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DOE OSTI2024

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Anchor-based optimization of energy density functionals

A new anchor-based optimization method of defining energy density functionals (EDFs) is proposed. In this approach, the optimization of the parameters of EDFs is carried out for a selected set of spherical anchor nuclei, the physical observables of which are modified by the correction function, which takes into account the global performance of EDFs. It is shown that the use of this approach leads to a substantial improvement in the global description of binding energies for several classes of covariant EDFs. Here, the computational cost of defining a new functional within this approach is drastically lower as compared with the one for the optimization which includes the global experimental data on spherical, transitional, and deformed nuclei in the fitting protocol.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Industry 4.0 and Intelligent Manufacturing Processes: A Review of Modern Sensing Technologies

Digital Manufacturing technologies have quickly become ubiquitous in the manufacturing industry. The transformation commonly referred to as the fourth industrial revolution, or Industry 4.0, has ushered in a wide range of communication technologies, connection mechanisms, and data analysis capabilities. These technologies provide powerful tools to create a more lean, profitable, and data-driven manufacturing processes. In this paper, we review modern communication technologies and connection architectures for Digital Manufacturing and Industry 4.0 applications. An introduction to Cyber-Physical Systems and a review of digital manufacturing trends is followed by an overview of data acquisition methods for manufacturing processes. Numerous communication protocols are presented and discussed for connecting disparate machines and processes. Flexible data architectures are discussed and examples of machine monitoring implementations are provided. Finally, select implementations of these communication protocols and architectures are surveyed with recommendations for future architecture implementations.

42 ENGINEERING↗

DOE OSTI2023

Quantum JPEG

The joint photographic expert group algorithm compresses a digital image by filtering its high spatial-frequency components. Similarly, we introduce a quantum algorithm that uses the quantum Fourier transform to discard the high spatial-frequency qubits of an image, downsampling it to a lower resolution. This allows one to capture, compress, and send images even with limited quantum resources for storage and communication. We show under which conditions this protocol is advantageous with respect to its classical counterpart.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Experimental measurement of the effective contact angle for solvent/packing interactions in a structured packed column for CO 2 capture

The contact angle is a critical factor for determining the effective mass transfer area for carbon dioxide (CO 2 ) capture via the chemical absorption process in a packed column, and thus the overall capture efficiency of the packed column. Many widely used commercial packings involve microscale features (perforation, corrugation, etc.) that may also affect the wetting behavior. This study proposes a systematic method of using a modified Wilhelmy plate to measure the effective contact angle to characterize the solvent and featured packing interaction. In lieu of computational efforts relying on assumptions guided by semi-informed correlation, the proposed method directly measures the effective contact angle as a function of the solvent and packing thermophysical and hydrodynamic properties. The characterization of the effective contact angle is then integrated in the computational fluid dynamics modeling to reduce uncertainty in the prediction of effective mas transfer area. Experiments were conducted for stainless steel coupons using water and aqueous sodium hydroxide (NaOH) solvent for verification of the proposed experimental protocol. The surface tension of the aqueous NaOH solvent was altered using surfactant and antifoam. The effective contact angle increases with the increased value of the surface tension for flat stainless steel sheets. On the other hand, effective contact angles do not vary in Mellapak coupons for aqueous monoethanolamine (MEA) and NaOH solvent. In this case, surface textures and sheet design play a dominant role in the surface tension of solvents. Furthermore, CO 2 loading has a significant effect on the contact angle for Mellapak coupons. As expected, the contact angle decreases with the increasing temperature of CO 2 capture solvents (MEA, EEMPA). The effective contact angle measurement using the Wilhelmy plate method can provide more accurate and efficient solvents for characterizing the solvent-packing surface interactions. Subsequently, the present method enhances the accuracy of the prediction of the effective mass transfer area in carbon capture by solvent absorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Co-optimizing water-alternating-carbon dioxide injection projects using a machine learning assisted computational framework

In this report, a robust machine-learning-based computational framework that couples multi-layer neural network (MLNN) proxies and a multi-objective particle swarm optimizer (MOPSO) to design water-alternating-carbon dioxide injection (CO 2 -WAG) projects is presented. The proposed optimization protocol considers various objectives, including oil recovery and CO 2 storage volume. Expert MLNN systems are trained and employed as surrogate models of the high-fidelity compositional simulator in the optimization workflow. When multiple objective functions are considered, two approaches are employed to treat the objectives: the weighted sum method and the Pareto-front-based scheme. A field-scale implementation focusing on tertiary recovery in the Morrow B formation at Farnsworth Unit (FWU) is presented. The developed Pareto-optimal solutions indicate the maximal available oil production can be 1.64 × 10 7 barrels and maximal carbon storage can achieve 2.35 × 10 7 tons. Trade-offs factor is defined to divide the constructed Pareto front into 4 sections with the trade-off factors’ value ranges from 0.35 to 49.9. This work also compares the optimum solution found by the aggregative objective function and the solution repository covered by the Pareto front that considers the physical and operational constraints and reduces uncertainties involved by the multi-objective optimization process. Our comparison indicates multiple solutions exist to satisfy the objective criteria of the WAG design, and these results cannot be found using the traditional weighted sum method. The Pareto front solution can provide more options for project designers, but decisions regarding necessary trade-offs must be made using the solution repository to balance the project economics and CO 2 storage amount.

10 SYNTHETIC FUELS↗

DOE OSTI2024

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Adapting Grid Criticality for Data Centers

This presentation explores the evolving definition of “critical load” in the electric grid, emphasizing the growing importance of digital infrastructure—particularly data centers—in grid resilience, restoration, and modernization. As utilities increasingly rely on AI-driven analytics and software-defined control systems, data centers have shifted from passive electricity consumers to essential computational hubs that enable National Critical Functions (NCFs) and support real-time grid operations. The deck examines the scale and impact of digital loads, the need for grid modernization to manage rapid load growth, and the diverse computing paradigms required for AI deployment. It introduces a tiered taxonomy for classifying critical loads, highlights operational dependencies between the grid and digital infrastructure, and discusses policy implications for integrating data centers into emergency planning and restoration protocols. Through case studies and practical frameworks, the presentation provides actionable insights for utilities, regulators, and planners navigating the digital transformation of the power sector.

29 - ENERGY PLANNING, POLICY AND ECONOMY↗

DOE OSTI2024

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. Our approach uses simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine from their molten states. Our graph latent variables when biased in well-tempered metadynamics consistently show transitions between states and achieve accurate free energy calculations in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our graph neural net variables for improved sampling. Furthermore, the protocol shown here should be applicable for other systems and with other sampling methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Supporting Cyber Security of Power Distribution Systems by Detecting Differences Between Real-time Micro-Synchrophasor Measurements and Cyber-Reported SCADA (Final Report)

As modern power grids tend towards greater levels of automation and communication, the challenges of identifying and mitigating vulnerabilities to cyber-attacks are ones that are increasingly demanding attention. Today’s power system has evolved to form the foundational bedrock of modern society, and an attack on this infrastructure could prove disastrous. In this project we were tasked to investigate the use of distribution synchrophasors as an independent isolated sensor network with which we can corroborate, or flag potentially spoofed,Supervisory Control And Data Acquisition (SCADA) data. We adapted an approach to marry the underlying physical properties of power systems with the network communications used by power systems in order to offer insights unattainable by either data stream isolation. While the concept of intrusion detection systems (IDS) is well understood for monitoring network traffic and traditional IT computing systems, the approach discussed in this report is motivated by several key notions: first, current SCADA communications alone presents an incomplete view of the grid. Second, the power grid, and the equipment controlling it, is grounded by laws of physics. Given this, we leverage high-frequency physical grid measurements to understand the physical condition of the grid, and combine this with SCADA. While high-frequency physical grid measurements and SCADA communication over Internet Protocol (IP) networks are fundamentally disparate information sources, when collectively examined through appropriate lenses, they offer a much more nuanced depiction of the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2019

Upper urinary tract urothelial carcinoma on multidetector CT: spectrum of disease

Urothelial carcinoma of the upper urinary tract (UUT) is a relatively uncommon genitourinary malignancy, accounting for about 5–7% of urothelial tumors. The significant features of this tumor are multifocality and high rate of recurrence. Computed tomography urography (CTU) has replaced excretory urography (EU) and retrograde pyelography (RP) for imaging of upper tract urothelial carcinoma. While many studies have confirmed high sensitivity (88–100%) and specificity (93–100%) of CTU, an optimized CT protocol is of critical importance in screening, staging, and post-operative follow-up of patients (Chlapoutakis, Eur J Radiol 73(2):334–338, 2010; Caoli and Cohan, Abdom Radiol (NY) 41(6):1100–1107, 2016). The key element of the CT protocol is to have adequate distension of the collecting system with excreted contrast, to detect subtle lesions at an early stage. In this article, we discuss the background of upper urinary tract TTC, pathogenesis, CT protocol and the role of imaging in evaluation of this malignancy, staging, as well as different imaging appearances.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2024

Building a controlled-NOT gate between polarization and frequency

By harnessing multiple degrees of freedom (DoFs) within a single photon, controlled quantum unitaries, such as the two-qubit controlled-NOT ( cnot ) gate, play a pivotal role in advancing quantum communication protocols such as dense coding and entanglement distillation. In this work, we devise and realize a cnot operation between polarization and frequency DoFs by exploiting directionally dependent electro-optic phase modulation within a fiber Sagnac loop. Alongside computational basis measurements, we validate the effectiveness of this operation through the synthesis of all four Bell states in a single photon, all with fidelities greater than 98%. This demonstration opens new avenues for manipulating hyperentanglement across these two crucial DoFs, marking a foundational step toward leveraging polarization-frequency resources in fiber networks for future quantum applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Temperature Rise on Liner Surfaces of Fuel Cell Electric Vehicle Tanks during Fueling Process

Herein, the temperature of the inner tank walls, or plastic liners, of composite pressure tanks in fuel cell electric vehicles during fueling using three‐dimensional computational fluid dynamics (CFD) models is evaluated. The liner materials are limited to 85.0 °C to prevent thermal stress causing material failure that would result in a hydrogen leak. Therefore, the temperature of hydrogen gas must be limited to below 85.0 °C during the fueling process as dictated by the current fueling protocol. However, there are limited experimental or simulation data confirming that the temperature changes do not exceed the threshold. Herein, the liner temperatures with CFD tank models for two sizes of type IV tanks representative of the upper and lower system bounds that are close to the SAE J2601 fueling protocol (36.0 and 244.0 L) are evaluated. First, each model's reliability is validated with experimental data and then analyzed, and the data are used to evaluate the maximum hydrogen and liner temperatures under real‐world fueling conditions. The evaluation shows that the maximum liner surface temperature of each tank model is at least 7 °C lower than that of the hydrogen. Additionally, there is at least 12 °C difference found between the upper limit and actual liner temperatures.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Efficient, Predictive Tomography of Multi-Qubit Quantum Processors

After decades of R&D, quantum computers comprising more than 2 qubits are appearing. If this progress is to continue, the research community requires a capability for precise characterization (“tomography”) of these enlarged devices, which will enable benchmarking, improvement, and finally certification as mission-ready. As world leaders in characterization -- our gate set tomography (GST) method is the current state of the art – the project team is keenly aware that every existing protocol is either (1) catastrophically inefficient for more than 2 qubits, or (2) not rich enough to predict device behavior. GST scales poorly, while the popular randomized benchmarking technique only measures a single aggregated error probability. This project explored a new insight: that the combinatorial explosion plaguing standard GST could be avoided by using an ansatz of few-qubit interactions to build a complete, efficient model for multi-qubit errors. We developed this approach, prototyped it, and tested it on a cutting-edge quantum processor developed by Rigetti Quantum Computing (RQC), a US-based startup. We implemented our new models within Sandia’s PyGSTi open-source code, and tested them experimentally on the RQC device by probing crosstalk. We found two major results: first, our schema worked and is viable for further development; second, while the Rigetti device is indeed a “real” 8-qubit quantum processor, its behavior fluctuated significantly over time while we were experimenting with it and this drift made it difficult to fit our models of crosstalk to the data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

TF9 Dataset Analysis

Incident Overview: In the time between November 2, 2019 and November 11, 2019, WheelByte was plagued by breaches in security. These insecurities led to breaches in customer data, company data, and even the death of an employee, Matthew Swift. They have launched an investigation into the company’s computer systems in hopes to find the root cause. We have been provided with the following artifacts from WheelByte: memory images, disk images, network packet captures, and emails. We have found multiple cyber-system attacks against WheelByte. Our investigation lasted from July 13th - August 3rd, 2023. WheelByte allowed us to look at any and every file, and there were no restrictions on what we could or could not use in our investigation. By the end of our investigation, we have been able to deduce who is behind the attack, what they have done, and why they did it. A company that is closely related to WheelByte is called Slyde. Slyde sells electric scooters and it is known that the Chief Executive Officer (CEO) of Slyde, Kimberly Holmes, sees WheelByte as a threat to business, as Wheelbyte sells electric skateboards. We have been able to deduce that Slyde is likely behind many of the malicious attacks. We have seen exfiltration addresses to Slyde domains, along with other Slyde information within their malware. We can see lots of traffic to and from Slyde Internet Protocol (IP) addresses. This may be an attempt to cripple WheelByte’s productivity to remove Slyde’s competitor from the market.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Raspberry Pi–powered temperature monitoring of growth chamber microclimates

While controlled environments are desirable for growing and measuring plants, growth chambers and greenhouses typically have microclimates that impact plant growth, development, and stress responses. Furthermore, opening and closing the doors of a controlled environment introduces variation in the environment, especially at temperature extremes, affecting both the measurements and the organisms within. Using multiple temperature data loggers to normalize results can be cost-prohibitive and rarely offers real-time feedback on temperature status. We used low-cost single-board computers, cameras, and temperature sensors to manage and capture growth chamber temperatures while acquiring plant image data. Detailed here are methods to document microclimates within a growth chamber so that data can be normalized to measured temperature information. This protocol describes a low-cost method for automated temperature monitoring, which enables both high-throughput measurements of temperature along with plant growth and stress responses via plant imaging.

Plant Sciences↗

DOE OSTI2021

Photon-recoil and laser-focusing limits to Rydberg gate fidelity

Limits to Rydberg gate fidelity that arise from the entanglement of internal states of neutral atoms with the motional degrees of freedom due to the momentum kick from photon absorption and re-emission is quantified. This occurs when the atom is in a superposition of internal states but only one of these states is manipulated by visible or UV photons. The Schrödinger equation that describes this situation is presented and two cases are explored. In the first case, the entanglement arises because the spatial wave function shifts due to the separation in time between excitation and stimulated emission. For neutral atoms in a harmonic trap, the decoherence can be expressed within a sudden approximation when the duration of the laser pulses are shorter than the harmonic oscillator period. In this limit, the decoherence is given by simple analytic formulas that account for the momentum of the photon, the temperature of the atoms, the harmonic oscillator frequency, and atomic mass. In the second case, there is a reduction in gate fidelity because the photons causing absorption and stimulated emission are in focused beam modes. This leads to a dependence of the optically induced changes in the internal states on the center of mass atomic position. In the limit where the time between pulses is short, the decoherence can be expressed as a simple analytic formula involving the laser waist, temperature of the atoms, the trap frequency, and the atomic mass. These limits on gate fidelity are studied for the standard π-2π-π Rydberg gate and a protocol based on a single adiabatic pulse with a Gaussian envelope.

74 ATOMIC AND MOLECULAR PHYSICS↗