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Frontiers in Scientific Workflows: Pervasive Integration With High-Performance Computing

Herein we address the increasing complexity of scientific workflows in the context of high-performance computing (HPC) and their associated need for robust, adaptable, and flexible computational support systems. We explore five key trends as well as future challenges and opportunities for scientific workflows and HPC technologies.

97 MATHEMATICS AND COMPUTING

Integration of Silica in G4CMP for Phonon Simulations: Framework and Tools for Material Integration

Superconducting detectors with sub-eV energy resolution have demonstrated success setting limits on Beyond the Standard Model (BSM) physics due to their unique sensitivity to low-energy events. G4CMP, a Geant4-based extension for condensed matter physics, provides a comprehensive toolkit for modeling phonon and charge dynamics in cryogenic materials. This paper introduces a technical formalism to support the superconducting qubit and low-threshold detector community in implementing phonon simulations in custom materials into the G4CMP. As a case study, we present the results of a detailed analysis of silica phonon transport properties relevant for simulating substrate backgrounds in Beryllium Electron capture in Superconducting Tunnel junctions (BeEST)-style experiments using G4CMP. Additionally, Python-based tools were developed to aid users in implementing their own materials and are available on the G4CMP repository.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life

Agent-based models (ABMs) in transportation modeling simulate activity and travel decisions at the disaggregate level of households and individuals. To do this, ABMs require detailed and realistic information on agents’ socioeconomic and demographic characteristics. Various synthetic population generators have been proposed to address this need. However, most of those currently in practice are cross-sectional in nature and do not account for the dynamics within households and individuals as they progress through life events over time. This is a major shortcoming, as literature has shown that transportation decisions are affected by the transition between and co-occurrence of life cycle events. While some demographic evolution simulators have been proposed to address this issue, they are developed using cross-sectional data and capture only a small set of life cycle events and their interdependence. Addressing these drawbacks, we propose a demographic microsimulator (DEMOS) that captures the “continuum of life” by considering a range of household- and individual-level life cycle events. DEMOS is developed using the Panel Survey of Income Dynamics, one of the world’s longest-running longitudinal surveys. The DEMOS submodels consider key life cycle events that are influenced by agents’ demographic variables. DEMOS is applied to evolve the population of the San Francisco Bay Area over a 9-year horizon. Results demonstrate how DEMOS generates life trajectories and how DEMOS outputs match the observed demographic trends. DEMOS is expected to enable longitudinal analysis in the context of ABMs and expand ABMs analyses relating to dynamic processes such as household-level vehicle transactions.

Demographic evolution

Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. Here, we validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.

59 BASIC BIOLOGICAL SCIENCES

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando

Sensory integration for neuroprostheses: from functional benefits to neural correlates

In the field of sensory neuroprostheses, one ultimate goal is for individuals to perceive artificial somatosensory information and use the prosthesis with high complexity that resembles an intact system. To this end, research has shown that stimulation elicited somatosensory information improves prosthesis perception and task performance. While studies strive to achieve sensory integration, a crucial phenomenon that entails naturalistic interaction with the environment, this topic has not been commensurately reviewed. Therefore, here we present a perspective for understanding sensory integration in neuroprostheses. First, we review the engineering aspects and functional outcomes in sensory neuroprosthesis studies. In this context, we summarize studies that have suggested sensory integration. We focus on how they have used stimulation-elicited percepts to maximize and improve the reliability of somatosensory information. Next, we review studies that have suggested multisensory integration. These works have demonstrated that congruent and simultaneous multisensory inputs provided cognitive benefits such that an individual experiences a greater sense of authority over prosthesis movements (i.e., agency) and perceives the prosthesis as part of their own (i.e., ownership). Thereafter, we present the theoretical and neuroscience framework of sensory integration. We investigate how behavioral models and neural recordings have been applied in the context of sensory integration. Sensory integration models developed from intact-limb individuals have led the way to sensory neuroprosthesis studies to demonstrate multisensory integration. Neural recordings have been used to show how multisensory inputs are processed across cortical areas. Lastly, we discuss some ongoing research and challenges in achieving and understanding sensory integration in sensory neuroprostheses. Here, resolving these challenges would help to develop future strategies to improve the sensory feedback of a neuroprosthetic system.

60 APPLIED LIFE SCIENCES

Thermal Integration of Advanced Nuclear Reactors with a Reference Refinery, Methanol Synthesis, and a Wood Pulp Plant (Rev.1)

The present report is intended to provide process flow diagrams (PFDs) and energy and mass balance data sheets for a U.S. industrial sector subset with which nuclear heat and power could be integrated—a subset that includes the oil refining, methanol and pulp and paper industries. Coupling options for integrating nuclear energy into these industries are quantitatively outlined for reference systems, and future work will extend this analysis in greater detail. Opportunities for integrating small modular nuclear reactors (SMNRs) were investigated for each of the industrial process configurations. Aspen HYSYS and Cycle-Tempo models for a high-temperature gas-cooled reactor were developed to evaluate the proposed integration. This introductory evaluation provides a general description and assessment of the operating principles, reactor coolant core outlet temperature, and reactor size to be integrated with industry. The industrial processes of oil refining and the production of methanol, pulp and paper were simulated by using Aspen HYSYS, Aspen Plus, and the PRELIM (Petroleum Refinery Life Cycle Inventory Model) tool to develop process details. Cycle-Tempo models then extend the process modeling results to obtain net energy demands (e.g., heat, steam, and electricity) when accounting for process steam and waste heat recovery. This information is intended to foster the analysis of integrating an SMNR to decarbonize industrial facilities. The SMNR would provide reliable, competitive, and sustainable clean energy while reducing carbon emissions and other environmental impacts, such as water withdrawals, consumption, and contamination. The refining industry, exhibited in Figure ES1, is a leading consumer of fossil -fuel-based heat, power, and hydrogen in the U.S. industrial sector, generating over 164 million metric tons (MMT) of CO 2 emissions in 2023. The overall mass and energy pertaining to a generalized complex refinery in the United States is reflected in Figure ES1, along with energy metrics regarding integration with a nuclear power plant (NPP). Data sheets were developed to indicate the energy requirements for the overall refinery and each refinery process. The data sheet for the overall refinery is shown in Table ES2.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Understanding drivers of oil and gas well integrity issues in the greater wattenberg area of Colorado

Well integrity is critically important to maintain to minimize the environmental impacts of oil and gas development and other subsurface energy operations. The Wattenberg Field of Colorado—a top producing field with >40,000 wells—has one of the most robust publicly reported well integrity programs in the country. Here, in this study, we analyzed annular pressure and annular-fluid geochemical test results collected from Wattenberg wells through the end of 2019 to characterize the frequency and spatial variability of integrity issues in the field and understand their drivers. Estimated frequencies of integrity issues among tested wells were 8.2-17.1% between 1955 and 2019 and 6.1-11.4% in 2019 alone. The frequency of integrity issues was nearly four times greater in wells located above the Longmont Wrench Fault Zone. Potential drivers of integrity issues were identified using ensemble decision tree models trained with a broad set of relevant information. Models show that well integrity issues are spatially clustered on regional and sub-regional scales and suggest the relatively high frequency of integrity issues observed is likely attributed to geologic factors. These findings are valuable for regulatory agencies and operators seeking to inform well integrity monitoring, plugging, and emissions reduction efforts and design future subsurface energy projects.

03 NATURAL GAS

Integrated-photonics-based systems for polarization-gradient cooling of trapped ions

Trapped ions are a promising modality for quantum systems, with demonstrated utility as the basis for quantum processors and optical clocks. However, traditional trapped-ion systems are implemented using complex free-space optical configurations, whose large size and susceptibility to vibrations and drift inhibit scaling to large numbers of qubits. In recent years, integrated-photonics-based systems have been demonstrated as an avenue to address the challenge of scaling trapped-ion systems while maintaining high fidelities. While these previous demonstrations have implemented both Doppler and resolved-sideband cooling of trapped ions, these cooling techniques are fundamentally limited in efficiency. In contrast, polarization-gradient cooling can enable faster and more power-efficient cooling and, therefore, improved computational efficiencies in trapped-ion systems. While free-space implementations of polarization-gradient cooling have demonstrated advantages over other cooling mechanisms, polarization-gradient cooling has never previously been implemented using integrated photonics. In this paper, we design and experimentally demonstrate key polarization-diverse integrated-photonics devices and utilize them to implement a variety of integrated-photonics-based polarization-gradient-cooling systems, culminating in the first experimental demonstration of polarization-gradient cooling of a trapped ion by an integrated-photonics-based system. By demonstrating polarization-gradient cooling using an integrated-photonics-based system and, in general, opening up the field of polarization-diverse integrated-photonics-based devices and systems for trapped ions, this work facilitates new capabilities for integrated-photonics-based trapped-ion platforms.

atom optics

Ion Traps and Packaging for Heterogenous Integration - Chimera

Microfabricated surface ion traps and silicon-based photonics are critical technologies for scaling quantum systems. Current ion trap architectures face scalability and integration challenges due to limitations in optical access, fabrication techniques, and material compatibility. State-of-the-art quantum computers and atomic clocks are investigating monolithic integration, which necessitates custom traps for each ion species and has not overcome the integration hurdles presented by merging these technologies. The Chimera (Ion Traps and Packaging for Heterogeneous Integration) project proposes a novel approach utilizing heterogeneous integration (HI) of ion traps and photonic circuits. This separation of components allows for flexibility in ion trap design and reduces fabrication compromises. The Chimera project specifically designed an ion trap to interface vertically with a separately fabricated waveguide chip and demonstrates the first steps to integrating them at the packaging level. The ion trap features a large area of removed silicon, allowing the photonics chip outputs closer to the ion trap, improving alignment and packaging processes. The alignment must be accurate to < 1 µm to ensure that the light from the waveguide can overlap with the trapping region. This fine alignment must also be maintained through an ultra-high vacuum bake, a critical step in preparing an ion trap experiment. By combining separate chips, we demonstrate a new path for scaling trapped ion technology that is less reliant on monolithic integration. We successfully fabricated a trap with a large area of oxide removed, resulting in a region thinned to about 40 µm, a key milestone toward successful integration.

42 ENGINEERING

On-PIC Light Source Integration & Micro-dispensing of Solder Paste for Flip Chip Application

To reach the next level benefits of photonic integrated circuits (PICs), the Integrated Photonic Systems Roadmap-International describes the necessity of either heterogeneous or hybrid integration of light sources [1]. A new approach for hybrid integration is Photonic Wire Bonding where 3D nanolithography is used to pattern a polymer waveguide that connects light sources to PIC waveguides. The waveguides resemble electrical wire bonds and essentially do the same as their electrical counterpart for packaging photonic chips together. In order to reap the full benefits of a photonic wire bonds, the light source must be carefully packaged. In this work I seek to expand RIT’s photonic packaging capability by establishing a packaging process to integrate light sources, specifically an Indium Phosphide distributed feedback lasers and a reflective semiconductor optical amplifiers, directly onto a photonic integrated circuits. Another necessary requirement for PIC packaging is densely integrated electrical connectivity. In this thesis I developed a fine pitch flip chip interconnect technique demonstrated using gold stud bumps in conjunction with micro-dispensed solder paste. This work opens the door to high density photonic flip chip applications. The micro-dispensed solder paste dots having diameters 50-125 µm are currently being tested at a pitch of 150 µm . The gold stud bumps are formed with 1mil gold wire creating bumps with a diameter of 40-60 µm depending on specific parameter values. These capabilities will allow RIT to assemble and test novel photonic integrated devices, cutting down on the time and cost associated with third party assembly and tests facilities. Thereby keeping RIT at the forefront of photonic research.

Wongk, Nicole

Design of Quasi-Integral Experiments at the Flexible Neutron Source at the University of Tennessee

Nuclear reaction data libraries make use of experimental data that are differential in reaction and neutron energy for evaluation and data that are integral in reaction and energy for validation. In many cases, integral measurements can provide lower experimental uncertainties than differential measurements, but the impact of individual reactions and energies cannot generally be determined from the single experimental observable. “Quasi-integral” or “quasi-differential” measurements, which are integral in one characteristic (energy or reaction) and differential in the other, can often provide a middle ground of lower experimental uncertainties combined with some ability to unpack the impact of individual reactions or energies. Furthermore, the Flexible Neutron Source (FNS) at the University of Tennessee, Knoxville, is a new experimental facility that can perform integral and quasi-integral measurements by removing components of the integral configuration to determine the impact of specific reactions. Possible flux-averaged cross-section measurements, flux perturbation measurements, and neutron downscattering measurements are simulated here to show the value of the FNS to evaluation and validation of nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Nyström type exponential integrators for strongly magnetized charged particle dynamics

Solving for charged particle motion in electromagnetic fields (i.e. the particle pushing problem) is a computationally intensive component of particle-in-cell (PIC) methods for plasma physics simulations. This task is especially challenging when the plasma is strongly magnetized due numerical stiffness arising from the wide range of time scales between highly oscillatory gyromotion and long term macroscopic behavior. A promising approach to solve these problems is by a class of methods known as exponential integrators that can solve linear problems exactly and are A-stable. This work extends the standard exponential integration framework to derive Nyström-type exponential integrators that integrates the Newtonian equations of motion as a second-order differential equation directly. In particular, we derive second-order and third-order Nyström-type exponential integrators for strongly magnetized particle pushing problems. Numerical experiments show that the Nyström-type exponential integrators exhibit significant improvement in computation speed over the standard exponential integrators.

general physics

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF

Technical and Economic Assessment and Gap Analysis of Advanced Nuclear Reactor Integration with a Reference Oil Refinery

Efforts to identify the most-economic methods to decarbonize several sectors of the U.S. economy are underway. Industrial processes such as crude-oil refining rely heavily on energy-dense and easily stored and transported fossil fuels for powering their operations. Refineries use large amounts of energy, primarily derived from fossil sources to separate crude-oil components, break down heavier hydrocarbons into lighter compounds, remove impurities, reform hydrocarbon molecules, and generate steam and electricity for pumps and compressors and other various auxiliary systems. Crude-oil refining operations such as distillation, cracking, desulfurization, reforming, utilities systems and some offsite facilities collectively account for most of the energy consumption. Other operations such as hydrocracking or hydrotreating also require hydrogen for developing hydrogenation reactions which involve substantial heating to keep the reactors at high-temperature and pressure levels. All heat and energy demands are typically provided by natural gas (NG), oil, or other fuels, which makes refinery industry one of the most-difficult sectors to decarbonize. Nuclear power is a viable and energy-dense source of clean electricity, heat, and hydrogen to provide the large, sustainable energy supply that the refining industry demands. The U.S. Department of Energy’s (DOE’s) Integrated Energy Systems (IES) program is working to perform research and development, design, economic siting, and risk analysis. This state-of-the-art work will enable the first on-site demonstrations and commercial deployments of advanced small modular nuclear reactors (SMNRs) integrated with industries such as chemical production, refining, iron and steel making, and more. IES seeks to demonstrate the ability of advanced nuclear reactors to meet the heat and power demands of these industries while reducing carbon emissions in a sustainable and cost-competitive way. The primary objective of this research effort is to analyze industrial-scale SMNR integration intended to decarbonize refining facilities. The foreseen outcome is the provision of reliable, cost-competitive, and sustainable clean energy, alongside a reduction of carbon emissions. Specifically, the focus of this work lies on meeting the reference facilities’ heat and electricity demands with nuclear power while also supplying clean hydrogen via integrated high-temperature steam electrolysis (HTSE). This report presents a comprehensive technical and economic assessment of the integration of advanced nuclear reactors into a reference refinery, leveraging financial incentives from the Inflation Reduction Act (IRA). The evaluation aims to explore the potential economic benefits and challenges associated with incorporating advanced nuclear reactors into refinery operations, particularly in terms of energy efficiency, economic implications and environmental impact. By examining both the technical feasibility and economic viability, this analysis seeks to identify existing gaps and propose solutions for successful nuclear integration implementation. The findings are intended to provide valuable insights for stakeholders considering the adoption of advanced nuclear reactors in the refining sector. A refinery reference-plant was developed, using an open-source refinery model, Petroleum Refinery Lifecycle Inventory Model (PRELIM) and expert assessment, as a base case for comparison with various nuclear integration options. The capacity of 100 kbd/day (KBD) of heavy crude-oil feed was selected to represent a general coking-type refinery with deep conversion capabilities (incorporating heavy-oil upgrading with FCC, coking, and associated hydrotreating process units), using a heavy crude-oil feed, which represents about 70% of U.S. refineries configurations. A summary of all cases considered in this study is shown in Table 1.

13 HYDRO ENERGY