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DOE OSTI2025

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗

DOE OSTI2026

Real-Time Detection of Charge Jumps in Superconducting Qubits with a Convolutional Neural Network

Ionizing radiation from cosmic rays and gammas can induce discontinuous jumps in the environmental charge of superconducting qubits (charge jumps), causing correlated errors that challenge fault-tolerant quantum computing while simultaneously providing a detection signature for quantum sensing applications. Current detection methods operate offline, introducing latency incompatible with in-the-loop qubit control. In this paper, an online detector of charge jumps for superconducting qubits, based on a dilated causal convolutional neural network (DCCNN) designed for in-the-loop deployment on the Quantum Instrumentation Control Kit (QICK) platform, is presented. The network is trained on synthetic Ramsey tomography scans generated from qubit templates measured at the Northwestern Experimental Underground Site (NEXUS) at Fermilab, and translated to FPGA firmware via hls4ml with ap_fixed$\langle 16,6 \rangle$ quantization, reaching a per-inference latency of $6.19 μ$s on the Zynq UltraScale+ RFSoC ZCU216. At this operating point the DCCNN matches the detection efficiency of the established offline $χ^2$ algorithm ($0.843 \pm 0.022$ vs. $0.866 \pm 0.020$ on $|Δq| \in [0.1, 0.5] e$ at matched false-positive rate), while requiring no per-qubit hyperparameter tuning. This shifts charge-jump detection from a post-hoc diagnostic to a control-loop primitive, enabling adaptive protocols that respond to radiation-induced events in situ, with applications to quantum-computing error mitigation and to the use of superconducting qubits as particle detectors.

Gaytan-Villarreal, Daniel [Carnegie Mellon U.]↗

NASA NTRS1990

Flight crew aiding for recovery from subsystem failures

Some of the conceptual issues associated with pilot aiding systems are discussed and an implementation of one component of such an aiding system is described. It is essential that the format and content of the information the aiding system presents to the crew be compatible with the crew's mental models of the task. It is proposed that in order to cooperate effectively, both the aiding system and the flight crew should have consistent information processing models, especially at the point of interface. A general information processing strategy, developed by Rasmussen, was selected to serve as the bridge between the human and aiding system's information processes. The development and implementation of a model-based situation assessment and response generation system for commercial transport aircraft are described. The current implementation is a prototype which concentrates on engine and control surface failure situations and consequent flight emergencies. The aiding system, termed Recovery Recommendation System (RECORS), uses a causal model of the relevant subset of the flight domain to simulate the effects of these failures and to generate appropriate responses, given the current aircraft state and the constraints of the current flight phase. Since detailed information about the aircraft state may not always be available, the model represents the domain at varying levels of abstraction and uses the less detailed abstraction levels to make inferences when exact information is not available. The structure of this model is described in detail.

Hudlicka, E.↗

NASA NTRS2010

Flow, Aurora and PI2 Associations Observed by Themis

It has been known for decades that auroral substorm onset occurs on (or at least near) the most equatorward auroral arc, which is thought to map to the near geosynchronous region. The lack of auroral signatures poleward of this arc prior to onset has been a major criticism of flow-burst driven models of sub storm onset. The combined THEMIS 5 spacecraft in-situ and ground array measurements provide an unprecedented opportunity to examine the causal relationship between midtail plasma flows, aurora, and ground magnetic signatures. I first present an event from 2008 using multi-spectral all sky imager data from Gillam and in-situ data from THEMIS. The multispectral data indicate an equatorward moving auroral form prior to sub storm onset. When this forms reaches the most equatorward arc, the arc brightens and an auroral substorm begins. The THEMIS data show fast Earthward flows prior to onset as well. I suggest that the results strongly support flow-burst driven models of magnetospheric activity. I discuss further the association of flow bursts and Pi2 pulsations, and discuss the possibility of using Pi2 waveforms to infer midtail reconnection dynamics

Kepko, E. I.↗

DOE OSTI2025

Indicators of carbon alteration (ICAs) suggest patterns in reservoir methane emissions

Reservoir operations influence emissions via multiple causal pathways. In this paper, we quantify indicators of carbon alteration (ICAs) focused on methane. ICAs were chosen to reflect the potential for methane emission along four causal pathways: 1) water column mixing, 2) wet-dry cycles in sediment, 3) sediment redistribution, and 4) vegetation. We developed algorithms to calculate ICAs for three reservoirs along a longitudinal gradient in the Tennessee River basin of the southeast US. The ICAs revealed interesting longitudinal patterns. Indicators of both methane production and destruction increased downstream. The potential for ebullitive methane emissions driven by sub-daily water level fluctuations and emissions mediated by vegetation were higher in downstream mainstem reservoirs than in the upstream tributary reservoir. Along the remaining two pathways, longitudinal patterns were equivocal (sediment pathway) or suggested decreased emissions downstream (water-column mixing). We also observed seasonal patterns and, by combining ICAs, inferred times when ramping could be achieved with lower risk of emissions. The ICAs demonstrated here are the first step in quantifying mechanistic relationships between reservoir operation and methane emissions. In future, they may lead to improved operations in reservoir cascades and regional-scale estimates of emissions that account for differences among reservoirs.

Greenhouse gases↗

DOE OSTI2024

Bayesian inference of multi-messenger astrophysical data: Joint and coherent inference of gravitational waves and kilonovae

Multi-messenger observations of binary neutron star mergers can provide information on the neutron star’s equation of state (EOS) above the nuclear saturation density by directly constraining the mass-radius diagram. We present a Bayesian framework for joint and coherent analyses of multi-messenger binary neutron star signals. As a first application, we analyze the gravitational-wave GW170817 and the kilonova (kN) AT2017gfo data. These results are then combined with the most recent X-ray pulsar analyses of PSR J0030+0451 and PSR J0740+6620 to obtain new EOS constraints.We extend the bajes infrastructure with a joint likelihood for multiple datasets, support for various semi-analytical kN models, and numerical-relativity (NR)-informed relations for the mass ejecta, as well as a technique to include and marginalize over modeling uncertainties. The analysis of GW170817 used the TEOBResumS effective-one-body waveform template to model the gravitational-wave signal. The analysis of AT2017gfo used a baseline multicomponent spherically symmetric model for the kN light curves. Various constraints on the mass-radius diagram and neutron star properties were then obtained by resampling over a set of ten million parameterized EOSs, which was built under minimal assumptions (general relativity and causality).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Limiting masses and radii of neutron stars and their implications

We combine the equation of state of dense matter up to twice nuclear saturation density 𝑛 sat obtained using chiral effective field theory (𝜒⁢EFT) and recent observations of neutron stars to gain insights about the high-density matter encountered in their cores. A key element in our study is the recent Bayesian analysis of correlated EFT truncation errors based on order-by-order calculations up to next-to-next-to-next-to-leading order in the 𝜒⁢EFT expansion. We refine the bounds on the maximum mass imposed by causality at high densities and provide stringent limits on the maximum and minimum radii of ∼1.4M ⊙ and ∼2.0M ⊙ stars. Including 𝜒⁢EFT predictions from 𝑛sat to 2𝑛 sat reduces the permitted ranges of the radius of a ~1.4M ⊙ star, 𝑅 1.4 , by ∼3.5km. If observations indicate 𝑅 1.4 < 11.2km, then our study implies that either the squared speed of sound 𝑐$^{2}_{𝑠}$ > 1/2 for densities above 2𝑛 sat or that 𝜒⁢EFT breaks down below 2𝑛 sat . Here, we also comment on the nature of the secondary compact object in GW190814 with mass ≃ 2.6M ⊙ and discuss the implications of massive neutron stars > 2.1⁢M ⊙ ⁡(2.6M ⊙ ) in future radio and gravitational-wave searches. Some form of strongly interacting matter with 𝑐$^{2}_{𝑠}$ > 0.35⁢(0.55) must be realized in the cores of such massive neutron stars. In the absence of phase transitions below 2𝑛 sat , the small tidal deformability inferred from GW170817 lends support for the relatively small pressure predicted by 𝜒⁢EFT for the baryon density 𝑛 B in the range 1–2𝑛 sat . Together they imply that the rapid stiffening required to support a high maximum mass should occur only when 𝑛 B ≳ 1.5–1.8 𝑛 sat .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Constraining aerosol–cloud adjustments by uniting surface observations with a perturbed parameter ensemble

Abstract. Aerosol–cloud interactions (ACIs) are the largest source of uncertainty in inferring the magnitude of future warming consistent with the observational record. The effective radiative forcing due to ACI (ERFaci) is dominated by liquid clouds and is composed of two terms: the change in cloud albedo due to redistributing liquid over a larger number of cloud droplets (Nd) and the change in cloud macrophysical properties due to changes in cloud microphysics. These terms are, respectively, referred to as the radiative forcing due to ACI (RFaci) and aerosol–cloud adjustments. While the magnitude of RFaci is uncertain, its sign is confidently negative and results in a cooling in the historical record. In contrast, the adjustment of cloud liquid water path (LWP) to enhanced Nd and associated radiative forcing is uncertain in sign. Increased LWP in response to increased Nd is consistent with precipitation suppression, while decreased LWP in response to increased Nd is consistent with enhanced evaporation from cloud top. Observational constraints of these processes are poor in part because of causal ambiguity in the relationship between Nd and LWP. To better understand this relationship, precipitation (P), Nd, and LWP surface observations from the Eastern North Atlantic (ENA) atmospheric observatory are combined with the output from a perturbed parameter ensemble (PPE) hosted in the Community Atmosphere Model version 6 (CAM6). This allows for causal interpretation of observed covariability. Observations of precipitation and cloud from ENA constrain the range of possible LWP aerosol–cloud adjustments relative to the prior from the PPE by 15 %, resulting in a global value that is confidently positive (a historical cooling) ranging from 2.1 to 6.9 g m−2. It is found that observed covariability between Nd and LWP is dominated by coalescence scavenging and that this observed covariability is not strongly related to aerosol–cloud adjustments.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2011

Thoughts Without Content are Empty, Intuitions Without Concepts are Blind - Determinism and Contingency Revisited

Was the emergence of life a predictable outcome of chemical evolution on earth? Could evolution produce life very different from ours? These are one of the oldest questions in the field of the origin of life that not only have broad philosophical implications but also impact how we approach the problem from the methodological standpoint. Framing the issue in terms of the dichotomy between contingency and determinism is not a fortunate because these two terms in their conventional meaning are neither mutually exclusive nor jointly exhaustive. Determinism, represented in natural sciences by Newtonian physics, relies on the assumption that every event is causally determined by a chain of previous events. In the context of the origin of life it means that once the initial conditions on the early earth have been specified further evolution follows inevitably. Considering uncertainties about conditions on the prebiotic earth, many plausible sets of initial conditions can be defined, each followed by a separate deterministic trajectory. This conventional understanding of determinism does not admit contingency. Further, it has no implications for evaluating how many sets of initial conditions lead to the emergence of life. It appears that a better framing of the problem is as follows: given plausible sets of initial conditions on the early earth how probable and broadly spread are evolutionary trajectories that lead to life? Instead of undertaking an impossible task of specifying microscopic initial conditions for all components of the system one uses a reduced representation of this system and specify only a small set of essential macroscopic parameters, values (or ranges of values) of which can be identified, inferred or estimated from experiment, theory or historical record. The following evolutionary trajectories are still governed by laws of physics and chemistry but become probabilistic and "contingency" is admitted as variations in other variables in the system. A similar reasoning is common in other fields of science, for example in statistical mechanics. Some trajectories lead to life, perhaps in different forms, whereas others do not. Of our true interest is the ratio of these two outcomes. The issue of determinism does not directly enter the picture. The debate about the likelihood of the emergence of life is quite old. One view holds that the origin of life is an event governed by chance, and the result of so many random events (contingencies) is unpredictable. This view was eloquently expressed by Monod. In his book "Chance or Necessity" he argued that life was a product of "nature's roulette." In an alternative view, expressed in particular by deDuve and Morowitz, the origin of life is considered a highly probable or even inevitable event (although its details need not be determined in every respect). Only in this sense the origin of life can be considered a "deterministic event".

Pohorille, Andrew↗

NASA NTRS2012

Mars Atmospheric CO2 Condensation Above the North and South Poles as Revealed by Radio Occultation, Climate Sounder, and Laser Ranging Observations

We study the condensation of CO2 in Mars atmosphere using temperature profilesretrieved from radio occultation measurements from Mars Global Surveyor (MGS) as wellas the climate sounding instrument onboard the Mars Reconnaissance Orbiter (MRO),and detection of reflective clouds by the MGS Mars Orbiter Laser Altimeter (MOLA). Wefind 11 events in 1999 where MGS temperature profiles indicate CO2 condensation andMOLA simultaneously detects reflective clouds. We thus provide causal evidence thatMOLA non-ground returns are associated with CO2 condensation, which strongly indicatestheir nature being CO2 clouds. The MGS and MRO temperature profiles together revealthe seasonal expansion and shrinking of the area and the vertical extent of atmosphericsaturation. The occurrence rate of atmospheric saturation is maximized at high latitudes inthe middle of winter. The atmospheric saturation in the northern polar region exhibits moreintense seasonal variation than in the southern polar region. In particular, a shrinking ofsaturation area and thickness from LS 270 to 300 in 2007 is found; this is probablyrelated to a planet-encircling dust storm. Furthermore, we integrate the condensation areaand the condensation occurrence rate to estimate cumulative masses of CO2 condensatesdeposited onto the northern and southern seasonal polar caps. The precipitation flux isapproximated by the particle settling flux which is estimated using the impulse responses ofMOLA filter channels. With our approach, the total atmospheric condensation mass canbe estimated from these observational data sets with average particle size as the onlyfree parameter. By comparison with the seasonal polar cap masses inferred from thetime-varying gravity of Mars, our estimates indicate that the average condensate particleradius is 822 mm in the northern hemisphere and 413 mm in the southern hemisphere.Our multi-instrument data analysis provides new constraints on modeling the global climateof Mars.

MOLA↗

DOE OSTI2023

Assessment of Potential Ergonomic Injury Risk in the Nuclear Material Processing Glovebox Environment [Capstone Project]

Gloveboxes are isolation barriers that are used within many different industries such as pharmaceuticals, electronic parts fabrication, nuclear, and biological. The research on glovebox ergonomics is currently limited with few ergonomic professionals that focusing exclusively on glovebox working environments. There is existing documentation on occupational injuries, such as musculoskeletal disorders (MSD), sustained as a direct result of working in gloveboxes. The main elements that pose ergonomic risks to glovebox workers are operational repetition, duration, force, vibration, lifting heavy (more than 15lbs with two hands) objects, and awkward postures. This paper examines a small sample of the potential causal or risk factors that lead to the ergonomic injuries. A meta-analysis utilizing a random effect model is used to examine data from several studies which focus on, dexterity and strength changes as result of glove thickness, and robotic assistive technology as a means to improve postural mechanics. With the meta-analysis technique, similar data sets from different research studies can be coalesced into a single weighted, statistically significant result for subsequent consideration. The results from the analysis show that increased glove thickness results in decreased dexterity for operators thus increasing ergonomic risk factors such as task duration. It is also shown that glove thickness decreases grip strength but a similar decrease in pinch strength is not definitively demonstrated. With decreased grip strength, operators will need to exert more force (a known ergonomic risk factor) on processing tools, etc. during operations thus increasing the risk of ergonomic injury. The use of robotic assistive technology as a means to improve operator posture (risk factor) was also examined. Although it may be intuitively assumed that human-robotic collaboration would be beneficial in reducing risk factors, the result from this study’s analysis was not statistically significant. It is inferred that with additional directed research on this topic another study/analysis could be statistically significant demonstrating the benefits of the technology.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Antarctic permafrost processes and antiphase dynamics of cold-based glaciers in the McMurdo Dry Valleys inferred from 10 Be and 26 Al cosmogenic nuclides

Abstract. Soil and sediment mixing and associated permafrost processes are not widely studied or understood in the McMurdo Dry Valleys of Antarctica. In this study, we investigate the stability and depositional history of near-surface permafrost sediments to ∼ 3 m depth in the Pearse and lower Wright valleys using measured cosmogenic 10Be and 26Al depth profiles. In Pearse Valley, we estimate a minimum depositional age of ∼ 74 ka for the active layer and paleoactive-layer sediments (< 0.65 m). Combined depth profile modelling of 10Be and 26Al gives a depositional age for near-surface (< 1.65 m) permafrost in Pearse Valley of 180 +20/-40 ka, implying that the deposition of permafrost sediments predates MIS 5 advances of Taylor Glacier. Deeper permafrost sediments (> 2.09 m) in Pearse Valley are thus inferred to have a depositional age of > 180 ka. At a coastal, lower-elevation site in neighbouring lower Wright Valley, 10Be and 26Al depth profiles from a second permafrost core exhibit near-constant concentrations with depth and indicate the sediments are either vertically mixed after deposition or sufficiently young so that post-depositional nuclide production is negligible relative to inheritance. 26Al/10Be concentration ratios for both depth profiles range between 4.0 and 5.2 and are all lower than the nominal surface production rate ratio of 6.75, indicating that prior to deposition, these sediments experienced complex, yet similar, exposure–burial histories. Assuming a single-cycle exposure–burial scenario, the observed 26Al/10Be ratios are equivalent to a total minimum exposure–burial history of ∼ 1.2 Myr. In proximity to the depth profile core site, we measured cosmogenic 10Be and 26Al in three granite cobbles from thin, patchy drift (Taylor 2 Drift) in Pearse Valley to constrain the timing of retreat of Taylor Glacier. Assuming simple continuous exposure, our minimum, zero-erosion exposure ages suggest Taylor Glacier partially retreated from Pearse Valley no later than 65–74 ka. The timing of retreat after 65 ka and until the Last Glacial Maximum (LGM) when Taylor Glacier was at a minimum position remains unresolved. The surface cobble ages and permafrost processes reveal Taylor Glacier advances during MIS 5 were non-erosive or mildly erosive, preserving the underlying permafrost sediments and peppering boulders and cobbles upon an older, relict surface. Our results are consistent with U/Th ages from central Taylor Valley and suggest changes in moisture delivery over Taylor Dome during MIS 5e, 5c, and 5a appear to be associated with the extent of the Ross Ice Shelf and sea ice in the Ross Sea. These data provide further evidence of antiphase behaviour through retreat of a peripheral lobe of Taylor Glacier in Pearse Valley, a region that was glaciated during MIS 5. We suggest a causal relationship of cold-based glacier advance and retreat that is controlled by an increase in moisture availability during retreat of sea ice and perhaps the Ross Ice Shelf, as well as, conversely, a decrease during times of sea ice and Ross Ice Shelf expansion in the Ross Sea.

58 GEOSCIENCES↗