Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Advanced Computing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Context-aware learning of hierarchies of low-fidelity models for multi-fidelity uncertainty quantification

Multi-fidelity Monte Carlo methods leverage low-fidelity and surrogate models for variance reduction to make tractable uncertainty quantification even when numerically simulating the physical systems of interest with high-fidelity models is computationally expensive. This work proposes a context-aware multi-fidelity Monte Carlo method that optimally balances the costs of training low-fidelity models with the costs of Monte Carlo sampling. It generalizes the previously developed context-aware bi-fidelity Monte Carlo method to hierarchies of multiple models and to more general types of low-fidelity models. When training low-fidelity models, the proposed approach takes into account the context in which the learned low-fidelity models will be used, namely for variance reduction in Monte Carlo estimation, which allows it to find optimal trade-offs between training and sampling to minimize upper bounds of the mean-squared errors of the estimators for given computational budgets. This is in stark contrast to traditional surrogate modeling and model reduction techniques that construct low-fidelity models with the primary goal of approximating well the high-fidelity model outputs and typically ignore the context in which the learned models will be used in upstream tasks. Further, the proposed context-aware multi-fidelity Monte Carlo method applies to hierarchies of a wide range of types of low-fidelity models such as sparse-grid and deep-network models. Numerical experiments with the gyrokinetic simulation code Gene show speedups of up to two orders of magnitude compared to standard estimators when quantifying uncertainties in small-scale fluctuations in confined plasma in fusion reactors. This corresponds to a runtime reduction from 72 days to four hours on one node of the Lonestar6 supercomputer at the Texas Advanced Computing Center.

42 ENGINEERING↗
DOE OSTI2023

Nonvolatile Memristive Effect in Few-Layer CrI 3 Driven by Electrostatic Gating

The potential of memristive devices for applications in nonvolatile memory and neuromorphic computing has sparked considerable interest, particularly in exploring memristive effects in two-dimensional (2D) magnetic materials. However, the progress in developing nonvolatile, magnetic field-free memristive devices using 2D magnets has been limited. In this work, we report an electrostatic-gating-induced nonvolatile memristive effect in CrI 3 -based tunnel junctions. The few-layer CrI 3 -based tunnel junction manifests notable hysteresis in its tunneling resistance as a function of gate voltage. We further engineered a nonvolatile memristor using the CrI 3 tunneling junction with low writing power and at zero magnetic field. We show that the hysteretic transport observed is not a result of trivial effects or inherent magnetic properties of CrI 3 . We propose a potential association between the memristive effect and the newly predicted ferroelectricity in CrI 3 via gating-induced Jahn–Teller distortion. Furthermore, our work illuminates the potential of 2D magnets in developing next-generation advanced computing technologies.

2D magnet↗
DOE OSTI2022

A level-of-details framework for representing occupant behavior in agent-based models

We report agent-based modeling is an advanced computational technique capable of representing complex and dynamic processes of human behavior in building performance simulation. Though the agent-based approach supports diverse applications concerning human behavior modeling within the built environment, there is no consensus on the optimal amount of information or level of granularity needed for occupant information representation. This paper attempts to formalize the level of details (LoD) needed for occupant behavior representation in agent-based environments. A novel framework, grounded on the concept of LoD, is proposed to select the required details in representing occupants in agent-based models. Ten attributes related to occupants' presence, movement, behavioral processes, and repertoire are considered to define the LoD. The framework identifies use case parameters as the guiding principle and allows a hybrid approach for selecting varying degrees of occupant attributes to serve the purpose of simulation. A discussion on the pertinence of different occupant behavior LoDs in relation to the desired objective and simulation context is also presented. The study intends to support the occupant behavior research by advancing agent-based occupant modeling in building performance simulation.

42 ENGINEERING↗
DOE OSTI2022

Two-Stage Reinforcement Learning Policy Search for Grid-Interactive Building Control

This paper develops an intelligent grid-interactive building controller, which optimizes building operation during both normal hours and demand response (DR) events. To avoid costly on-demand computation and to adapt to non-linear building models, the controller utilizes reinforcement learning (RL) and makes real-time decisions based on a near-optimal control policy. Learning such a policy typically amounts to solving a hard non-convex optimization problem. We propose to address this problem with a novel global-local policy search method. In the first stage, an RL algorithm based on zero-order gradient estimation is leveraged to search for the optimal policy globally, due to its scalability and the potential to escape some poor performing local optima. The obtained policy is then fine-tuned locally to bring the first-stage solution closer to that of the original unsmoothed problem. Experiments on a simulated five-zone commercial building demonstrate the advantages of the proposed method over existing learning approaches. They also show that the learned control policy outperforms a pragmatic linear model predictive controller (MPC) and approaches the performance of an oracle MPC in testing scenarios. Using a state-of-the-art advanced computing system, we demonstrate that the controller can be learned and deployed within hours of training.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2016

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Numerical Simulation of Critical Factors Controlling Heat Extraction from Geothermal Systems Using a Closed-Loop Heat Exchange Method

Closed-loop heat exchange for geothermal energy production involves injecting working fluid down a well that extends through the geothermal resource over a significant length to absorb heat by conduction through the well pipe. The well then needs to return to the surface for energy recovery and fluid re-injection to complete the cycle. We have carried out mixed convective-conductive fluid-flow modeling using a wellbore flow model for TOUGH2 called T2Well to investigate the critical factors that control closed-loop geothermal energy recovery. T2Well solves a mixed explicit-implicit set of momentum equations for flow in the pipe with full coupling to the implicit three-dimensional integral finite difference equations for Darcy flow in the porous medium. T2Well has the option of modeling conductive heat flow from the porous medium to the pipe by means of a semi-analytical solution which makes the computation very efficient because the porous medium does not have to be discretized. When the fully three-dimensional option is chosen, the porous medium is discretized and heat flow to the pipe is by conduction and convection, depending on reservoir permeability and other factors. Simulations of the closed-loop system for a variety of parameter values have been carried out to elucidate the heat recovery process. To the extent that convection may occur to aid in heat delivery to the pipe, the permeability of the geothermal reservoir, whether natural or stimulated, is an important property in heat extraction. The injection temperature and flow rate of the working fluid strongly control the ultimate energy recovery. Pipe diameter also plays a strong role in heat extraction, but is correlated with flow rate. Similarly, the choice of working fluid plays an important role, with water showing better heat extraction than CO2 for certain flow rates, while the CO2 has higher pressure at the production wellhead which can aid in surface energy recovery. In general, we find complex interactions between the critical factors that will require advanced computational approaches to fully optimize.

Oldenburg, Curtis↗
DOE OSTI2019

Probabalistic Modeling of Minibangs and Megabands (Final Report)

This project was original proposed as a fundamental advance in the treatment of probabilistic modeling as it applies to nuclear fission calculations of nuclear database inputs and produced particle distributions in heavy-ion collisions. However, funding decisions made within LLNL and the DOE Office of Science led to the project proceeding through three distinct stages. The first two, probabilistic calculations of the fission and jet energy loss relate follow directly from the proposed research. The fission task led to the development of a proof-of-principle Gaussian Process Emulator for time-dependent generator coordinate method (TDGCM) calculation for the fission of Pu-240. To study energy loss in heavy-ion collisions with a probabilistic model, we generated a training data set using the Pythia event generator superimposed on a heavy-ion background with a single quench-factor parameter. We then used kernel density estimation (KDE) to recover the distribution of quench-factors for a calibration data set. In the third stage, we proceeded to work through collaborations, collecting new data within the ATLAS experiment at the Large Hadron Collider (LHC), and further developing bayesian methodology within the Jet Energy-loss Tomography with a Statistically and Computationally Advanced Program Envelope (JETSCAPE) Collaboration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Artificial intelligence-driven approaches for materials design and discovery

Materials design is an important component of modern science and technology, yet traditional approaches rely heavily on trial and error and can be inefficient. Computational techniques, enhanced by modern artificial intelligence, have reshaped the landscape of designing new materials. Among these approaches, inverse design has shown great promise in designing materials that meet specific property requirements. Here, in this Review, we present key computational advances in materials design over the past few decades. We follow the evolution of relevant materials design techniques, from high-throughput forward machine learning methods and evolutionary algorithms, to advanced artificial intelligence strategies such as reinforcement learning and deep generative models. We highlight the paradigm shift from conventional screening approaches to inverse generation driven by deep generative models. Finally, we discuss current challenges and future perspectives of materials inverse design. This Review may serve as a brief guide to the approaches, progress and outlook of designing future functional materials with technological relevance.

computational methods↗
DOE OSTI2025

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗
DOE OSTI2020

Experimental Study on the Effect of Localized Blockages on the Friction Factor of a 61-Pin Wire-Wrapped Bundle

Abstract The thermal-hydraulic behavior of the flow in rod bundles has motivated numerous experimental and computational investigations. Previous studies have identified potential for accumulation of debris within the small subchannels of typical wire-wrapped assemblies with subsequent total or partial blockage of subchannel coolant flow. A test campaign was conducted to study the effects of localized blockages on the bundle averaged friction factor of a tightly packed wire-wrapped rod bundle. Blockages were installed within the bundle, and fluid pressure drop was measured across one wire pitch for a Reynolds number range of 500–17,200. The Darcy–Weisbach friction factor of the perturbed rod bundle geometry was compared with that of the unblocked bundle, as well as with the predictions of a well-established friction factor correlation. Differing effects based on blockage size and location for various flow regimes were studied. A number of conclusions can be made about the effects of the blockages on the friction factor, such as an increasing effect of the blockage on friction factor with an increase in Reynolds number, a change in flow behavior in the turbulent transition flow regime near Reynolds number 3000, differences in effect on friction factor for different types of subchannel blockage, and a nonlinear trend in friction factor variation with flow area impeded for edge subchannels. To this end, all data and quantified uncertainty produced in this study are made available for comparison and validation of advanced computational tools.

Engineering↗
DOE OSTI2012

Status of the Short-Pulse X-ray Project at the Advanced Photon Source

The Advanced Photon Source Upgrade (APS-U) Project at Argonne will include generation of short-pulse x-rays based on Zholents deflecting cavity scheme. We have chosen superconducting (SC) cavities in order to have a continuous train of crabbed bunches and flexibility of operating modes. In collaboration with Jefferson Laboratory, we are prototyping and testing a number of single-cell deflecting cavities and associated auxiliary systems with promising initial results. In collaboration with Lawrence Berkeley National Laboratory, we are working to develop state-of-the-art timing, synchronization, and differential rf phase stability systems that are required for SPX. Collaboration with Advanced Computations Department at Stanford Linear Accelerator Center is looking into simulations of complex, multi-cavity geometries with lower- and higher-order modes waveguide dampers using ACE3P. This contribution provides the current R&D status of the SPX project.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

First principles reactive simulation for equation of state prediction

The high cost of density functional theory (DFT) has hitherto limited the ab initio prediction of the equation of state (EOS). In this article, we employ a combination of large scale computing, advanced simulation techniques, and smart data science strategies to provide an unprecedented ab initio performance analysis of the high explosive pentaerythritol tetranitrate (PETN). Comparison to both experiment and thermochemical predictions reveals important quantitative limitations of DFT for EOS prediction and thus the assessment of high explosives. In particular, we find that DFT predicts the energy of PETN detonation products to be systematically too high relative to the unreacted neat crystalline material, resulting in an underprediction of the detonation velocity, pressure, and temperature at the Chapman–Jouguet state. The energetic bias can be partially accounted for by high-level electronic structure calculations of the product molecules. Furthermore we demonstrate a modeling strategy for mapping chemical composition across a wide parameter space with limited numerical data, the results of which suggest additional molecular species to consider in thermochemical modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Building Towards Discovery: Preparing for New Physics at the LHC [Final papers]

Particle physics today is at a crossroads. The Standard Model (SM) has survived four decades of experimental scrutiny and spurred multiple landmark discoveries, culminating with the 2012 discovery of the Higgs boson at the Large Hadron Collider (LHC). Yet we know that this model is incomplete. We live in a universe dominated by matter and energy unaccounted for by the SM– and the Higgs boson itself is improbably light. It falls to the current generation of high-energy physicists to go beyond the model and enter a new era of discovery. Andeen is leading a new research group at the University of Texas at Austin (UT-Austin) that is endeavoring to reveal novel physical phenomena through the discovery of new particles with the ATLAS detector at the LHC. A key element of our experience thus far has been collaborating closely with theorists to identify both interesting new physics models. In addition we work closely with electrical engineers in detector development. Our approach is therefore unique in its integration of theory, analysis and instrumentation, and is encapsulated in a three-pronged strategy. First is the essential task of analyzing our rapidly expanding dataset. I am directing my group in searches for vector-like quarks (VLQs). Should they exist, these hypothetical particles would indicate physics scenarios beyond the SM. Experimental constraints suggest VLQs decay preferentially to a third generation quark and a Higgs, W or Z boson. Today at 13 TeV, both multi-lepton (electron and muon) and jet substructure signatures are sensitive to identifying the VLQ decay products. The large Run 2 dataset (collected through 2018) of up to 150 fb -1 will allow us to simultaneously use multi-lepton signatures with jet-substructure in searches for new physics. UT-Austin is well positioned to be a leader in this area. Prof. P. Onyisi’s postdoctoral researchers and graduate students are searching for ttH signatures in three- and four-lepton channels and we benefit from their experience. We are also aided by the availability of the Texas Advanced Computing Center, which provides us with easy access to several high performance computing (HPC) systems. My previous experience in VLQ searches propels the work today. I have published both the first investigation into the single production of top partners (signatures of composite Higgs Models) of any LHC experiment 1 as well as one of the first analyses utilizing jet-substructure techniques to search for the single production of vector-like quarks. 2 Adding to this is my group’s work with the Liquid Argon (LAr) calorimeter, the primary instrument we use in detecting electrons. Second, my group is contributing to the operations of the LAr calorimeter while preparing to install and commission new electronic hardware (the Phase 1 upgrade) to this crucial component of the ATLAS detector. I have played a leading role in the development of a critical, radiation-hard, high-speed Analog-to-Digital Convertor (ADC) that is essential inselecting data collected by the LAr calorimeter. 3 This upgrade will improve the e!ciency with which we can select events in our detector. Postdoctoral researcher N. Nikiforou (based at CERN May 2016 onward) and graduate students (one based at CERN from the start of 2018 onward, with one additional graduate students from summer 2018) are growing our already deep experience in the operation of the LAr calorimeter to prepare for installation and commissioning of the new trigger readout in 2018-2019. My group will then be positioned to be the first to exploit the potential of the improved triggers in our multi-lepton searches for new physics. Third, a suite of preparations for a major detector upgrade, scheduled to be completed in 2024, are underway. My group is building hardware that will improve the electronic readout of the ATLAS detector. I am partnering with a group in the Electrical and Computer Engineering (ECE) Department at UT-Austin (Prof. N. Sun) to employ his work at the cutting edge of ADC research. We will support an ECE grad student for the layout of this design, and collaborate with engineering groups at Nevis Laboratory and the Electrical Engineering Department (Prof. P. Kinget) at Columbia University to integrate our ADC with gain selection circuits. We will provide this critical component of the ASIC at the challenging boundary of the analog and digital signals in the LAr calorimeter readout chain. Furthermore UT-Austin will lead the testing of this device during development and production (approximately 55,000 four-channel chips). This effort compliments my work as the deliverables manager for the LAr front-end ASICs for the US ATLAS HL-LHC project and strengthens the US commitment to that upgrade.In so doing, my group at the UT-Austin will be at the forefront of efforts to probe the structure of the universe to an unmatched degree both at the current LHC and with its future upgrades. Through both the ongoing analysis of data at the ATLAS detector and improvements to the detector itself, an answer to what lies beyond the SM may come within our grasp. My background in instrumentation and analysis allows my group to establish a singular research effort on the ATLAS experiment. In addition to answering fundamental questions about the subatomic world, the technologies developed could advance the broader scientific community and result in valuable spin-offs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Automatic Imagery Data Analysis for Proactive Computer-Based Workflow Management during Nuclear Power Plant Outages

This report is being submitted for the task “Final Report” of DOE NEUP Project 15-8121 “Automatic Imagery Data Analysis for Proactive Computer-Based Workflow Management during Nuclear Power Plant Outages.” Typical nuclear power plant (NPP) outages always involve thousands of maintenance and refueling activities and a large number of workers in limited workspaces, while having tight schedules and zero-tolerance for accidents. During an outage, thousands of workers will be working in various workspaces across the NPP. High outage costs and expensive delays (approximately 1.5 million dollars of loss per day of delay) in NPP maintenance demand tight outage schedules. In packed workspaces, an automatic system that monitors human behaviors in real-time and provides insights about current and pending schedule deviations from the plan is critical for ensuring: 1) effective collaboration among workers and worker teams from different trades; 2) less waste of time and resources due to the lack of situational awareness; and 3) proactive outage project control. The overall goal of this project is to test the hypothesis that real-time imagery-based object tracking and spatial analysis, as well as human behavior modeling of outage participants, will significantly improve the efficiency of outage control while lowering the rates of accidents and incidents. Three objectives of this project are: 1) Establish real-time object tracking and spatiotemporal analysis methods that automatically assess the productivity of field activities and detect anomalous spatiotemporal relationships among activities that cause inefficiencies and risks; 2) Establish realtime human tracking and human factor modeling methods for automatically diagnosing unexpected actions of and interactions between outage participants, those which cause inefficient collaborations between Advanced Outage Control Center (AOCC), satellite outage centers, NPP workers, and maintenance service providers; and 3) Test the proposed automated object tracking, human behavior modeling, and spatiotemporal analysis methods in outage control case studies in order to characterize the effectiveness of automated imagery-data-driven methods in proactively improving the efficiency and safety of workflows in outage coordination and risk management. Recent studies of detailed human behavior monitoring on construction sites have examined the potential of applying advanced computer vision algorithms in detecting and tracking anomalous workers (i.e., workers who do not wear hard hats or safety vests) for ensuring job site safety. Some studies of human factor studies revealed the importance of modeling detailed interactions between individuals within and across teams in better understanding the impact of human in proactive project control. Other studies in the construction domain have developed computational simulation frameworks that formalize detailed spatiotemporal interactions between tasks in order to simulate the impacts of individual tasks on the performance of workflows. While integrated analyses that combine human factor assessment, as well as image processing and simulation, are in demand for effective decision-making, limited studies have examined the potential of such integrated analyses in NPP outage control. This research project has examined an automatic outage monitoring and control system that integrates human factor analysis, computer vision techniques, and simulation methods in order to enable engineers to better understand the interactions between humans, resources, and workflows during outage processes. The project aims at providing NPP maintenance agencies insights into more efficient use of limited resources in extending the life of a nuclear plant, as well as reducing waste while ensuring sufficient generation of electricity. This study is significant for the safety of nuclear plants, sustainable electricity generation for livable communities, and cost savings for maintaining electricity infrastructures in the United States.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Accomplishments of Sandia and Kitware CMake/CTest/CDash Contract for (FY2017-2020)

We describe the accomplishments jointly achieved by Kitware and Sandia over the fiscal years 2016 through 2020 to benefit the Advanced Scientific Computed (ASC) Advanced Technology Development and Mitigation (ATDM) project. As a result of our collaboration, we have improved the Trilinos and ATDM application developer experience by decreasing the time to build, making it easier to identify and resolve build and test defects, and addressing other issues . We have also reduced the turnaround time for continuous integration (CI) results. For example, the combined improvements likely cut the wall clock time to run automated builds of Trilinos posting to CDash by approximately 6x or more in many cases. We primarily achieved these benefits by contributing changes to the Kitware CMake/CTest/CDash suite of open source software development support tools. As a result, ASC developers can now spend more time improving code and less time chasing bugs. And, without this work, one can argue that the stabilization of Trilinos for the ATDM platforms would not have been feasible which would have had a large negative impact on an important internal FY20 L1 milestone.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The Challenging World of Simple Inorganic Rings: Revisiting Roesky's Ketone and Roesky's Sulfoxide

Abstract The surprising differences between the experimental solid‐state and calculated gas‐phase structures of 5‐oxo‐1,3,2,4‐dithiadiazole (Roesky's ketone,1) and 1‐oxo‐1,2,4,3,5‐trithiadiazole (Roesky's sulfoxide,2), identified and studied in a series of papers published between 2004 and 2010 but then never satisfactorily explained, have been revisited, making use of the more advanced computational possibilities currently available. The previous calculations’ considerable overestimations of the C−S and S−S bond lengths in1and2, respectively, have been partly explained based on the results of periodic calculations and the application of Valence Bond (VB) Theory. In the case of1, the crystal environment appears to stabilize a structure with a highly polarized C=O bond, which features a C−S bond with considerable double‐bond character – an effect which does not exist for the isolated molecule – explaining the much shorter bond in the solid state. For2, a similar conclusion can be drawn for the S−S distance. For both compounds, though, packing effects are not the sole source of the differences: the inability of Density Functional Theory (DFT) to properly deal with the electronic structures of these apparently simple main‐group systems remains a contributing factor.

Chemistry↗
DOE OSTI2020

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2

Motion-activated wildlife cameras (or “camera traps”) are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the “species model,” and one that determines if an image is empty or if it contains an animal, the “empty-animal model.” Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%–91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%–94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Abstract Host‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

59 BASIC BIOLOGICAL SCIENCES↗