SeQUeNCe: a customizable discrete-event simulator of quantum networks
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71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
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Traveler: Navigating Task Parallel Traces for Performance Analysis
Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace —a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. Here, to address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler , an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.
97 MATHEMATICS AND COMPUTING↗
Etching of Si 3 N 4 induced by electron beam plasma from hollow cathode plasma in a downstream reactive environment
An etching system based on the interaction of electrons extracted from a direct current (DC) hollow-cathode (HC) Ar plasma and injected towards a Si3N4 covered silicon substrate located in the downstream reactive environment created by an additional remote CF 4 /O 2 plasma source was developed and evaluated. By controlling the properties of the injected beam electrons, this approach allows to deliver energy to a surface functionalized by exposure to reactive species, and initiate surface etching. The energy of the primary beam electrons is controlled by the acceleration voltage relative to the HC discharge. Ar atoms flow from the high-pressure HC discharge into the low pressure downstream reactive environment in the process chamber. For an acceleration voltage greater than the ionization potential of Ar and/or process gas species, the energetic primary beam electrons produce a secondary plasma in the process chamber, and can also cause additional dissociation. We have characterized the properties of the secondary plasma and also surface etching of Si 3 N 4 as a function of process parameters, including acceleration voltage (0-80 V), discharge current of the HC discharge (1-2 A), pressure (3.5-20 mTorr), source to substrate distance (1.5 to 5 cm), and feed gas composition (20% and 80% O2 in CF 4 /O 2 ). The electron energy probability function (EEPF) measured with a Langmuir probe about 2.5 cm below the extraction ring suggests several major groups of electrons for this situation, including high energy primary beam electrons with an energy that varies as the acceleration voltage is changed and low energy electrons produced by beam electron-induced ionization of the Ar gas in the process chamber. When a remote CF 4 /O 2 plasma is additionally coupled to the process chamber, Si 3 N 4 surfaces can be functionalized, and by varying the energy of the beam electrons, Si 3 N 4 etching can be induced by electron-neutral synergy effect with plasma-surface interaction. For conditions without beam electron injection, the remote plasma etching rate (ER) of Si 3 N 4 depends strongly on the O 2 concentration in the CF 4 /O 2 processing gas mixture and can be suppressed for O 2 -rich process conditions by the formation of a SiONF passivation layer on the Si 3 N 4 surface. The combination of the HC electron beam source with the remote plasma source (HCEB-RP) makes it possible to induce Si 3 N 4 etching for O 2 -rich remote plasma conditions where remote plasma by itself produces negligible Si 3 N 4 etching. The electron enhanced etching of Si 3 N 4 depends strongly on O 2 /CF 4 mixing ratio reflecting changing arrival rates of O and F species at the surface. Optical emission spectroscopy was used to estimate the ratio of gas phase F and O densities and found to be controlled by the gas mixing ratio and independent of HC EB operating conditions. At this time the detailed sequence of events operative in the etching mechanism is unclear. While the increase of the electron energy is ultimately responsible for initiating surface etching, at present we cannot rule out a role of ions from the simultaneously produced secondary plasma in plasma surface interaction mechanisms.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Maximizing Strength: The Stimuli and Mediators of Strength Gains and Their Application to Training and Rehabilitation
Abstract Spiering, BA, Clark, BC, Schoenfeld, BJ, Foulis, SA, and Pasiakos, SM. Maximizing strength: the stimuli and mediators of strength gains and their application to training and rehabilitation. J Strength Cond Res 37(4): 919–929, 2023—Traditional heavy resistance exercise (RE) training increases maximal strength, a valuable adaptation in many situations. That stated, some populations seek new opportunities for pushing the upper limits of strength gains (e.g., athletes and military personnel). Alternatively, other populations strive to increase or maintain strength but cannot perform heavy RE (e.g., during at-home exercise, during deployment, or after injury or illness). Therefore, the purpose of this narrative review is to (a) identify the known stimuli that trigger gains in strength; (b) identify the known factors that mediate the long-term effectiveness of these stimuli; (c) discuss (and in some cases, speculate on) potential opportunities for maximizing strength gains beyond current limits; and (d) discuss practical applications for increasing or maintaining strength when traditional heavy RE cannot be performed. First, by conceptually deconstructing traditional heavy RE, we identify that strength gains are stimulated through a sequence of events, namely: giving maximal mental effort, leading to maximal neural activation of muscle to produce forceful contractions, involving lifting and lowering movements, training through a full range of motion, and (potentially) inducing muscular metabolic stress. Second, we identify factors that mediate the long-term effectiveness of these RE stimuli, namely: optimizing the dose of RE within a session, beginning each set of RE in a minimally fatigued state, optimizing recovery between training sessions, and (potentially) periodizing the training stimulus over time. Equipped with these insights, we identify potential opportunities for further maximizing strength gains. Finally, we identify opportunities for increasing or maintaining strength when traditional heavy RE cannot be performed.
Sport Sciences↗
Adverse Neurological Effects of Wildfire Smoke
The respiratory and cardiovascular effects of smoke exposure are well documented from cigarette smoking and particulate matter (PM) associated with air-pollution studies, but epidemiological data also suggests exposure to high levels of woodsmoke correlate with central-nervous-system (CNS) dysfunction, including elevated rates of Alzheimer’s disease (AD) and dementia. Neuro-inflammation is believed to initiate the majority of Alzheimer’s and other neurodegenerative diseases attributed to environmental factors. We investigated whether inhaled PM and specific classes of compounds in wildfire smoke condensate extract (WSE) reach the brain and cause neuro-inflammation that can lead to progressive neurological degeneration, using isotope tracing of labeled particulate matter and major compound classes, biomarkers of blood-brain barrier (BBB) integrity, and biomarkers of neuro-inflammation. This project showed that inhalation exposure to PM and major compound classes present in WSE reached the brain through absorption in the nasal cavity and systemic circulation across the BBB. Twenty-four exposures of WSE to brain endothelial cells that form the main physical barrier of the BBB produced dose-dependent increases in biomarkers of inflammation and decreases in tight junction markers between cells. Intranasal exposure to WSE caused inflammatory disfunction in lung and brain. Biomarkers of inflammation increased and an enzyme inhibiting inflammation decreased. Similar patterns of chemical-induced changes in the lung and brain suggest either: (1) chemicals may act through shared molecular pathways upon entering lung and brain, or (2) that mediators originating in the lung circulate systemically to the brain and drive neuroinflammation. These findings warrant further mechanistic studies to delineate the temporal sequence of events to establish the lung-brain axis.
54 ENVIRONMENTAL SCIENCES↗
From Qualitative to Quantitative AOP: A Case Study of Neurodegeneration
Adverse outcome pathways (AOPs) include a sequence of events that connect a molecular-level initiating event with an adverse outcome at the cellular level for human health endpoints, or at the population level for ecological endpoints. When there is enough quantitative understanding of the relationships between key events in an AOP, a mathematical model may be developed to connect key events in a quantitative AOP (qAOP). Ideally, a qAOP will reduce the time and resources spent for chemical toxicity testing and risk assessment and enable the extrapolation of data collected at the molecular-level by in vitro assays, for example, to predict whether an adverse outcome may occur. Here, we review AOPs in the AOPWiki, an AOP repository, to determine best practices that would facilitate conversion from AOP to qAOP. Then, focusing on a particular case study, acetylcholinesterase inhibition leading to neurodegeneration, we describe specific methods and challenges. Examples of challenges include the availability and collection of quantitative data amenable to model development, the lack of studies that measure multiple key events, and model accessibility or transferability across platforms. We conclude with recommendations for improving key event and key event relationship descriptions in the AOPWiki that facilitate the transition of qualitative AOPs to qAOPs.
Sinitsyn, Dennis↗
The Great Inequality and the Dynamical Disintegration of the Outer Solar System
Using an ensemble of N-body simulations, this paper considers the fate of the outer gas giants (Jupiter, Saturn, Uranus, and Neptune) after the Sun leaves the main sequence and completes its stellar evolution. Due to solar mass loss—which is expected to remove roughly half of the star’s mass—the orbits of the giant planets expand. This adiabatic process maintains the orbital period ratios, but the mutual interactions between planets and the width of mean-motion resonances (MMR) increase, leading to the capture of Jupiter and Saturn into a stable 5:2 resonant configuration. The expanded orbits, coupled with the large-amplitude librations of the critical MMR angle, make the system more susceptible to perturbations from stellar flyby interactions. Accordingly, within about 30 Gyr, stellar encounters perturb the planets onto the chaotic subdomain of the 5:2 resonance, triggering a large-scale instability, which culminates in the ejections of all but one planet over the subsequent ∼10 Gyr. After an additional ∼50 Gyr, a close stellar encounter (with a perihelion distance less than ∼200 au) liberates the final planet. Through this sequence of events, the characteristic timescale over which the solar system will be completely dissolved is roughly 100 Gyr. Our analysis thus indicates that the expected dynamical lifetime of the solar system is much longer than the current age of the universe, but is significantly shorter than previous estimates.
79 ASTRONOMY AND ASTROPHYSICS↗
Applying Waveform Correlation and Waveform Template Metadata to Aftershocks in the Middle East to Reduce Analyst Workload
Organizations that monitor for underground nuclear explosive tests are interested in techniques that automatically characterize recurring events such as aftershocks to reduce the human analyst effort required to produce high-quality event bulletins. Waveform correlation is a technique that is effective in finding similar waveforms from repeating seismic events. In this study, we apply waveform correlation in combination with template event metadata to two aftershock sequences in the Middle East to seek corroborating detections from multiple stations in the International Monitoring System of the Preparatory Commission for the Comprehensive Nuclear-Test-Ban Treaty Organization. We use waveform templates from stations that are within regional distance of aftershock sequences to detect subsequent events, then use template event metadata to discover what stations are likely to record corroborating arrival waveforms for recurring aftershock events at the same location, and develop additional waveform templates to seek corroborating detections. We evaluate the results with the goal of determining whether applying the method to aftershock events will improve the choice of waveform correlation detections that lead to bulletin-worthy events and reduction of analyst effort.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Evaluating the Aftershock Duration of Induced Earthquakes
As the carbon sequestration community prepares to scale up the number and size of commercial operations, the need for tools and methods to assess and mitigate risks associated with these operations becomes increasingly important. One outstanding question is whether aftershocks of induced events decay quickly after injection operations cease or if aftershock activity persists for hundreds of years before returning to background levels more akin to tectonic events (Stein and Liu, 2009). Appropriate estimates of the aftershock duration impact several operational management decisions including mitigation strategies and post-injection monitoring for seismic activity. It is hypothesized that induced earthquake rates may diminish more quickly after injection is stopped, owing to higher stressing rates from injected fluids. Alternatively, it is plausible that only the first event in the sequence is induced by increased fluid overpressures, whereas subsequent events (e.g., aftershocks) respond to the stored tectonic stresses and static and dynamic stress changes due to the mainshock (Keranen et al., 2013). Further, if the aftershock duration can be linked to stressing rates due to injection, then it follows that operational strategies to reduce seismic hazard by reducing injection rates or volumes may be successful. However, if aftershocks of induced events are relieving stored tectonic stresses, then altering injection volumes may not alleviate ongoing seismic activity. Furthermore, knowledge of an aftershock duration could aid in the determination of an appropriate post-injection monitoring period for ongoing seismicity, which is a factor in overall operational costs. In this study, we model induced seismicity sequences in Oklahoma with a coupled Coulomb rate–state earthquake rate model (Dieterich, 1994; Kroll et al., 2017) to estimate aftershocks durations. Results for the current study indicate that elevated rates of aftershock activity following induced mainshocks return to background seismicity rates in less than five years, contrary to the tens to hundreds of years observed for tectonic aftershocks.
58 GEOSCIENCES↗
Detecting anomalous sequences in electronic health records using higher-order tensor networks
Detecting anomalous sequences is an integral part of building and protecting modern large-scale health information technology (HIT) systems. These HIT systems generate a large volume of records of patients’ state and significant events, which provide a valuable resource to help improve clinical decisions, patient care processes, and other issues. However, detecting anomalous sequences in electronic health records (EHR) remains a challenge in healthcare applications for several reasons, including imbalances in the data, complexity of relationships between events in the sequence, and the curse of dimensionality. Conventional anomaly detection methods use the finite sequence of events to discriminate sequences. They fail to incorporate salient event details under variable higher-order dependencies (e.g., duration between events) that can provide better discrimination of sequences in their models. To address this problem, we propose event sequence and subsequence anomaly detection algorithms that (1) use network-based representations of interactions in the data, (2) account for variable higher-order dependencies in the data, and (3) incorporate events duration for adequate discrimination of the data. The proposed approach identifies anomalies by monitoring the change in the graph after the test sequence is removed from the network. The change is quantified using graph distance metrics so that dramatic changes in the network can be attributed to the removed sequence. Furthermore, the proposed subsequence algorithm recommends plausible paths and salient information for the detected anomalous subsequences. Our results show that the proposed event sequence anomaly detection algorithm outperforms the baseline methods for both synthetic data and real-world EHR data.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Formal verification and validation of run-to-completion style state charts using Event-B
State chart notations with ‘run to completion’ semantics are popular with engineers for designing controllers that react to environment events with a sequence of state transitions but lack formal refinement and rigorous verification methods. State chart models are typically used to design complex control systems that respond to environmental triggers with a sequential process. The model is usually constructed at a concrete level and verified and validated using animation techniques relying on human judgement. Event-B, on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. Abstraction and formal verification provide greater assurance that critical (e.g. safety or security) properties are not violated by the control system. In this paper, we introduce a notion of refinement into a ‘run to completion’ state chart modelling notation and leverage Event-B’s tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Event-B refinements and suggest a solution. We illustrate our approach and show how models can be validated at different refinement levels using our scenario checker animation tools. We show how critical invariant properties can be verified by proof despite the reactive nature of the system and how behavioural aspects of the system can be verified by testing the expected reactions using a temporal logic, model checking approach. To verify liveness, we outline a proof that the run to completion is deadlock-free and converges to complete the run.
97 MATHEMATICS AND COMPUTING↗
Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions
The CRISPR-Cas9 system has been deployed for precision mutagenesis in an ever-growing number of species, including agricultural crops and forest trees. Its application to closely linked genes with extremely high sequence similarities has been less explored. In this study, we used CRISPR-Cas9 to mutagenize a tandem array of seven Nucleoredoxin1 (NRX1) genes spanning ~100 kb in Populus tremula × Populus alba. We demonstrated efficient multiplex editing with one single guide RNA in 42 transgenic lines. The mutation profiles ranged from small insertions and deletions and local deletions in individual genes to large genomic dropouts and rearrangements spanning tandem genes. We also detected complex rearrangements including translocations and inversions resulting from multiple cleavage and repair events. Target capture sequencing was instrumental for unbiased assessments of repair outcomes to reconstruct unusual mutant alleles. The work highlights the power of CRISPR-Cas9 for multiplex editing of tandemly duplicated genes to generate diverse mutants with structural and copy number variations to aid future functional characterization.
59 BASIC BIOLOGICAL SCIENCES↗
Charge accumulation and solvation in $β$-NiOOH: Surface chemistry of an OER catalyst from ML-aided simulations
Electrochemical water splitting is a key technology for a sustainable energy transition, providing a route to store surplus electricity from renewable sources. A central bottleneck is the sluggish oxygen evolution reaction (OER), which drives the search for catalysts that are active, stable, and inexpensive enough for large-scale deployment. Within this context, pure and doped NiO x H y combine high activity with low cost, making them prime candidates for alkaline OER. Yet, despite extensive study, the atomistic structure of NiOOH under operando conditions and the associated reaction mechanisms remain debated. Here, we investigate the structural complexity of pure β-NiOOH, the scaffold for its doped derivatives. We systematically investigate the oxidation of the surface adsorbates via proton-coupled electron transfer steps across relevant facets and sites, identifying the most probable sequence of deprotonation events. Our results reveal asymmetric charge accumulation on Wulff-relevant surfaces and show how applied potential can promote morphological restructuring. Explicit solvation is included through machine-learning interatomic potential molecular dynamics of the NiOOH/water interface, which allows us to resolve the hydrophobic and hydrophilic character of different surfaces and the associated interfacial water structure. Together, these insights demonstrate how surface chemistry and solvation jointly govern the stability of NiOOH and the accumulation of surface charge, with possible implications for catalytic performance.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Learning reference governor for cycle-to-cycle combustion control with misfire avoidance in spark-ignition engines at high exhaust gas recirculation–diluted conditions
Cycle-to-cycle feedback control is employed to achieve optimal combustion phasing while maintaining high levels of exhaust gas recirculation by adjusting the spark advance and the exhaust gas recirculation valve position. The control development is based on a control-oriented model that captures the effects of throttle position, exhaust gas recirculation valve position, and spark timing on the combustion phasing. Under the assumption that in-cylinder pressure information is available, an adaptive extended Kalman filter approach is used to estimate the exhaust gas recirculation rate into the intake manifold based on combustion phasing measurements. The estimation algorithm is adaptive since the cycle-to-cycle combustion variability (output covariance) is not known a priori and changes with operating conditions. A linear quadratic regulator controller is designed to maintain optimal combustion phasing while maximizing exhaust gas recirculation levels during load transients coming from throttle tip-in and tip-out commands from the driver. During throttle tip-outs, however, a combination of a high exhaust gas recirculation rate and an overly advanced spark, product of the dynamic response of the system, generates a sequence of misfire events. In this work, an explicit reference governor is used as an add-on scheme to the closed-loop system in order to avoid the violation of the misfire limit. The reference governor is enhanced with model-free learning which enables it to avoid misfires after a learning phase. Experimental results are reported which illustrate the potential of the proposed control strategy for achieving an optimal combustion process during highly diluted conditions for improving fuel efficiency.
42 ENGINEERING↗
Generic Pressurized Water Reactor Model for SAPHIRE
Generic Pressurized Water Reactor Model for SAPHIRE This report contains a data dump from a SAPHIRE Generic Pressurized Water Reactor (PWR) model. The intent is to have this information reviewed for export control and classification so that the generic model can be used external to INL. The facility model is not applicable to any existing nuclear reactors. The Generic PWR model does not represent any existing power plant and was created to support research and training purposes. Three distinct types of data are used to create a SAPHIRE risk model: - Event trees representing typical PWR sequences - Fault trees representing generic system performance - Basic events (e.g., component failure information) Where possible, we have taken information from publicly available documents and referenced that information tagged to a specific item.
99 GENERAL AND MISCELLANEOUS↗
Evaluation of sequence tracking methods for Compton cameras based on CdZnTe arrays
In this study, the performance of sequence tracking methods for multiple interaction events in specific CdZnTe Compton imagers was evaluated using Monte Carlo simulations. The Compton imager consisted of a 6 × 6 array of virtual Frisch-grid CZT crystals, where the dimensions of each crystal were 5 × 5 × 12 mm 3 . The sequence tracking methods for another Compton imager that consists of two identical CZT crystals arrays were also evaluated. When 662 keV radiation was incident on the detectors, the percentages of the correct sequences determined by the simple comparison and deterministic methods for two sequential interactions were identical (~80 %), while those evaluated using the minimum squared difference method (55-59 %) and Three Compton method (45-55 %) for three sequential interactions, differed from each other. The reconstructed images of a 662 keV point source detected using single and double arrays were evaluated based on their angular resolution and signal-to-noise ratio, and the results showed that the double arrays outperformed single arrays.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Gamma-ray imaging of Np-237 metal using an organic glass imager
Neutron and gamma-ray imaging systems are deployed within the field of nuclear safeguards for the detection and localization of special nuclear materials and other materials of interest. 237 Np is one of these materials of interest due its presence in spent nuclear fuel and potential for use in nuclear weapons when purified. Here, for the first time, a 6 kg neptunium sphere (98.8 wt% 237 Np) was measured using a dual-particle imager, from the University of Michigan, consisting of organic glass and inorganic scintillators. The novel composition of organic glass scintillator was recently developed at Sandia National Labs and has been used in particle imaging systems due to its time resolution and particle discrimination capabilities. Gamma-ray energy spectra from single and coincident events were extracted and the sequencing of Compton scatter and photoelectric absorption gamma-ray events was used to generate images using simple backprojection. The emissions of interest in this work are the 312 keV and 416 keV gamma rays from 233 Pa, a daughter isotope from the neptunium decay series. The results of this work show that there is close agreement between the true source location in angular space and the converged location from the gamma ray images created using the system. The gamma spectroscopy from single and coincident events also identified the characteristic emission from the daughter isotope and could be used to assist with the identification of 237 Np. Furthermore, successful localization of the source with 5 s of data demonstrates the practical application of the imaging system for imaging and detection of material in weapons-useable quantities.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Safety Analysis for the Versatile Test Reactor Conceptual Design
Safety analysis simulations have been carried out using the SAS4A/SASSYS-1 safety analysis code system to update the baseline set of results for the Versatile Test Reactor conceptual design. Results from a previous revision of this work provided input for the Conceptual Safety Design Report summarizing the overall safety basis for the VTR. This work will also support future analyses that will be required for Chapter 13, “Accident Analysis,” of a preliminary safety analysis report. A number of transients have been evaluated based on categories of postulated accident sequences suggested for consideration in NUREG-1537. Ultimately, the full spectrum of event initiators and subsequent accident sequences will be defined through a probabilistic risk assessment of the plant design following the implementation of the Licensing Modernization Project guidelines as described in the VTR Safety Design Strategy. Since that process is ongoing, the present analysis addresses several transients that are expected to be bounding accident scenarios that represent the three key ways to perturb a reactor: through changes to the core inlet temperature, mass flow rate, or reactivity. These correspond to a loss of heat sink (LOHS), loss of flow (LOF) or station blackout (SBO), and transient overpower (TOP), respectively. Both Protected and Unprotected versions of these transients have been evaluated, along with additional transients that include transient overpower with one stuck rod, pump coast-down failures, seismic events, and overcooling events. At the current stage of design, transient simulation results for the Versatile Test Reactor indicate that large safety margins exist for many event initiators. However, several “enabling” assumptions have been made, in terms of both design features and design limits, in order to perform the analyses; and these assumptions will need to be revised as the design matures. In addition, a larger spectrum of events needs to be evaluated as part of the on-going probabilistic risk assessment process.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗