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At least 523 records · Page 29

Assessing mechanisms for microbial taxa and community dynamics using process models

Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

Uncertainty quantification and propagation in lithium-ion battery electrodes using bayesian convolutional neural networks

The complex nature of manufacturing processes stipulates electrodes to possess high variability with increased heterogeneity during production. X-ray computed tomography imaging has proved to be critical in visualizing the complicated stochastic particle distribution of as-manufactured electrodes in lithium-ion batteries. However, accurate prediction of their electrochemical performance necessitates precise evaluation of kinetic and transport properties from real electrodes. Image segmentation that characterizes voxels to particle/pore phase is often meticulous and fraught with subjectivity owing to a myriad of unconstrained choices and filter algorithms. Here we utilize a Bayesian convolutional neural network to tackle segmentation subjectivity and quantify its pertinent uncertainties. Otsu inter-variance and Blind/Referenceless Imaging Spatial Quality Evaluator are used to assess the relative image quality of grayscale tomograms, thus evaluating the uncertainty in the derived microstructural attributes. We analyze how image uncertainty is correlated with the uncertainties and magnitude of kinetic and transport properties of an electrode, further identifying pathways of uncertainty propagation within microstructural attributes. The coupled effect of spatial heterogeneity and microstructural anisotropy on the uncertainty quantification of transport parameters is also understood. This work demonstrates a novel methodology to extract microstructural descriptors from real electrode images through quantification of associated uncertainties and discerning the relative strength of their propagation, thus facilitating feedback to manufacturing processes from accurate image based electrochemical simulations.

25 ENERGY STORAGE↗

Simulation-based characterization of the variability of earthquake risk to buildings in the near-field

Recent advancements in high performance computing platforms and computational workflow for regional-scale simulations are enabling unprecedented modeling of fault-to-structure earthquake processes. Regional simulations resolving ground motions at frequencies relevant to engineered systems are becoming computationally viable and provide a new capability to improve understanding of the geographical distribution and intensity of risk to buildings and critical infrastructure. As computational capabilities advance, it is essential to move beyond illustrative single rupture realizations for scenario earthquake events towards the development of a full suite of rupture realizations that appropriately characterize the range of risk to building systems. The work described in this article investigates the application of a suite of fault rupture realizations with the objective of assessing near-fault, site-specific seismic demand variability for building structures. A representative high-performance regional-scale computational model is utilized to execute ground motion and building response simulations based on 18 kinematic rupture realizations of an M7 strike-slip scenario earthquake. The fault rupture models for the scenario earthquake are created by systematically perturbing the hypocenter location and stochastically generating rupture parameters (slip, rise time, rake angle) to represent a breadth of ground motion intensities resulting from the spatial and temporal variabilities of an earthquake rupture process. The resulting seismic demand variability for three-story (short period) and forty-story (long period) steel moment-resisting frame buildings is characterized in terms of the median and distribution of peak inter-story drift ratio for a range of near-fault sites. The full suite of 18 fault rupture realizations and approximately 280,000 nonlinear dynamic building simulations indicate that the three-story building undergoes higher median seismic demand and significantly greater variability of demand at a given site than the forty-story building, which has important implications for the level of certainty in predicting building performance during an earthquake. The simulations performed provide deeper insight into the relationship between fault rupture parameterization and building response, which is essential information for developing a representative suite of rupture realizations for specific earthquake scenarios.

58 GEOSCIENCES↗

Generation and representation of synthetic smart meter data

Advanced energy algorithms running at big-data scale will be necessary to identify, realize, and verify energy savings to meet government and utility goals of building energy efficiency. Any algorithm must be well characterized and validated before it is trusted to run at these scales. Smart meter data from real buildings will ultimately be required for the development, testing, and validation of these energy algorithms and processes. However, for initial development and testing, smart meter data are difficult to work with due to privacy restrictions, noise from unknown sources, data accessibility, and other concerns which can complicate algorithm development and validation. This paper describes a new methodology to generate synthetic smart meter data of electricity use in buildings using detailed building energy modeling, which aims to capture the variability and stochastics of real energy use in buildings. The methodology can create datasets tailored to represent specific scenarios with known truth and controllable amounts of synthetic noise. Knowledge of ground truth also allows the development and validation of enhanced processes which leverage building metadata, such as building type or size (floor area), in addition to smart meter data. The methodology described in this paper includes the key influencing factors of real-world building energy use including weather data, occupant-driven loads, building operation and maintenance practices, and special events. Data formats to support workflows leveraging both synthetic meter data and associated metadata are proposed and discussed. Finally, example use cases of the synthetic meter data are described to illustrate potential applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Time-Sequenced Flow Field Prediction in an Optima Spark-Ignition Direct-Injection Engine Using Bidirectional Recurrent Neural Network (bi-RNN) with Long Short-Term Memory

To further improve the energy conversion efficiency of internal combustion engine, the transient and complex air flow movement inside the cylinder needs to be better understood and controlled. Although the in-cylinder flow fields are highly stochastic with strong cycle-to-cycle fluctuations, machine learning can still provide an efficient way to learn and regress the complex flow movement process inside the cylinder. In this work, a bidirectional recurrent neural network (bi-RNN) model with long short-term memory was applied to predict the in-cylinder flow fields at different time steps using training data from mull-cycle particle image velocimetry (PIV) measurements. To evaluate the agreement between the true and predicted flow fields, structure and magnitude comparison indices are calculated both globally and locally. The comparison results show that the bi-RNN model can accurately predict the bulk flow and vortex motions from early intake stroke to compression stroke. This work demonstrates that the machine learning model has the potential to predict the underlying dynamics of the interaction between in-cylinder flows and provides a reliable way to improve temporal resolution in PIV flow data to better reveal transient in-cylinder flow features.

Bi-RNN model↗

Reshaping of Truncated Pd Nanocubes: Energetic and Kinetic Analysis Integrating Transmission Electron Microscopy with Atomistic-Level and Coarse-Grained Modeling

Stability against reshaping of metallic fcc nanocrystals synthesized with tailored far-from-equilibrium shapes is key to maintaining optimal properties for applications such as catalysis. Yet Arrhenius analysis of experimental reshaping kinetics, and appropriate theory and simulation, is lacking. As such, we use TEM to monitor the reshaping of Pd nanocubes of ~25 nm side length between 410 °C (over ~4.5 h) and 440 °C (over ~0.25 h), extracting a high effective energy barrier of E eff ≈ 4.6 eV. We also provide an analytic determination of the energy variation along the optimal pathway for reshaping that involves transfer of atoms across the nanocube surface from edges or corners to form new layers on side {100} facets. The effective barrier from this analysis is shown to increase strongly with the degree of truncation of edges and corners in the synthesized nanocube. Theory matches experiment for the appropriate degree of truncation. In addition, we perform simulations of a stochastic atomistic-level model incorporating a realistic description of diffusive hopping for undercoordinated surface atoms, thereby providing a visualization of the initial reshaping process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Production of neutron-rich isotopes for 𝑍 ≥ 98 in the 238 U + 248 Cm reaction

Multinucleon transfer (MNT) reactions in actinide systems are a promising method to synthesize transuranium neutron-rich elements. Appropriate theoretical approaches are needed to understand the mechanisms behind MNT. We employ a microscopic approach to calculate neutron-rich isotope production in the reaction 238 U + 248 Cm system. Here, the stochastic mean-field (SMF) approach is used to calculate the primary cross sections in MNT reactions based on the quasifission and inverse quasifission processes, and a statistical de-excitation model with GEMINI ++ code to calculate the secondary fragment cross sections. The calculated cross sections using SMF and GEMINI ++ explain available experimental results for the 238 U + 248 Cm system at 𝐸 c.m. = 898.7 MeV energy. This shows the effectiveness and applicability of the quantal diffusion approach, based on the SMF theory, in heavy-ion collisions. Production of transuranium neutron-rich elements with a proton number up to 𝑍=101 is obtained with sizable cross sections. Theoretical results calculated for the 𝑍=102–105 region, for which there are no experimental data, show that the cross-section values would be lower than the microbarn level. SMF theory does not contain any adjustable parameters other than the standard parameters of the energy density functional used in the TDHF theory and is an important approach for the microscopic understanding of reaction mechanisms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

HERON

HERON is a modeling toolset and plugin for RAVEN to accelerate stochastic technoeconomic assessment of the economic viability of various grid-energy system configurations, especially with application to electrical grids and integrated energy systems (IES). The frameworks enabling this toolset are INL's RAVEN and its TEAL plugin. The toolset includes automated RAVEN workflow generation tools for performing stochastic analysis and optimization driven by technoeconomic factors. The workflows generated employ RAVEN for parametric or optimizing study of grid component characteristics, and again for stochastic sampling of regulated and deregulated markets, load, and weather histories. The toolset further provides methods for economically-optimal dispatch of system components given the stochastic samples of market, load, and weather histories. The toolset allows assembling of existing and new models through the RAVEN interface to the Modelica process modeling language.

Talbot, PaulW↗

Adaptive Sampling-Based Bi-Fidelity Stochastic Trust Region Method for Stochastic Derivative-Free Optimization

Bi-fidelity stochastic optimization has gained increasing attention as an efficient approach to reduce computational costs by leveraging a low-fidelity (LF) model to optimize an expensive high-fidelity (HF) objective. In this paper, we propose ASTRO-BFDF, an adaptive sampling trust-region method specifically designed for unconstrained bi-fidelity stochastic derivative-free optimization problems. In ASTRO-BFDF, the LF function serves two purposes: (i) to identify better iterates for the HF function when the optimization process indicates a high correlation between them and (ii) to reduce the variance of the HF function estimates using bi-fidelity Monte Carlo (BFMC). The algorithm dynamically determines sample sizes while adaptively choosing between crude Monte Carlo and BFMC to balance the trade-off between optimization and sampling errors. We prove that the iterates generated by ASTRO-BFDF converge to a first-order stationary point almost surely. Additionally, we demonstrate the effectiveness of the proposed algorithm through numerical experiments on synthetic benchmarks and simulation optimization problems involving discrete event systems.

97 MATHEMATICS AND COMPUTING↗

A Machine Learning Model for Predicting Composition of Catalytic Coprocessing Products from Molecular Beam Mass Spectra

Demand for the development of an automated and integrated refining process for biofuels has increased in recent years due to the lack of generalized process inspection tools. In bio-oil upgrading processes, all process variables are maintained based on the offline specification of intermediates and products. A lack of real-time product specifications in batch-wise monitoring can cause process failure and wasted resources. Therefore, there is a need for a fast and accurate intermediates/product specification tool that can be used for real-time specification to reduce waste and mitigate the risk of process failure. Here, to address this gap, we developed a machine learning (ML) model for predicting speciated bio-oil composition, including paraffin, iso-paraffins, olefins, naphthene, and aromatics. The model is trained using the mass spectra from upgraded products collected in the vapor phase before condensation and predicts the composition of the condensed product. Training ML models using raw mass spectra is challenging due to numerous overlapped peaks originating from different parent compounds. With this in mind, we propose a protocol that (i) transforms raw mass spectra to chemistry-inspired predefined features and (ii) trains decision tree-based models using these features. Our results show that the random forest model was robust against overfitting and had the highest accuracy compared to other models. Moreover, a stochastic ablation method determined the eight most significant features while maximizing the accuracy. Our protocol facilitates real-time compositional analysis of upgraded bio-oils and thus real-time process monitoring. Additionally, this protocol enables the rational design of efficient catalysts and the determination of optimal process conditions.

09 BIOMASS FUELS↗

Training reinforcement learning models via an adversarial evolutionary algorithm

When training for control problems, more episodes used in training usually leads to better generalizability, but more episodes also requires significantly more training time. There are a variety of approaches for selecting the way that training episodes are chosen, including fixed episodes, uniform sampling, and stochastic sampling, but they can all leave gaps in the training landscape. In this work, we describe an approach that leverages an adversarial evolutionary algorithm to identify the worst performing states for a given model. We then use information about these states in the next cycle of training; this process can be repeated until the desired level of model performance is met. We demonstrate this approach with the OpenAI Gym cart-pole problem. With this problem, we show that the adversarial evolutionary algorithm did not reduce the number of episodes required in training needed to attain model generalizability when compared with stochastic sampling, and actually performed slightly worse.

Coletti, Mark↗

Incorporation of market signals for the optimal design of post combustion carbon capture systems

Recent studies have shown that fossil generators equipped with post-combustion carbon capture (PCC) systems are needed to reduce the cost of deep decarbonization. Such generators need to be flexible and responsive to grid conditions, particularly in a high variable renewable energy (VRE) environment. In this work, we evaluate the net present value (NPV) of retrofitting an existing natural gas combined cycle (NGCC) unit with a flexible PCC system while incorporating market signals from a high VRE grid. We use our industrial partner’s NGCC configuration as representative of existing NGCC units and Svante’s rapid-temperature swing adsorption (TSA) for PCC. Because of its ability to rapidly startup/shutdown and ramp-up/ramp-down, the chosen capture technology is very attractive for load-following operations. For a given set of market signals, we formulate a two-stage stochastic multi-period optimization problem, under the price-taker assumption, to simultaneously optimize the design of the capture system and operation of the entire plant. Rigorous models for the NGCC unit, PCC system, and compression system are developed using commercial process simulators and validated with either plant or vendor data. For computational tractability, we develop surrogate/reduced-order models for use in the optimization problem. The surrogate model for the NGCC plant is constructed by linearizing the rigorous dynamic model at 75% load, while data-driven nonlinear surrogate models for the capture and compression systems are constructed using simulation data from the rigorous models. The optimization problem, formulated as a mixed integer bilinear program, is implemented in the IDAES® integrated platform and solved to global optimality using Gurobi 9.5. Using this formulation, we determine the profitability of retrofitting an existing NGCC unit with the chosen capture system for multiple regions in the U.S. under two scenarios with different carbon prices. Importantly, the results show that the optimal decision strongly depends on the region and on the carbon price, thereby demonstrating the importance of the inclusion of market signals in the design process.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Parallel interior-point solver for block-structured nonlinear programs on SIMD/GPU architectures

Here, we investigate how to port the standard interior-point method to new exascale architectures for block-structured nonlinear programs with state equations. Computationally, we decompose the interior-point algorithm into two successive operations: the evaluation of the derivatives and the solution of the associated Karush-Kuhn-Tucker (KKT) linear system. Our method accelerates both operations using two levels of parallelism. First, we distribute the computations on multiple processes using coarse parallelism. Second, each process uses SIMD/GPU accelerators locally to accelerate the operations using fine-grained parallelism. The KKT system is reduced by eliminating the inequalities and the state variables from the corresponding equations. We demonstrate our method's capability on the supercomputer Polaris, a testbed for the future exascale Aurora system. Each node is equipped with four GPUs, a setup amenable to our two-level approach. Our experiments on the stochastic optimal power flow problem show that the reduction method is 50x faster than the sparse linear solver HSL MA57 running in serial on the CPU, and 6x faster than Pardiso running in parallel on CPU on the same number of processes.

97 MATHEMATICS AND COMPUTING↗

Theory of mean E × B shear in a stochastic magnetic field: ambipolarity breaking and radial current

The mean E $ \times $ B shear in a stochastic magnetic field is calculated, using the radial force balance relation and transport equations. This analysis is relevant to the L → H transition with resonant magnetic perturbations, and special focus is placed upon the physics of non-ambipolar transport and radial current. The key physical process is the flow of fluctuating currents along wandering magnetic fields. The increments in poloidal and toroidal rotation, density and ion pressure are calculated. The radial envelope of the magnetic perturbations inside the plasma defines a new scale ${\ell _{{\text{env}}}}$, which is the characteristic scale of the magnetic fluctuation intensity profile. Here, the net particle outflow due to stochastic magnetic fields is calculated and is determined by the net radial current through the separatrix. Implications for the L → H transition are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Machine learning and atomic layer deposition: Predicting saturation times from reactor growth profiles using artificial neural networks

In this work, we explore the application of deep neural networks to the optimization of atomic layer deposition (ALD) processes. In particular, we focus on a one-shot optimization problem, where we try to predict the optimal dose time that leads to saturation everywhere in the reactor based on thickness values measured at different points of an ALD reactor after a single trial growth. In order to tackle this problem, we introduce a dataset designed to train neural networks to predict saturation times based on these inputs for a cross-flow ALD reactor. Here, we then explore the predictive ability of artificial neural networks of different depths and sizes using a separate testing dataset to evaluate their accuracies. The results obtained show that networks trained using stochastic gradient descent methods can accurately predict saturation times without requiring any additional information on the surface kinetics. This provides a viable approach to minimize the number of experiments required to optimize new ALD processes in a known reactor, and it highlights the way machine learning can be leveraged for thin film growth and manufacturing. While the datasets and training procedure depend on the reactor geometry, the trained neural networks provide a general surrogate model connecting thickness values and trial dose times with optimal saturation times that can be reused for different ALD processes within the same reactor.

36 MATERIALS SCIENCE↗

Computational Aspects of Single-Molecule Kinetics for Coupled Catalytic Cycles: A Spectral Analysis

Catalysis from single active sites is analyzed using methods developed from single molecule kinetics. Using a stochastic Markov state description, the observable properties of general catalytic networks of reactions are expressed using an eigenvalue decomposition of the transition matrix for the Markov process. By the use of a sensitivity analysis, the necessary eigenvalues and eigenvectors are related to the energies of controlling barriers and wells located along the reaction routes. A generalization of the energetic span theory allows the eigenvalues to be computed from several activation energies corresponding to distinct barrier-well pairings. The formalism is demonstrated accurately for model problems for a physically realistic mechanism for an alkene hydrogenation reaction on a single atom catalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Robust Parameter Design on Dual Stochastic Response Models With Constrained Bayesian Optimization

In engineering system design, minimizing the variations of the quality measurements while guaranteeing their overall quality up to certain levels, namely the robust parameter design (RPD), is crucial. Recent works have dealt with the design of a system whose response-control variables relationship is a deterministic function with a complex shape and function evaluation is expensive. In this work, we propose a Bayesian optimization method for the RPD of stochastic functions. Dual stochastic response models are carefully designed for stochastic functions. The heterogeneous variance of the sample mean is addressed by the predictive mean of the log variance surrogate model in a two-step approach. We establish an acquisition function that favors exploration across the feasible and optimality-improvable regions to effectively and efficiently solve the stochastic constrained optimization problem. Further, the performance of our proposed method is demonstrated by the extensive numerical and case studies. Note to Practitioners-Many manufacturing processes involve undesirable variations, which create variations in the final products. For example, many emerging manufacturing processes, such as nanomanufacturing, involve complex physical and chemical dynamics and transformation, creating variations in the manufacturing output. In such processes, it is crucial to design the manufacturing processes or products so that they have minimum variations in their quality. Meanwhile, it is also important to maintain the overall quality of the designed processes or products. Furthermore, acquiring data from many advanced manufacturing processes is often very costly, especially in the designing stage. In this work, we propose a data-driven method that automatically finds the best setting of manufacturing processes or products with the minimum variations of quality and a given constraint on the average quality satisfied. Our proposed method is used before conducting every experiment; It analyzes the historical data from previous experiments and provides a setting to be used in the next experiment. Our proposed method efficiently utilizes the historical data, and thus finds the best robust setting by conducting only a small number of experiments.

42 ENGINEERING↗

Jarzynski Equality for Conditional Stochastic Work

It has been established that the inclusive work for classical, Hamiltonian dynamics is equivalent to the two-time energy measurement paradigm in isolated quantum systems. However, a plethora of other notions of quantum work has emerged, and thus the natural question arises whether any other quantum notion can provide motivation for purely classical considerations. In the present analysis, we propose the conditional stochastic work for classical, Hamiltonian dynamics, which is inspired by the one-time measurement approach. This novel notion is built upon the change of expectation value of the energy conditioned on the initial energy surface. As main results, we obtain a generalized Jarzynski equality and a sharper maximum work theorem, which account for how non-adiabatic the process is. Our findings are illustrated with the parametric harmonic oscillator.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗