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Thermal insulation versus capacitance: A simulation experiment comparing effects of shade and hyporheic exchange on daily and seasonal stream temperature cycles

In streams where water temperatures stress native biota, management of riparian shade or hyporheic exchange are both considered viable management strategies for reducing the peaks of daily and seasonal stream channel temperature cycles. Although shade and hyporheic exchange may have similar effects on stream temperatures, their mechanisms differ. Improved understanding of the heat-exchange mechanisms influenced by shade and hyporheic exchange will aid in the appropriate application of either stream temperature management strategy. To illustrate a conceptual model highlighting shade as ‘thermal insulation’ and hyporheic exchange imparting ‘thermal capacitance’ to a stream reach, we conducted an in-silico simulation modelling experiment increasing shade or hyporheic exchange parameters on an idealized, hypothetical stream. We assessed the potential effects of increasing shade or hyporheic exchange on a stream reach using an established process-based heat-energy budget model of stream-atmosphere heat exchange and incorporated an advection-driven hyporheic heat exchange routine. The model tracked heat transport through the hyporheic zone and exchange with the stream channel, while including the effects of hyporheic water age distribution on upwelling hyporheic temperatures. Results showed that shade and hyporheic exchange similarly damped diurnal temperature cycles and differentially altered seasonal cycles of our theoretical stream. In winter, hyporheic exchange warmed simulated channel temperatures whereas shade had little effect. In summer, both shade and hyporheic exchange cooled channel temperatures, though the effects of shade were more pronounced. Our simple-to-grasp analogies of ‘thermal insulation’ for shade effects and ‘thermal capacitance’ for hyporheic exchange effects on stream temperature encourage more accurate conceptualization of complex, dynamic heat exchange processes among the atmosphere, stream channel, and alluvial aquifer.

54 ENVIRONMENTAL SCIENCES↗

Measurement of the Z boson production cross-section in pp collisions at $ \sqrt{s}$ = 5.02 TeV

The first measurement of the Z boson production cross-section at centre-of-mass energy $\sqrt{s}$ = 5.02 TeV in the forward region is reported, using pp collision data collected by the LHCb experiment in year 2017, corresponding to an integrated luminosity of 100 ± 2 pb –1 . The production cross-section is measured for final-state muons in the pseudorapidity range 2.0 < η < 4.5 with transverse momentum p T > 20 GeV/c. The integrated cross-section is determined to be ${\sigma}_{Z\to \mu +\mu -}=39.6\pm 0.7\left(\textrm{stat}\right)\pm 0.6\left(\textrm{syst}\right)\pm 0.8\left(\textrm{lumi}\right)\textrm{pb}$ for the di-muon invariant mass in the range 60 < M μμ < 120 GeV/c 2 . This result and the differential cross-section results are in good agreement with theoretical predictions at next-to-next-to-leading order in the strong coupling constant. Based on a previous LHCb measurement of the Z boson production cross-section in pPb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV, the nuclear modification factor RpPb is measured for the first time at this energy. The measured values are ${1.2}_{-0.3}^{+0.5}$ (stat) ± 0.1(syst) in the forward region (1.53 < ${y}_{\mu}^{\ast }$ < 4.03) and ${3.6}_{-0.9}^{+1.6}$ (stat) ± 0.2(syst) in the backward region (–4.97 < ${y}_{\mu}^{\ast }$ < –2.47), where ${y}_{\mu}^{\ast }$ represents the muon rapidity in the centre-of-mass frame.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantitative and Predictive Genetic Parts for Plant Synthetic Biology

Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.

59 BASIC BIOLOGICAL SCIENCES↗

On a simplified solution of climate-carbon dynamics in idealized flat10MIP simulations

Abstract. Idealized experiments with coupled climate-carbon Earth system models (ESMs) provide a basis for understanding the response of the carbon cycle to external forcing and for quantifying climate-carbon feedbacks. Here, we analyze globally-averaged results from idealized esm-flat10 experiments and show that most models exhibit a quasi-linear relationship between cumulative carbon uptake on land and in the ocean during a period of constant fossil fuel emissions of 10 Pg C yr−1. We hypothesize that this relationship does not depend on emission pathways. Further, as a simplification, we quantify the relationship between cumulative ocean carbon uptake and changes in ocean heat content using a linear approximation. In this way, changes in oceanic heat content and atmospheric CO2 concentration become interdependent variables, reducing the coupled temperature-CO2 system to just one differential equation. The equation can be solved analytically or numerically for the atmospheric CO2 concentration as a function of fossil fuel emissions. This approach leads to a simplified description of global carbon and climate dynamics, which could be used for applications beyond existing analytical frameworks.

Brovkin, Victor↗

Combined Numerical/Analytical Perturbation Solutions of the Navier-Stokes Equations for Aerodynamic (Ejector Nozzle) Flows

In spite of the rapid advances in both scalar and parallel computational tools, the large number and breadth of variables involved in aerodynamic systems make the use of parabolized or even boundary layer fluid flow models impractical for both preliminary design and inverse design problems. Given this restriction, we have concluded that reduced or approximate models are an important family of tools for design purposes. This study of a combined perturbation/numerical modeling methodology with an application to ejector-mixer nozzles (shown schematically in the following figure) is nearing completion. The work is being funded by a grant from the NASA Lewis Research Center to Texas A&M University. These ejector-mixer nozzle models are designed to be of use to the High Speed Civil Transport Program and may be adopted by both NASA and industry. A computer code incorporating the ejector-mixer models is under development. This code, the Differential Reduced Ejector/Mixer Analysis (DREA), can be run fast enough to be used as a subroutine or to be called by a design optimization routine. Simplified conservation equations--x-momentum, energy, and mass conservation--are used to define the model. Unlike other preliminary design models, DREA requires minimal empirical input and includes vortical mixing and a fully compressible formulation among other features. DREA is being validated by comparing it with results obtained from open literature and proprietary industry data. Preliminary results for a subsonic ejector and a supersonic ejector are shown. In addition, dedicated experiments have been performed at Texas A&M. These experiments use a hydraulic/gas flow analog to provide information about the inviscid mixing interface structure. Final validation and documentation of this work is expected by May of 1997. However, preliminary versions of DREA can be expected in early 1997. In summary, DREA provides a sufficiently detailed and realistic ejector-mixer nozzle model at a computational cost compatible with preliminary design applications.

DeChant, Lawrence J.↗

In-Flight Aeroelastic Stability of the Thermal Protection System on the NASA HIAD, Part II: Nonlinear Theory and Extended Aerodynamics

Conical shell theory and a supersonic potential flow aerodynamic theory are used to study the nonlinear pressure buckling and aeroelastic limit cycle behavior of the thermal protection system for NASA's Hypersonic Inflatable Aerodynamic Decelerator. The structural model of the thermal protection system consists of an orthotropic conical shell of the Donnell type, resting on several circumferential elastic supports. Classical Piston Theory is used initially for the aerodynamic pressure, but was found to be insufficient at low supersonic Mach numbers. Transform methods are applied to the convected wave equation for potential flow, and a time-dependent aerodynamic pressure correction factor is obtained. The Lagrangian of the shell system is formulated in terms of the generalized coordinates for all displacements and the Rayleigh-Ritz method is used to derive the governing differential-algebraic equations of motion. Aeroelastic limit cycle oscillations and buckling deformations are calculated in the time domain using a Runge-Kutta method in MATLAB. Three conical shell geometries were considered in the present analysis: a 3-meter diameter 70 deg. cone, a 3.7-meter 70 deg. cone, and a 6-meter diameter 70 deg. cone. The 6-meter configuration was loaded statically and the results were compared with an experimental load test of a 6-meter HIAD. Though agreement between theoretical and experimental strains was poor, the circumferential wrinkling phenomena observed during the experiments was captured by the theory and axial deformations were qualitatively similar in shape. With Piston Theory aerodynamics, the nonlinear flutter dynamic pressures of the 3-meter configuration were in agreement with the values calculated using linear theory, and the limit cycle amplitudes were generally on the order of the shell thickness. The effect of axial tension was studied for this configuration, and increasing tension was found to decrease the limit cycle amplitudes when the circumferential elastic supports were neglected, but resulted in more complex behavior when the supports were included. The nominal flutter dynamic pressure of the 3.7-meter configuration was significantly lower than that of the 3-meter, and it was found that two sets of natural modes coalesce to flutter modes near the same dynamic pressure. This resulted in a significant drop in the limit cycle frequencies at higher dynamic pressures, where the flutter mode with the lower frequency becomes more critical. Pre-buckling pressure loads and the aerodynamic pressure correction factor were studied for all geometries, and these effects resulted in significantly lower flutter boundaries compared with Piston Theory alone. The maximum dynamic pressure predicted by aerodynamic simulations of a proposed 3.7-meter HIAD vehicle was still lower than any of the calculated flutter dynamic pressures, suggesting that aeroelastic effects for this vehicle are of little concern.

Goldman, Benjamin D.↗

Accelerating Continuous Variable Coherent Ising Machines Via Momentum

The Coherent Ising Machine (CIM) is a non-conventional architecture that takes inspiration from physical annealing processes to solve Ising problems heuristically. Its dynamics are naturally continuous and described by a set of ordinary differential equations that have been proven to be useful for the optimization of continuous variables nonconvex quadratic optimization problems. The dynamics of such Continuous Variable CIMs (CV-CIM) encourage optimization via optical pulses whose amplitudes are determined by the negative gradient of the objective; however, standard gradient descent is known to be trapped by local minima and hampered by poor problem conditioning. In this work, we propose to modify the CV-CIM dynamics using more sophisticated pulse injections based on tried-and-true optimization techniques such as momentum and Adam. Through numerical experiments, we show that the momentum and Adam updates can significantly speed up the CV-CIM’s convergence and improve sample diversity over the original CV-CIM dynamics. We also find that the Adam-CV-CIM’s performance is more stable as a function of feedback strength, especially on poorly conditioned instances, resulting in an algorithm that is more robust, reliable, and easily tunable. More broadly, we identify the CIM dynamical framework as a fertile opportunity for exploring the intersection of classical optimization and modern analog computing.

Ising Model↗

Preferential heating of light ions during an ionospheric AR(+) injection experiment

The ARCS 4 sounding rocket was launched northward into high altitude from Poker Flat Research Range on February 23, 1990. The vehicle crossed geomagnetic field lines containing discrete auroral activity. An instrumented subpayload released 100 ev and 200 ev Ar(+) ion beams sequentially, in a direction largely perpendicular to both the local geomagnetic field and the subpayload spin axis. The instrumented main payload was separated along field lines from the beam emitting subpayload by a distance which increased at a steady rate of approx. 2.4 m/s. Three-dimensional mass spectrometric ion observations of ambient H(+) and O(+) ions, obtained onboard the main payload, are presented. Main payload electric field observations in the frequency range 0-16 kHz, are also presented. These observations are presented to demonstrate the operation of transverse ion acceleration, that was differential with respect to ion mass, primarily during 100-ev beam operations. The preferential transverse acceleration of ambient H(+) ions, as compared with ambient O(+) ions during the second, third, fourth, and fifth 100-ev beam operations, is attributed to a resonance at the injected the beam drift velocity among the thermal H(+) ions and plasma waves generated by the injected beam and propagating at the beam drift speed. This work provides experimental support of processes predicted by previously published theory and simulations.

Pollock, C. J.↗

Formulation, Implementation and Validation of a 1D Boundary Layer Inflow Scheme for the QUIC Modeling System

Recent studies have highlighted the importance of accurate meteorological conditions for urban transport and dispersion calculations. In this work, we present a novel scheme to compute the meteorological input in the Quick Urban & Industrial Complex () diagnostic urban wind solver to improve the characterization of upstream wind veer and shear in the Atmospheric Boundary Layer (ABL). The new formulation is based on a coupled set of Ordinary Differential Equations (ODEs) derived from the Reynolds Averaged Navier–Stokes (RANS) equations, and is fast to compute. Building upon recent progress in modeling the idealized ABL, we include effects from surface roughness, turbulent stress, Coriolis force, buoyancy and baroclinicity. We verify the performance of the new scheme with canonical Large Eddy Simulation (LES) tests with the GPU-accelerated FastEddy"Equation missing" solver in neutral, stable, unstable and baroclinic conditions with different surface roughness. Furthermore, we evaluate QUIC calculations with and without the new inflow scheme with real data from the Urban Threat Dispersion (UTD) field experiment, which includes Lidar-based wind measurements as well as concentration observations from multiple outdoor releases of a non-reactive tracer in downtown New York City. Compared to previous inflow capabilities that were limited to a constant wind direction with height, we show that the new scheme can model wind veer in the ABL and enhance the prediction of the surface cross-isobaric angle, improving evaluation statistics of simulated concentrations paired in time and space with UTD measurements.

54 ENVIRONMENTAL SCIENCES↗

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗

High-Order Mesh r-Adaptivity with Tangential Relaxation and Guaranteed Mesh Validity

High-order meshes are crucial for achieving optimal convergence rates in curvilinear domains, preserving symmetry, and aligning with key flow features in moving mesh simulations [1], but their quality is challenging to control. In prior work, we have developed techniques based on Target-Matrix Optimization Paradigm (TMOP) to adapt a given high-order mesh to the geometry and solution of the partial differential equation (PDE) [2, 3]. Here, we extend this framework to address two key gaps in the literature for highorder mesh 𝑟-adaptivity. First, we introduce tangential relaxation on curved surfaces using solely the discrete mesh representation, eliminating the need for access to underlying geometry (e.g., CAD model). Second, we ensure a continuously positive Jacobian determinant throughout the domain. This determinant positivity is essential for using the high-order mesh resulting from 𝑟-adaptivity with arbitrary quadrature schemes in simulations. The proposed approach is demonstrated to be robust using a variety of numerical experiments.

Mathematics and Computing↗

Calculation of the polarization potential for e-N2 collisions

A polarization potential V(pol) for e-N2 collisions is calculated by the generalization of the static part of the method of polarized orbitals to molecular targets. Partial differential equations (PDE) are derived for polarized orbitals, which are functions of the distance (r) from the molecular center and angle (theta) from the molecular axis. The equations are solved with the use of the noniterative PDE technique. From the polarized orbitals a polarization potential can be constructed whose r and theta dependence is found to be significantly different from the well-known phenomenological one. The two potentials are further compared by carrying out limited hybrid-theory scattering calculations. Only those scattering results based on the calculated V(pol) are in satisfactory accord with experiment.

Onda, K.↗

Calculations of particle-laden flows by second-moment closures

A differential second-moment closure is applied to calculate nonswirling turbulent particle-laden jet flow. The closure is effected by extending constant-density single-phase turbulence models to the continuous (carrier) phase of two-phase flow. The dispersed (discrete) phase is treated by stochastic-Lagrangian technique. To reduce the effects of numerical (false) diffusion on the predicted results, a higher order differencing scheme, namely the flux-spline, is employed. In addition, an experimental study is conducted to provide data of good quality, especially near the inlet, for model assessment. The experiment consists of a confined coaxial jet flow of air with glass beads. The beads' diameter is 105 microns and is injected from the inner jet with a mass loading ratio of 0.9. The computed results are in good agreement with experimental data, especially for the carrier phase. However, the predicted turbulence fluctuations associated with the discrete phase are lower than the data at the downstream region of the flow field.

Nikjooy, M.↗

Analytical, Experimental, and Modelling Studies of Lunar and Terrestrial Rocks

The goal of our research has been to understand the paths and the processes of planetary evolution that produced planetary surface materials as we find them. Most of our work has been on lunar materials and processes. We have done studies that obtain geological knowledge from detailed examination of regolith materials and we have reported implications for future sample-collecting and on-surface robotic sensing missions. Our approach has been to study a suite of materials that we have chosen in order to answer specific geologic questions. We continue this work under NAG5-4172. The foundation of our work has been the study of materials with precise chemical and petrographic analyses, emphasizing analysis for trace chemical elements. We have used quantitative models as tests to account for the chemical compositions and mineralogical properties of the materials in terms of regolith processes and igneous processes. We have done experiments as needed to provide values for geochemical parameters used in the models. Our models take explicitly into account the physical as well as the chemical processes that produced or modified the materials. Our approach to planetary geoscience owes much to our experience in terrestrial geoscience, where samples can be collected in field context and sampling sites revisited if necessary. Through studies of terrestrial analog materials, we have tested our ideas about the origins of lunar materials. We have been mainly concerned with the materials of the lunar highland regolith, their properties, their modes of origin, their provenance, and how to extrapolate from their characteristics to learn about the origin and evolution of the Moon's early igneous crust. From this work a modified model for the Moon's structure and evolution is emerging, one of globally asymmetric differentiation of the crust and mantle to produce a crust consisting mainly of ferroan and magnesian igneous rocks containing on average 70-80% plagioclase, with a large, mafic, trace-element-rich geochemical province, and a regolith that globally contains trace-element-rich material distributed from this province by the Imbrium basin-forming impact. This contrasts with earlier models of a concentrically zoned Moon with a crust of ferroan anorthosite overlying a layer of urKREEP overlying ultramafic cumulates. From this work, we have learned lessons useful for developing strategies for studying regolith materials that help to maximize the information available about both the evolution of the regolith and the igneous differentiation of the planet. We believe these lessons are useful in developing strategies for on-surface geological, mineralogical, and geochemical studies, as well. The main results of our work are given in the following brief summaries of major tasks. Detailed accounts of these results have been submitted in the annual progress reports.

Haskin, Larry A.↗

Direct Probe of Dark Energy Interactions with a Solar System Laboratory: NASA Innovative Advanced Concepts (NIAC) - Phase 1 Final Report

In this NIAC (NASA Innovative Advanced Concepts) study, we embrace the challenge of direct detection of the galileon dark energy field in the Vainshtein model. We developed a mission concept to directly measure the galileon field using the solar system as a laboratory. The experiment scheme involves precise measurements of the trace of the total scalar force gradient tensor. A tetrahedral constellation off our spacecraft measures the "local" traces while orbiting about 1 AU (Astronomical Unit) away from the Sun and faraway from planets (Figure 1). The trace measurement is insensitive to the much stronger gravity field which satisfies the inverse square law and thus is traceless. Atomic test masses and atom interferometer measurement techniques are used as precise drag-free inertial references while laser ranging interferometers are employed to connect among atom interferometer pairs in spacecraft for the differential gradient force measurements. We conclude that such a mission is scientifically and technologically feasible. We show that a mission of 3-year measurement time would be able to provide high confidence statements (over 3 standard deviations) about the existence and strength of the cubic galileon field of the Sun. In addition, such a mission would also provide rich and diverse scientific data for testing any gravitational theory in general beyond the Newtonian gravity, hunting for ultra-light fields of dark matter, and detecting gravitational waves in the mid-frequency band between those of LIGO (Laser Interferometer Gravitational-Wave Observatory) and LISA (Laser Interferometer Space Antenna). For these reasons, we will term the mission concept Gravity Observation and Dark energy Detection Explorer in the Solar System (GODDESS).

Dark Energy↗

Composition and Evolution of Southeast Asian Biomass Burning Trace Gas Emissions during a September 2019 Borneo Burning Event

Biomass burning in Southeast Asia is a major pollutant source contributing to poor air quality throughout the region. Thus, understanding these emissions is critical for predicting and mitigating their health impacts. While there have been many studies reporting ground-based and satellite measurements, regional scale measurements to tie the two together have not been common in this region. The 2019 Cloud, Aerosol and Monsoon Processes Philippines Experiment (CAMP2Ex) field campaign examined Southeast Asian regional sources and their effects on aerosol/cloud interactions using a combination of airborne, shipborne, and ground-based measurements. On 16 September, a major biomass burning event primarily located on Borneo was sampled via aircraft in the near-field over the Sulu Sea, while on 17 September, the aged plume from the event was sampled again east of the Philippines over the Philippine Sea. We discuss the emissions from this event, using tracer-tracer ratios (e.g. MCE, NOy/CO), HYSPLIT back trajectories, and HSRL-2 lidar retrievals to differentiate sources and provide insight into the composition and chemical evolution of the plume. This case study provides a valuable perspective into the accuracy of emission inventories as well as a rare opportunity for satellite validation.

Joshua P DiGangi↗

HemoCue ISS Tech Demo - Results and Lessons Learned

During long duration space missions, astronauts experience immune system dysregulation [1], and white blood cell (WBC) count can give vital information about the body’s immune response. The ability to measure WBC count is currently an unmet need on the International Space Station (ISS) and for future exploration missions. To address this need, the Human Research Program’s (HRP) Exploration Medical Capability (ExMC) Element, along with the Research Operations and Integration (ROI) Element and the NASA Johnson Space Center Immunology Lab, flew HemoCue®, a commercial-off-the-shelf analyzer with the ability to measure whole blood WBC count with 5-part differential to ISS in December 2020.

Exploration Medical Capability↗

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗

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