TOWARDS LEARNING ON MULTIPLE PLATFORMS USING FUGU
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Daram, Anurag Reddy↗
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A consensus mathematical model of vaccine-induced antibody dynamics for multiple vaccine platforms and pathogens
Introduction: Vaccine platforms used in successful, licensed vaccines have varied among pathogens. However, antibody level is still the main clinical correlate of protection in most approved vaccines. Decisions as to the best vaccine platform to pursue for a given pathogen may be informed through improved understanding of the process of antibody generation and its temporal dynamics, as well as the relationship between these processes and the type of vaccine. Methods: We have analyzed the dynamics of antibody generation for different vaccine platforms against diverse pathogens, and developed a consensus mathematical model that captures antibody dynamics across these diverse systems. Initially, the model was fitted to a rich dataset of antibody and immune cell concentrations in a SARS-CoV-2 vaccine experiment. We then used concepts from machine learning, such as transfer learning, to apply the same model to a variety of systems, involving different pathogens, vaccine platforms, and booster dose use/timing, fixing most parameter values relating to the dynamics of the immune system. Results: The model includes B cell proliferation and differentiation, as well as the generation of plasma cells, which secrete large amounts of antibody, and memory B cells. Overall, the model describes antibody generation in all systems tested well and shows that the main differences across platforms are related to the dynamics of antigen presentation. Discussion: This model can be used to predict antibody generation in pairs of vaccine platform/pathogen, allowing for the use of in silico results to narrow down experimental burden in vaccine development.
59 BASIC BIOLOGICAL SCIENCES↗
Programming approaches for scalability, performance, and portability of combustion physics codes
Here, this paper presents the process, strategy, and results associated with porting a typical combustion physics flow solver to current state-of-the-art and future massively-parallel computer architectures. Major focus is placed on the distinct algorithmic structure of these types of codes and how it can be integrated with modern programming paradigms for heterogeneous platforms (i.e., distributed many-core systems with accelerators). An end-to-end case study is presented that exemplifies the process in a generic manner, which then serves as a clear guide with respect to the strategy and best practices leading to a robust and adaptable framework that performs well, is durable over time, is portable, and requires minimal human-effort. This end is accomplished beginning with the use of a mature, validated, structured, multiblock code framework optimized for application of both Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS). This code has been ported to a variety of platforms over the past decade, including most recently the Oak Ridge Leadership Computing Facility’s “Summit” Platform. The experience gained on these multiple platforms provides general insights and thus the results presented are not specific to any one code or platform other than the overarching trend toward distributed many-core systems with accelerators in order to move toward exascale performance. The resultant performance and scalability of the ported code is demonstrated on a real-world application; a state-of-the-art rotating detonation rocket engine simulation that matches the complex geometry and boundary conditions imposed as part of a companion experimental campaign.
97 MATHEMATICS AND COMPUTING↗
Precise ROCOF estimation algorithm for low inertia power grids
The precise estimation of Rate Of Change Of Frequencies (ROCOFs) in a generation trip event can be helpful on power system inertia estimation, fast system response, and accurate event capturing. However, the ROCOF estimations from the existing Synchronized Measurement Devices (SMDs) are usually simply calculated by the finite difference between two adjacent frequency measurement points. The ineluctable noises, disturbances, and spikes from real-world frequency measurements can bring large dynamics to the ROCOF estimation and thus can result in an inaccurate estimation of the initial ROCOF. This issue becomes more serious when the target power grid has low inertia, and a large amount of distributed energy sources are deployed. To address this issue, a precise ROCOF estimation algorithm is designed based on least square method with flexible window size. In addition, a median filter is also designed and applied on the frequency measurements before using the proposed algorithm. The window size and thresholds in the proposed algorithm are determined with historical event data analysis. The proposed algorithm is deployed in a low cost, flexible, and distribution level universal grid analyzer (UGA) platform. In conclusion, multiple experiments are conducted in both a laboratory and the Hawaiian Islands to verify the effectiveness of the proposed algorithm.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities
Abstract Multimodal multiscale characterization provide opportunities to study organic semiconducting thin films with multiple length scales, across multiple platforms, to elucidate crystallization mechanisms of the various microstructures that impact functionality. With polarized scanning transmission X‐ray and 4D‐scanning transmission electron microscopy, hybrid crystalline structures in rubrene thin films in which large crystalline domains surround a common nucleus and transition to a spherulite morphology at larger radii is observed. These high‐resolution techniques reveal how azimuthal orientational discontinuities at smaller radii are erased as spherulite morphology takes hold. In situ crystallization in the films with optical microscopy is also captured, discovering the importance of considering the initial temperature increase of a film during thermal annealing over the crystallization timescale. This kinetic information of the radial crystallization rate and of corresponding film heating kinetics is used to estimate the temperature at which the larger crystalline regions transition into a spherulite. By combining the results obtained from the different characterization modes, it is learned that thermal conditions can sensitively affect the crystallization of rubrene and other organic thin films. The observations suggest opportunities for more complex temperature‐dependent processing to maximize hybrid structures’ functionality in organic thin films and demonstrate that multimodal studies deepen the understanding of structure‐function dynamics.
Tan, Jenna A.↗
Machine learning for automated experimentation in scanning transmission electron microscopy
Abstract Machine learning (ML) has become critical for post-acquisition data analysis in (scanning) transmission electron microscopy, (S)TEM, imaging and spectroscopy. An emerging trend is the transition to real-time analysis and closed-loop microscope operation. The effective use of ML in electron microscopy now requires the development of strategies for microscopy-centric experiment workflow design and optimization. Here, we discuss the associated challenges with the transition to active ML, including sequential data analysis and out-of-distribution drift effects, the requirements for edge operation, local and cloud data storage, and theory in the loop operations. Specifically, we discuss the relative contributions of human scientists and ML agents in the ideation, orchestration, and execution of experimental workflows, as well as the need to develop universal hyper languages that can apply across multiple platforms. These considerations will collectively inform the operationalization of ML in next-generation experimentation.
36 MATERIALS SCIENCE↗
Correlated Hofstadter spectrum and flavour phase diagram in magic-angle twisted bilayer graphene
In magic-angle twisted bilayer graphene, the moiré superlattice potential gives rise to narrow electronic bands that support a multitude of many-body quantum phases. Further richness arises in the presence of a perpendicular magnetic field, where the interplay between moiré and magnetic length scales leads to fractal Hofstadter subbands. In this strongly correlated Hofstadter platform, multiple experiments have identified gapped topological and correlated states, but little is known about the phase transitions between them in the intervening compressible regimes. Here we simultaneously unveil sequences of broken-symmetry Chern insulators and resolve sharp phase transitions between competing states with different topological quantum numbers and different occupations of the spin-valley flavour. Our measurements determine the energy spectrum of interacting Hofstadter subbands in magic-angle twisted bilayer graphene and map out the phase diagram of flavour occupancy. In addition, we observe full lifting of the degeneracy of the zeroth Landau levels together with level crossings, indicating moiré valley splitting. We propose a unified flavour polarization mechanism to understand the intricate interplay of topology, interactions and symmetry breaking as a function of density and applied magnetic field in this system.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Spack-Manager
SAND2022-3282 O Spack-Manager is a lightweight wrapper for streamlining the software development and deployment cycle using Spack. Spack-Manager creates a uniform framework for developing, testing, and deploying specific software stacks for projects across multiple platforms while utilizing Spack as much as possible. It organizes Spack extensions, machine configurations, project customizations, and tools for features that are mostly project specific. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Sakievich, Philip↗
Real-Twin
Real-Twin is a unified, model-agnostic scenario generation tool designed to streamline and standardize the evaluation of emerging mobility technologies. It provides an end-to-end framework that includes robust workflows, integrated tools, and comprehensive metrics to generate, calibrate, and benchmark microscopic traffic simulation scenarios across multiple platforms. Key Features of Real-Twin include: - Unified Scenario Generation: generate transferable, simulation-ready scenarios from heterogeneous data sources using a consistent workflow. - Automated Calibration Workflow: bridges simulation and real-world data, minimizing manual effort and making traffic simulation more accessible to researchers and engineers. - Model-Agnostic Compatibility: supports SUMO, VISSIM, and AIMSUN for cross-platform scenario generation and benchmarking. Enables reliable comparisons and reproducibility across different simulation tools. - Consistent Scenarios across Different Simulators: generate comparable simulation scenarios across different microscopic traffic simulators, providing users the ability to conduct benchmarking and cross-validation that are crucial for ensuring the reliability and reproducibility of simulation results. - Emerging Technology Support: includes a scenario database and pipeline for studying autonomous vehicles (AVs), with planned extensions to CAVs, EVs, and other advanced technologies.
Wang, Chieh (Ross) [Oak Ridge National Laboratory ↗
Dataset for "A primer on forest structure measurement with lidar for ecologists"
This repository includes data and code accompanying the case study included in the manuscript "A primer on forest structure measurement with lidar for ecologists" (submitted to Ecosphere). We compiled lidar datasets from multiple platforms in a common area to: 1. Demonstrate how differences in sensor characteristics influence density and resolution of lidar data. 2. Provide open-source, co-located datasets for users to further inspect differences in lidar data. 3. Provide example code to perform basic lidar analysis. This case study is meant to allow readers to get hands-on experience with real-world data from different platforms. This case study is not meant to be a rigorous comparison of derived ecological metrics among all sensors; such comparisons can be found throughout other publications referenced throughout the main manuscript. Code includes basic functions in R commonly used to visualize and manipulate lidar data accessible with a normal laptop computer; more sophisticated algorithms for advanced users are also referenced throughout the main manuscript. Terrestrial laser scanning (TLS), mobile laser scanning (MLS), UAS laser scanning (ULS), airborne laser scanning (ALS), and spaceborne laser scanning (SLS) data were collected within the Smithsonian Environmental Research Center (SERC) forest dynamics plot in Maryland, USA. TLS, MLS, and ALS data were collected within 1 month of the 2021 growing season; ULS data were collected in November 2020 (“leaf-off” data) and July 2022 (“leaf-on” data).
54 ENVIRONMENTAL SCIENCES↗
EOSPAC User's Manual: Version 6.5 Second Edition (Rev. 3)
The EOSPAC utility package is a collection of interface routines, which can be used to access the SESAME data library and perform various data adjustments and interpolations on the SESAME data. The SESAME data library contains both thermodynamic (e.g., equation of state) and transport coefficients (e.g., opacity and conductivity). Note, for simplicity, the term EOS (equation of state) used herein includes both thermodynamic variables and transport coefficients. The EOSPAC utility package is designed to be used by physics codes (henceforth ”host codes”) written in multiple languages and on multiple platforms. The remainder of this manual is organized into several sections. Chapter 2 discusses conventions such as data organization and routine names. Chapter 3 provides a general overview of basic theory and models implemented within EOSPAC. Chapter 4 provides a general overview of how to use the EOSPAC interface library. Chapters 5 to 7 describe the public interfaces of EOSPAC in detail. Chapter 8 provides a brief introduction to some related tools, which may be of use to the user. Chapter 9 provides details related to some selected numerical features of EOSPAC. Chapter 10 gives examples for using the interface routines described in chapters 5 to 7. Chapter 11 provides technical support contact information. Chapter 12 contains a brief set of acknowledgments. Chapter 13 contains a list of referenced documents. Finally, chapter 14 lists the “table types: mnemonic conventions”, “table types: grouped by category, sorted by name”, “table types: eospac version 5 cross reference”, “options: setup phase”, “data information parameters”, “meta-data information parameters”, “options: interpolation phase”, and the “error codes”.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Triton Initiative: FY22 Communications, Outreach, and Engagement End-of-Year Report
The Department of Energy (DOE) Water Power Technologies Office (WPTO) Triton Initiative supports the advancement of the marine energy (ME) industry through environmental monitoring research and technology development. This report presents the results and analysis of the Triton Initiative’s communications, outreach, and engagement (TCOE) efforts in fiscal year 2022. The primary TCOE goals were to: (1) educate and raise awareness of ME and the role of Triton's environmental monitoring research in supporting the industry; (2) build trust with audiences through transparent communications and outreach; and (3) evaluate and refine TCOE tactics based on feedback and metrics. To support these goals, the TCOE team used multiple platforms and approaches. Notable achievements include: (1) 12 newsletter issues sent to 185 subscribers with an average open rate of 56.4%. (2) 10 Triton Stories, resulting in 2,871 collective views contributing to 46% of all Triton website views. (3) 78 Triton-specific social media posts, which generated a total of 81,896 impressions, 1,037 post-clicks, and 7,814 video views. (4) 6,320 Triton website views with increased search engine optimization ranking in several categories. (5) 3 Triton researchers interviewed as guests on two different podcasts, Water Women and Big Deep: An Ocean Podcast. (6) A Triton special issue of the Journal of Marine Science and Engineering (JMSE) featuring 10 peer reviewed publications. All articles ranked in the top 25%, and two in the top 5%, for digital attention of all research outputs scored by Altmetric. (7) A seven-part webinar series called Triton Talks to share and discuss research and results from the research published in the JMSE special issue. Triton leveraged unique opportunities, particularly the JMSE special issue, to disseminate research results to end users, educate stakeholders, and gain valuable feedback. These concerted communication efforts increased exposure across platforms ultimately resulting in greater reach and access across audiences. Based on audience analyses of webinar attendees and newsletter subscribers, the TCOE team was able to successfully engage with general audiences, research partners, and ME stakeholders, including subject matter experts from government agencies, research organizations, and the regulatory community. The TCOE task established channels to gather input and create opportunities for two-way communication with people engaged with Triton’s outreach efforts. The feedback received will enable the TCOE team to support its goals for ongoing evaluation of outreach and engagement tools while continuing to build trust in the ME community and educate diverse audiences about the impactful research conducted by the Triton Initiative. This report is a Triton Initiative Fiscal Year 2022 Quarter 4 Milestone Deliverable due to the DOE WPTO Sponsor on 9/30/2022. An updated version to include data through 9/30/2022 will be delivered in October 2022.
16 TIDAL AND WAVE POWER↗
Understanding Aitken Mode Aerosol Variability over the Southern Ocean and Antarctica: Insights from Cloud Condensation Nuclei Data
Aitken mode aerosol particles play an important role influencing cloud properties and sustenance, acting as a reservoir of potential cloud condensation nuclei against precipitation scavenging. However, there is limited data on Aitken mode aerosols. In this study, we develop a method to estimate Aitken mode aerosol concentrations and size distribution using cloud condensation nuclei measurements (CCN) and κ-Köhler theory. The performance of this method is evaluated using scanning mobility particle sizer (SMPS) data from recent field campaigns to demonstrate its skills and applicability. The method reasonably estimates Aitken- and accumulation-mode aerosol concentrations, achieving correlations of 0.7–0.9 with only modest biases (mean fractional bias within ±23% for Aitken mode and ±34% for accumulation-mode). This method is further applied to measurements collected over the Southern Ocean and Antarctica in recent years from multiple platforms, including ground sites, aircraft, and ships, to derive Aitken and accumulation-mode aerosol concentrations. Using the derived data, we examine the seasonal cycle, latitudinal variations, and vertical distribution of aerosols. Aitken mode aerosol concentrations are elevated over the Southern Ocean and Antarctica during the austral summer similar to the accumulation mode. In the austral summer, the free troposphere has more Aitken mode aerosols and fewer accumulation mode aerosols than the boundary layer, and thus likely serves as an important source of cloud-forming aerosol while also diluting the accumulation mode.
Kang, Litai [University of Washington] (ORCID:0000↗
Intercomparison of airborne and surface-based measurements during the CLARIFY, ORACLES and LASIC field experiments
Data are presented from intercomparisons between two research aircraft, the FAAM BAe-146 and the NASA Lockheed P3, and between the BAe-146 and the surface-based DOE (Department of Energy) ARM (Atmospheric Radiation Monitoring) Mobile Facility at Ascension Island (8 S, 14.5W, a remote island in the mid-Atlantic). These took place from 17 August to 5 September 2017, during the African biomass burning season. The primary motivation was to give confidence in the use of data from multiple platforms with which to evaluate numerical climate models. The three platforms were involved in the CLouds-Aerosol-Radiation Interaction and Forcing for Year 2017 (CLARIFY-2017), ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES), and Layered Atlantic Smoke and Interactions with Clouds (LASIC) field experiments. Comparisons from flight segments on six days where the BAe-146 flew alongside the ARM facility on Ascension Island are presented, along with comparisons from wing-tip to wing-tip flight of the P3 and BAe-146 on 18 th August 2017. The intercomparison flight sampled a relatively clean atmosphere overlying a moderately polluted boundary layer, while the 6 fly-bys of the ARM site sampled both clean and polluted conditions 2–4 km upwind. We compare and validate characterisations of aerosol physical, chemical, and optical properties, atmospheric radiation, and cloud microphysics between platforms. We assess the performance of measurement instrumentation in the field, under conditions where sampling conditions are not tightly controlled as in laboratory measurements where calibrations are performed. Solar radiation measurements compared well between airborne platforms. Optical absorption coefficient measurements compared well across all three platforms, even though absolute magnitudes were often low (< 10 Mm -1 ) and close to the sensitivity limits of measurement instrumentation thereby confounding assessments of the comparability of absorption Ångström exponent characterisations. Aerosol absorption measurements from airborne platforms were more comparable than aircraft-to-ground observations. Scattering coefficient observations compared well between airborne platforms, but agreement with ground-based measurements was worse, potentially caused by small differences in sampling conditions or actual aerosol population differences. Chemical composition measurements followed a similar pattern, with better comparisons between the airborne platforms. Thermodynamics, aerosol, and cloud microphysical properties generally compared well.
54 ENVIRONMENTAL SCIENCES↗
From Count Rates to Quantifying Isotopic Activities – Field Analysis of Radiation Monitoring Data
The Nevada National Security Site (NNSS) provides a comprehensive bicoastal radiological and nuclear emergency response to United States Department of Energy/National Nuclear Security Administration. A major part of the support is to provide systematic radiological search for lost or stolen sources, Radiological search is a core competency of the NNSS with its origin dating back to nuclear weapons test era. Search operations from multiple platforms is the common thread among the various NNSS assets, which include Aerial Measuring System (AMS), Maritime Support Team (MST), National Capitol Response (NCR), National Search Team (NST) and Radiological Assistance Program (RAP). Information collected and analyzed during search operations add to the actionable intelligence for the law enforcement agencies and provide valuable guidance for the tactical resolution of a nuclear or radiological crisis. Search is an intelligence and situational awareness driven operation and most often called upon during a radiological emergency, however it can be brought into play to thwart a potential threat by providing monitoring and surveillance support. The Office of Nuclear Incident Response (NA-84) serves as the technical leader in responding to and resolving nuclear and radiological threats worldwide and integrates its efforts with other NNSA stakeholders (e.g., NNSA office of Defense Nuclear Non-proliferation NA-22). The response includes expertise in the areas of radiological search, render safe, and consequence management. This article will discuss the methodologies, tools, procedures, and techniques to extract maximum radiological characterization information (isotopic composition, activities for individual isotopes, threat assessment etc.) from field monitoring or Search operation data.
61 RADIATION PROTECTION AND DOSIMETRY↗
Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.
59 BASIC BIOLOGICAL SCIENCES↗
A consolidated bioprocess design to produce multiple high-value platform chemicals from lignocellulosic biomass and its technoeconomic feasibility
5-Hydroxymethyl furfural (HMF) and furfurals are DOE-listed platform chemicals that can be derived from the renewable carbon in the lignocellulosic biomasses and have the potential to replace petroleum-derived alter- natives. High substrate cost and use of expensive solvents limit the economic feasibility of bio-based HMF production on an industrially relevant scale. The study presents an experimental optimized condition that maximizes the chemical-free production of HMF and furfurals without lowering the yield of total fermentable sugars from Saccharum bagasse. Hydrothermal pretreatment at 210 °C for 15 min yielded approximately 10%, 12%, and 46% of HMF, furfurals, and fermentable sugars per gram of dry biomass, respectively. Additionally, the study proposes a consolidated bioprocess model to produce and recover four high-value bioproducts i.e., HMF, furfurals, ethanol, and acetic acid based on the experimental results and evaluates its technoeconomic feasibility considering HMF as the main product. The minimum selling price (MSP) of HMF was estimated to be 930.6 USD/ t which is competitive with its petroleum-derived precursor alternative p-xylene (1,113 USD/t). The sensitivity analysis performed for the process parameters suggests that pretreatment cost and revenues from coproducts immensely influence the MSP of HMF. The preliminary technoeconomic analysis performed on the consolidated bioprocess design indicates that additional revenue streams from diversified coproducts in biorefineries aid in lowering the MSP of high-value bioproducts.
09 BIOMASS FUELS↗