accuracy at 1.0 wt% MnO, and 4.4 wt% accuracy at 100 wt% MnO. Precision is estimated using the standard deviation of the test set measurements, and is ±0.01 wt% MnO at the quantification limit, ±0.09 wt% MnO at 1.0 wt% MnO, and ± 2.1 wt% MnO at 100 wt% MnO (all 1 standard deviation). This new calibration is important for understanding the variation of manganese in the bedrock with the Curiosity rover on Mars, which provides insight into past redox conditions on Mars.
Sharing is caring: An extensive analysis of parameter-based transfer learning for the prediction of building thermal dynamics
In recent years deep neural networks have been proposed as a lightweight data-driven model to capture high-dimensional, nonlinear physical processes to predict building thermal responses. However, the need of a large amount of data for the training process of deep neural networks clashes with the potential limited data availability in most existing or new buildings. Transfer learning aims to enhance the performance of a target learner exploiting knowledge from related and similar environments. This study conducted a suite of experiments that leveraged 250 data-driven models based on a synthetic dataset of a building archetype to study the influence of data availability, energy efficiency level, occupancy and climate for the transfer process of thermal dynamics. The performance of the transfer learning process was compared against a classical machine learning approach. Here, the results suggest that building thermal dynamics can be effectively transferred under the same climatic conditions, increasing performance when dealing with different occupancy schedules, efficiency levels and low data availability. Furthermore, the paper compares the performance of both transfer learning and machine learning approaches in an online fashion, to support the implementation in real-world deployment.
Rapid failure mode classification and quantification in batteries: A deep learning modeling framework
Unique, rapid identification and quantification of the dominant aging modes in lithium-ion batteries (LiBs) with early and non-specialized test data is a significant scientific challenge. Leveraging synthetic-data, deep-learning (DL) techniques have great potential to enable fast and robust classification and quantification of battery aging modes that produce different patterns of cell aging. This study, for the first time, presents a synthetic–data-based DL modeling framework for rapid and automatic classification and quantification of battery-aging modes and resultant aging with experimental validation. Availing synthetic dQ.dV -1 curves for ~26000 initial conditions and aging modes, the framework classified the dominant aging modes, for cells undergoing fast charge, in fewer than 100 cycles. Upon classification, the framework quantified the evolution of the aging modes, which were often nonuniform with cycling, for 22 gr/NMC532 pouch cells tested up to 600 cycles at different charging rates (1C–9C).
Encoding nonlinear and unsteady aerodynamics of limit cycle oscillations using nonlinear sparse Bayesian learning
This article investigates the applicability of a recently proposed, nonlinear sparse Bayesian learning (NSBL) algorithm to identify and estimate the complex aerodynamics of limit cycle oscillations. NSBL provides a semi-analytical framework for determining the data-optimal sparse model nested within a (potentially) over-parameterized model. This is particularly relevant to nonlinear dynamical systems where modelling approaches involve the use of physics-based and data-driven components. In such cases, the data-driven components, where analytical descriptions of the physical processes are not readily available, are often prone to overfitting, meaning that the empirical aspects of these models will often involve the calibration of an unnecessarily large number of parameters. While an overparameterized model may fit the observed data well, such models may be inadequate for making predictions in regimes that are different from those wherein the data were recorded. In view of this, it is desirable to not only calibrate the model parameters, but also identify the optimal compromise between data fit and model complexity. In this article, we exhibit the optimal model discovery for an aeroelastic system wherein the structural dynamics are well-known and described by a differential equation model, coupled with a semi-empirical aerodynamic model for laminar separation flutter, resulting in low-amplitude limit cycle oscillations (LCO). To illustrate the performance of the algorithm, in this article, we use synthetic data and demonstrate the ability of the algorithm to correctly rediscover the optimal model and model parameters, given a known data-generating model. The synthetic data are generated from a forward simulation of a known differential equation model with parameters selected so as to mimic the dynamics observed in wind-tunnel experiments. Subsequently, we demonstrate the performance of the algorithm for model selection using noisy LCO data from wind tunnel experiments. As there is no ground truth available for the experimental data case, we provide a comparison between NSBL and Bayesian model selection to validate the results, and demonstrate the use of NSBL as an efficient alternative to traditional methods.
EpiCast: Simulating Epidemics with Extreme Detail
In early 2020, COVID-19 swept the globe. Governments attempted to “flatten the curve” through business shutdowns and stay-at-home orders, but the United States was hit hard. By the end of March, mere months after the virus first emerged in humans 7,000 miles away, the U.S. had recorded 192,300 cases and 5,300 deaths. While this unprecedented disaster sent shockwaves through every level of society and clouded an uncertain future, state and local governments turned to computational and mathematical epidemiology researchers to help formulate intervention strategies to limit the spread of the disease. Traditional forecasting models provided a reasonable understanding of how the near future was likely to look, but local policy makers and public health communities still struggled to understand how potential mitigations ought to be implemented. Decision makers needed a way to measure the impact of their policy choices—they needed better technology. EpiCast answered the call, bringing urgently needed answers to policymakers grappling with how to adjust school and business schedules. EpiCast is modeling software that generates a synthetic, representative population to simulate infectious disease transmission in the United States with extreme detail and granularity. The software models human behavior combined with community-specific information to provide a fine-grained preview of the effect of potential mitigation strategies for decision makers.
Energy Conversion and Electron Acceleration and Transport in 3D Simulations of Solar Flares
Recent observations and simulations indicate that solar flares undergo extremely complex 3D evolution, making 3D particle transport models essential for understanding electron acceleration and interpreting flare emissions. In this study, we investigate this problem by solving Parker’s transport equation with 3D MHD simulations of solar flares. By examining energy conversion in the 3D system, we evaluate the roles of different acceleration mechanisms, including reconnection current sheet (CS), termination shock (TS), and supra-arcade downflows (SADs). We find that large-amplitude turbulent fluctuations are generated and sustained in the 3D system. The model results demonstrate that a significant number of electrons are accelerated to hundreds of keV and even a few MeV, forming power-law energy spectra. These energetic particles are widely distributed, with concentrations at the TS and in the flare looptop region, consistent with results derived from recent hard X-ray (HXR) and microwave (MW) observations. By selectively turning particle acceleration on or off in specific regions, we find that the CS and SADs effectively accelerate electrons to several hundred keV, while the TS enables further acceleration to MeV. However, no single mechanism can independently account for the significant number of energetic electrons observed. Instead, the mechanisms work synergistically to produce a large population of accelerated electrons. Our model provides spatially and temporally resolved electron distributions in the whole flare region and at the flare footpoints, enabling synthetic HXR and MW emission modeling for comparison with observations. These results offer important insights into electron acceleration and transport in 3D solar flare regions.
Sensitivity of modelled passive margin stratigraphy to variations in sea level, sediment supply and subsidence
Abstract We produced a 10 Myr synthetic stratigraphic section using a forward stratigraphic model that generates marine deltaic stratigraphy over geological timescales. We recursively fit the model using a Bayesian inversion algorithm to test: (1) if it could be accurately reconstructed; (2) if the parameters used to create it could be recovered; and (3) the sensitivity of the model output to given model parameters and the attendant physical processes. The original synthetic stratigraphic section was produced with cyclical sea‐level variations of 40 and 30 m with 2.4 and 10 Myr periods respectively. Sediment was also supplied cyclically, in 2.4 and 10 Myr cycles with amplitudes of 30 and 80 tons/100 kyr, respectively, varying from a mean of 232 tons/100 kyr. Parameter values were sampled to fit the model using a Markov chain Monte Carlo algorithm, resulting in a ±5 m (1σ) variation between the experimental output and the original. Sea level varied by ±7 m (1σ) within the posterior distribution of parameters. As a result, both the 10 Myr and 2.4 Myr sea‐level cycles could be extracted from the original output. The variation in sediment supply was approximately ±38 tons/100 kyr (1σ) and, as a result, only the larger long‐term supply variations could be accurately recovered in refitting the model. The variation in thermal, flexural and total subsidence across those parameter sets is less than ±10 m (1σ). The original section experienced 150 m of total subsidence at the depocentre. Our results demonstrate the distinct and interpretable imprint of sea level and subsidence on continental margin stratigraphy can be quantified. Moreover, we conclude that sea‐level change produces a defined effect on the geometries of stratigraphic architecture, and that techniques applied for the purpose of delineating sea‐level variation from continental margin strata have a well‐founded conceptual basis.
A Siamese CNN + KNN-Based Classification Framework for Non-intrusive Load Monitoring
Through the development of smart grids, programs such as demand side response, have been presented as auxiliary services to the real-time operation of distributed networks. In order to provide consumers information on their energy consumption, so that a modulation in consumption is possible, non-intrusive load monitoring has been introduced as an solution to this pattern recognition problem. Non-intrusive load monitoring enables the modeling of electrical loads connected to the low-voltage system, considering only a single measurement point. Presented state-of-the-art solutions though, consider availability of data as well as representation of all possible classes of the environment. This is of course a most conservative hypothesis, since in real-life applications availability of such data is much difficult, as well as the dynamic behavior of models is implicitly evolving in time. Here, a framework that uses neural Siamese networks with k-nearest neighbor clustering is presented toward non-intrusive load monitoring. Online learning feature is implemented, which relaxes the hypothesis of data requirements as well addresses the evolving nature of load profile. k-nearest clustering allows nonlinear characteristic space modelling. Test results using synthetics and real-life data show that the solution, besides obtaining a good generalizability in the classification, also obtained results with an accuracy of 95.77%.