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Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗

Designing a User Interface for Real-Time Magnetometer Data Acquisition

The Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) is a next-generation quantum sensor designed to search for ultralight dark matter and explore new frontiers in quantum mechanics. Due to the experiment s sensitivity to magnetic interference, a magnetometer trolley system was developed to scan magnetic fields along a vacuum tube. Interacting with the system required command-line inputs, creating usability challenges. To improve accessibility and streamline data acquisition, I developed a graphical user interface (GUI) using Python and the customtkinter library. The GUI supports real-time data display, state/mode switching, command execution, and CSV file management. I collaborated with another intern to integrate data visualization features into the GUI, allowing users to generate 3D plots of post-acquisition magnetic field data. In the future, I aim to fix the real-time plotting feature as it results in an unresponsive GUI.

Mendez, Milagros [DuPage Coll.]↗

Designing a User Interface for Real-Time Magnetometer Data Acquisition

The Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) is a next-generation quantum sensor designed to search for ultralight dark matter and explore new frontiers in quantum mechanics. Due to the experiment’s sensitivity to magnetic interference, a magnetometer trolley system was developed to scan magnetic fields along a vacuum tube. Interacting with the system required command-line inputs, creating usability challenges. To improve accessibility and streamline data acquisition, I developed a graphical user interface (GUI) using Python and the customtkinter library. The GUI supports real-time data display, state/mode switching, command execution, and CSV file management. I collaborated with another intern to integrate data visualization features into the GUI, allowing users to generate 3D plots of post-acquisition magnetic field data. In the future, I aim to fix the real-time plotting feature as it results in an unresponsive GUI.

Mendez, Milagros [DuPage Coll.]↗

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗

Optical properties of Peaked Spectrum radio sources

ABSTRACT In this work, we study the optical properties of compact radio sources selected from the literature in order to determine the impact of the radio-jet in their circumnuclear environment. Our sample includes 58 Compact Steep Spectrum (CSS) and GigaHertz Peaked Spectrum (GPS) and 14 Megahertz-Peaked spectrum (MPS) radio sources located at z ≤ 1. The radio luminosity (LR) of the sample varies between Log LR ∼ 23.2 and 27.7 W Hz−1. We obtained optical spectra for all sources from SDSS-DR12 and performed a stellar population synthesis using the starlight code. We derived stellar masses (M⋆), ages 〈t⋆〉, star formation rates (SFR), metallicities 〈Z⋆〉 and internal reddening AV for all young AGNs of our sample. A visual inspection of the SDSS images was made to assign a morphological class for each source. Our results indicate that the sample is dominated by intermediate to old stellar populations and there is no strong correlation between optical and radio properties of these sources. Also, we found that young AGNs can be hosted by elliptical, spiral and interacting galaxies, confirming recent findings. When comparing the optical properties of CSS/GPS and MPS sources, we do not find any significant difference. Finally, the Mid-Infrared WISE colours analysis suggests that the compact radio sources defined as powerful AGNs are, in general, gas-rich systems.

79 ASTRONOMY AND ASTROPHYSICS↗

Bridging Time-series Image Phenotyping and Functional–Structural Plant Modeling to Predict Adventitious Root System Architecture

Root system architecture (RSA) is an important measure of how plants navigate and interact with the soil environment. However, current methods in studying RSA must make tradeoffs between precision of data and proximity to natural conditions, with root growth in germination papers providing accessibility and high data resolution. Functional–structural plant models (FSPMs) can overcome this tradeoff, though parameterization and evaluation of FSPMs are traditionally based in manual measurements and visual comparison. Here, we applied a germination paper system to study the adventitious RSA and root phenology of Populus trichocarpa stem cuttings using time-series image-based phenotyping augmented by FSPM. We found a significant correlation between timing of root initiation and thermal time at cutting collection (P value = 0.0061, R 2 = 0.875), but little correlation with RSA. We also present a use of RhizoVision [1] for automatically extracting FSPM parameters from time series images and evaluating FSPM simulations. A high accuracy of the parameterization was achieved in predicting 2D growth with a sensitivity rate of 83.5%. This accuracy was lost when predicting 3D growth with sensitivity rates of 38.5% to 48.7%, while overall accuracy varied with phenotyping methods. Despite this loss in accuracy, the new method is amenable to high throughput FSPM parameterization and bridges the gap between advances in time-series phenotyping and FSPMs.

60 APPLIED LIFE SCIENCES↗

Conceptual Model Update of Mercury Sources and Flux at Y-12 and Upper East Fork Poplar Creek, Oak Ridge,Tennessee

The interactions between the key processes that control the fate and transport of mercury (Hg) in the sediments, groundwater, and stream water within the Y-12 National Security Complex (Y-12) in Oak Ridge, Tennessee are complex, and many aspects are not well understood. In contaminated environments such as Y-12, conceptual models are frequently developed to aid in visualizing and understanding the dynamic nature of the hydrologic, geochemical, and physical environment. These conceptual models integrate data in an internally consistent manner to understand processes that control the fate and transport of contaminants. Over the past few decades of environmental investigation at Y-12, a number of conceptual models have been developed to identify and define various technical processes at various scales. The main purpose of the activities described in this report is to update the 2011 conceptual model for Upper East Fork Poplar Creek using the most recent Hg concentration and flux data and informed scientific interpretation. Emphasis was placed on improving the previous model by implementing a more detailed spatial and temporal approach to visualize transport pathways in the watershed and trends in flux and concentration over time, and to compare baseflow and stormflow system dynamics. Detailed descriptions of historical and current Hg sources and transport pathways are also provided for the east and west ends of the facility. This conceptual model will allow the US Department of Energy to evaluate past and present remedial activities and provide a strong technical basis for prioritizing and optimizing remedial responses in a cost-effective and efficient manner. Twenty years ago, Hg flux from Outfall (OF) 200 at the headwaters of East Fork Poplar Creek represented approximately 20% of the overall flux leaving Y-12. By the time of the 2011 conceptual model report, that percentage had increased to 70%–80%. Flux estimates compiled for this report using data from 2009 to 2018 show that OF200 accounted for roughly 60% of the flux leaving Y-12. The relative role of the four storm drain conduits to OF200 appeared similar to 2011, with OF163 being the greatest contributor to downstream flux. An increase in Hg concentrations and flux occurred throughout and downstream of west end storm drains in 2011 in response to a storm drain cleanout. Leading up to the 2011 storm drain cleanout, annual baseflow flux was higher at OF200A6 than at Station 17. From 2011 to 2018, the trend reversed with concentrations and flux being higher at Station 17 than at OF200A6. A spike in concentrations occurred in July 2018, potentially due to a one-time influx of Hg that occurred during COLEX decontamination and decommissioning activities at Y-12. This report includes recommendations for improving our conceptual understanding of Hg sources, transport pathways, and flux at Y-12. Important recommendations include further evaluation of transport pathways, concurrent measurement of Hg concentration and flux under baseflow and stormflow conditions at multiple sites, and research to understand the connections among periphyton and methylmercury concentration, bioavailability, and bioaccumulation. Ongoing facility decontamination and decommissioning efforts, site characterization, remedial actions, and research are facilitating the collection of new Hg data at Y-12. The conceptual model update provided herein takes advantage of the extensive recent Hg sampling to provide an updated assessment of Hg mass balance and support a refined understanding of Hg behavior at or near Y-12. This assessment should assist in future environmental management decisions and in mitigating the impacts of Hg on the surrounding environment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

PathTrace and MPVEASI: A Path Analysis Comparative Validation Study

Developed in 2018, PathTrace is a software package built with the intention of making path analysis simple and intuitive. PathTrace is a top-down pathway analysis software where a user is able to explore vulnerable pathways into a facility. The intention of utilizing a software tool like PathTrace is to characterize an existing physical protection system (PPS) and to upgrade the system to achieve a high level of response interruption, or probability of interruption (P I ) of the adversary. There are four steps for conducting path analysis using PathTrace. The first step is to identify an image to use to build the model and scale the model within PathTrace using a section of known distance (wall or fence perimeter, for example). The scaling process will produce a grid of cells through which the user is able to build a model. The second step is to fill out the grid of cells with four categories of materials: Barriers, Detection Areas, Jumps, and Targets. These materials apply associated delay and detection values to the cells in which they are applied. The third step is to represent the adversary and response forces. The adversaries are represented by their capabilities in interacting with the materials identified in step two, and the response is represented by how quickly they will be able to respond to an adversary attack. Finally, the user is able to take all of the information from the previous three steps and perform a Most Vulnerable Path (MVP) analysis. In this stage, the user is able to visualize vulnerable adversary pathways and reason about how to upgrade these pathways to provide a high level of P I .

97 MATHEMATICS AND COMPUTING↗

Live-Cell Quantum Dot-Based Tracking of Plant & Microbial Extracellular Vesicles

All cellular organisms examined to date release various types of small vesicles called extracellular vesicles (EVs). They were originally thought to be unimportant, but research into EVs as carriers of key messages for communication within large, multicellular organisms or between interacting organisms has gained interest in many different scientific areas of study. Recently, it was discovered that both plants and their pathogenic fungi generate EVs and they are important vehicles for sending plant signals to thwart invasion by fungal pathogens, and in response, fungi use EVs to help evade plant defenses. This project aimed to develop new ways to visualize EVs and their potential nucleic acid cargo isolated from the crop plant, sorghum. We adapted a click chemistry-based method for making quantum dot-based RNA sensors, which will be a useful tool for others studying small RNAs. These sensors were not used detect RNA in sorghum EVs because unlike EVs from Arabidopsis, sorghum EVs were not enriched for specific small RNAs. This interesting difference shifted the project in an exciting direction, which focused on comparing EV proteomes. Our study discovered that greater than 60% of Arabidopsis EV proteins were also found in the sorghum EV proteome, revealing a partial conservation between a eudicot and monocot plant. These studies have raised new, fundamental questions on the conserved function of EVs in plants.

59 BASIC BIOLOGICAL SCIENCES↗

Manipulating single excess electrons in monolayer transition metal dihalide

Polarons are entities of excess electrons dressed with local response of lattices, whose atomic-scale characterization is essential for understanding the many body physics arising from the electron-lattice entanglement, yet difficult to achieve. Here, using scanning tunneling microscopy and spectroscopy (STM/STS), we show the visualization and manipulation of single polarons in monolayer CoCl 2 , that are grown on HOPG substrate via molecular beam epitaxy. Two types of polarons are identified, both inducing upward local band bending, but exhibiting distinct appearances, lattice occupations and polaronic states. First principles calculations unveil origin of polarons that are stabilized by cooperative electron-electron and electron-phonon interactions. Both types of polarons can be created, moved, erased, and moreover interconverted individually by the STM tip, as driven by tip electric field and inelastic electron tunneling effect. This finding identifies the rich category of polarons in CoCl 2 and their feasibility of precise control unprecedently, which can be generalized to other transition metal halides.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Effect of Laser Cutting Heuristic Presentation Modality on Design Learning

Abstract The goal of this work is to study the way student designers use heuristics to effectively design for laser-cut manufacturing methods. With the recent advent of academic makerspaces, digital fabrication tools like laser cutters are relatively new additions to the classroom. Therefore, there is a gap in formal education or training on these tools, and students can find it challenging to design effectively for them. A study was performed to investigate the way students apply heuristics to redesign laser-cut assemblies when received in different modalities. All participants were given an identical lecture on laser cutting heuristics. Then, a redesign problem was presented to students, and three different experimental groups were given the heuristics in different modalities: Text-Only, text with Visual aids, and text with Tactile aids. The novelty and quality of each of the resulting redesigns were evaluated. It was hypothesized that participants would have more difficulty interpreting and applying the Text-Only heuristics, lowering the quality of their redesigned solutions relative to the other two conditions. It was also hypothesized that participants would experience fixation caused by interacting with the tactile aids, leading to the lower novelty of their redesigned solutions relative to the other two conditions. Results showed that modality played a significant role in participants’ feelings of self-efficacy after the intervention, as well as in their understanding of laser cutter design skills when responding to quiz-style questions. However, analysis of novelty and quality showed little significant impact of the intervention and varying modalities on participants’ designs.

Engineering↗

Exploring Wholesale Energy Price Trends: The Renewables and Wholesale Electricity Prices (ReWEP) tool (Ver. 2024.1)

The Renewables and Wholesale Electricity Prices (ReWEP) visualization tool from Berkeley Lab has been updated with nodal electricity pricing and wind and solar generation data through the end of 2023. ReWEP users can explore trends in wholesale electricity prices and their relationship to wind and solar generation. ReWEP includes nodal pricing trends across locations, regions, and different timeframes. The tool consists of maps, time series, and other interactive figures that provide: (1) a general overview of how average pricing, negative price frequency, and extreme high prices vary over time, and (2) a summary of how pricing patterns are related to wind and solar generation. Interactive functionality allows investigation by year, season, time of day, and region, where region is defined as the Independent System Operators (ISO) or Regional Transmission Organizations (RTO) region. ReWEP also contains prices throughout much of the western United States from the Western Energy Imbalance Market and the Western Energy Imbalance Service Market.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Exploring Wholesale Energy Price Trends: The Renewables and Wholesale Electricity Prices (ReWEP) tool (Ver. 2024.1)

The Renewables and Wholesale Electricity Prices (ReWEP) visualization tool from Berkeley Lab has been updated with nodal electricity pricing and wind and solar generation data through the end of 2023. ReWEP users can explore trends in wholesale electricity prices and their relationship to wind and solar generation. ReWEP includes nodal pricing trends across locations, regions, and different timeframes. The tool consists of maps, time series, and other interactive figures that provide: (1) a general overview of how average pricing, negative price frequency, and extreme high prices vary over time, and (2) a summary of how pricing patterns are related to wind and solar generation. Interactive functionality allows investigation by year, season, time of day, and region, where region is defined as the Independent System Operators (ISO) or Regional Transmission Organizations (RTO) region. ReWEP also contains prices throughout much of the western United States from the Western Energy Imbalance Market and the Western Energy Imbalance Service Market.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400–700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700–800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL–PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Continuous cultivation of the lithoautotrophic nitrate‐reducing Fe( II )‐oxidizing culture KS in a chemostat bioreactor

Abstract Laboratory‐based studies on microbial Fe(II) oxidation are commonly performed for 5–10 days in small volumes with high substrate concentrations, resulting in geochemical gradients and volumetric effects caused by sampling. We used a chemostat to enable uninterrupted supply of medium and investigated autotrophic nitrate‐reducing Fe(II)‐oxidizing culture KS for 24 days. We analysed Fe‐ and N‐speciation, cell‐mineral associations, and the identity of minerals. Results were compared to batch systems (50 and 700 mL—static/shaken). The Fe(II) oxidation rate was highest in the chemostat with 7.57 mM Fe(II) d −1 , while the extent of oxidation was similar to the other experimental setups (average oxidation of 92% of all Fe(II)). Short‐range ordered Fe(III) phases, presumably ferrihydrite, precipitated and later goethite was detected in the chemostat. The 1 mM solid phase Fe(II) remained in the chemostat, up to 15 μM of reactive nitrite was measured, and 42% of visualized cells were partially or completely mineral‐encrusted, likely caused by abiotic oxidation of Fe(II) by nitrite. Despite (partial) encrustation, cells were still viable. Our results show that even with similar oxidation rates as in batch cultures, cultivating Fe(II)‐oxidizing microorganisms under continuous conditions reveals the importance of reactive nitrogen intermediates on Fe(II) oxidation, mineral formation and cell–mineral interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells

Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle in a haystack. Scouting gross cellular changes with fluorescent microscopy is only possible for well-established viruses, where fluorescent tagging is developed. Soft X-ray tomography (SXT) offers 3D imaging of entire cells without the need for chemical fixation or labeling. Here, we use full-rotation SXT to visualize entire human B cells infected by the herpes simplex virus 1 (HSV-1). We have mapped the temporospatial remodeling of cells during the infection and observed changes in cellular structures, such as the presence of cytoplasmic stress granules and multivesicular structures, formation of nuclear virus-induced dense bodies, and aggregates of capsids. Our results demonstrate the power of SXT imaging for scouting virus-induced changes in infected cells and understanding the orchestration of virus-host remodeling quantitatively.

59 BASIC BIOLOGICAL SCIENCES↗

Flowable Cementitious Grouts for False Bottoms in Hanford Waste Tanks – 26085

Cementitious grouts with epoxy coatings are being evaluated as an approach to refurbish the bottom of waste tanks at the Hanford Site. This work studies four grout concept materials for this application, two grouts being from commercial vendors and two grouts based off formulations used to close reactors and tanks at the Savannah River Site. All the candidate grouts demonstrate flowability and pumpability at the 0.5 cu ft scale. The commercial vendor products demonstrate the best flow and have lower water/premix ratio and are less likely to have bleed, which would impact epoxy bonding to the grout. The commercial products also demonstrate increased compression strengths compared to the reactor closure grouts. Additional fresh and cured properties for all the grout formulations were similar. The grouts in the tank waste simulant without epoxy coating do not crack but show visual changes to the grout and the surrounding simulant solution, and simulant absorption into the grout. The grout/epoxy bond in ambient conditions has strengths of over 7 MPa and needs to be evaluated for simulant chemical durability. Overall, the results to date justify testing the flowability, pumpability, and placement of the grouts at larger, engineering scale and for further studies of the interactions between the grout and epoxy.

Valdes, Nicholas [Savannah River National Laborato↗