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DOE OSTI2021

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Heterogeneous oxidation of amorphous organic aerosol surrogates by O 3 , NO 3 , and OH at typical tropospheric temperatures

Typical tropospheric temperatures render possible phase states of amorphous organic aerosol (OA) particles of solid, semisolid, and liquid. This will affect the multiphase oxidation kinetics involving the organic condensed-phase and gaseous oxidants and radicals. To quantify this effect, we determined the reactive uptake coefficients (γ) of O 3 , NO 3 , and OH by substrate films composed of single and binary OA surrogate species under dry conditions for temperatures from 213 to 313 K. A temperature-controlled coated-wall flow reactor coupled to a chemical ionization mass spectrometer was applied to determine γ with consideration of gas diffusion transport limitation and gas flow entrance effects, which can impact heterogeneous reaction kinetics. The phase state of the organic substrates was probed via the poke-flow technique, allowing the estimation of the substrates' glass transition temperatures. γ values for O 3 and OH uptake to a canola oil substrate, NO 3 uptake to a levoglucosan and a levoglucosan / xylitol substrate, and OH uptake to a glucose and glucose / 1,2,6-hexanetriol substrate have been determined as a function of temperature. We observed the greatest changes in γ with temperature for substrates that experienced the largest changes in viscosity as a result of a solid-to-liquid phase transition. Organic substrates that maintain a semisolid or solid phase state and as such a relatively higher viscosity do not display large variations in heterogeneous reactivity. From 213 to 293 K, γ values of O 3 with canola oil, of NO 3 with a levoglucosan / xylitol mixture, and of OH with a glucose / 1,2,6-hexanetriol mixture and canola oil, increase by about a factor of 34, 3, 2, and 5, respectively, due to a solid-to-liquid phase transition of the substrate. These results demonstrate that the surface and bulk lifetime of the OA surrogate species can significantly increase due to the slowed heterogeneous kinetics when OA species are solid or highly viscous in the middle and upper troposphere. This experimental study will further our understanding of the chemical evolution of OA particles with subsequent important consequences for source apportionment, air quality, and climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Examining the vertical heterogeneity of aerosols over the Southern Great Plains

Abstract. Atmospheric aerosols affect the global energy budget by scattering and absorbing sunlight (direct effects) and by changing the microphysical structure, lifetime, and coverage of clouds (indirect effects). Both aerosol direct and indirect effects are affected by the vertical distribution of aerosols in the atmosphere, which is further influenced by a range of processes, such as aerosol dynamics, long-range transport, and entrainment. However, many observations of these processes are based on ground measurements, limiting our ability to understand the vertical distribution of aerosols and simulate their impact on clouds and climate. In this work, we examined the vertical heterogeneity of aerosols over the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) using data collected from the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) campaign. The vertical profiles of meteorological and aerosol physiochemical properties up to 2500 m above are examined based on the 38 flights conducted during the HI-SCALE campaign. The aerosol properties over the SGP show strong vertical heterogeneity and seasonal variabilities. The aerosol concentrations at the surface are the highest due to strong emissions at ground level. In general, the mode diameter of aerosols during summer (∼ 100 nm) is larger than that during spring (∼ 30 nm), a result of enhanced condensational growth due to enriched volatile organic compounds in summer. The concentration of aerosols below 30 nm in the boundary layer (BL) (e.g., below 1000 m) during spring is higher than that during summer, a result of the stronger new particle formation (NPF) events due to the reduced condensation sink in spring. In the BL, the size of the aerosols gradually increases with altitude due to condensational growth and cloud processing. However, the chemical composition of the aerosols remained similar, with organics and sulfates representing 59.8 ± 2.2 % and 22.7 ± 2.1 %, respectively, of the total mass in the BL. Through the vertical profiles of aerosol properties, we observed NPF events in the upper BL during 7 out of 38 research flights, where the newly formed particles continue to grow as they are mixed down to the surface. There is also an indication that deep convection brings aerosols from the free troposphere (FT) to the surface, where they grow to contribute to the cloud condensation nuclei (CCN). Overall, the vertical heterogeneity of aerosols over the SGP is influenced by aerosol dynamics (new particle formation, growth, and cloud processing) and transport processes (mixing in the BL, long-range transport, entrainment, and convective downward transport). Case studies showing the influence of these factors are discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A new parameterization of ice heterogeneous nucleation coupled to aerosol chemistry in WRF-Chem model version 3.5.1: evaluation through ISDAC measurements

In the Arctic, during polar night and early spring, ice clouds are separated into two leading types of ice clouds (TICs): (1) TIC1 clouds characterized by a large concentration of very small crystals and TIC2 clouds characterized by a low concentration of large ice crystals. Using a suitable parameterization of heterogeneous ice nucleation is essential for properly representing ice clouds in meteorological and climate models and subsequently understanding their interactions with aerosols and radiation. Here, we describe a new parameterization for ice crystal formation by heterogeneous nucleation in water-subsaturated conditions coupled to aerosol chemistry in the Weather Research and Forecasting model coupled with chemistry (WRF-Chem). The parameterization is implemented in the Milbrandt and Yau (2005a, b) two-moment cloud microphysics scheme, and we assess how the WRF-Chem model responds to the run-time interaction between chemistry and the new parameterization. Well-documented reference cases provided us with in situ data from the spring 2008 Indirect and Semi-Direct Aerosol Campaign (ISDAC) over Alaska. Our analysis reveals that the new parameterization clearly improves the representation of the ice water content (IWC) in polluted or unpolluted air masses and shows the poor performance of the reference parameterization in representing ice clouds with low IWC. The new parameterization is able to represent TIC1 and TIC2 microphysical characteristics at the top of the clouds, where heterogenous ice nucleation is most likely occurring, even with the known bias of simulated aerosols by WRF-Chem over the Arctic.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

The revised FLORIDyn model: implementation of heterogeneous flow and the Gaussian wake

In this paper, a new version of the FLOw Redirection and Induction Dynamics (FLORIDyn) model is presented. The new model uses the three-dimensional parametric Gaussian FLORIS model and can provide dynamic wind farm simulations at a low computational cost under heterogeneous and changing wind conditions. Both FLORIS and FLORIDyn are parametric models which can be used to simulate wind farms, evaluate controller performance and can serve as a control-oriented model. One central element in which they differ is in their representation of flow dynamics: FLORIS neglects these and provides a computationally very cheap approximation of the mean wind farm flow. FLORIDyn defines a framework which utilizes this low computational cost of FLORIS to simulate basic wake dynamics. This is achieved by creating so-called observation points (OPs) at each time step at the rotor plane which inherit the turbine state. In this work, we develop the initial FLORIDyn framework further considering multiple aspects. The underlying FLORIS wake model is replaced by a Gaussian wake model. The distribution and characteristics of the OPs are adapted to account for the new parametric model but also to take complex flow conditions into account. To achieve this, a mathematical approach is developed to combine the parametric model and the changing, heterogeneous world conditions and link them with each OP. We also present a computationally lightweight wind field model to allow for a simulation environment in which heterogeneous flow conditions are possible. FLORIDyn is compared to Simulator for Offshore Wind Farm Applications (SOWFA) simulations in three- and nine-turbine cases under static and changing environmental conditions. The results show a good agreement with the timing of the impact of upstream state changes on downstream turbines. They also show a good agreement in terms of how wakes are displaced by wind direction changes and when the resulting velocity deficit is experienced by downstream turbines. A good fit of the mean generated power is ensured by the underlying FLORIS model. In the three-turbine case, FLORIDyn simulates 4 s simulation time in 24.49 ms computational time. The resulting new FLORIDyn model proves to be a computationally attractive and capable tool for model-based dynamic wind farm control.

17 WIND ENERGY↗

DOE OSTI2022

Near-Surface Hydrology and Soil Properties Drive Heterogeneity in Permafrost Distribution, Vegetation Dynamics, and Carbon Cycling in a Sub-Arctic Watershed: Modeling Archive

This Modeling Archive is in support of a NGEE-Arctic publication: Shirley et al. (2022) “Near-Surface Hydrology and Soil Properties Drive Heterogeneity in Permafrost Distribution, Vegetation Dynamics, and Carbon Cycling in a Sub-Arctic Watershed". [DOI].The dataset contains outputs from the global sensitivity analysis (GSA) of the “ecosys” model as reported in Shirley et al. (2022). The study showed that discontinuous permafrost environments are characterized by complex feedback loops and strong spatial heterogeneity which is created by variability in near-surface hydrology and soil properties. Additionally, the study demonstrated that missing representation of sub-grid heterogeneity in terrestrial ecosystem models can lead to biased estimates of the high-latitude carbon budget. Included in this dataset are the factor values for each run in the GSA and the model outputs used in this study. Included are two *.csv data files and one *.pdf.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1983

Lateral heterogeneity and azimuthal anistropy of the upper mantle: Love and Rayleigh waves 100-250 sec

The lateral heterogeneity and apparent anisotropy of the upper mantle are studied by measuring Rayleigh and Love wave phase velocities in the period range 100-250 sec. Spherical harmonic descriptions of the lateral heterogeneity are obtained for order and degree up to 1=m=10. Slow regions are evident at the East Pacific rise, northeast Africa, Tibet, Tasman sea, southwestern North America and triple junctions in the Northern Atlantic and Indian oceans. Fast regions occur in Australia, western Pacific and the eastern Atlantic. Details which are not evident in previous studies include two fast regions in the central Pacific and the subduction zone in the Scotia Arc region. Inversion for azimuthal dependence showed (1) little correlation between the fast phase velocity directions and the plate motion vector in plate interiors, but (2) correlation of the fast direction with the perpendicular direction to trenches and ridges. Phase velocity is high when waves propagate perpendicular to these structures. Severe tradeoffs exist between heterogeneity and azimuthal dependence because of the yet unsatisfactory path coverage.

Tanimoto, T.↗

NASA NTRS1983

ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.

Voecks, G. E.↗

NASA NTRS1984

The Effect of Point-spread Function Interaction with Radiance from Heterogeneous Scenes on Multitemporal Signature Analysis

The point-spread function is an important factor in determining the nature of feature types on the basis of multispectral recorded radiance, particularly from heterogeneous scenes and particularly from scenes which are imaged repetitively, in order to provide thematic characterization by means of multitemporal signature. To demonstrate the effect of the interaction of scene heterogeneity with the point spread function (PSF)1, a template was constructed from the line spread function (LSF) data for the thematic mapper photoflight model. The template was in 0.25 (nominal) pixel increments in the scan line direction across three scenes of different heterogeneity. The sensor output was calculated by considering the calculated scene radiance from each scene element occurring between the contours of the PSF template, plotted on a movable mylar sheet while it was located at a given position.

Duggin, M. J.↗

NASA NTRS1983

Oxygen isotopic heterogeneities, their petrological correlations, and implications for melt origins of chondrules in unequilibrated ordinary chondrites

Clayton et al. (1976, 1982) established that equilibrated ordinary chondrites (EOC's) can be divided into the H- and L-groups on the basis of their oxygen isotopic composition. The present investigation is concerned with new oxygen isotopic analyses of petrologically well-characterized individual chondrules from the unequilibrated chondrites Dhajala (H3,4), Hallingeberg (L3), and Semarkona (LL3). A study is conducted regarding the implications of isotopic/petrologial correlations for the origin of chondrules in ordinary chondrites. It is found that the oxygen isotopic heterogeneities among chondrules are reminiscent of the bulk elemental and phase compositional heterogeneities among the same and other chondrules as reported by Gooding et al. (1979, 1980). It is concluded that chondrules formed possibly as a result of the melting of preexisting materials which were both chemically and isotopically heterogeneous.

Gooding, J. L.↗

NASA NTRS1985

Lateral heterogeneity and azimuthal anisotropy of the upper mantle - Love and Rayleigh waves 100-250 sec

Tanimoto, T.↗

NASA NTRS1989

Ozone destruction through heterogeneous chemistry following the eruption of El Chichon

The results of ozone observations at northern midlatitudes in late 1982 through 1983, following the eruption of El Chichon are discussed, together with the observations of other trace gases which may be linked to possible variations in ozone chemistry. These results are related to the in situ aerosol observations following the El Chicon eruption, with particular attention given to data relevant to heterogeneous reactions, such as the aerosol surface area and weight percent H2SO4. It is shown that, at midlatitudes, the observed volcanic-particle surface area reached a maximum of about 50 sq microns/cu m (above a typical background value of about 0.75) at an altitude of 18-20 km in early 1983; this enhancement of surface area is about the same as that encountered in stratospheric clouds in the Antarctic, suggesting a possible basis for ozone depletion through heterogeneous chemistry. The fraction of ozone reduction that may have occurred as a result of heterogeneous chemicl effects is estimated.

Hofmann, David J.↗

NASA NTRS1990

Heterogeneous chemistry on liquid sulfate aerosols - A comparison of in situ measurements with zero-dimensional model calculations

The possibility that stratospheric chlorine is converted from reservoir to reactive forms by heterogeneous reactions on background sulfate aerosols is examined. Tightly constrained photochemical models have been used to calculate ClO abundances for the morning and the afternoon conditions observed on January 24, 1989 outside the Arctic polar vortex by instruments on the NASA ER-2 aircraft. Calculations involving gas-phase chemistry only and calculations with heterogeneous chemistry including HCl evaporation from the aerosol both produce ClO abundances that agree with observations; calculations in which HCl removal from the aerosol is controlled by heterogeneous reactions produce ClO abundances that are 3 to 3.5 times larger than observations. These results suggest that HCl evaporation must be included in a model of the chemistry of background aerosols.

Mather, J. H.↗

NASA NTRS1991

Measuring the effects of heterogeneity on distributed systems

Distributed computer systems in daily use are becoming more and more heterogeneous. Currently, much of the design and analysis studies of such systems assume homogeneity. This assumption of homogeneity has been mainly driven by the resulting simplicity in modeling and analysis. A simulation study is presented which investigated the effects of heterogeneity on scheduling algorithms for hard real time distributed systems. In contrast to previous results which indicate that random scheduling may be as good as a more complex scheduler, this algorithm is shown to be consistently better than a random scheduler. This conclusion is more prevalent at high workloads as well as at high levels of heterogeneity.

El-Toweissy, Mohamed↗

NASA NTRS1991

A distributed scheduling algorithm for heterogeneous real-time systems

Much of the previous work on load balancing and scheduling in distributed environments was concerned with homogeneous systems and homogeneous loads. Several of the results indicated that random policies are as effective as other more complex load allocation policies. The effects of heterogeneity on scheduling algorithms for hard real time systems is examined. A distributed scheduler specifically to handle heterogeneities in both nodes and node traffic is proposed. The performance of the algorithm is measured in terms of the percentage of jobs discarded. While a random task allocation is very sensitive to heterogeneities, the algorithm is shown to be robust to such non-uniformities in system components and load.

Zeineldine, Osman↗

NASA NTRS1992

Heterogeneous conversion of N2O5 to HNO3 on background stratospheric aerosols - Comparisons of model results with data

The effects of heterogeneous processing by a parameterized lower stratospheric sulfate aerosol layer on model calculations were examined using a 2D photochemical model. Model results were compared with zonally averaged LIMS data on HNO3 and NO2 and in situ measurements of NO, NO(y), and ClO, taken by the ER-2 aircraft. The results obtained are contradictory: some comparisons favor heterogeneous chemistry, and some do not. It is suggested that the assumptions made to parameterize the sulfate aerosol chemistry result in a rate of heterogeneous processing that is too vigorous.

Considine, David B.↗

NASA NTRS1993

Heterogeneous chemistry on Antarctic polar stratospheric clouds - A microphysical estimate of the extent of chemical processing

A detailed model of polar stratospheric clouds (PSCs), which includes nucleation, condensational growth. and sedimentation processes, has been applied to the study of heterogeneous chemical reactions. For the first time, the extent of chemical processing during a polar winter has been estimated for an idealized air parcel in the Antarctic vortex by calculating in detail the rates of heterogeneous reactions on PSC particles. The resulting active chlorine and NO(x) concentrations at first sunrise are analyzed with respect to their influence upon the Antarctic ozone hole using a photochemical model. It is found that the species present at sunrise are primarily influenced by the relative values of the heterogeneous reaction rate constants and the initial gas concentrations. However, the extent of chlorine activation is also influenced by whether N2O5 is removed by reaction with HCl or H2O. The reaction of N2O5 with HCl, which occurs rapidly on type 1 PSCs, activates the chlorine contained in the reservoir species HCl. Hence the presence and surface area of type 1 PSCs early in the winter are crucial in determining ozone depletion.

Drdla, K.↗

NASA NTRS1993

Node assignment in heterogeneous computing

A number of node assignment schemes, both static and dynamic, are explored for the Algorithm to Architecture Mapping Model (ATAMM). The architecture under consideration consists of heterogeneous processors and implements dataflow models of real-time applications. Terminology is developed for heterogeneous computing. New definitions are added to the ATAMM for token and assignment classifications. It is proved that a periodic execution is possible for dataflow graphs. Assignment algorithms are developed and proved. A design procedure is described for satisfying an objective function in an heterogeneous architecture. Several examples are provided for illustration.

Som, Sukhamoy↗