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DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗

DOE OSTI2022

COVID-19 through Adverse Outcome Pathways: Building networks to better understand the disease – 3rd CIAO AOP Design Workshop

On April 28-29, 2021, 50 scientists from different fields of expertise met for the 3rd online CIAO workshop. The CIAO project “Modelling the Pathogenesis of COVID-19 using the Adverse Outcome Pathway (AOP) framework” aims at building a holistic assembly of the available scientific knowledge on COVID-19 using the AOP framework. An individual AOP depicts the disease progression from the initial contact with the SARS-CoV-2 virus through biological key events (KE) toward an adverse outcome such as respiratory distress, anosmia or multiorgan failure. Assembling the individual AOPs into a network highlights shared KEs as central biological nodes involved in multiple outcomes observed in COVID-19 patients. During the workshop, the KEs and AOPs established so far by the CIAO members were presented and positioned on a timeline of the disease course. Modulating factors influencing the progression and severity of the disease were also addressed as well as factors beyond purely biological phenomena. CIAO relies on an interdisciplinary crowdsourcing effort, therefore, approaches to expand the CIAO network by widening the crowd and reaching stakeholders were also discussed. To conclude the workshop, it was decided that the AOPs/KEs will be further consolidated, integrating virus variants and long COVID when relevant, while an outreach campaign will be launched to broaden the CIAO scientific crowd.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

A QUBO formulation for top-τ eigencentrality nodes

The efficient calculation of the centrality or “hierarchy” of nodes in a network has gained great relevance in recent years due to the generation of large amounts of data. The eigenvector centrality (aka eigencentrality) is quickly becoming a good metric for centrality due to both its simplicity and fidelity. In this work we lay the foundations for solving the eigencentrality problem of ranking the importance of the nodes of a network with scores from the eigenvector of the network, using quantum computational paradigms such as quantum annealing and gate-based quantum computing. The problem is reformulated as a quadratic unconstrained binary optimization (QUBO) that can be solved on both quantum architectures. The results focus on correctly identifying a given number of the most important nodes in numerous networks given by the sparse vector solution of our QUBO formulation of the problem of identifying the top- τ highest eigencentrality nodes in a network on both the D-Wave and IBM quantum computers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

MPC-Based Local Voltage Control Strategy of DGs in Active Distribution Networks

The increasing penetration of distributed generators (DGs) exacerbates the voltage violations in active distribution networks (ADNs). The commonly used centralized voltage control may aggravate the burden of computation and communication. Local voltage control can realize fast response to frequent voltage fluctuations. However, effective local control for DGs still needs to be further investigated. In this paper, a model predictive control (MPC)-based local voltage control strategy of DGs is proposed to cope with voltage violation problems and enhance the adaptation to the DG volatility. DGs are regulated with local Q-V control curves to respond to voltage fluctuations rapidly. Based on the dynamic network partition, a unified control curve for DGs is set in the same area to realize efficient operation. To further improve the performance of voltage control, the parameter tuning of control curves is regularly conducted based on decentralized inter-area coordination with the rolling of the control horizon. Finally, case study is verified on the modified IEEE 33-node distribution system. The proposed local control strategy of DGs can effectively improve the voltage profile and reduce power losses of the whole network without high computation and communication burden.

active distribution network (ADN)↗

DOE OSTI2020

Preliminary Design Process for Networked Microgrids

Changes in economic, technology, and environmental policies are resulting in a re-evaluation of the dependence on large central generation facilities and their associated transmission networks. Emerging concepts of smart communities/cities are examining the potential to leverage cleaner sources of generation, and the potential to integrate electricity generation with other municipal functions. When grid-connected, these generation assets can supplement the existing interconnections with the bulk transmission system, and in the event of an extreme event, they can provide power via networks of microgrids. While the design process for a single stand-alone microgrid is relatively well understood, the process of designing the infrastructure for networked microgrid operations has not been well studied. Because of the wide range of potential operational goals for microgrids, it is typical to follow the engineering process of developing an initial conceptual design, a preliminary design, a detailed design, and then a final as-built design. The conceptual design is typically completed without detailed engineering analysis, and the preliminary design is the first stage that requires it. This paper presents a process for developing the preliminary design for networked microgrids, which can then be used as a basis for the final as-built design.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Most transcriptomic studies of SARS-CoV-2 infection have focused on differentially expressed genes, which do not necessarily reveal the genes mediating the transcriptomic changes. In contrast, exploiting curated biological network, our PathExt tool identifies central genes from the differentially active paths mediating global transcriptomic response. Here we apply PathExt to multiple cell line infection models of SARS-CoV-2 and other viruses, as well as to COVID-19 patient-derived PBMCs. The central genes mediating SARS-CoV-2 response in cell lines were uniquely enriched for ATP metabolic process, G1/S transition, leukocyte activation and migration. In contrast, PBMC response reveals dysregulated cell-cycle processes. In PBMC, the most frequently central genes are associated with COVID-19 severity. Importantly, relative to differential genes, PathExt-identified genes show greater concordance with several benchmark anti-COVID-19 target gene sets. We propose six novel anti-SARS-CoV-2 targets ADCY2, ADSL, OCRL, TIAM1, PBK, and BUB1, and potential drugs targeting these genes, such as Bemcentinib, Phthalocyanine, and Conivaptan.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Breaking the curse of dimensionality: Solving configurational integrals for crystalline solids by tensor networks

Accurately evaluating configurational integrals for dense solids remains a central and difficult challenge in the statistical mechanics of condensed systems. Here, we present a tensor network approach that reformulates the high-dimensional configurational integral for identical-particle crystals into a sequence of computationally efficient summations. We represent the integrand as a high-dimensional tensor and apply tensor-train (TT) decomposition together with a custom TT-cross interpolation. This approach circumvents the need to explicitly construct the full tensor. We introduce tailored rank-1 and rank-2 schemes optimized for sharply peaked Boltzmann probability densities, typical for identical-particle crystals. When applied to the calculation of internal energy and pressure-temperature curves for crystalline Cu and Ar at high (GPa) pressures, as well as the alpha-to-beta phase transition diagram of Sn, our method accurately reproduces molecular dynamics simulation results using tight-binding, machine learning, hierarchical interacting particle–neural network, and modified embedded atom method potentials,all within seconds of computation time.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Signatures of a liquid–liquid transition in an ab initio deep neural network model for water

Significance Water is central across much of the physical and biological sciences and exhibits physical properties that are qualitatively distinct from those of most other liquids. Understanding the microscopic basis of water’s peculiar properties remains an active area of research. One intriguing hypothesis is that liquid water can separate into metastable high- and low-density liquid phases at low temperatures and high pressures, and the existence of this liquid–liquid transition could explain many of water’s anomalous properties. We used state-of-the-art approaches in computational quantum chemistry, statistical mechanics, and machine learning and obtained evidence consistent with a liquid–liquid transition, supporting the argument for the existence of this phenomenon in real water.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The Edge of Exploration: An Edge Storage and Computing Framework for Ambient Noise Seismic Interferometry Using Internet of Things Based Sensor Networks

Recent technological advances have reduced the complexity and cost of developing sensor networks for remote environmental monitoring. However, the challenges of acquiring, transmitting, storing, and processing remote environmental data remain significant. The transmission of large volumes of sensor data to a centralized location (i.e., the cloud) burdens network resources, introduces latency and jitter, and can ultimately impact user experience. Edge computing has emerged as a paradigm in which substantial storage and computing resources are located at the “edge” of the network. In this paper, we present an edge storage and computing framework leveraging commercially available components organized in a tiered architecture and arranged in a hub-and-spoke topology. The framework includes a popular distributed database to support the acquisition, transmission, storage, and processing of Internet-of-Things-based sensor network data in a field setting. We present details regarding the architecture, distributed database, embedded systems, and topology used to implement an edge-based solution. Lastly, a real-world case study (i.e., seismic) is presented that leverages the edge storage and computing framework to acquire, transmit, store, and process millions of samples of data per hour.

58 GEOSCIENCES↗

DOE OSTI2025

Designing reinforcement learning algorithms for building HVAC control: From experimental observation to simulation comparisons

Advanced supervisory-level control with reinforcement learning (RL) is regarded as a promising solution for HVAC systems to minimize energy consumption while maintaining thermal comfort and indoor air quality. However, most RL applications were conducted in the simulation environment rather than real-world HVAC systems. This paper developed a value-based RL controller termed Deep Q-Network (DQN) for a typical central HVAC system and evaluated its performance in a building test facility. By comparing DQN with a rule-based controller, the study not only demonstrated the cases where DQN could properly maintain indoor comfort but also discussed possible reasons why DQN failed in some other situations. Recognizing the limitations of value-based RL algorithms from the experimental tests, a simulation study was conducted to compare DQN with an alternative RL approach, an actor–critic algorithm termed Deep Deterministic Policy Gradient (DDPG). In scenarios with a relatively large action space, DDPG outperformed DQN by requiring fewer computational resources and achieving better thermal comfort, lower energy consumption, and more stable control actions. The findings suggest that the ability of DDPG to handle continuous control variables more effectively allows for faster convergence in training and more precise control in practice, which enhances the overall efficiency and reliability of the HVAC system.

Guo, Fangzhou↗

DOE OSTI2023

Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils

As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. In this report we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for ‘Cull-the-Winner’ dynamics, whereby viruses infect and cull but do not decimate dominant host populations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Universal Monte Carlo Event Generator

With the Jefferson Lab 12 GeV physics program underway and plans for the future Electron-Ion Collider (EIC), the nuclear physics community is entering a new era of exploration of QCD phenomena involving extensive data taking and event-level processing. This brings with it the potential for unprecedented access to multidimensional particle momentum distributions (PMDs) that can be connected to various theoretical frameworks by unfolding the emergent quantum mechanical properties of QCD using the PMDs. In practice, the PMDs are rendered as discretized histograms (typically one- or two-dimensional projections), and detector effects must be taken into account to unfold the pure detector effect-free PMDs that can be connected with theory. One of the challenges in this new era is obtaining faithful reconstructions of the multidimensional PMDs that preserve all of the inherent particle correlations. In this LDRD project we developed a novel approach using machine learning (ML) that solves this challenge, by avoiding entirely the need to use histograms as the main numerical technique to obtain the detector effect-free PMDs. The new approach is, moreover, scalable to higher dimensional PMDs. The central idea involves training neural networks (NNs) to generate synthetic event-level data (momenta 4-vectors of final state particles) to preserve all correlations among the particles. This is achieved by converting the trial synthetic vertex-level events to detector-level events using detector simulators. The NNs are then tuned using a specialized distance metric between the synthetic detector events and the real detector events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Videoshare

SAND2023-05132O Videoshare is an application that allows users to communicate in a variety of ways, including voice, video, and text, over a local network without having to use a central server or an internet connection. The software features: • Screen-sharing and connecting to external IP cameras. • Ability to hold group calls on computers running the same software and network. • Ability to connect to other computers running the same software. • Curating potential connections and manually adding IP addresses to available connections. 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.

McIlraith, Aiden↗

DOE OSTI2022

Hierarchical distributed voltage regulation

Embodiments of the disclosure provide for hierarchically distributed voltage regulation and power flow optimization in a power distribution network. According to one embodiment, a regional coordinator system may determine power flow for an autonomous grid (AG) representing a portion of the distribution network based on a set of voltage parameters from nodes in the AG. The set of voltage parameters my include a current voltage magnitude. The regional coordinator system may provide, to a central controller system of the distribution network, one or more power flow parameters based on the determined power flow for the AG.

Zhou, Xinyang↗

DOE OSTI2022

Hypothesis-Agnostic Network-Based Analysis of Real-World Data Suggests Ondansetron is Associated with Lower COVID-19 Any Cause Mortality

Background: The COVID-19 pandemic generated a massive amount of clinical data, which potentially hold yet undiscovered answers related to COVID-19 morbidity, mortality, long-term effects, and therapeutic solutions.Objectives: The objectives of this study were (1) to identify novel predictors of COVID-19 any cause mortality by employing artificial intelligence analytics on real-world data through a hypothesis-agnostic approach and (2) to determine if these effects are maintained after adjusting for potential confounders and to what degree they are moderated by other variables.Methods: A Bayesian statistics-based artificial intelligence data analytics tool (bAIcis®) within the Interrogative Biology® platform was used for Bayesian network learning and hypothesis generation to analyze 16,277 PCR+ patients from a database of 279,281 inpatients and outpatients tested for SARS-CoV-2 infection by antigen, antibody, or PCR methods during the first pandemic year in Central Florida. This approach generated Bayesian networks that enabled unbiased identification of significant predictors of any cause mortality for specific COVID-19 patient populations. These findings were further analyzed by logistic regression, regression by least absolute shrinkage and selection operator, and bootstrapping.Results: We found that in the COVID-19 PCR+ patient cohort, early use of the antiemetic agent ondansetron was associated with decreased any cause mortality 30 days post-PCR+ testing in mechanically ventilated patients.Conclusions: The results demonstrate how a real-world COVID-19-focused data analysis using artificial intelligence can generate unexpected yet valid insights that could possibly support clinical decision making and minimize the future loss of lives and resources.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Insights from application of a hierarchical spatio-temporal model to an intensive urban black carbon monitoring dataset

Existing regulatory pollutant monitoring networks rely on a small number of centrally located measurement sites that are purposefully sited away from major emission sources. While informative of general air quality trends regionally, these networks often do not fully capture the local variability of air pollution exposure within a community. Recent technological advancements have reduced the cost of sensors, allowing air quality monitoring campaigns with high spatial resolution. The 100×100 black carbon (BC) monitoring network deployed 100 low-cost BC sensors across the 15 km 2 West Oakland, CA community for 100 days in the summer of 2017, producing a nearly continuous site-specific time series of BC concentrations which we aggregated to one-hour averages. Leveraging this dataset, we employed a hierarchical spatio-temporal model to accurately predict local spatio-temporal concentration patterns throughout West Oakland, at locations without monitors (average cross-validated hourly temporal R 2 =0.60). Using our model, we identified spatially varying temporal pollution patterns associated with small-scale geographic features and proximity to local sources. In a sub-sampling analysis, here we demonstrated that fine scale predictions of nearly comparable accuracy can be obtained with our modeling approach by using ~30% of the 100×100 BC network supplemented by a shorter-term high-density campaign.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Graph identification of proteins in tomograms ( GRIP‐Tomo )

Abstract In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three‐dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo‐multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single‐domain protein native topologies as well as distinct single‐domain proteins from multimeric complexes within noisy volumes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The MOSAiC Distributed Network: Observing the coupled Arctic system with multidisciplinary, coordinated platforms

Central Arctic properties and processes are important to the regional and global coupled climate system. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Distributed Network (DN) of autonomous ice-tethered systems aimed to bridge gaps in our understanding of temporal and spatial scales, in particular with respect to the resolution of Earth system models. By characterizing variability around local measurements made at a Central Observatory, the DN covers both the coupled system interactions involving the ocean-ice-atmosphere interfaces as well as three-dimensional processes in the ocean, sea ice, and atmosphere. The more than 200 autonomous instruments (“buoys”) were of varying complexity and set up at different sites mostly within 50 km of the Central Observatory. During an exemplary midwinter month, the DN observations captured the spatial variability of atmospheric processes on sub-monthly time scales, but less so for monthly means. They show significant variability in snow depth and ice thickness, and provide a temporally and spatially resolved characterization of ice motion and deformation, showing coherency at the DN scale but less at smaller spatial scales. Ocean data show the background gradient across the DN as well as spatially dependent time variability due to local mixed layer sub-mesoscale and mesoscale processes, influenced by a variable ice cover. The second case (May–June 2020) illustrates the utility of the DN during the absence of manually obtained data by providing continuity of physical and biological observations during this key transitional period. We show examples of synergies between the extensive MOSAiC remote sensing observations and numerical modeling, such as estimating the skill of ice drift forecasts and evaluating coupled system modeling. The MOSAiC DN has been proven to enable analysis of local to mesoscale processes in the coupled atmosphere-ice-ocean system and has the potential to improve model parameterizations of important, unresolved processes in the future.

54 ENVIRONMENTAL SCIENCES↗