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DOE OSTI2022

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Nonlinear modeling of the scaling law for the m/n = 3/2 error field penetration threshold

The scaling law for the m/n=3/2 error field (EF) penetration threshold is predicted numerically based on nonlinear single-fluid and two-fluid modeling using the TM1 code. The simulated penetration threshold of radial magnetic field b r at the plasma edge is scaled to the electron density n e , temperature T e , viscous time τ μ , toroidal field B t and the natural frequency ω in the form of b r /B t ∝n e αn T e αT τ μ αμ B t αB ω αω by scanning these parameters separately. Here, α n , α T , α μ , α B and α ω are the scaling coefficients on n e , T e , τ μ , B t and ω, respectively. Single-fluid modeling shows that the 3/2 EF threshold scales as b r /B t ∝n e 0.56 T e 0.6 τ μ -0.59 B t -1.15 ω, which is similar with the analytical scaling law in both the Rutherford and visco-resistive regimes. Yet, two-fluid modeling shows that the scaling law differs significantly in particular regarding the dependence on plasma rotation. In detail, the scaling coefficient α n on density decreases from 0.67 to 0.56 and α T on temperature decreases from 0.67 to 0.32, while α μ on viscous time is around -0.45 and α B on toroidal field decreases slightly from -1.15 to -1, when the ratio |ω E /ω *e | between plasma rotation frequency ω E and diamagnetic drift frequency ω *e varies from 0 to 10. Scans of the plasma rotation reveals that the penetration threshold linearly depends on the perpendicular rotation frequency (or natural frequency) ω ⊥e =ω E +ω *e , and there is a minimum in the required field amplitude when ω ⊥e 0. In addition, the enduring mystery of non-zero penetration threshold at zero plasma natural frequency in EF experiments is resolved by two-fluid simulations. We report that the very small island and smooth bifurcation in EF penetration near zero frequency is hard to detect in the experiment, leading to a finite penetration threshold within the capability of the experimental measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

DLSIA: Deep Learning for Scientific Image Analysis

DLSIA (Deep Learning for Scientific Image Analysis) is a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing. DLSIA features easy-to-use architectures, such as autoencoders, tunable U-Nets and parameter-lean mixed-scale dense networks (MSDNets). Additionally, this article introduces sparse mixed-scale networks (SMSNets), generated using random graphs, sparse connections and dilated convolutions connecting different length scales. For verification, several DLSIA-instantiated networks and training scripts are employed in multiple applications, including inpainting for X-ray scattering data using U-Nets and MSDNets, segmenting 3D fibers in X-ray tomographic reconstructions of concrete using an ensemble of SMSNets, and leveraging autoencoder latent spaces for data compression and clustering. As experimental data continue to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration and advance research in scientific image analysis.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

Controlled vortical flow on delta wings through unsteady leading edge blowing

The vortical flow over a delta wing contributes an important part of the lift - the so called nonlinear lift. Controlling this vortical flow with its favorable influence would enhance aircraft maneuverability at high angle of attack. Several previous studies have shown that control of the vortical flow field is possible through the use of blowing jets. The present experimental research studies vortical flow control by applying a new blowing scheme to the rounded leading edge of a delta wing; this blowing scheme is called Tangential Leading Edge Blowing (TLEB). Vortical flow response both to steady blowing and to unsteady blowing is investigated. It is found that TLEB can redevelop stable, strong vortices even in the post-stall angle of attack regime. Analysis of the steady data shows that the effect of leading edge blowing can be interpreted as an effective change in angle of attack. The examination of the fundamental time scales for vortical flow re-organization after the application of blowing for different initial states of the flow field is studied. Different time scales for flow re-organization are shown to depend upon the effective angle of attack. A faster response time can be achieved at angles of attack beyond stall by a suitable choice of the initial blowing momentum strength. Consequently, TLEB shows the potential of controlling the vortical flow over a wide range of angles of attack; i.e., in both for pre-stall and post-stall conditions.

Lee, K. T.↗

NASA NTRS1991

Sensitivity-based scaling for correlating structural response from different analytical models

A sensitivity-based linearly varying scale factor is described used to reconcile results from refined models for analysis of the same structure. The improved accuracy of the linear scale factor compared to a constant scale factor as well as the commonly used tangent approximation is demonstrated. A wing box structure is used as an example, with displacements, stresses, and frequencies correlated. The linear scale factor could permit the use of a simplified model in an optimization procedure during preliminary design to approximate the response given by a refined model over a considerable range of design changes.

Chang, Kwan J.↗

NASA NTRS1956

Determination of the structural damping coefficients of six full-scale helicopter rotor blades of different materials and methods of construction

Results of an experimental investigation of the structural damping of six full-scale helicopter rotor blades, made to determine the variation of structural damping with materials and methods of construction, are presented. The damping of the blades was determined for the first three flapwise bending modes, first chordwise bending mode, and first torsion mode. The contribution of structural damping to the total damping of the blades is discussed for several aerodynamic conditions in order to point out situations where structural damping is significant.

WINGS, ROTATING - EXPERIMENTAL STUDIES↗

NASA NTRS1990

Catalytic ignition model in a monolithic reactor with in-depth reaction

Two transient models have been developed to study the catalytic ignition in a monolithic catalytic reactor. The special feature in these models is the inclusion of thermal and species structures in the porous catalytic layer. There are many time scales involved in the catalytic ignition problem, and these two models are developed with different time scales. In the full transient model, the equations are non-dimensionalized by the shortest time scale (mass diffusion across the catalytic layer). It is therefore accurate but is computationally costly. In the energy-integral model, only the slowest process (solid heat-up) is taken as nonsteady. It is approximate but computationally efficient. In the computations performed, the catalyst is platinum and the reactants are rich mixtures of hydrogen and oxygen. One-step global chemical reaction rates are used for both gas-phase homogeneous reaction and catalytic heterogeneous reaction. The computed results reveal the transient ignition processes in detail, including the structure variation with time in the reactive catalytic layer. An ignition map using reactor length and catalyst loading is constructed. The comparison of computed results between the two transient models verifies the applicability of the energy-integral model when the time is greater than the second largest time scale of the system. It also suggests that a proper combined use of the two models can catch all the transient phenomena while minimizing the computational cost.

Tien, Ta-Ching↗

DOE OSTI2024

Impact of baryonic feedback on HSC-Y1 weak lensing non-Gaussian statistics

Baryonic feedback is a major systematic in weak lensing cosmology. Its most studied effect is the suppression of the lensing power spectrum, a second-order statistic, on small scales. Motivated by the growing interest in statistics beyond the second order, we investigate the effect of baryons on lensing non-Gaussian statistics and the resulting biases in the matter clustering amplitude S 8 = σ 8 Ω m / 0.3 . We focus on the Subaru Hyper Suprime-Cam Year 1 (HSC-Y1) data which, with its high source number density, closely resembles those expected from the upcoming Euclid and Rubin Legacy Survey of Space and Time. We study four non-Gaussian statistics of convergence maps—peak counts, minimum counts, the probability distribution function, and the scattering transform coefficients—in addition to the usual power spectrum. We first estimate the biases in S 8 using mock observations built from the IllustrisTNG and BAHAMAS hydrodynamical simulations and theoretical models built from dark-matter-only simulations. We find up to 1 σ bias in S 8 when the smallest scales (2 arcmin) and the highest feedback level are considered. We then analyze the HSC-Y1 data and compare the S 8 obtained for each statistic with different smoothing scales or scale cuts. As we expect that baryons mostly affect the small scales, comparing the results obtained from including and excluding small scales can indicate the level of impact from baryons. With HSC data, we find only minor ( ≤ 0.5 σ ) differences in S 8 for all statistics, even when considering very small scales (2 arcmin). Our results suggest that the effect of baryons is insignificant at the level of HSC-Y1 down to 2 arcmin for all statistics examined here, or it is canceled by other scale-dependent systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Multi-scale, Multi-disciplinary, and Multi-agent Explainable AI with Koopman-Undergirded Learning, Prediction, and Analysis (M3EA KULPA) (Project Closeout Report)

The goal of this project was to develop and use domain-aware machine learning formulations, based on the Koopman Operator (KO), for modelling multi-scale, multi-disciplinary (e.g., multi-physics), and/or multi-agent systems. The project developed these formulations for the following cases: • Systems with dynamics at two separate time scales, • Systems with a bi-level hierarchical control structure, • Systems with bi-level hierarchical control and dynamics at two separate time scales (the lower level controls operating at the faster time scale), and • Systems with n separate but interacting agents/disciplines (with/without control, respectively); the controls for each agent could include bi-level hierarchical control and dynamics at two separate time scales as described above. The project then defined a set of dynamical systems consisting of different nonlinear oscillators that could be used to test these different formulations and then subsequently learned the KO models for those systems. With the KO models, we were able to do the following: • Quantify system stability, including both long-term and transient behavior, • Quantify the effects of feedbacks between the different time scales and agents/disciplines in terms of those feedbacks’ effects on system stability, • Replace a standard Proportional-Integral (PI) control in the hierarchical control structure with a KO-based Linear-Quadratic Regular (LQR), a form of optimal control, • Calculate optimal supervisory control policies a) with and without time scale separated dynamics at the lower level control levels and b) with both PI and KO-based LQR lower level control policies, and • Calculate dynamic Nash equilibria for multi-agent systems where each agent makes its own control decisions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Economic Perspectives of Biogas Production via Anaerobic Digestion

As the demand for utilizing environment-friendly and sustainable energy sources is increasing, the adoption of waste-to-energy technologies has started gaining attention. Producing biogas via anaerobic digestion (AD) is promising and well-established; however, this process in many circumstances is unable to be cost competitive with natural gas. In this research, we provide a technical assessment of current process challenges and compare the cost of biogas production via the AD process from the literature, Aspen Plus process modeling, and CapdetWorks software. We also provide insights on critical factors affecting the AD process and recommendations on optimizing the process. We utilize four types of wet wastes, including wastewater sludge, food waste, swine manure, and fat, oil, and grease, to provide a quantitative assessment of theoretical energy yields of biogas production and its economic potential at different plant scales. Our results show that the cost of biogas production from process and economic models are in line with the literature with a potential to go even lower for small-scale plants with technological advancements. This research illuminates potential cost savings for biogas production using different wastes and guide investors to make informed decisions, while achieving waste management goals.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

Connecting Atmospheric Science and Atmospheric Models for Aerocaptured Missions to Titan and the Outer Planets

Many atmospheric measurement systems, such as the sounding instruments on Voyager, gather atmospheric information in the form of temperature versus pressure level. In these terms, there is considerable consistency among the mean atmospheric profiles of the outer planets Jupiter through Neptune, including Titan. On a given planet or on Titan, the range of variability of temperature versus pressure level due to seasonal, latitudinal, and diurnal variations is also not large. However, many engineering needs for atmospheric models relate not to temperature versus pressure level but atmospheric density versus geometric altitude. This need is especially true for design and analysis of aerocapture systems. Aerocapture drag force available for aerocapture is directly proportional to atmospheric density. Available aerocapture "corridor width" (allowable range of atmospheric entry angle) also depends on height rate of change of atmospheric density, as characterized by density scale height. Characteristics of hydrostatics and the gas law equation mean that relatively small systematic differences in temperature-versus-pressure profiles can integrate at high altitudes to very large differences in density-versus-altitude profiles. Thus a given periapsis density required to accomplish successful aerocapture can occur at substantially different altitudes (approx. 150 - 300 km) on the various outer planets, and significantly different density scale heights (approx. 20 - 50 km) can occur at these periapsis altitudes. This paper will illustrate these effects and discuss implications for improvements in atmospheric measurements to yield significant impact on design of aerocapture systems for future missions to Titan and the outer planets. Relatively small- scale atmospheric perturbations, such as gravity waves, tides, and other atmospheric variations can also have significant effect on design details for aerocapture guidance and control systems. This paper will also discuss benefits that would result from improved understanding of Titan and outer planetary atmospheric perturbation characteristics. Details of recent engineering-level atmospheric models for Titan and Neptune will be presented, and effects of present and future levels of atmospheric uncertainty and variability characteristics will be examined.

Justus, C. G.↗

NASA NTRS2015

Volcanism on Mars

Spacecraft exploration has revealed abundant evidence that Mars possesses some of the most dramatic volcanic landforms found anywhere within the solar system. How did a planet half the size of Earth produce volcanoes like Olympus Mons, which is several times the size of the largest volcanoes on Earth? This question is an example of the kinds of issues currently being investigated as part of the space-age scientific endeavor called "comparative planetology." This chapter summarizes the basic information currently known about volcanism on Mars. The volcanoes on Mars appear to be broadly similar in overall morphology (although, often quite different in scale) to volcanic features on Earth, which suggests that Martian eruptive processes are not significantly different from the volcanic styles and processes on Earth. Martian volcanoes are found on terrains of different age, and Martian volcanic rocks are estimated to comprise more than 50% of the Martian surface. This is in contrast to volcanism on smaller bodies such as Earth's Moon, where volcanic activity was mainly confined to the first half of lunar history (see "Volcanism on the Moon"). Comparative planetology supports the concept that volcanism is the primary mechanism for a planetary body to get rid of its internal heat; smaller bodies tend to lose their internal heat more rapidly than larger bodies (although, Jupiter's moon Io appears to contradict this trend; Io's intense volcanic activity is powered by unique gravitational tidal forces within the Jovian system; see "Volcanism on Io"), so that volcanic activity on Mars would be expected to differ considerably from that found on Earth and the Moon.

Mars↗

NASA NTRS2020

A Multi-scaled Analysis of Forest Structure using Individual-Based Modeling in a Costa Rican Rainforest

Consideration of scale is essential when examining structural relationships in forests. In this study, we present a parameterization of the FORMIND individual-based forest model for old growth Atlantic lowland rainforest in La Selva, Costa Rica. Results show that the simulated forest reproduces the structural complexity of Costa Rican rainforest within 2.3% of aboveground biomass values, based on comparisons with CARBONO inventory plot data. The Costa Rica FORMIND simulation was then used to investigate the relationship between canopy height and aboveground biomass (AGB), leaf area index (LAI) and gross primary productivity (GPP) at different spatial scales (20 × 20 m, 60 × 60 m, 100mx100m). The relationship between aboveground biomass and height is of particular importance toward the calibration of various remote sensing products including lidar and radar, whereas the LAI and GPP relationships are understudied in this context. We found that the relationship between all three variables and height varies considerably: the relationship is stronger at finer scales and weaker at coarser resolution. However, in all three comparisons, RMSE also decreased as scales coarsened, with the largest difference shown between 100 m and 10 m resolutions in relating AGB to Lorey's height (R^2 decreased by 0.3; RMSE decreased by 114.5 Mg/ha). This suggests that a trade-off between accuracy and precision exists, and further highlights the importance of spatial scale in determining the relatability of forest structure variables.

A.H.Armstrong↗

DOE OSTI2024

A MPET 2 -mPBPK model for subcutaneous injection of biotherapeutics with different molecular weights: From local scale to whole-body scale

Subcutaneous injection of biotherapeutics has attracted considerable attention in the pharmaceutical industry. However, there is limited understanding of the mechanisms underlying the absorption of drugs with different molecular weights and the delivery of drugs from the injection site to the targeted tissue. Here, we propose the MPET 2 -mPBPK model to address this issue. This multiscale model couples the MPET 2 model, which describes subcutaneous injection at the local tissue scale from a biomechanical view, with a post-injection absorption model at injection site and a minimal physiologically-based pharmacokinetic (mPBPK) model at whole-body scale. Utilizing the principles of tissue biomechanics and fluid dynamics, the local MPET 2 model provides solutions that account for tissue deformation and drug absorption in local blood vessels and initial lymphatic vessels during injection. Additionally, we introduce a model accounting for the molecular weight effect on the absorption by blood vessels, and a nonlinear model accounting for the absorption in lymphatic vessels. The post-injection model predicts drug absorption in local blood vessels and initial lymphatic vessels, which are integrated into the whole-body mPBPK model to describe the pharmacokinetic behaviors of the absorbed drug in the circulatory and lymphatic system. We establish a numerical model which links the biomechanical process of subcutaneous injection at local tissue scale and the pharmacokinetic behaviors of injected biotherapeutics at whole-body scale. With the help of the model, we propose an explicit relationship between the reflection coefficient and the molecular weight and predict the bioavalibility of biotherapeutics with varying molecular weights via subcutaneous injection. The considered drug absorption mechanisms enable us to study the differences in local drug absorption and whole-body drug distribution with varying molecular weights. This model enhances the understanding of drug absorption mechanisms and transport routes in the circulatory system for drugs of different molecular weights, and holds the potential to facilitate the application of computational modeling to drug formulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Dual-scale folding in cutting of commercially pure aluminum alloys

We examine a, hitherto, little-studied and curious machining chip morphology, with tell-tale signs of folding at two different length scales, that is common in cutting of certain ductile and highly strain-hardening metals like soft aluminum alloys, tantalum and niobium. This chip morphology does not appear in the usual catalogues of common chip types. The mechanics of formation of the “dual-scale folded chip” is studied in model material systems of commercially pure aluminum alloys (AA 1100 and AA 8040), that prominently exhibit this chip morphology. The flow, folding and associated plastic instabilities are investigated using micro/macro structure observations of the chip in a plane-strain cutting framework, with high-speed in situ imaging and image analysis of material flow; and force measurements. The smaller-scale folding is shown to develop in the primary deformation zone while the larger-scale folding occurs as the chip traverses the rake face of the tool. The resulting chip is composed of irregularly-spaced large folds, superimposed onto which are the quasi periodic small folds. The representative wavelengths of the two folds differ on average by an order of magnitude, 0.1 mm vs. 2 mm. The observations reveal a direct coupling between the material flow and chip morphology, and how specific attributes of the dual-scale folded chip arise from the flow mechanism. Plastic buckling is found to play a key role in the folding at both length scales. The small-scale folds are characteristic of a sinuous plastic flow mode, while the large-scale folding is characterized by buckling and stick-slip along the tool rake face, triggered by adhesive pinning of the chip to the tool. Important consequences of the dualscale folding are very large cutting forces, and force oscillations of large amplitude, despite the alloys being very soft, only ~ 25 HV. Here, the dual-scale folding is why many of these alloys are classified as “gummy” to machine. Since the dual-scale folded chip is associated with large cutting forces and poor surface quality, there is much to be gained by disrupting this flow type in practical machining applications. Methods for controlling the folding to improve machining performance with the gummy alloys are briefly discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Comparison of the Distribution of the In Situ Ring Current Density Based on Magnetic Field Observations From THEMIS, MMS and Cluster

Abstract We review and extend previous work on the ring current density distribution by applying the curlometer technique to multi‐spacecraft magnetic field data on different spatial scales, directly comparing the results of three space missions: Time History of Events and Macroscale Interactions during Substorms (THEMIS), The Magnetospheric Multiscale (MMS) and Cluster, that have so far accrued decades of data on a range of spatial separation scales. We suggest that the statistical results of Cluster data over two decades can illustrate well the overall form of the ring current (in the ring plane), but can underestimate the current density, while THEMIS (partially) and MMS are able to observe the detailed structure of the ring current and indeed show different behavior on some (smaller) spatial scales. These results suggest that, in addition to the local time and radial form, reported previously, the morphology of the ring current may also depend on magnetic latitude, as influenced by the tilt angle between the inner and outer magnetic fields.

Tan, X. [School of Space and Earth Sciences Beihan↗

DOE OSTI2023

Heat Transfer and Pressure Loss of Additively Manufactured Internal Cooling Channels With Various Shapes

Abstract Additive manufacturing (AM) provides the ability to fabricate highly customized internal cooling passages that are relevant to gas turbine components. This experimental study examines the pressure loss and heat transfer performance of a range of fundamental channel shapes that were produced using direct metal laser sintering. Circular, hexagonal, pentagonal, elliptical, diamond, square, rectangular, trapezoidal, and triangular channel cross sections were investigated. To maintain the same convective surface area between shapes, the wetted perimeters of the channel cross sections were kept constant. Parallel computational fluid dynamic simulations were performed to understand the relationships in cooling performance between several channel shapes. Several characteristic length scales were evaluated to scale the pressure loss and heat transfer measurements. Among the channel shapes investigated, the diamond channel showed the lowest Nusselt number and friction factor. The pentagon exhibited a similar Nusselt number as the circular channel despite having a lower friction factor. There was no difference in scaling the friction factor or Nusselt number results of the different channel shapes between using the square root of cross-sectional area compared to hydraulic diameter as the characteristic length scale

Engineering↗