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At least 505 records · Page 28

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗

Identifying Nuclear Data Correlated Through Predicting Bias in Integral Experiments via Applying Principal Component Analysis to Random Forest

ABSTRACT Nuclear data (ND) are the input data for neutron‐transport simulations to answer questions related to nuclear technologies. Subsets of ND, here > 20,000 data points, are validated with respect to thousands of criticality experiments that represent various applications on a small scale. The aim of validation with these experiments is to find errors in ND or methods. The key challenge here is that several hundreds of ND are used to simulate one integral value. Hence, one cannot clearly identify what ND are leading to bias in criticality measurements. In fact, a mistake in one nuclear‐data observable can be compensated with an error in another, and the predicted criticality value would still be predicted in agreement with experimental data. Random forest (RF) was previously employed to predict bias in criticality measurements using sensitivities of simulated criticality experiments to ND. The SHapley Additive exPlanations (SHAP) metric was then applied to attribute the importance of each ND experiment and observable to bias prediction. This, however, did not highlight what ND were jointly related to predicting bias. This is important as it could inform us about where compensating errors in ND could hide. We tackle this shortcoming here by first decomposing the ND sensitivities to integral‐experiment simulations into principal components. Then we use principal component projections to predict bias via the RF and SHAP. The SHAP values and principal components are employed to reconstruct detailed SHAP values for each ND observable. We demonstrate that these extended SHAP bias predictions are more robust, less noisy, and more efficient. In addition, we show that this approach accounts for covariance in ND sensitivities and automates the identification of where compensating errors could hide in ND.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Do parcel lockers reduce delivery times? Evidence from the field

Common-carrier parcel lockers have emerged as a secure, automated, self-service means of delivery consolidation in congested urban areas, which are believed to mitigate last-mile delivery challenges through reducing out-of-vehicle delivery times and consequently vehicle dwell times at the curb. However, little research exists to empirically demonstrate the environmental and efficiency gains from this technology. In this study, we designed a nonequivalent groups pre-test/post-test control experiment to estimate the causal effects of a parcel locker on delivery times in a residential building in downtown Seattle, WA. Here, the causal effects are measured in terms of vehicle dwell time and the time delivery couriers spend inside the building, through the difference-in-difference method and using a similar nearby residential building as a control. The results showed a statistically significant decrease in time spent inside the building, and small yet insignificant reduction in delivery vehicle dwell time at the curb. The locker was also well received by the building managers and residents.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

CCSI Toolset 3.21 Release

CCSI Toolset 3.21 Release Highlights Parallelization support was added for Sequential Design of Experiments (SDOE) computations using Dask (preliminary). Input type dependent ordering capability was added to the SDOE module. With this implementation the user can specify the level of difficulty to change an input (Easy or Hard) and FOQUS will generate the appropriate ordered design depending on the input difficulty combination. Python version support was extended. FOQUS is now compatible with Python 3.8 through 3.12. Platforms used for automated testing were expanded to include macOS ARM (Apple Silicon). Updates to the FOQUS documentation to include information on how to set paths for SimSinter and TurbineLite. Turbine configuration section was added to Debugging Documentation.

AS↗

Shielding Benchmark Comparison - MCNP6.2

This report documents the calculations performed for a shielding code comparison between various Department of Energy (DOE) sites. These shielding calculations were performed using an experiment drawn from the International Handbook of Evaluated Criticality Safety Benchmark Experiments, published by the Organisation for Economic Cooperation and Development/Nuclear Energy Agency (OECD/NEA). The benchmark selected for comparison is ALARM-CF-AIR-LAB-001 (“Neutron Fields in the Three-Section Concrete Labyrinth from Cf-252 Source, Benchmark ALARM CF AIR LAB-001”). The Y-12 submission for this code comparison was performed with Monte Carlo N Particle (MCNP) Transport Code System, Version 6.2 and Automated Variance Reduction Generator (ADVANTG).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

An Online Dynamic Amplitude-Correcting Gradient Estimation Technique to Align X-ray Focusing Optics

High-brightness X-ray pulses, as generated at synchrotrons and X-ray free electron lasers (XFELs), are used in a variety of scientific experiments. At these facilities, measurements often require optical equipment, e.g Compound Refractive Lenses (CRLs) to be precisely aligned and focused. The lateral alignment of CRLs to a beamline requires precise positioning along four axes: two translational, and the two rotational. At a synchrotron, alignment is often accomplished manually. However, XFEL beamlines present a beam brightness that fluctuates stochastically, making manual alignment a time-consuming endeavor. Automation using simplex or classic stochastic descent often fails, given the errant gradient estimates. Herein we present a dynamic-amplitude correction to the usual gradient based on the combination of a generalized finite difference stencil and a time-dependent sampling pattern. Intensity is recorded periodically, then used to normalize numerical derivatives against fluctuations. Error expectation is analyzed, and efficacy is demonstrated on classic benchmarks. We provide a proof of concept by laterally aligning optics on a simulated XFEL beamline using data recorded at both synchrotron and XFEL facilities.

97 MATHEMATICS AND COMPUTING↗

Enabling energy‐efficient manufacturing of pharmaceutical solid oral dosage forms via integrated techno‐economic analysis and advanced process modeling

Abstract The global pharmaceutical industry is a trillion‐dollar market. However, the pharmaceutical sector often lags in manufacturing innovation and automation which limits its potential to maximize energy efficiency. The integration of techno‐economic analysis (TEA) with advanced process models as part of an overarching smart manufacturing platform, can help industries create business models, which can be adapted for manufacturing to reduce energy consumption and operating costs while ensuring product quality which can further enable a more sustainable process operation. In this study, a rational design of experiment on three unit‐operations (wet granulation, drying, and milling) was performed on a batch (case 1) and continuous (case 2) pharmaceutical process to obtain experimental data. Process models for predicting product quality and energy efficiency of each of the three‐unit operations were developed. The experimental data were used to validate the models and good agreement was observed. The energy consumption of each unit operation was calculated using statistical models relating the power consumption and the process parameters. The developed process models and energy models were further integrated into a TEA framework, which quantified the energy and monetary cost of manufacturing for both batch and continuous manufacturing cases. With this integrated framework, energy costs savings of ~33% was obtained in the continuous manufacturing process (case 2) over the batch process (case 1).

Sampat, Chaitanya↗

Machine learning for surrogate process models of bioproduction pathways

Technoeconomic analysis and life-cycle assessment are critical to guiding and prioritizing bench-scale experiments and to evaluating economic and environmental performance of biofuel or biochemical production processes at scale. Traditionally, commercial process simulation tools have been used to develop detailed models for these purposes. However, developing and running such models can be costly and computationally intensive, which limits the degree to which they can be shared and reproduced in the broader research community. This study evaluates the potential of an automated machine learning approach to develop surrogate models based on conventional process simulation models. The analysis focuses on several high-value biofuels and bioproducts for which pathways of production from biomass feedstocks have been well-established. The results demonstrate that surrogate models can be an accurate and effective tool for approximating the cost, mass and energy balance outputs of more complex process simulations at a fraction of the computational expense.

09 BIOMASS FUELS↗

Delivering real-time multi-modal materials analysis with enterprise beamlines

Contemporary advancements in low-cost automation and computation, reduced barrier to entry in developing artificial intelligence/machine learning (AI/ML), and increased ability to represent complex materials in digital form have led to a number of accelerated materials discovery platforms. However, many of these approaches operate with completely rigid vertical integration in an isolated feedback loop using limited modalities. In order to make a substantial impact on discovering new energy materials, AI-driven experiments must operate collaboratively with each other and researchers and over multiple measurement modalities. Herein, we describe the potential for an “internet of things” approach to self-driving enterprise beamlines that merges core information technologies, robotics, and multi-modal AI. The approach will enable full utility of light sources, collaborate effectively with other remote materials acceleration platforms, and help stride toward the world’s energy future.

36 MATERIALS SCIENCE↗

Predicting third-body collision efficiencies for water and other polyatomic baths

Low-pressure-limit microcanonical (collisional activation) and thermal rate constants are predicted using a combination of automated ab initio potential energy surface construction, classical trajectories, transition state theory, and a detailed energy- and angular-momentum-resolved collision kernel. Several systems are considered, including CH 4 (+M) and HO 2 (+M), with an emphasis on systems where experimental information is available for comparison. The a priori approach involves no adjustable parameters, and we show that the predicted thermal rate constants are in excellent agreement with experiments, with average deviations of less than 25%. Notably, the a priori approach is shown to perform equally well for atomic, diatomic, and polyatomic baths, including M = H 2 O, CO 2 , and “fuel” baths like M = CH 4 and NH 3 . Additionally, the utility of microcanonical rate constants for interpreting trends and inferring mechanistic details in the thermal kinetics is demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Role of Blockchains in Multi-Stakeholder Transactive Energy Systems

Power grids are undergoing major changes due to rapid growth in renewable energy and improvements in battery technology. Prompted by the increasing complexity of power systems, decentralized solutions are emerging that arrange local communities into transactive microgrids. This paper addresses the problem of implementing transactive energy mechanisms in a distributed setting, providing both privacy and safety. Specifically, we design and implement an automated auction and matching system that ensures safety (e.g., satisfaction of line capacity constraints), preserves privacy, and promotes local trade and market efficiency for transactive energy systems. This design problem is challenging because safety, market efficiency, and privacy are competing objectives. We implement our solution as a decentralized trading platform built on blockchain technology and smart contracts. To demonstrate the viability of our platform, we analyze the results of experiments with dozens of embedded devices and energy production and consumption profiles using an actual dataset from the transactive energy domain.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Connecting Large‐Scale Meteorological Patterns to Extratropical Cyclones in CMIP6 Climate Models Using Self‐Organizing Maps

Abstract Extratropical cyclones (ETCs) are responsible for the majority of cool‐season extreme events in the northeastern United States (NEUS), often leading to high‐impact weather conditions that can have wide‐ranging socioeconomic impacts. Evaluating the ability of climate models to adequately simulate ETC dynamics is essential for improving model performance and increasing confidence in future projections used by stakeholders and policymakers. ETCs are traditionally studied using techniques such as case studies and synoptic typing, however, these approaches can be time‐consuming, require subjective analysis, and do not necessarily identify the coincident large‐scale meteorological patterns (LSMPs). Here, we apply self‐organizing maps (SOMs) as an automated machine‐learning approach to characterize the LSMPs and associated frequency and intensity of discrete ETC events over NEUS. The dominant patterns of geopotential height variability are identified through SOM analysis of five reanalysis products during the last four decades. ETC events are tracked using TempestExtremes and are integrated with SOMs to classify the accumulated cyclone activity (ACA) associated with each pattern. We then evaluate the skill of CMIP6 historical experiments in simulating the LSMPs and ETC events identified in the SOM. Our results identify a robust bias toward more zonal patterns, with models struggling to reproduce the more amplified patterns typically associated with the highest cyclone activity. While model resolution has some impact on simulation credibility, model configuration appears to be more important in LSMP representation. The vast majority of CMIP6 models produce too few ETCs, although model errors are distributed around historical reanalyses when ACA is normalized by storm frequency.

54 ENVIRONMENTAL SCIENCES↗

Machine learning the metastable phase diagram of covalently bonded carbon

Abstract Conventional phase diagram generation involves experimentation to provide an initial estimate of the set of thermodynamically accessible phases and their boundaries, followed by use of phenomenological models to interpolate between the available experimental data points and extrapolate to experimentally inaccessible regions. Such an approach, combined with high throughput first-principles calculations and data-mining techniques, has led to exhaustive thermodynamic databases (e.g. compatible with the CALPHAD method), albeit focused on the reduced set of phases observed at distinct thermodynamic equilibria. In contrast, materials during their synthesis, operation, or processing, may not reach their thermodynamic equilibrium state but, instead, remain trapped in a local (metastable) free energy minimum, which may exhibit desirable properties. Here, we introduce an automated workflow that integrates first-principles physics and atomistic simulations with machine learning (ML), and high-performance computing to allow rapid exploration of the metastable phases to construct “metastable” phase diagrams for materials far-from-equilibrium. Using carbon as a prototypical system, we demonstrate automated metastable phase diagram construction to map hundreds of metastable states ranging from near equilibrium to far-from-equilibrium (400 meV/atom). We incorporate the free energy calculations into a neural-network-based learning of the equations of state that allows for efficient construction of metastable phase diagrams. We use the metastable phase diagram and identify domains of relative stability and synthesizability of metastable materials. High temperature high pressure experiments using a diamond anvil cell on graphite sample coupled with high-resolution transmission electron microscopy (HRTEM) confirm our metastable phase predictions. In particular, we identify the previously ambiguous structure of n -diamond as a cubic-analog of diaphite-like lonsdaelite phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

hi_class background evolution, initial conditions and approximation schemes

Cosmological datasets have great potential to elucidate the nature of dark energy and test gravity on the largest scales available to observation. Theoretical predictions can be computed with hi_class (www.hiclass-code.net), an accurate, fast and flexible code for linear cosmology, incorporating a wide range of dark energy theories and modifications to general relativity. We introduce three new functionalities into hi_class: (1) Support for models based on covariant Lagrangians, including a constraint-preserving integration scheme for the background evolution and a series of worked-out examples: Galileon, nKGB, quintessence (monomial, tracker) and Brans-Dicke. (2) Consistent initial conditions for the scalar-field perturbations in the deep radiation era, identifying the conditions under which modified-gravity isocurvature perturbations may grow faster than adiabatic modes leading to a loss of predictivity. (3) An automated quasistatic approximation scheme allowing order-of-magnitude improvement in computing performance without sacrificing accuracy for wide classes of models. These enhancements bring the treatment of dark energy and modified gravity models to the level of detail comparable to software tools restricted to standard $\Lambda$CDM cosmologies. Finally, the hi_class code is publicly available (https://github.com/miguelzuma/hi_class_public), ready to explore current data and prepare for next-generation experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

Testing and validating SMDS algorithms implemented in the cloud

Pacific Northwest National Laboratory (PNNL) provided technical assistance to NorthWrite Inc. under the Small Business Vouchers (SBV) Pilot. NorthWrite delivered services to owners of small commercial buildings, using a cloud-based service to monitor, control, and optimize building operations, saving energy and reducing operating costs for the owners while ensuring that occupant comfort needs were consistently met. NorthWrite had a longstanding desire to add a new suite of diagnostic capabilities to their service offering and had been trying, without success, to incorporate several diagnostic algorithms published by PNNL. These algorithms arise from research previously supported by BTO. Through the SBV awarded to NorthWrite, PNNL made available technical knowledge regarding the derivation and application of the following sets of algorithms for use in the NorthWrite Cloud-based service delivery system: • algorithms for monitoring rooftop packaged air conditioners and heat pumps (often referred to as rooftop units or RTUs) and diagnosing faults in these units, • advanced algorithms for automated fault detection and diagnosis of other equipment found in small buildings, and • algorithms for identifying, prioritizing, and assessing the economic effectiveness of implementing energy saving measures in small commercial buildings based on sensed data. The PNNL researchers involved were the original developers of these algorithms, had a unique understanding of the derivation of the algorithms, and had the source data used for this derivation. Further, the PNNL researchers had extensive experience using these algorithms in the laboratory, unique experience applying these algorithms in real-world small commercial buildings and could solve a number of key problems that NorthWrite and other users faced in using these algorithms at scale. In addition, PNNL had recently installed a pair of RTUs in a laboratory setting that were instrumented and connected with data acquisition systems that provided a unique test rig for validating the algorithms before NorthWrite began to deploy their new services in the field.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The Next Stage for Smart Cities: Metrics to Spur an Evolution from Technology for Efficiency to Technology for People's Needs

The Smart Cities movement is about a decade old, energized by the USDOT Smart Cities grant that sparked cities to dream big. Now, 10 years later, and multitudes of conferences and papers later, the biggest question regarding Smart Cities is whether any progress has been made? Smart Cities forums are typically led by the technology sector, either telecommunications, internet access, or most recently artificial intelligence (AI) concerns. Each of these areas have grown and found new applications in the context of Smart Cities, however, these technology applications are just tools toward ends. Do digital communications and assistance enable or foster improved access to real, tactile, non-virtual goods and services such as transportation, food, housing, trash removal, health care, education, social interaction? These and other topics are not 'big tech', but are each critical to quality of life outcomes and are day-to-day necessities, comprising many of the touch points through which citizens interact with municipal agencies. Regarding Smart Cities, relationships have not been fully refined as to how best to merge the emerging generation of technology and related trends with more mundane but essential requirements of tactile services. How should municipal managers and operators bring the range of new technology tools (e.g. on-demand transit, automated vehicles, digital connectivity) to bear to improve functions serving real- physical- non-virtual needs? How do we make cities more efficient in providing access to services and opportunities for improved quality of life? This paper examines the current Smart City movement, emerging trends, and the need to put metrics with respect to the delivery, access, and provision of real-life needs. Using a few case studies of past, present, and projected future scenarios, this paper attempts to bring Smart Cities into the real cities domain, perhaps pushing the moniker away from 'Smart' to 'Efficient' - something that can be measured, counted, and assessed. Through the consideration of the next stage of the evolution of cities from 'Smart' to 'Efficient', the combined efforts and experience of multiple researchers at the NREL and their network of collaborators highlights the need for updates metrics that can be used to start guiding efforts toward productive initiatives to improve quality of life.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Development of a data-driven neural network model for electron thermal transport in NSTX

A data-driven electron thermal transport neural network (ETT-NN) model, trained on TRANSP interpretative analysis results of National Spherical Torus Experiment (NSTX), was developed to enable faster and more accurate ETT computation for spherical tokamaks (STs). The model incorporates both convolutional NNs and recurrent NNs, allowing it to simultaneously account for the spatial and temporal non-localities and multi-scale features of turbulent transport, which have been considered only in a limited manner in conventional models. The model was validated through interpretative analysis and predictive simulations using Tokamak Reactor Integrated Automated Suite for Simulation and Computation, demonstrating relatively high accuracy. Additionally, parameter scans were performed on test discharges known to exhibit specific turbulent modes, such as microtearing mode, trapped electron mode, kinetic ballooning mode, and electron temperature gradient mode. The scanning results revealed that the ETT-NN model exhibits the same trends as those observed in conventional gyrokinetic simulations or theories, while also capturing the global nature of turbulent transport, indicating that the data-driven model accurately reflects the underlying physical characteristics. Furthermore, due to the dimensionless nature of the model, we can feasibly expand its applicability by incorporating data from other devices and uncovering the characteristics of ETT in STs in the future.

NSTX↗

Active sampling of volatile chemicals for non-invasive classification of chicken eggs by sex early in incubation

According to industry estimates, approximately 7 billion day-old male chicks are disposed of annually worldwide because they are not of use to the layer industry. A practical process to identify the sex of the egg early in incubation without penetrating the egg would improve animal welfare, reduce food waste and mitigate environmental impact. We implemented a moderate vacuum pressure system through commercial egg-handling suction cups to collect volatile organic compounds (VOCs). Three separate experiments were set up to determine optimal conditions to collect eggs VOCs to discriminate male from female embryos. Optimal extraction time (2 min), storage conditions (short period of incubation during egg storage (SPIDES) at days 8–10 of incubation), and sampling temperature (37.5°C) were determined. Our VOC-based method could correctly differentiate male from female embryos with more than 80% accuracy. These specifications are compatible with the design of specialized automation equipment capable of high-throughput, in-ovo sexing based on chemical sensor microchips.

Borras, Eva↗