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The presentation discusses the scope of EMPIRE, EMPIRE's convenience, the EMPIRE-3.2 (Malta) Nuclear Reaction Model Code, reaction models, and what is needed to improve EMPIRE's predictive power.
This is the final report for the early career award for Prof. Egemen Kolemen that aimed to develop the physics and technical basis of real-time transient – i.e. disruptions and Edge Localized Modes (ELMs) – avoidance and feedback control at the DIII-D nuclear fusion facility for the ITER era. During this project, we reconstructed high quality real-time DIII-D equilibria using kinetic information from the motional Stark effect (MSE), Thomson Scattering (TS), and Charge Exchange Recombination (CER) spectroscopy. These equilibria were analyzed in real-time to determine the low-n ideal MHD stability and the pedestal stability thresholds, and to obtain plasma response models. These calculations were used to understand which physical process evolves to lead to the onset of disruption in ITER-relevant scenarios at DIII-D, and how disruption can be predicted using stability analysis as opposed to the current methods of correlation of various signals, which are descriptive but lack predictive power. In the disruption studies, we focused on tearing modes, since these constitute the vast majority of disruptions in this regime. With this knowledge, real-time disruption avoidance algorithms were developed and tested. The enhanced situation awareness and physics insight were used in advanced real-time feedback control of pedestal and core profiles, which allowed the pursuit and sustainment of transient-free high-confinement regimes that cannot be achieved via feed-forward design based on in-between shot analysis.
This collaborative project combines synthesis, measurement, and theory by three faculty members at the Eddleman Quantum Institute of UC Irvine to effectively investigate the quantum properties of molecules in the space, time, and frequency domains. Through synthetic chemistry, molecules are tailored for their magnetic and coherent properties. By combining femtosecond (fs) terahertz (THz) light and a continuous wave (cw) THz laser with a low temperature scanning tunneling microscope (STM), quantum phenomena are probed with simultaneous femtosecond temporal and atomic-scale spatial resolution. In particular, the invention of the quantum superposition microscope (QSM) advances quantum sensing for enhanced spectroscopy and imaging capabilities. Coupling theory to the experimental efforts offers a deeper understanding and predictive power for the molecular systems. The phenomena of superposition, entanglement, and coherence is central to quantum information science and can be realized in qubit states. Many systems can be modeled by a double-well potential in which two levels are formed in the two lowest energy states interacting with the environment and external radiation. In focusing on molecules as two-level systems, the underlying expectation is that their tunable composition and structure allows an effective parameter space to optimize their use as qubits for quantum sensing and computing. The THz radiation induces the superposition between the two states, appearing as temporal oscillations that damp in amplitude. Enhanced spectroscopy and imaging in the time and frequency domains is achieved through the extreme sensitivity of the frequency and damping of coherence of two-level systems to its environment. A single hydrogen molecule trapped in the STM tunneling gap experiences a double-well potential and absorption of THz femtosecond pulses of light creates the superposition of its two levels, appearing as damped oscillations in the light induced direct current (DC). The oscillation frequency depends sensitively on the electric field distribution of the copper nitride (Cu 2 N) surface, through the Stark effect, and associated with the different charge distributions at the copper and nitrogen sites and in between. This QSM can resolve variation in the surface electric field with 0.02 nanometer resolution. In addition, the single hydrogen molecule entaes with nearby hydrogen molecules as seen in the avoided level crossings of energy (oscillation frequency) versus the voltage across the tunneling gap. Thus, the first application of the QSM senses and images the surface electric field at the atomic scale. Results from this project advance fundamental understanding of quantum phenomena, develop novel synthesis, measurement, and theory, provide the knowledge foundation for molecule-based qubits and sensing that enable the development of the QSM and emergent technologies. This project trained researchers in quantum information science, extended knowledge in classrooms, and outreached to the community.
With the rise of cheap data and sensors, more use cases are emerging for multi-input models. Research has shown that including multiple data modalities can improve performance, suggesting that deep learning models can successfully learn to leverage complementary information from different modalities. However, this improved predictive power comes with unanticipated costs: additional inputs change model resiliency and expand the threat space for adversarial attacks. We first provide theoretical underpinnings for how adversarial success scales with input dimension. We then characterize the performance of a suite of multispectral deep learning models with different fusion approaches, quantify their relative reliance on different input bands, and evaluate their robustness to naturalistic and adversarial image corruptions.
This project covered theoretical studies in particle physics, particle astrophysics and cosmology, aiming to bridge theoretical models with observable phenomena. The central focus was on exploring innovative mechanisms that could simultaneously address several outstanding puzzles in these areas, including the nature of dark matter, the muon g-2 anomaly, the existence of topologically stable monopoles, the generation of observable gravitational waves from early universe phenomena and high energy cosmic rays. One of the major achievements of this project was the development of models that predict new physics accessible through current and forthcoming experimental setups, both in particle colliders and astrophysical observations. These models have been instrumental in proposing verifiable predictions concerning supersymmetric extensions, the dynamics of cosmic strings and monopoles, and the intricate processes underpinning baryogenesis and reheating post-inflation. In tackling the dark matter conundrum, the project proposed several candidates within extended frameworks, such as light Z' models, pseudo-Goldstone dark matter, and scenarios integrating dark matter with inflationary cosmology. Each model outlined pathways for detection through direct, indirect, and collider search strategies, marking significant strides in the hunt for dark matter. Another cornerstone of the project was the in-depth analysis of inflationary models compliant with the Trans-Planckian Censorship Conjecture, highlighting the compatibility of axion dark matter within such frameworks. This not only provided a coherent picture of early universe cosmology but also delineated clear experimental signatures. The exploration of grand unified theories yielded insights into the potential discovery of monopoles and novel particle configurations at energy scales accessible to current and future colliders. This endeavor expanded the predictive power of these theories, particularly in the context of proton decay and the properties of Higgs-portal dark matter. Throughout the project, significant emphasis was placed on ensuring the theoretical developments were grounded in experimental testability. This led to a series of publications across prestigious journals, each contributing to the vibrant discourse at the intersection of particle physics and cosmology. In summary, this project has elucidated pathways beyond the Standard Model that are ripe for exploration through both ongoing and upcoming experimental efforts. The comprehensive approach adopted herein not only enhances our understanding of the fundamental forces and constituents of the universe but also propels the field towards new frontiers in high-energy physics and cosmology.
Deep learning (DL) models have enjoyed increased attention in recent years because of their powerful predictive capabilities. While many successes have been achieved, standard deep learning methods suffer from a lack of uncertainty quantification (UQ). While the development of methods for producing UQ from DL models is an active area of current research, little attention has been given to the quality of the UQ produced by such methods. In order to deploy DL models to high-consequence applications, high-quality UQ is necessary. This report details the research and development conducted as part of a Laboratory Directed Research and Development (LDRD) project at Sandia National Laboratories. The focus of this project is to develop a framework of methods and metrics for the principled assessment of UQ quality in DL models. This report presents an overview of UQ quality assessment in traditional statistical modeling and describes why this approach is difficult to apply in DL contexts. An assessment on relatively simple simulated data is presented to demonstrate that UQ quality can differ greatly between DL models trained on the same data. A method for simulating image data that can then be used for UQ quality assessment is described. A general method for simulating realistic data for the purpose of assessing a model’s UQ quality is also presented. A Bayesian uncertainty framework for understanding uncertainty and existing metrics is described. Research that came out of collaborations with two university partners are discussed along with a software toolkit that is currently being developed to implement the UQ quality assessment framework as well as serve as a general guide to incorporating UQ into DL applications.
The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we plan to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We also plan to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task to identify pan-coronavirus protease inhibitors such as SARS-CoV-2. While the overall goals and milestones remain consistent with the original proposal, certain technical details have been modified, which we will describe in this report.
The auxiliary field quantum Monte Carlo method developed by the PIs has been shown to provide the most accurate description of strongly correlated electronic systems, from molecules to solids. Unlike other explicitly many‐body approaches, the quantum Monte Carlo method scales as a low order polynomial of systems size, similar to mean‐field methods such as density functional theory. However, the auxiliary field quantum Monte Carlo algorithm is significantly more expensive than traditional density functional calculations. This creates a bottleneck for applications to extended systems, such as large molecules and solids. One principal objective of this proposal was to develop new auxiliary field quantum Monte Carlo computational strategies to achieve improved scaling with system size, using downfolding and localization schemes, without sacrificing the predictive power of the calculations. A second goal is to extend the reach of auxiliary field quantum Monte Carlo to calculate excited states. This final report summarizes what has been achieved during the course the project toward these goals.
Multiple sensor packages were deployed at Alpha-4 by SRNL, in collaboration with United Cleanup Oak Ridge LLC (UCOR), to monitor mercury vapor concentrations and meteorological parameters. These sensors collected data, inside and outside of the legacy-use facility, for approximately two years. Though data gaps still exist, particularly in colder months, several controlling variables were identified that govern mercury vapor concentrations within Alpha-4. Temperature, barometric pressure gradients, humidity, and wind speed have been identified as controlling variables. A strong positive correlation was seen between mercury vapor concentrations and temperature which generally followed diurnal fluctuations. Temperatures below approximately 10 degrees Celsius did not show any spikes above the PEL, indicating more work can be performed at any time during the winter months – more data should be collected to confirm consistency in this finding. Additionally, spikes in mercury vapor concentrations above that of the permissible exposure limit (PEL; 100 µg/m 3 ) occurred primarily in late afternoon or evening/overnight hours (between 3 PM and 6 AM), which suggests D&D operations might be best scheduled during morning or daytime hours prior to the late afternoon. However, a limited number of spikes did occur outside of the identified window, although this may be attributed to disturbances in air flow and mercury vapor release from work activities performed inside of the Alpha-4 building. The analysis conducted allows for a strong predictive capability for estimating mercury vapor concentrations based upon accurate meteorological parameters. Still, additional data collection, particularly in the winter months, could help to strengthen the predictive power and validate the identified data trends. Further, increased temporal resolution could also help to better characterize the incipient stages of the increases and decreases in the mercury vapor concentration. Continued monitoring support by SRNL at Y-12 is underway at Alpha-4 to further close remaining data gaps and support deactivation and decommissioning work. Within a collaborative effort with UCOR, the SRNL team is collecting mercury vapor data to study the efficacy of a novel mercury suppressant, FerroBlack® which was recently deployed at Alpha-4. In addition, modifications to the current monitoring setup to increase measurement resolution is also being investigated.
The Zirconium isotopes exhibit structural properties that present multiple challenges to nuclear theory. Investigations of the coupling present within isoscalar modes and within isovector modes are scarce but important for advancing our understanding of the microscopic picture of nuclei. To explore some of these underlying coupling features, and to test the predictive power of a state-of the-art nuclear structure approach, we provide a detailed analysis of the properties of 90,96,98Zr. This region includes a benchmarking case and offers insights into nuclear deformation phenomena. To investigate the coupling between collective modes in deformed nuclei, we focused our analysis on the ground and excited-state properties of these isotopes, employing a consistent approach with the axially-symmetric deformed Hartree-Fock-Bogoliubov (HFB) and the Quasiparticle Random Phase Approximation (QRPA) framework, both using the Gogny D1M force. This approach effectively describes both low-lying and giant-resonance states. We devoted special attention to the deformed 98Zr nucleus, where we confirm the existence of coupling between monopole and quadrupole excitations through the K π = 0 + QRPA components and demonstrate an analogous dipole-octupole coupling through the K π = 0 − and K π = 1 − components. Intrinsic transition densities and associ ated radial projections illustrate the coupling. Our work complements and extends earlier studies carried out using density-functional-based methods and notably, we included the complete Coulomb interaction also in the pairing fields, i.e. we treat terms exactly that are approximated in typical calculations that use the Gogny D1 and D2 interaction families.
Our project established and demonstrated a transfer learning framework that enables prediction of antibody–antigen interactions across related viruses. The approach focused on three major activities: 1. Conserved region and epitope identification – We compared viral protein structures and sequences to identify shared receptor-binding domains and neutralizing epitope regions across variants and related viruses. These conserved features formed the foundation for discovering broadly functional antibodies. 2. Machine learning model development – We built neural network–based models that integrate epitope features with antibody sequence information. Instead of relying solely on structural or physical properties, the models learned transferable patterns that describe antibody binding potential across different viral families. 3. Transfer learning and validation – Using SARS-CoV-2 and Ebola as source systems, we successfully transferred learned epitope features to predict antibody interactions for SARS CoV-1 and Marburg virus. Iterative cycles of dataset generation, retraining, and evaluation improved generalization and predictive power, ensuring the framework can adapt to new threats.
The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.
A well-known parable is that of the blind men studying an elephant each of which assert the elephant is the part they first hold in their hands, e.g., “rope!” says the tail holder while the leg holder asserts “tree!” The various subdisciplines of ecology appear similar in that we each engage in our enthusiastic but at least somewhat myopic study with remarkably limited agreement or even discussion about the overall system which we all study. Allometric trophic network (ATN) theory offers a path out of this dilemma by integrating across scales, taxa, habitats and organizational levels from physiology to ecosystems based on consumer-resource interactions among co-existing organisms. The network architecture and the metabolic and behavioral processes that determine the structure and dynamics of these interactions form the first principles of ATN theory, which in turn provides a synthetic overview and powerfully predictive framework for ecology from organisms to ecosystems. Beyond ecology, ATN theory also synthesizes eco-evolutionary and socio-ecological research still largely based on consumer-resource mechanisms but respectively integrated with different processes including natural selection and market mechanisms. This paper briefly describes foundations, advances, and future directions of ATN theory including predicting an ecosystem’s phenotype from its community’s genotype in order to accelerate more predictive and unified understanding of the complex systems studied by ecologists and other environmental scientists.
Increased mitotic activity is associated with the genesis and aggressiveness of many cancers. To assess the clinical value of mitotic activity as prognostic biomarker, we performed a pan-cancer study on the mitotic network activity index (MNAI) constructed based on 54-gene mitotic apparatus network. Our pan-cancer assessment on TCGA (33 tumor types, 10,061 patients) and validation on other publicly available cohorts (23 tumor types, 9,209 patients) confirmed the significant association of MNAI with overall survival, progression-free survival, and other prognostic endpoints in multiple cancer types, including lower-grade gliomas (LGG), breast invasive carcinoma (BRCA), as well as many others. We also showed significant association between MNAI and genetic instability, which provides a biological explanation of its prognostic impact at pan-cancer landscape. Our association analysis revealed that patients with high MNAI benefitted more from anti-PD-1 and Anti-CTLA-4 treatment. In addition, we demonstrated that multimodal integration of MNAI and the AI-empowered Cellular Morphometric Subtypes (CMS) significantly improved the predictive power of prognosis compared to using MNAI and CMS alone. Our results suggest that MNAI can be used as a potential prognostic biomarker for different tumor types toward different clinical endpoints, and multimodal integration of MNAI and CMS exceeds individual biomarker for precision prognosis.
Microbial decomposition of organic matter (OM) in river corridors is a major driver of nutrient and energy cycles in natural ecosystems. Recent advances in omics technologies enabled high-throughput generation of molecular data that could be used to inform biogeochemical models. With ultrahigh-resolution OM data becoming more readily available, in particular, the substrate-explicit thermodynamic modeling (SXTM) has emerged as a promising approach due to its ability to predict OM degradation and respiration rates from chemical formulae of compounds. This model implicitly assumes that all detected organic compounds are bioavailable, and that aerobic respiration is driven solely by thermodynamics. Despite promising demonstrations in previous studies, these assumptions may not be universally valid because OM degradation is a complex process governed by multiple factors. To identify key drivers of OM respiration, we performed a comprehensive analysis of diverse river systems using Fourier-transform ion cyclotron resonance mass spectrometry OM data and associated respiration measurements collected by the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium. In support of our argument, we found that the incorporation of all compounds detected in the samples into the SXTM resulted in a poor correlation between the predicted and measured respiration rates. The data-model consistency was significantly improved by the selective use of a small subset (i.e., only about 5%) of organic compounds identified using an optimization method. Through a subsequent comparative analysis of the subset of compounds (which we presume as bioavailable) against the full set of compounds, we identified three major traits that potentially determine OM bioavailability, including: (1) thermodynamic favorability of aerobic respiration, (2) the number of C atoms contained in compounds, and (2) carbon/nitrogen (C/N) ratio. We found that all three factors serve as “filters” in that the compounds with undesirable properties in any of these traits are strictly excluded from the bioavailable fraction. This work highlights the importance of accounting for the complex interplay among multiple key traits to increase the predictive power of biogeochemical and ecosystem models.
Models based on vision transformer architectures are considered state-of-the-art when it comes to image classification tasks. However, they require extensive computational resources both for training and deployment. The problem is exacerbated as the amount and complexity of the data increases. Quantum-based vision transformer models could potentially alleviate this issue by reducing the training and operating time while maintaining the same predictive power. Although current quantum computers are not yet able to perform high-dimensional tasks, they do offer one of the most efficient solutions for the future. In this work, we construct several variations of a quantum hybrid vision transformer for a classification problem in high-energy physics (distinguishing photons and electrons in the electromagnetic calorimeter). We test them against classical vision transformer architectures. Our findings indicate that the hybrid models can achieve comparable performance to their classical analogs with a similar number of parameters.
Machine learning (ML) is growing in popularity for various particle accelerator applications including anomaly detection such as faulty beam position monitor or RF fault identification, for non-invasive diagnostics, and for creating surrogate models. ML methods such as neural networks (NN) are useful because they can learn input-output relationships in large complex systems based on large data sets. Once they are trained, methods such as NNs give instant predictions of complex phenomenon, which makes their use as surrogate models especially appealing for speeding up large parameter space searches which otherwise require computationally expensive simulations. However, quickly time varying systems are challenging for ML-based approaches because the actual system dynamics quickly drifts away from the description provided by any fixed data set, degrading the predictive power of any ML method, and limits their applicability for real time feedback control of quickly time-varying accelerator components and beams. In contrast to ML methods, adaptive model-independent feedback algorithms are by design robust to un-modeled changes and disturbances in dynamic systems, but are usually local in nature and susceptible to local extrema. In this work, we propose that the combination of adaptive feedback and machine learning, adaptive machine learning (AML), is a way to combine the global feature learning power of ML methods such as deep neural networks with the robustness of model-independent control. We present an overview of several ML and adaptive control methods, their strengths and limitations, and an overview of AML approaches.
We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.