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DOE OSTI2022

The Chocolate Chip Cookie Model: Dust Geometry of Milky Way–like Disk Galaxies

We present a new two-component dust geometry model, the Chocolate Chip Cookie model, where the clumpy nebular regions are embedded in a diffuse stellar/interstellar medium disk, like chocolate chips in a cookie. By approximating the binomial distribution of the clumpy nebular regions with a continuous Gaussian distribution and omitting the dust scattering effect, our model solves the dust attenuation process for both the emission lines and stellar continua via analytical approaches. Our Chocolate Chip Cookie model successfully fits the inclination dependence of both the effective dust reddening of the stellar components derived from stellar population synthesis and that of the emission lines characterized by the Balmer decrement for a large sample of Milky Way–like (MW-like) disk galaxies selected from the main galaxy sample of the Sloan Digital Sky Survey. Our model shows that the clumpy nebular disk is about 0.55 times thinner and 1.6 times larger than the stellar disk for MW-like galaxies, whereas each clumpy region has a typical optical depth of τ cl,V ~ 0.5 in the V band. After considering the aperture effect, our model prediction on the inclination dependence of dust attenuation is also consistent with observations. Not only that, in our model, the dust attenuation curve of the stellar population naturally depends on the inclination, and its median case is consistent with the classical Calzetti law. As the modeling constraints are from the optical wavelengths, our model is unaffected by the optically thick dust component, which however could bias the model's prediction of the infrared emissions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Water dynamics in C–S–H and M-S-H cement pastes: A revised jump-diffusion and rotation-diffusion model

The Quasi-Elastic Neutron Scattering (QENS) spectra from four cement pastes are re-analyzed by a new revised jump-diffusion and rotation-diffusion model (rJRM). From the QENS fit, it can be seen that the rJRM is an improved model to fit QENS spectra within the whole detected neutron energy transfer and scattering vector. By the rJRM fitting, the structure parameters extracted from QENS spectra show that both the additives aluminum-silicate nanotubes (ASN) and carboxyl group functionalized ASN (ASN-COOH) can improve magnesium-silicate-hydrate (M-S-H) toward calcium-silicate-hydrate (C–S–H) direction in mechanical properties, but the improvement is weakened with decreasing temperatures. The extracted dynamical parameters show that there is a dynamic anomaly near 230 K in not only translational but also rotational diffusion of water confined in all the investigated samples. In conclusion, the anomaly in rotational diffusion is new compared with those results obtained by the QENS fit using other models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Unraveling the Pyrolytic Behavior and Kinetics of Single Polymers and Plastic-Rich Municipal Solid Waste Using Thermal Analysis

Pyrolysis is a highly promising thermochemical recycling technology for converting heterogenous plastic waste into sustainable fuels in a single step. Therefore, understanding the pyrolysis mechanism is essential for enabling rational reactor design and enhancing efficient recycling techniques. In this study, the thermal degradation behaviors and corresponding kinetics of pure polymers (PE, PP, and PET) and plastic-rich MSW were examined using simultaneous thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Experiments were carried out in the temperature range of 30-800°C with variable heating rates from 5°C/min to 20°C/min in an ultra-high purity Argon atmosphere. Our results indicated that the plastic pyrolysis was an endothermic process, with varying decomposition temperature ranges depending on their structure and composition. Various iso-conversional model-free methods (Friedman, Flynn-Wall-Ozawa, Starink, and Kissinger-Akahira-Sunose) were utilized to determine the apparent activation energy of the plastic degradation, which increased in the following order: PET (214 kJ/mol), PP (218 kJ/mol), PE (245 kJ/mol), and MSW (249 kJ/mol). Finally, Criado’s master plots were employed to identify the best-fitting reaction model and the pre-exponential factor was subsequently determined.

Bashir, Muhammad Aamir↗

DOE OSTI2020

A Climatology and Extreme Value Analysis of Large Hail in China

In this paper, hail size records are analyzed at 2254 stations in China and a hail size climatology is developed based on gridded hail observations for the period 1960–2015. It is found that the annual percentiles of hail size records changed sharply and national-wide after 1980, therefore two periods, 1960–79 and 1980–2015, are studied. There are some similarities between the two periods in terms of the characteristics of hail size such as the spatial distribution patterns of mean annual maximum hail size and occurrence week of annual maximum hail size. The 1980–2015 period had higher observation density than the 1960–79 period, but showed smaller mean annual maximum hail size, especially in northern China. In the majority of grid boxes, the annual maximum hail size experienced a decreasing trend during the 1980–2015 period. A Gumbel extreme value model is fitted to each grid box to estimate the return periods of maximum hail size. The scale and location parameter of the fitted Gumbel distributions are higher in eastern China than in western China, thereby reflecting a greater likelihood of large hail in eastern China. In southern China, the maximum hail size exceeds 127 mm for a 10-yr return period, whereas in northern China maximum hail size exceeds this threshold for a 50-yr return period. Furthermore, the Gumbel model is found to potentially underestimate the maximum hail size for certain return periods, but provides a more informed picture of the spatial distribution of extreme hail size and the regional differences.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Structure of the Bastnäsite (001) Surface by Crystal Truncation Rod X-ray Diffraction and Ab Initio Molecular Dynamics: Implications for Separations of a Rare Earth Ore Mineral

Bastnäsite ((Ce,La)FCO 3 ) is the primary mineral source of light rare earth elements, but its surface structure is not well understood. This presents a major challenge in improving beneficiation strategies. In this work, a synergistic combination of X-ray scattering and ab initio molecular dynamics (AIMD) was used to gain atomistic insight into the interfacial structure of bastnäsite. Surface X-ray scattering was used to measure crystal truncation rods (CTRs) of the bastnäsite (001) surface, a significant crystal face with a previously unknown termination. The best-fit atomic-scale model of the CTR data features a carbonate layer at the surface, which is stabilized by the relaxation of carbonate groups from their bulk structural positions. AIMD simulations predict similar surface relaxations, which are shown to be influenced by the protonation of oxygen atoms at the surface. Evidence of ordered water at the interface is also observed in the best-fit model and AIMD simulations. Further, the presence of a carbonate layer at this dominant crystal surface is significant for improving separation technologies because most commonly used ligands utilize anionic functional groups to chelate metal cations at particle surfaces. Without modification, anionic ligands are expected to have poor affinity for the carbonate-terminated (001) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Characterization of shale using Helium and Argon at high pressures

In order to estimate the shale gas in place and the eventual recovery during shale gas operations, one of the key requirements is to accurately characterize the shale’s petrophysical and transport properties such as porosity, permeability, diffusivity, and storage capacity. Despite the many efforts reported in the technical literature aiming to provide an improved understanding of the complex pore structures and the associated fluid flow in gas shales, complete characterization of organic-rich shale samples still poses a big challenge. Here, we have characterized mass transfer and sorption in shale at different length scales using Helium (He) and Argon (Ar) as probe gases. Thermogravimetric analysis (TGA) with a shale cube of ~1 cm 3 in size and gas expansion experiments with a full-diameter core (3.5” in diameter) were used to measure sorption kinetics/isotherms and mass transfer, respectively. Both samples are from the same depth/location in the Marcellus shale formation. The TGA steady-state technique was initially used to generate excess sorption isotherms for Ar, while dynamic TGA experiments were used to study its sorption kinetics. The TGA experiments demonstrate that Ar, which has a similar sorption potential as Methane, but is generally assumed to be inert, adsorbs onto the surfaces of the mesoporous and microporous regions of the shale samples according to a Langmuir-type behavior. Helium expansion experiments, on the full-diameter core, were used to measure the overall porosity, on the basis that He is a non-sorbing and inert gas as compared to Ar. The He expansion experiments, furthermore, allow us to delineate the mass transfer of gas across the inherent hierarchy of pore sizes, including macropores (macro- and microcracks), mesopores and micropores. Similar expansion experiments were also performed with Ar to study the combined impact of mass transfer and sorption. A triple-porosity model (TPM) was utilized to interpret the He expansion experiments with the shale core and to extract (estimate) relevant transport parameters. We report and compare here the diffusivities and permeabilities of the whole core for both He and Ar, as calculated from the modeling and fitting of the experimental data. On the premise that the shale cube is representative of the matrix region of the core, the Ar sorption kinetics from the cube experiments were subsequently combined with the transport parameters extracted from the He experiments to predict the behavior of the Ar expansion test with the full-diameter core. An excellent agreement is observed between the model predictions and the experimental data. The experimental observations and their interpretation indicate that one must be cautious when using Ar to estimate the true porosity and permeability of shales. In addition, we demonstrate that He and Ar probe gases, when used in tandem, can be employed effectively as a tool to characterize shales in terms of mass transfer and sorption dynamics across scales.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2020

Efficient, Predictive Tomography of Multi-Qubit Quantum Processors

After decades of R&D, quantum computers comprising more than 2 qubits are appearing. If this progress is to continue, the research community requires a capability for precise characterization (“tomography”) of these enlarged devices, which will enable benchmarking, improvement, and finally certification as mission-ready. As world leaders in characterization -- our gate set tomography (GST) method is the current state of the art – the project team is keenly aware that every existing protocol is either (1) catastrophically inefficient for more than 2 qubits, or (2) not rich enough to predict device behavior. GST scales poorly, while the popular randomized benchmarking technique only measures a single aggregated error probability. This project explored a new insight: that the combinatorial explosion plaguing standard GST could be avoided by using an ansatz of few-qubit interactions to build a complete, efficient model for multi-qubit errors. We developed this approach, prototyped it, and tested it on a cutting-edge quantum processor developed by Rigetti Quantum Computing (RQC), a US-based startup. We implemented our new models within Sandia’s PyGSTi open-source code, and tested them experimentally on the RQC device by probing crosstalk. We found two major results: first, our schema worked and is viable for further development; second, while the Rigetti device is indeed a “real” 8-qubit quantum processor, its behavior fluctuated significantly over time while we were experimenting with it and this drift made it difficult to fit our models of crosstalk to the data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Effect of Pressurization on Solid Oxide Cell Oxygen Electrodes: the Role of PrO x Nanoparticle Infiltration

Pressurization of solid oxide cells improves performance by reducing electrode polarization resistance (R P ) and facilitates system integration with balance of plant components such as pressurized storage tanks. However, there are few reports on pressurization effects for electrodes designed for low-temperature operation and utilizing infiltrated catalysts. Here we report an electrochemical impedance spectroscopy study of high performing oxygen electrode materials, SrTi 0.3 Fe 0.63 Co 0.07 O 3-∂ (STFC) and PrO x infiltrated STFC, for oxygen partial pressures ($p$ $o$ 2 ) from 0.1 to 8 atm and temperatures from 550 to 650 °C. decreases more with pressurization for STFC:PrO x , fitting well to with an exponent n~0.3, compared to n~0.25 for STFC. The combination of PrO x infiltration and pressurization yields a substantial R P decrease, e.g., at 600 °C by ~7 times from 0.36 Ω cm 2 at $p$ $o$ 2 = 0.2 atm for STFC to 0.055 Ω cm 2 at $p$ $o$ 2 = 4 atm for STFC:PrO x . Here, a transmission-line-based circuit model impedance fit reveals that the significant oxygen surface reaction (R surf ) resistance contribution decreases substantially with PrO x infiltration; and its $p$ $o$ 2 dependence become more pronounced, with n increasing from ~0.25 to ~0.5. R surf for STFC:PrO x decreases so much at elevated $p$ $o$ 2 that the electrode/electrolyte interface resistance dominates.

25 ENERGY STORAGE↗

DOE OSTI2023

Suppression of Midinfrared Plasma Resonance Due to Quantum Confinement in δ-Doped Silicon

The classical Drude model provides an accurate description of the plasma resonance of three-dimensional materials, but only partially explains two-dimensional systems where quantum mechanical effects dominate such as P:δ layers—atomically thin sheets of phosphorus dopants in silicon that induce electronic properties beyond traditional doping. Previously it was shown that P:δ layers produce a distinct Drude tail feature in ellipsometry measurements. However, the ellipsometric spectra could not be properly fit by modeling the δ layer as a discrete layer of classical Drude metal. In particular, even for large broadening corresponding to extremely short relaxation times, a plasma resonance feature was anticipated but not evident in the experimental data. In this work, we develop a physically accurate description of this system, which reveals a general approach to designing thin films with intentionally suppressed plasma resonances. Our model takes into account the strong charge-density confinement and resulting quantum mechanical description of a P:δ layer. Here, we show that the absence of a plasma resonance feature results from a combination of two factors: (i) the sharply varying charge-density profile due to strong confinement in the direction of growth; and (ii) the effective mass and relaxation time anisotropy due to valley degeneracy. The plasma resonance reappears when the atoms composing the δ layer are allowed to diffuse out from the plane of the layer, destroying its well-confined two-dimensional character that is critical to its distinctive electronic properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Testing H 0 in Acoustic Dark Energy with Planck and ACT Polarization

The canonical acoustic dark energy model (cADE), which is based on a scalar field with a canonical kinetic term that rapidly converts potential to kinetic energy around matter radiation equality, alleviates the Hubble tension found in ΛCDM. Here, we show that it successfully passes new consistency tests in the CMB damping tail provided by the ACT data, while being increasingly constrained and distinguished from alternate mechanisms by the improved CMB acoustic polarization data from Planck. The best fit cADE model to a suite of cosmological observations, including the SH0ES H 0 measurement, has H 0 = 70.25 compared with 68.23 (km s –1 Mpc –1 ) in ΛCDM and a finite cADE component is preferred at the 2.8σ level. The ability to raise H0 is now mainly constrained by the improved Planck acoustic polarization data, which also plays a crucial role in distinguishing cADE from the wider class of early dark energy models. ACT and Planck TE polarization data are currently mildly discrepant in normalization and drive correspondingly different preferences in parameters. Improved constraints on intermediate scale polarization approaching the cosmic variance limit will be an incisive test of the acoustic dynamics of these models and their alternatives.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

A ``Tail" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL

I describe $SIR$ modeling of the COVID-19 pandemic in two U.S. urban environments, New York City (NYC) and Cook County, IL, from onset through the month of June, 2020. Since testing was not widespread early in the pandemic in the U.S., I do not use data on confirmed cases and rely solely on public fatality data to estimate model parameters. Fits to the first 20 days of data determine a degenerate combination of the basic reproduction number, $R_0$, and the mean time to removal from the infectious population, $\gamma^{-1}$, with $\gamma (R_0-1) = 0.25 (0.21)$ inverse days for NYC (Cook County). Equivalently, the initial doubling time was $t_d = 2.8 (3.4)$ days for NYC (Cook). The early fatality data suggest that both locations had infections in early February. I model the mitigation measures implemented in mid-March in both locations (distancing, quarantine, isolation, etc) via a time-dependent reproduction number $R_t$ that declines monotonically from $R_0$ to a sma ller asymptotic value, with a parameterized functional form. The timing (mid-March) and duration (several days) of the transitions in $R_t$ appear well determined by the data. However, the fatality data determine only a degenerate combination of the parameters $R_0$, the percentage reduction in social contact due to mitigation measures, $X$, and the infection fatality rate (IFR), $f$. With flat priors, based on simulations the NYC model parameters have 95.45\% credible intervals of $R_0 = 3.0-5.4$, $X= 80-99.9\%$ and $f=2-6\%$, with $5-13\%$ of the population asymptotically infected. A strong external prior indicating a lower value of $f$ or of $\gamma^{-1}$ would imply lower values of $R_0$ and $X$ and higher percentage infection of the population. For Cook County, the evolution was qualitatively different: after mitigation measures were implemented, the daily fatality counts reached a plateau for about a month before tailing off. This is consistent with an $SIR$ model that exhibits ``critical slowing-down", in which $R_t$ plateaus ! at a value just above unity. For Cook County, the 95.45\% credible intervals for the model parameters are much broader and shifted downward, $R_0=1.4-4.7$, $X=26-54\%$, and $f=0.1-0.6\%$ with $15-88\%$ of the population asymptotically infected. Despite the apparently lower efficacy of its social contact reduction measures, Cook County has had significantly fewer fatalities per population than NYC, $D_\infty/N=100$ vs. 270 per 100,000. In the model, this is attributed to the lower inferred IFR for Cook; an external prior pointing to similar values of the IFR for the two locations would instead chalk up the difference in $D/N$ to differences in the relative growth rate of the disease. I derive a model-dependent threshold, $X^{crit}_e$, for `safe' re-opening, that is, for easing of contact reduction that would not trigger a second wave; for NYC, the models predict that increasing social contact by more than 20\% from post-mitigation levels will lead to renewed spread, while for Cook County the threshold value is very uncertain, given the parameter degeneracies. The timing of 2nd-wave growth will depend on the amplitude of contact increase relative to $X^{crit}_e$ and on the asymptotic growth rate, and the impact in terms of fatalities will depend on the parameter $f$.

Frieman, Joshua↗

DOE OSTI2024

O'Hare Airport roadway traffic prediction via data fusion and Gaussian process regression

This study proposes an approach of leveraging information gathered from multiple traffic data sources at different resolutions to obtain approximate inference on the traffic distribution of Chicago's O'Hare Airport area. Specifically, it proposes the ingestion of traffic datasets at different resolutions to build spatiotemporal models for predicting the distribution of traffic volume on the road network. Due to its good adaptability and flexibility for spatiotemporal data, the Gaussian process (GP) regression was employed to provide short-term forecasts using data collected by loop detectors (sensors) and supplemented by telematics data. The GP regression is used to make predictions of the distribution of the proportion of sensor data traffic volume represented by the telematics data for each location of the sensors. Consequently, the fitted GP model can be used to determine the approximate traffic distribution for a testing location outside of the training points. Policymakers in the transportation sector can find the results of this work helpful for making informed decisions relating to current and future transportation conditions in the area.

42 ENGINEERING↗

DOE OSTI2023

Design and Analysis of Multifidelity Finite Element Simulations

Abstract The numerical accuracy of finite element analysis (FEA) depends on the number of finite elements used in the discretization of the space, which can be varied using the mesh size. The larger the number of elements, the more accurate the results are. However, the computational cost increases with the number of elements. In current practice, the experimenter chooses a mesh size that is expected to produce a reasonably accurate result, and for which the computer simulation can be completed in a reasonable amount of time. Improvements to this approach have been proposed using multifidelity modeling by choosing two or three mesh sizes. However, mesh size is a continuous parameter, and therefore, multifidelity simulations can be performed easily by choosing a different value for the mesh size for each of the simulations. In this article, we develop a method to optimally find the mesh sizes for each simulation and satisfy the same time constraints as a single or a double mesh size experiment. A range of different mesh sizes used in the proposed method allows one to fit multifidelity models more reliably and predict the outcome when meshes approach infinitesimally small, which is impossible to achieve in actual simulations. We illustrate our approach using an analytical function and a cantilever beam finite element analysis experiment.

Engineering↗

DOE OSTI2024

Geophysical and Environmental Monitoring Data, and Subsurface Flow Modelling Results for Chicken Bone Meadow, Mt. Snodgrass, Crested Butte, CO

This dataset includes geoelectrical monitoring data acquired between October 2021 and November 2022, soil moisture and temperature data, groundwater data obtained from borehole SNIB covering the period from June 2021 to September 2022, and hydrological modelling results. The data were acquired to investigate how variations in bedrock type and topography, and vegetation cover control subsurface flow dynamics. To provide insights into the subsurface flow dynamics and their controls, a monitoring transect was installed at the Chicken Bone Meadow, Mt. Snodgrass, Crested Butte, CO, measuring the spatio-temporal variations of soil moisture, soil and snow temperature, subsurface electrical resistivity variations, and groundwater dynamics. Field data are organized in a folder structure, with Electrical Resistivity Tomography (ERT) data being provided as one file per measurement, and data of the soil moisture and temperature sensors being provided as text files covering the entire monitoring period. The ‘Locations.csv’ file contains the location of all sensors, given in NAD83 – UTM Zone 13N. ERT monitoring data has been processed to filter data based on reciprocal errors (data with errors > 30% were removed), a linear error model was fitted to each survey, and to ensure a constant set of measurements for time-lapse inversion, filtered data were interpolated and assigned a 100% measurement error. Soil moisture and temperature data were acquired at 15 min intervals, and averaged to provide 1h data. Weather data and borehole data (groundwater depth, conductivity and temperature) were acquired at 30 min intervals, and are provided as daily measurements; all measurements are averaged, except of precipitation values, which are given as daily accumulation. The hydrological model was set up along the ERT monitoring transect, and net infiltration was used as surface boundary condition and derived from the weather data. Four different results are provided, (1) results for a parameterization using hydraulic permeability and porosity as derived from the ERT data through petrophysical relationships, and (2) three simplified model results, using 1 to 3 geological layers above the bedrock. Modelling was performed using PFLOTRAN, and for each model the PFLOTRAN input files are provided. The result files include weekly hydrological modelling results (e.g., saturation, velocities, pressures), as well as the model parameterization. The dataset additionally includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata; and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Learning electric vehicle driver range anxiety with an initial state of charge-oriented gradient boosting approach

This manuscript focuses on the modeling of electric vehicle (EV) driver’s range anxiety, a fear that a vehicle does not have sufficient range, or state of charge (SOC) of the battery pack, to reach its destination and would strand its occupants. Despite numerous research studies on the modeling of charging behaviors, modeling efforts to understand at what battery percentages do EV drivers charge their vehicles, and what are the associated contributing factors, are rather limited. To this end, an ensemble learning model based on gradient boosting is developed. The model sequentially fits new predictors to new residuals of the previous prediction and, then, minimizes the loss when adding the latest prediction. A total of 18 features are defined and extracted from the multisource data, which cover information on driver, vehicles, stations, traffic conditions, as well as spatial-temporal context information of the charging events. The analyzed dataset includes 4.5-year’s charging event log data from 3,096 users and 468 public charging stations in Kansas City Missouri, and the macroscopic travel demand model maintained by the metropolitan planning organization. Here, the result shows the proposed model achieved a satisfactory result with a R square value of 0.54 and root mean square error of 0.14, both better than multiple linear regression model and random forest model. To reduce range anxiety, it is suggested that the priorities of deploying new charging facilities should be given to the areas with higher daily traffic prediction, with more conservative EV users or that are further from residential areas.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2026

A dendritic strontium river isoscape for fisheries applications in the Sacramento River basin, California, USA

Objective Understanding the origins and movements of fish is fundamental to effective conservation and fisheries management. Strontium isotope ratios ( 87 Sr/ 86 Sr) in otoliths provide a powerful tracer of natal origin and migratory pathways. However, existing 87 Sr/ 86 Sr isoscapes for the Sacramento River basin, an ecosystem that supports ecologically and economically important salmon populations, rely on discrete classification approaches that overlook unsampled habitats and do not incorporate spatial uncertainty. Our objective was to develop a continuous, network-explicit 87 Sr/ 86 Sr isoscape with quantified uncertainty to fill in data gaps and enable probabilistic assignments of fish origin and movement. Methods We used river water 87 Sr/ 86 Sr data from 106 sites (1997–2021) to develop spatial stream network models that use dendritic connectivity and watershed characteristics (lithology, bedrock age, and land cover) to predict river water 87 Sr/ 86 Sr throughout the basin. Models were fitted using maximum and restricted likelihood and were evaluated via Akaike’s information criterion and leave-one-out cross validation. We produced both historical (pre-dam) and present-day (below-dam) isoscapes, delineated uncertainty-informed isotopic ranges using k -means clustering, and applied a proof-of-concept Bayesian assignment to estimate natal origins and early rearing habitats for two endangered winter-run Chinook Salmon Oncorhynchus tshawytscha. Results Cross validation indicated strong performance of the 87 Sr/ 86 Sr model (leave-one-out cross validation: R 2 = 0.91; root mean square error = 0.0005). Uncertainty-informed clustering identified 19 isotopic “suites” (reaches with indistinguishable 87 Sr/ 86 Sr values) in present-day anadromous habitats and 25 suites in the historical network. Example natal and early rearing assignments included predictions that challenged expectations for juvenile salmon migration based on predicted river 87 Sr/ 86 Sr compositions. Conclusions This study developed a continuous, network-explicit 87 Sr/ 86 Sr isoscape that integrates existing river data to predict 87 Sr/ 86 Sr in unsampled reaches and the likely achievable range and resolution of otolith-based origin and life history inference. The resulting river isoscape provides a valuable tool to predict salmon movements and identify habitats supporting their survival and growth that otherwise might remain undetected. Coupling these predictions with complementary approaches that ground-truth juvenile presence (e.g., targeted fish surveys) represents an important step toward science-informed restoration and management of critical habitats throughout the Sacramento River basin.

Environmental sciences↗

DOE OSTI2023

A data-driven method for modelling dissipation rates in stratified turbulence

We present a deep probabilistic convolutional neural network (PCNN) model for predicting local values of small-scale mixing properties in stratified turbulent flows, namely the dissipation rates of turbulent kinetic energy and density variance, $\varepsilon$ and $\chi$ . Inputs to the PCNN are vertical columns of velocity and density gradients, motivated by data typically available from microstructure profilers in the ocean. The architecture is designed to enable the model to capture several characteristic features of stratified turbulence, in particular the dependence of small-scale isotropy on the buoyancy Reynolds number $Re_b:=\varepsilon /(\nu N^2)$ , where $\nu$ is the kinematic viscosity and $N$ is the background buoyancy frequency, the correlation between suitably locally averaged density gradients and turbulence intensity and the importance of capturing the tails of the probability distribution functions of values of dissipation. Empirically modified versions of commonly used isotropic models for $\varepsilon$ and $\chi$ that depend only on vertical derivatives of density and velocity are proposed based on the asymptotic regimes $Re_b\ll 1$ and $Re_b\gg 1$ , and serve as an instructive benchmark for comparison with the data-driven approach. When trained and tested on a simulation of stratified decaying turbulence which accesses a range of turbulent regimes (associated with differing values of $Re_b$ ), the PCNN outperforms assumptions of isotropy significantly as $Re_b$ decreases, and additionally demonstrates improvements over the fitted empirical models. A differential sensitivity analysis of the PCNN facilitates a comparison with the theoretical models and provides a physical interpretation of the features enabling it to make improved predictions.

42 ENGINEERING↗

DOE OSTI2022

Exploring cryo-electron microscopy with molecular dynamics

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Biochemistry & Molecular Biology↗