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DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Multiple incommensurate magnetic states in the kagome antiferromagnet Na 2 Mn 3 Cl 8

The kagome lattice can host exotic magnetic phases arising from frustrated and competing magnetic interactions. However, relatively few insulating kagome materials exhibit incommensurate magnetic ordering. Here, we present a study of the magnetic structures and interactions of antiferromagnetic Na 2 Mn 3 Cl 8 with an undistorted Mn 2+ kagome network. Using neutron-diffraction and bulk magnetic measurements, we show that Na 2 Mn 3 Cl 8 hosts two different incommensurate magnetic states, which develop at T N1 = 1.6 K and T N2 = 0.6 K. Magnetic Rietveld refinements indicate magnetic propagation vectors of the form q=(q x , q y , $\frac{3}{2}$), and our neutron-diffraction data can be well described by cycloidal magnetic structures. By optimizing exchange parameters against magnetic diffuse-scattering data, we show that the spin Hamiltonian contains ferromagnetic nearest-neighbor and antiferromagnetic third-neighbor Heisenberg interactions, with a significant contribution from long-ranged dipolar coupling. This experimentally determined interaction model is compared with density-functional-theory simulations. Using classical Monte Carlo simulations, we show that these competing interactions explain the experimental observation of multiple incommensurate magnetic phases and may stabilize multi-q states. Here, our results expand the known range of magnetic behavior on the kagome lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Measurement of Conduction and Valence Bands g -Factors in a Transition Metal Dichalcogenide Monolayer

The electron valley and spin degree of freedom in monolayer transition-metal dichalcogenides can be manipulated in optical and transport measurements performed in magnetic fields. The key parameter for determining the Zeeman splitting, namely, the separate contribution of the electron and hole g factor, is inaccessible in most measurements. Here we present an original method that gives access to the respective contribution of the conduction and valence band to the measured Zeeman splitting. It exploits the optical selection rules of exciton complexes, in particular the ones involving intervalley phonons, avoiding strong renormalization effects that compromise single particle g -factor determination in transport experiments. These studies yield a direct determination of single band g factors. We measure g c1 = 0.86 ± 0.1, g c2 = 3.84 ± 0.1 for the bottom (top) conduction bands and g v = 6.1 ± 0.1 for the valence band of monolayer WSe 2 . These measurements are helpful for quantitative interpretation of optical and transport measurements performed in magnetic fields. In addition, the measured g factors are valuable input parameters for optimizing band structure calculations of these 2D materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Thermal Design Consideration of Medium Voltage High Frequency Transformers

This paper describes a thermal design using epoxy potting for high frequency transformer (HFT) for medium voltage high power electronic applications, namely emerging solid-state transformers. To address HFT’s thermal stress problem, thermal performance of the HFT with air and epoxy potting cooling method are both simulated by magnetothermal-fluid coupling method (MTFCM). The effectiveness of the simulation analysis is verified in a 100 kW DC-DC resonant converter. Influencing factors including distance between the high frequency transformer and the metal enclosure, epoxy thermal conductivity and heat sink placements are simulated and analyzed. Finally, an optimal cooling structure is proposed for future high power HFTs.

Wang, Haoming↗

DOE OSTI2020

Filtered Backprojection in Compton Imaging using a Spherical Harmonic Wiener Filter with Pixelated CdZnTe

Filtered backprojection is an image reconstruction technique for Compton imaging that provides reasonably high resolution at much lower computational costs when compared to iterative methods. Here, this work applies a Wiener filter that has been derived for spherical harmonics on Compton imaging using the OrionUM pixelated CdZnTe imaging-spectrometer. To regularize the filter, an investigation is made into the power spectral density of the signal and noise to develop an appropriate spectral signal-to-noise ratio model for the restoration process. Experimental measurements were conducted with two 228Th sources placed 30° apart. The resulting filtered image of the two sources have an average full-width-at-half-maximum (FWHM) of 9.8° or 7.5° when using a mean squared error and structural similarity optimization approach respectively; an improvement from the 29.0° FWHM image when using simple backprojection.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Digital quantum simulation of NMR experiments

Simulations of nuclear magnetic resonance (NMR) experiments can be an important tool for extracting information about molecular structure and optimizing experimental protocols but are often intractable on classical computers for large molecules such as proteins and for protocols such as zero-field NMR. We demonstrate the first quantum simulation of an NMR spectrum, computing the zero-field spectrum of the methyl group of acetonitrile using four qubits of a trapped-ion quantum computer. We reduce the sampling cost of the quantum simulation by an order of magnitude using compressed sensing techniques. We show how the intrinsic decoherence of NMR systems may enable the zero-field simulation of classically hard molecules on relatively near-term quantum hardware and discuss how the experimentally demonstrated quantum algorithm can be used to efficiently simulate scientifically and technologically relevant solid-state NMR experiments on more mature devices. Our work opens a practical application for quantum computation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice

Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Optimization of the first CUPID detector module

CUPID will be a next generation experiment searching for the neutrinoless double β decay, whose discovery would establish the Majorana nature of the neutrino. Based on the experience achieved with the CUORE experiment, presently taking data at LNGS, CUPID aims to reach a background free environment by means of scintillating Li 2 100 MoO 4 crystals coupled to light detectors. Indeed, the simultaneous heat and light detection allows us to reject the dominant background of α particles, as proven by the CUPID-0 and CUPID-Mo demonstrators. In this work we present the results of the first test of the CUPID baseline module. In particular, we propose a new optimized detector structure and light sensors design to enhance the engineering and the light collection, respectively. We characterized the heat detectors, achieving an energy resolution of (5.9 ± 0.2) keV FWHM at the Q-value of 100 Mo (about 3034 keV). We studied the light collection of the baseline CUPID design with respect to an alternative configuration which features gravity-assisted light detectors’ mounting. In both cases we obtained an improvement in the light collection with respect to past measures and we validated the particle identification capability of the detector, which ensures an α particle rejection higher than 99.9%, fully satisfying the requirements for CUPID.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Massively parallel and universal approximation of nonlinear functions using diffractive processors

Nonlinear computation is essential for a wide range of information processing tasks, yet implementing nonlinear functions using optical systems remains a challenge due to the weak and power-intensive nature of optical nonlinearities. Overcoming this limitation without relying on nonlinear optical materials could unlock unprecedented opportunities for ultrafast and parallel optical computing systems. Here, we demonstrate that large-scale nonlinear computation can be performed using linear optics through optimized diffractive processors composed of passive phase-only surfaces. In this framework, the input variables of nonlinear functions are encoded into the phase of an optical wavefront—e.g., via a spatial light modulator (SLM)—and transformed by an optimized diffractive structure with spatially varying point-spread functions to yield output intensities that approximate a large set of unique nonlinear functions–all in parallel. We provide proof establishing that this architecture serves as a universal function approximator for an arbitrary set of bandlimited nonlinear functions, also covering wavelength-multiplexed nonlinear functions as well as multi-variate and complex-valued functions that are all-optically cascadable. Our analysis also indicates the successful approximation of typical nonlinear activation functions commonly used in neural networks, including the sigmoid, tanh, ReLU (rectified linear unit), and softplus. We numerically demonstrate the parallel computation of one million distinct nonlinear functions, accurately executed at wavelength-scale spatial density at the output of a diffractive optical processor. Furthermore, we experimentally validated this framework using in situ optical learning and approximated 35 unique nonlinear functions in a single shot using a compact setup consisting of an SLM and an image sensor. These results establish diffractive optical processors as a scalable platform for massively parallel universal nonlinear function approximation, paving the way for new capabilities in analog optical computing based on linear materials.

Rahman, Md Sadman Sakib [University of California,↗

DOE OSTI2023

Defects in MX2 Phases (DMX) Dataset: STEM Digital Twins

DFT is used to optimize defects in monolayer MX2 phases. We calculate ~600 optimized defect structures, then use multislice simulations in abTEM to generate STEM digital twins, which can be used to train experimental ML. The reference paper for procedures and demonstration of their utility is https://arxiv.org/abs/2305.02917, and the images here correspond with the discussed Messy dataset.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Defects in MX2 (DMX) 2.0: STEM Digital Twins

36 MATERIALS SCIENCE↗

DOE OSTI2022

A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life

Potassium ion (K + ) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K + biosensors are promising tools to further improve our understanding of K + -dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K + biosensor, GINKO1, in the K + -bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K + biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K + dynamics in multiple model organisms, including bacteria, plants, and mice.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

New Approaches to Improved PEM Fuel Cell Catalyst Layers

Polymer-electrolyte membrane (PEM) fuel-cells are one of the most promising energy conversion technologies for renewable clean energy applications. A major challenge preventing their widespread commercialization is achieving high performance with lowloadings of platinum group metal (PGM) catalysts. One of the factors driving performance limitations in the cell is the mass transport losses within the cathode catalyst layers due to sluggish oxygen-reduction reactions occurring at the platinum-ionomer interface, which is believed to be linked to reduced transport of ions and oxygen. A viable solution to reduce the transport resistances in the catalyst layers is to create new ionomers that can provide good ion and oxygen transport needed to accomplish high-performing fuel cell catalysts. Characterization of transport properties of ionomers for various molecular architectures is the key step, in the effort to create and identify the optimized polymer structure with improved transport. Using this approach, Tetramer Technologies and LBNL propose improved fuel-cell catalyst ionomers based on Tetramers proprietary polymer chemistry, as highlighted under subtopic 17a Innovative Approaches Toward Discovery and Development of Improved Ionomers for Polymer Electrolyte Membrane Fuel Cell Catalyst Layer.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2025

Realizing the Materials-Designed-To-Environments Promise of Additive Manufacturing Through a Fundamentally Different Approach to Optimization of Nonlinear Solid Mechanics Structures

Additive Manufacturing (AM) is expected to play a large role in the labs-wide goals of accelerating innovation and leading in modern engineering. More specifically, AM is seen as a key enabling technology for increasing the agility of nuclear deterrence and other national security applications involving complex coupled environments. However, the impact of AM on these initiatives has not been as wide-ranging as hoped because – despite its unique qualities – the focus has mostly been on detailed qualification to force AM components into pre-existing performance envelopes. This paradigm fundamentally precludes the novel possibilities afforded by the geometric and material flexibility of AM. In particular, the engineering of small-scale features to undergo buckling and contact can cause large geometric and symmetry changes which provide responsiveness to different environments. Despite almost a decade of observing such behavior, there exists no way to systematically design for AM to exploit it. Our goal for this project was to connect material design to multi-environment component performance by reconceptualizing how to design for AM to exploit the buckling and contact of small-scale features.

36 MATERIALS SCIENCE↗

DOE OSTI2023

An Overview of Challenges and Strategies for Stabilizing Zinc Anodes in Aqueous Rechargeable Zn-Ion Batteries

Aqueous rechargeable zinc ion batteries (ZIBs) have been revived and are considered a promising candidate for scalable electrochemical energy storage systems due to their intrinsic safety, low cost, large abundance, mature recyclability, competitive electrochemical performance, and sustainability. However, the deployment of aqueous rechargeable ZIBs is still hampered by the poor electrochemical stability and reversibility of Zn anodes, which is a common, inherent issue for most metal-based anodes. This review presents a comprehensive and timely overview of the challenges and strategies of Zn anodes toward durable ZIBs. First, several challenges that significantly reduce the Coulombic efficiency and cycling stability of Zn anodes are briefly discussed including dendrite formation, hydrogen evolution, and corrosion. Then, the mitigation strategies are summarized in terms of modifying the electrode/electrolyte interfaces, designing electrode structures, and optimizing electrolytes and separators. Further, we comprehensively discuss the mechanisms behind these issues and improvement strategies with respect to the anodes, electrolytes, and separators. Lastly, we provide perspectives and critical analyses of remaining challenges, outlook, and future direction for accelerating the practical application of aqueous rechargeable ZIBs.

25 ENERGY STORAGE↗

DOE OSTI2022

Alicyclobacillus mali FL18 as a Novel Source of Glycosyl Hydrolases: Characterization of a New Thermophilic β-Xylosidase Tolerant to Monosaccharides

A thermo-acidophilic bacterium, Alicyclobacillus mali FL18, was isolated from a hot spring of Pisciarelli, near Naples, Italy; following genome analysis, a novel putative β-xylosidase, AmβXyl, belonging to the glycosyl hydrolase (GH) family 3 was identified. A synthetic gene was produced, cloned in pET-30a(+), and expressed in Escherichia coli BL21 (DE3) RIL. The purified recombinant protein, which showed a dimeric structure, had optimal catalytic activity at 80 °C and pH 5.6, exhibiting 60% of its activity after 2 h at 50 °C and displaying high stability (more than 80%) at pH 5.0–8.0 after 16 h. AmβXyl is mainly active on both para-nitrophenyl-β-D-xylopyranoside (K M 0.52 mM, k cat 1606 s -1 , and k cat /K M 3088.46 mM -1 ·s -1 ) and para-nitrophenyl-α-L-arabinofuranoside (K M 10.56 mM, k cat 2395.8 s -1 , and k cat /K M 226.87 mM -1 ·s -1 ). Thin-layer chromatography showed its ability to convert xylooligomers (xylobiose and xylotriose) into xylose, confirming that AmβXyl is a true β-xylosidase. Furthermore, no inhibitory effect on enzymatic activity by metal ions, detergents, or EDTA was observed except for 5 mM Cu 2+ . AmβXyl showed an excellent tolerance to organic solvents; in particular, the enzyme increased its activity at high concentrations (30%) of organic solvents such as ethanol, methanol, and DMSO. Lastly, the enzyme showed not only a good tolerance to inhibition by xylose, arabinose, and glucose, but was activated by 0.75 M xylose and up to 1.5 M by both arabinose and glucose. The high tolerance to organic solvents and monosaccharides together with other characteristics reported above suggests that AmβXyl may have several applications in many industrial fields.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Data-driven estimation of energy consumption for electric bus under real-world driving conditions

Reliable and accurate estimation of an electric bus’s instantaneous energy consumption is critical in evaluating energy impacts of planning and control of electric bus operations. In this study, we developed machine learning-based long short-term memory (LSTM) and artificial neural network (ANN) models to estimate 1 Hz energy consumption of electric buses based on continuous monitoring data of electric buses in Chattanooga, Tennessee, in 2019 and 2020. We propose a data-partitioning algorithm to separate energy charging and discharging modes before applying data-driven estimation models. Here, a K-fold cross-validation-based model selection process was conducted to identify the optimal model structure and input variables in terms of prediction accuracy. The estimation results show the predicted mean absolute percentage error rates of LSTM and ANN models were 3% and 5%, respectively. We compared the proposed models with existing models in the literature based on the same testing data to demonstrate the predictability of our models.

Artificial neural network↗

DOE OSTI2023

Exploration of superconducting multi-mode cavity architectures for quantum computing

Superconducting radio-frequency (SRF) cavities coupled to transmon circuits have proven to be a promising platform for building high-coherence quantum information processors. An essential aspect of this realization involves designing high quality factor three-dimensional superconducting cavities to extend the lifetime of quantum systems. To increase the computational capability of this architecture, we are exploring a multimode approach. This paper presents the design optimization process of a multi-cell SRF cavity to perform quantum computation based on an existing design developed in the scope of particle accelerator technology. We perform parametric electromagnetic simulations to evaluate and optimize the design. In particular, we focus on the analysis of the interaction between a nonlinear superconducting circuit known as the transmon and the cavity. This parametric design optimization is structured to serve as a blueprint for future studies on similar systems.

Reineri, Alessandro↗