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Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification

We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Historical Documentation of Buildings 0460 and 0463 at Technical Area 16 (Volume 1)

This report provides documentation as a standard mitigation measure to the adverse effects that occurred by the demolition of theses historic properties. To mitigate the adverse effects, LANL has followed Section 106 process contained in 36 CFR 800.6, resolution of adverse effects. In addition to these regulations and within this report, LANL has implemented the standards for documenting and reporting in accordance with the A Plan for the Management of the Cultural Heritage at Los Alamos National Laboratory, New Mexico (CRMP), LA-UR-19-21590, formerly LA-UR-15-27624. These standard reporting measures include archival-quality digital photographs of the building’s interior, exterior, outside landscape; updating LANL historic building survey forms including 11 in. x 17 in. copies (in a reduced scale) of key original and as-built drawings; identification and documentation of historically significant equipment and artifacts; a comprehensive list of LANL architectural drawings; construction-history maps of TA-16 including current Register Eligible and Ineligible Buildings; and a detailed use history of the building and technical division associated with its operation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Merefa Community Microgrid: Supporting Distributed Energy Resource Deployment in Ukraine

A conceptual design is described for a community microgrid in Ukraine. Microgrid resources include solar photovoltaics, battery energy storage, and conventional natural gas fueled reciprocating engine generators. The conceptual architecture was informed by the microgrid developer, NREL subject matter experts, and the application of REopt, an NREL-developed software tool created for identification of least-cost combination of resources for achieving cost savings, resilience, and renewable energy goals. This fact sheet is a summary of a previously published technical report; see NREL/TP-7A40-89527, which includes conceptual architecture, estimates of key summary financial metrics, and sequence of operations.

battery storage↗

ESI-MS Identification of the Cationic Phosphine-Ligated Gold Clusters Au1-Au22: Insight into the Gold-Ligand Ratio and Abundance of Larger Clusters

Triphenylphosphine (PPh3)-ligated gold clusters offer promising potential applications due to their relative ease of synthesis and usefulness in forming advanced cluster architectures. While previous studies reported cationic PPh3-ligated gold clusters with core sizes of Au1 - Au4, Au6 - Au11, and Au¬13 - Au14, there has not been definitive identification by mass spectrometry of larger clusters in the Au12 - Au25¬ range. Herein, we survey a polydisperse solution of cationic PPh3-ligated gold clusters using high mass-resolution (M/?M = 60,000) electrospray ionization mass spectrometry (ESI-MS). To improve the sensitivity and mass resolution of larger clusters for unambiguous identification, we increased the number of scan averages and reduced the range of mass collection windows to 200 m/z, thereby mitigating potential mass and ion abundance bias resulting from smaller “building block” gold clusters and other solution components present in higher abundance. In addition to the previously reported clusters, we identified several new species including Au5(PPh3)5+, Au12(PPh3)9HCl2+, Au15(PPh3)9Cl2+, Au16(PPh3)10Cl22+, Au17(PPh3)113+, Au18(PPh3)102+, Au19(PPh3)10Cl2+, Au20(PPh3)12H33+, Au21(PPh3)10Cl2+, and Au22(PPh3)10Cl22+, indicating that a full range of clusters between Au1 - Au22 may be observed in a single polydisperse solution. Considering all of the observed clusters, our findings provide evidence that the “magic number” icosahedral Au13 may be the transition point in cluster growth between smaller clusters, exhibiting a 1:1 gold-to-ligand ratio, and larger clusters, wherein subsequent gold atoms are added to the core without an equal number of accompanying ligands. Our method demonstrates that reducing the range of m/z collection windows and increasing the number of scan averages can improve instrument sensitivity for cationic gold clusters and enable a more complete survey of polydisperse solutions, thereby providing new insights to guide and validate the results of other characterization methods and theoretical calculations. This work was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MH acknowledges support from the DOE Science Undergraduate Laboratory Internship (SULI) program. HH acknowledges support from the DOE Office of Workforce Development for Teachers and Scientist (WDTS) under the Visiting Faculty Program (VFP). This work was performed using EMSL, a national scientific user facility sponsored by the DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle.

Hewitt, Michael↗

Materials loss measurements using superconducting microwave resonators

The performance of superconducting circuits for quantum computing is limited by materials losses. In particular, coherence times are typically bounded by two-level system (TLS) losses at single photon powers and millikelvin temperatures. The identification of low loss fabrication techniques, materials, and thin film dielectrics is critical to achieving scalable architectures for superconducting quantum computing. Superconducting microwave resonators provide a convenient qubit proxy for assessing performance and studying TLS loss and other mechanisms relevant to superconducting circuits such as non-equilibrium quasiparticles and magnetic flux vortices. In this review article, we provide an overview of considerations for designing accurate resonator experiments to characterize loss, including applicable types of losses, cryogenic setup, device design, and methods for extracting material and interface losses, summarizing techniques that have been evolving for over two decades. Results from measurements of a wide variety of materials and processes are also summarized. Finally, we present recommendations for the reporting of loss data from superconducting microwave resonators to facilitate materials comparisons across the field.

47 OTHER INSTRUMENTATION↗

SkX_NN: Neural Network for skyrmion identification in Lorentz TEM

A neural network for segmenting and processing Lorentz TEM images of skyrmion lattices. This software based on U-Net architecture is capable of identifying skyrmions in out-of-focus Lorentz TEM images based on training data. This isspecifically useful for analyzing large area data from in-situ experiments.

PHATAK, CHARUDATTA↗

High-bandwidth image-based predictive laser stabilization via optimized Fourier filters

Controlling the delivery of kHz-class pulsed lasers is of interest in a variety of industrial and scientific applications, from next-generation laser-plasma acceleration to laser-based x-ray emission and high-precision manufacturing. The transverse position of the laser pulse train on the application target is often subject to fluctuations by external drivers (e.g., room cooling and heating systems, motorized optics stages and mounts, vacuum systems, chillers, and/or ground vibrations). For typical situations where the disturbance spectrum exhibits discrete peaks on top of a broad-bandwidth lower-frequency background, traditional PID (proportional-integral-derivative) controllers may struggle, since as a general rule PID controllers can be used to suppress vibrations up to only about 5%–10% of the sampling frequency. Here, a predictive feed-forward algorithm is presented that significantly enhances the stabilization bandwidth in such laser systems (up to the Nyquist limit at half the sampling frequency) by online identification and filtering of one or a few discrete frequencies using optimized Fourier filters. Furthermore, the system architecture demonstrated here uses off-the-shelf CMOS cameras and piezo-electric actuated mirrors connected to a standard PC to process the alignment images and implement the algorithm. To avoid high-end, high-cost components, a machine-learning-based model of the piezo mirror’s dynamics was integrated into the system, which enables high-precision positioning by compensating for hysteresis and other hardware-induced effects. A successful demonstration of the method was performed on a 1 kHz laser pulse train, where externally-induced vibrations of up to 400 Hz were attenuated by a factor of five, far exceeding what could be done with a standard PID scheme.

Natal, Joseph↗

Distance-Weighted Graph Neural Networks on FPGAs for Real-Time Particle Reconstruction in High Energy Physics

Graph neural networks have been shown to achieve excellent performance for several crucial tasks in particle physics, such as charged particle tracking, jet tagging, and clustering. An important domain for the application of these networks is the FGPA-based first layer of real-time data filtering at the CERN Large Hadron Collider, which has strict latency and resource constraints. We discuss how to design distance-weighted graph networks that can be executed with a latency of less than one μs on an FPGA. To do so, we consider a representative task associated to particle reconstruction and identification in a next-generation calorimeter operating at a particle collider. We use a graph network architecture developed for such purposes, and apply additional simplifications to match the computing constraints of Level-1 trigger systems, including weight quantization. Using the hls4ml library, we convert the compressed models into firmware to be implemented on an FPGA. Performance of the synthesized models is presented both in terms of inference accuracy and resource usage.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Scalable Hybrid Large-Scale dc-ac Grid Analysis Methods (Phase II)

The goals of the project included the identification and evaluation of a voltage source converter multiterminal high-voltage direct current (VSC-MTdc) system architecture suitable for a high amount of power transfer through long transmission lines.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Identifying Transient Candidates in the Dark Energy Survey Using Convolutional Neural Networks

The ability to discover new transient candidates via image differencing without direct human intervention is an important task in observational astronomy. For these kind of image classification problems, machine learning techniques such as Convolutional Neural Networks (CNNs) have shown remarkable success. In this work, we present the results of an automated transient candidate identification on images with CNNs for an extant data set from the Dark Energy Survey Supernova program, whose main focus was on using Type Ia supernovae for cosmology. By performing an architecture search of CNNs, we identify networks that efficiently select non-artifacts (e.g., supernovae, variable stars, AGN, etc.) from artifacts (image defects, mis-subtractions, etc.), achieving the efficiency of previous work performed with random Forests, without the need to expend any effort in feature identification. The CNNs also help us identify a subset of mislabeled images. Performing a relabeling of the images in this subset, the resulting classification with CNNs is significantly better than previous results, lowering the false positive rate by 27% at a fixed missed detection rate of 0.05.

79 ASTRONOMY AND ASTROPHYSICS↗

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗

Identification of localized radiation damage in power MOSFETs using EBIC imaging

The rapidly increasing use of electronics in high-radiation environments and the continued evolution in transistor architectures and materials demand improved methods to characterize the potential damaging effects of radiation on device performance. Here, electron-beam-induced current is used to map hot-carrier transport in model metal-oxide semiconductor field-effect transistors irradiated with a 300 KeV focused He + beam as a localized line spanning across the gate and bulk Si. By correlating the damage to the electronic properties and combining these results with simulations, the contribution of spatially localized radiation damage on the device characteristics is obtained. Furthermore, this identified damage, caused by the He + beam, is attributed to localized interfacial P b centers and delocalized positive fixed-charges, as surmised from simulations. Comprehension of the long-term interaction and mobility of radiation-induced damage are key for future design of rad-hard devices.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Acoustic-based monitoring and machine learning of component status for microreactor applications

This report provides a description and assessment of recent efforts to couple acoustic-based experimental measurements and characterization with machine learning models in order to enhance structural health monitoring capabilities for nuclear microreactors. With resilient embedded sensors in development by others supported by programs funded by the US Department of Energy’s Office of Nuclear Energy, the work described herein builds upon ongoing efforts to improve non-destructive testing technology that relates measured acoustic signatures to component stresses and/or structural defects, using a combination of new experimental measurements and machine learning architectures. The experimental procedure remained similar to that developed for the previous year’s demonstration of damage detection by the authors, with the same damaged sample tested under similar applied stress conditions. Notably, a new mounting fixture was designed and implemented to improve measurement consistency and a more sophisticated laser Doppler vibrometer was employed to make high-fidelity vibration measurements. Two nominally identical sets of training data were collected for each experimental setup to better understand the repeatability of the experiment and to better test the generality of trained neural network models. Additionally, we obtained new high-quality 3D mode shapes of the damaged test article at various stress and excitation levels, providing greater insights into the physical response of the sample during testing. Previously, we demonstrated that a machine learning model based on a convolutional neural network can predict structural details of an artificially introduced interface (intact, rough cut, smooth cut), and the applied torque level. In this study, we have transitioned to graph-based neural network architectures to better develop and test a flexible framework that is more suitable to being transferred away from controlled benchtop experiments and into more applied settings where less-structured data inputs may be expected. In general, performance testing of a graph neural network on frequency-domain representations of the data indicates strong and consistent identification of test conditions for datasets recorded on damaged components. With goals of predicting damage location and other changing experimental conditions using limited datasets, predictive models using a graph neural network architecture correctly predicted the applied torque level with an accuracy of 85% using only a single measurement point and predicted within one torque level in 95% of test windows. Predictions of damage location had limited success due to the symmetry and minimal number of the damage scenarios presented during model training. Results were ambiguous as to whether the model could detect the location of the artificial damage, or if it was instead learning the location of a given measurement point on the part and subsequently detecting which points were closest to the location of the damage. This finding will be factored into upcoming planned work on damaged graphite components, where new experimental tests with a larger number and variety of damage scenarios are expected to provide improved validation of recent developments in monitoring methodology.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The genetic architecture of biomechanical traits in sorghum

Sorghum bicolor (L.) Moench is the fifth most commonly grown cereal crop worldwide with unrivaled drought tolerance compared with other cereal crops. Drought and heat tolerance and high biomass yield potential make sorghum a promising bioenergy crop. However, stem lodging is a significant problem that results in substantial yield losses. Stem biomechanical traits influence the mechanical stability of crops and breeding for desirable biomechanical traits may result in improved lodging resistance. In this study, we report the identification of quantitative trait loci (QTL) for stem mechanical and morphological traits in three recombinant inbred line (RIL; populations from Tx623/Rio, Tx623/Della, and Tx631/Della) crosses between elite grain and sweet sorghum parents. The genetic architecture of stem biomechanical traits in the three RIL populations is multigenic and pleiotropic. Additionally, eight QTL affecting mechanical and morphological traits were detected; two main effects of these QTL were consistently found in all populations and colocated with previously identified dwarfing genes Dw1 and Dw3. These results indicate that dwarfing genes affect the mechanical properties of sorghum stems and their lodging resistance, while also having demonstrable effects on stem morphology. The identification of these QTL provides new opportunities for improving stem lodging resistance via genomics-assisted breeding.

59 BASIC BIOLOGICAL SCIENCES↗

Accelerating End-to-End Deep Learning for Particle Reconstruction using CMS open data

Machine learning algorithms are gaining ground in high energy physics for applications in particle and event identification, physics analysis, detector reconstruction, simulation and trigger. Currently, most data-analysis tasks at LHC experiments benefit from the use of machine learning. Incorporating these computational tools in the experimental framework presents new challenges. This paper reports on the implementation of the end-to-end deep learning with the CMS software framework and the scaling of the end-to-end deep learning with multiple GPUs. The end-to-end deep learning technique combines deep learning algorithms and low-level detector representation for particle and event identification. We demonstrate the end-to-end implementation on a top quark benchmark and perform studies with various hardware architectures including single and multiple GPUs and Google TPU.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tuning magnetic antiskyrmion stability in tetragonal inverse Heusler alloys

The identification of materials supporting complex, tunable magnetic order at ambient temperatures is foundational to the development of new magnetic device architectures. In this work, we report the design of Mn 2 XY tetragonal inverse Heusler alloys that are capable of hosting magnetic antiskyrmions whose stability is sensitive to elastic strain. Here We first construct a universal magnetic Hamiltonian capturing the short- and long-range magnetic order which can be expected in these materials. This model reveals critical combinations of magnetic interactions that are necessary to approach a magnetic phase boundary, where the magnetic structure is highly susceptible to small perturbations such as elastic strain. We then computationally search for quaternary Mn 2 (X 1 , X 2 ) Y alloys where these critical interactions may be realized and which are likely to be synthesizable in the inverse Heusler structure. We identify the Mn 2 Pt 1–z X z Ga family of materials with X = Au, Ir, Ni as an ideal system for accessing all possible magnetic phases, with several critical compositions where magnetic phase transitions may be actuated mechanically.

36 MATERIALS SCIENCE↗

Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin ‘egg-box’ structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. Here, these changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

36 MATERIALS SCIENCE↗

Voxel carving–based 3D reconstruction of sorghum identifies genetic determinants of light interception efficiency

Changes in canopy architecture traits have been shown to contribute to yield increases. Optimizing both light interception and light interception efficiency of agricultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identification logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving algorithm to allow for fully automatic reconstruction of hundreds of plants. It was employed to generate 3D reconstructions of individual plants within a sorghum association population at the late vegetative stage of development. Light interception parameters estimated from these reconstructions enabled the identification of known and previously unreported loci controlling light interception efficiency in sorghum. The approach is generalizable and scalable, and it enables 3D reconstructions from existing plant high throughput phenotyping datasets. We also propose a set of best practices to increase 3D reconstructions’ accuracy.

3D plant reconstruction↗