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DOE OSTI2017

Estimating the reproductive number, total outbreak size, and reporting rates for Zika epidemics in South and Central America

As South and Central American countries prepare for increased birth defects from Zika virus outbreaks and plan for mitigation strategies to minimize ongoing and future outbreaks, understanding important characteristics of Zika outbreaks and how they vary across regions is a challenging and important problem. We developed a mathematical model for the 2015/2016 Zika virus outbreak dynamics in Colombia, El Salvador, and Suriname. We fit the model to publicly available data provided by the Pan American Health Organization, using Approximate Bayesian Computation to estimate parameter distributions and provide uncertainty quantification. The model indicated that a country-level analysis was not appropriate for Colombia. We then estimated the basic reproduction number to range between 4 and 6 for El Salvador and Suriname with a median of 4.3 and 5.3, respectively. We estimated the reporting rate to be around 16% in El Salvador and 18% in Suriname with estimated total outbreak sizes of 73,395 and 21,647 people, respectively. The uncertainty in parameter estimates highlights a need for research and data collection that will better constrain parameter ranges.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

WARM SPITZER OBSERVATIONS OF THREE HOT EXOPLANETS: XO-4b, HAT-P-6b, AND HAT-P-8b

We analyze Warm Spitzer/Infrared Array Camera observations of the secondary eclipses of three planets, XO-4b, HAT-P-6b, and HAT-P-8b. We measure secondary eclipse amplitudes at 3.6 {mu}m and 4.5 {mu}m for each target. XO-4b exhibits a stronger eclipse depth at 4.5 {mu}m than at 3.6 {mu}m, which is consistent with the presence of a temperature inversion. HAT-P-8b shows a stronger eclipse amplitude at 3.6 {mu}m and is best described by models without a temperature inversion. The eclipse depths of HAT-P-6b can be fitted with models with a small or no temperature inversion. We consider our results in the context of a postulated relationship between stellar activity and temperature inversion and a relationship between irradiation level and planet dayside temperature, as discussed by Knutson et al. and Cowan and Agol, respectively. Our results are consistent with these hypotheses, but do not significantly strengthen them. To measure accurate secondary eclipse central phases, we require accurate ephemerides. We obtain primary transit observations and supplement them with publicly available observations to update the orbital ephemerides of the three planets. Based on the secondary eclipse timing, we set upper boundaries for ecos ({omega}) for HAT-P-6b, HAT-P-8b, and XO-4b and find that the values are consistent with circular orbits.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Tape-in-tape-out (TITO): a new approach for in-situ contact resistance measurements in high temperature superconducting CORC® cables

One of the ongoing development challenges with ReBCO high-temperature superconducting (HTS) cables is normal zone initiation and local heating, which is associated with over-critical current flowing through and around local performance reductions in individual tapes. Although inter-tape contact resistances are well-reported for individual tapes and HTS cables, these measurements are a challenge in CORC® cables as current percolates through much of the cable. In this work, developments in tape-in-tape-out (TITO) automated individual tape powering experiments are presented, and a simplified modeling approach for current percolation in CORC® cables is developed. An optimization is formulated to fit the model parameters to a large set of TITO experiments on a single cable, allowing the layer-dependent inter-tape contact resistance to be extracted. Measurements are presented and discussed for a straight CORC® cable and a cable bent to a 152 mm and 76 mm radius. The approach provides both quantitative insight and facilitates better understanding of current sharing phenomena in HTS cables.

Teyber, Reed↗

DOE OSTI2012

Cosmological solutions in bimetric gravity and their observational tests

We obtain the general cosmological evolution equations for a classically consistent theory of bimetric gravity. Their analytic solutions are demonstrated to generically allow for a cosmic evolution starting out from a matter dominated FLRW universe and relaxing towards a de Sitter (anti-de Sitter) phase at late cosmic time. In particular, we examine a subclass of models which contain solutions that are able to reproduce the expansion history of the cosmic concordance model inspite of the nonlinear couplings of the two metrics. This is demonstrated explicitly by fitting these models to observational data from Type Ia supernovae, Cosmic Microwave Background and Baryon Acoustic Oscillations. In the appendix we comment on the relation to massive gravity.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of “stiff” equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A Novel Multiphysics Multiscale Multiporosity Shale Gas Transport Model for Geomechanics/Flow Coupling in Steady and Transient States

Summary A novel multiphysics multiscale multiporosity shale gas transport (M3ST) model was developed to investigate shale gas transport in both transient and steady states. The microscale model component contains a kerogen domain and an inorganic matrix domain, and each domain has its own geomechanical and gas transport properties. Permeabilities of various shale cores were measured in the laboratory using a pulse decay permeameter (PDP) with different pore pressure and confining stress combinations. The PDP-measured apparent permeability as a function of pore pressure under two effective stresses was fitted using the microscale M3ST model component based on nonlinear least squares fitting (NLSF), and the fitted model parameters were able to provide accurate model predictions for another effective stress. The parameters and petrophysical properties determined in the steady state were then used in the transient-state, continuum-scale M3ST model component, which performed history matching of the evolutions of the upstream and downstream gas pressures. In addition, a double-exponential empirical model was developed as a powerful alternative to the M3ST model to fit laboratory-measured apparent permeability under various effective stresses and pore pressures. The developed M3ST model and the research findings in this study provided critical insights into the role of the multiphysics mechanisms, including geomechanics, fluid dynamics and transport, and the Klinkenberg effect on shale gas transport across different spatial scales in both steady and transient states.

Engineering↗

DOE OSTI2016

Detection of enhancement in number densities of background galaxies due to magnification by massive galaxy clusters

We present a detection of the enhancement in the number densities of background galaxies induced from lensing magnification and use it to test the Sunyaev-Zel'dovich effect (SZE-) inferred masses in a sample of 19 galaxy clusters with median redshift z similar or equal to 0.42 selected from the South Pole Telescope SPT-SZ survey. These clusters are observed by the Megacam on the Magellan Clay Telescope though gri filters. Two background galaxy populations are selected for this study through their photometric colours; they have median redshifts zmedian similar or equal to 0.9 (low-z background) and z(median) similar or equal to 1.8 (high-z background). Stacking these populations, we detect the magnification bias effect at 3.3 sigma and 1.3 sigma for the low-and high-z backgrounds, respectively. We fit Navarro, Frenk and White models simultaneously to all observed magnification bias profiles to estimate the multiplicative factor. that describes the ratio of the weak lensing mass to the mass inferred from the SZE observable-mass relation. We further quantify systematic uncertainties in. resulting from the photometric noise and bias, the cluster galaxy contamination and the estimations of the background properties. The resulting. for the combined background populations with 1 sigma uncertainties is 0.83 +/- 0.24(stat) +/- 0.074(sys), indicating good consistency between the lensing and the SZE-inferred masses. We use our best-fitting eta to predict the weak lensing shear profiles and compare these predictions with observations, showing agreement between the magnification and shear mass constraints. This work demonstrates the promise of using the magnification as a complementary method to estimate cluster masses in large surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics

Abstract Drugs of abuse, such as opiates, have been widely associated with enhancing HIV replication, accelerating disease progression and diminishing host-immune responses, thereby making it harder to effectively manage HIV infection. It is thus important to study the effects of drugs of abuse on HIV-infection and immune responses. Here, we develop mathematical models that incorporate the effects of morphine-altered antibody responses on HIV/SIV dynamics. Based on fitting the model to experimental data from simian immunodeficiency virus (SIV) infections in control and morphine-addicted macaques, we found that two of the most significant effects of virus specific antibodies are neutralizing viral particles and enhancing viral clearance. Using our model, we quantified how morphine alters virus-specific antibody responses, and how this alteration affects the key components of virus dynamics such as infection rate, virus clearance, viral load, CD4 + T cell count, and CD4 + T cell loss in SIV-infected macaques under conditioning with morphine. We found that in a subpopulation of SIV-infected morphine addicted macaques, the presence of drugs of abuse may cause significantly diminished antibody responses, resulting in more severe infection with increased SIV infectivity, a decreased viral clearance rate, increased viral load, and higher CD4 + T cell loss.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

THE MASS-LOSS RETURN FROM EVOLVED STARS TO THE LARGE MAGELLANIC CLOUD. VI. LUMINOSITIES AND MASS-LOSS RATES ON POPULATION SCALES

We present results from the first application of the Grid of Red Supergiant and Asymptotic Giant Branch ModelS (GRAMS) model grid to the entire evolved stellar population of the Large Magellanic Cloud (LMC). GRAMS is a pre-computed grid of 80,843 radiative transfer models of evolved stars and circumstellar dust shells composed of either silicate or carbonaceous dust. We fit GRAMS models to {approx}30,000 asymptotic giant branch (AGB) and red supergiant (RSG) stars in the LMC, using 12 bands of photometry from the optical to the mid-infrared. Our published data set consists of thousands of evolved stars with individually determined evolutionary parameters such as luminosity and mass-loss rate. The GRAMS grid has a greater than 80% accuracy rate discriminating between oxygen- and carbon-rich chemistry. The global dust injection rate to the interstellar medium (ISM) of the LMC from RSGs and AGB stars is on the order of 2.1 Multiplication-Sign 10{sup -5} M{sub Sun} yr{sup -1}, equivalent to a total mass injection rate (including the gas) into the ISM of {approx}6 Multiplication-Sign 10{sup -3} M{sub Sun} yr{sup -1}. Carbon stars inject two and a half times as much dust into the ISM as do O-rich AGB stars, but the same amount of mass. We determine a bolometric correction factor for C-rich AGB stars in the K{sub s} band as a function of J - K{sub s} color, BC{sub K{sub s}}= -0.40(J-K{sub s}){sup 2} + 1.83(J-K{sub s}) + 1.29. We determine several IR color proxies for the dust mass-loss rate (M-dot{sub d}) from C-rich AGB stars, such as log M-dot{sub d} = (-18.90/((K{sub s}-[8.0])+3.37) - 5.93. We find that a larger fraction of AGB stars exhibiting the 'long-secondary period' phenomenon are more O-rich than stars dominated by radial pulsations, and AGB stars without detectable mass loss do not appear on either the first-overtone or fundamental-mode pulsation sequences.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Temperature- and Intensity-Dependent Photovoltaic Measurements to Identify Dominant Recombination Pathways

In novel photovoltaic absorbers, it is often difficult to assess the root causes of low open-circuit voltages, which may be due to bulk recombination or sub-optimal contacts. In the present work, we discuss the role of temperature- and illumination-dependent device electrical measurements in quantifying and distinguishing these performance losses - in particular, for determining bounds on interface recombination velocities, band alignment, and minority carrier lifetime. We assess the accuracy of this approach by direct comparison to photoelectron spectroscopy. Then, we demonstrate how more computationally intensive model parameter fitting approaches can draw more insights from this broad measurement space. We apply this measurement and modeling approach to high-performance III-V and thin-film chalcogenide devices.

14 SOLAR ENERGY↗

DOE OSTI2018

OSIF (Open Source Impedance Fitter)

OSIF is a tool that allows the user to easily fit electrochemical impedance spectra of proton exchange membrane fuel cells to a commonly accepted equivalent circuit model. The fitted parameters provide insight into the physical properties of the cell which allow the user to support experimental hypotheses.

Pfeilsticker, Jason↗

DOE OSTI2014

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells

HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. We used previously published data from five patients chronically infected with HIV-1 that initiated combination antiretroviral therapy (cART). Patient-matched PCR for unspliced and multiply spliced viral RNAs combined with limiting dilution analysis provided measurements of transcriptional profiles at the single cell level. Furthermore, measurement of intracellular transcripts and extracellular virion-enclosed HIV-1 RNA allowed us to distinguish productive from non-productive cells. We developed a mathematical model describing the dynamics of plasma virus and the transcriptional subclasses of HIV-1-infected cells. Fitting the model to the data allowed us to better understand the phenotype of different transcriptional subclasses and their contribution to the overall turnover of HIV-1 before and during cART. The average number of virus-producing cells in peripheral blood is small during chronic infection. We find that a substantial fraction of cells can become defectively infected. Assuming that the infection is homogenous throughout the body, we estimate an average in vivo viral burst size on the order of 104 virions per cell. Our study provides novel quantitative insights into the turnover and development of different subclasses of HIV-1-infected cells, and indicates that cells containing solely unspliced viral RNA are a good marker for viral latency. The model illustrates how the pool of latently infected cells becomes rapidly established during the first months of acute infection and continues to increase slowly during the first years of chronic infection. Having a detailed understanding of this process will be useful for the evaluation of viral eradication strategies that aim to deplete the latent reservoir of HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Reconstructing the Universe: Testing the Mutual Consistency of the Pantheon and SDSS/eBOSS BAO Data Sets with Gaussian Processes

We test the mutual consistency between the baryon acoustic oscillation measurements from the eBOSS SDSS final release and the Pantheon supernova compilation in a model-independent fashion using Gaussian process regression. We also test their joint consistency with the ΛCDM model in a model-independent fashion. We also use Gaussian process regression to reconstruct the expansion history that is preferred by these two data sets. While this methodology finds no significant preference for model flexibility beyond ΛCDM, we are able to generate a number of reconstructed expansion histories that fit the data better than the best-fit ΛCDM model. These example expansion histories may point the way toward modifications to ΛCDM. We also constrain the parameters Ω{sub k} and H {sub 0} r {sub d} both with ΛCDM and with Gaussian process regression. We find that H {sub 0} r {sub d} = 10,030 ± 130 km s{sup −1} and Ω{sub k} = 0.05 ± 0.10 for ΛCDM and that H {sub 0} r {sub d} = 10,040 ± 140 km s{sup −1} and Ω{sub k} = 0.02 ± 0.20 for the Gaussian process case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2012

Predictors of High-grade Esophagitis After Definitive Three-dimensional Conformal Therapy, Intensity-modulated Radiation Therapy, or Proton Beam Therapy for Non-small cell Lung Cancer

Introduction: We analyzed the ability of various patient- and treatment-related factors to predict radiation-induced esophagitis (RE) in patients with non-small cell lung cancer (NSCLC) treated with three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), or proton beam therapy (PBT). Methods and Materials: Patients were treated for NSCLC with 3D-CRT, IMRT, or PBT at MD Anderson from 2000 to 2008 and had full dose-volume histogram (DVH) data available. The endpoint was severe (grade {>=}3) RE. The Lyman-Kutcher-Burman (LKB) model was used to analyze RE as a function of the fractional esophageal DVH, with clinical variables included as dose-modifying factors. Results: Overall, 652 patients were included: 405 patients were treated with 3D-CRT, 139 with IMRT, and 108 with PBT; corresponding rates of grade {>=}3 RE were 8%, 28%, and 6%, respectively, with a median time to onset of 42 days (range, 11-93 days). A fit of the fractional DVH LKB model demonstrated that the fractional effective dose was significantly different (P=.046) than 1 (fractional mean dose) indicating that high doses to small volumes are more predictive than mean esophageal dose. The model fit was better for 3D-CRT and PBT than for IMRT. Including receipt of concurrent chemotherapy as a dose-modifying factor significantly improved the LKB model (P=.005), and the model was further improved by including a variable representing treatment with >30 fractions. Examining individual types of chemotherapy agents revealed a trend toward receipt of concurrent taxanes and increased risk of RE (P=.105). Conclusions: Fractional dose (dose rate) and number of fractions (total dose) distinctly affect the risk of severe RE, estimated using the LKB model, and concurrent chemotherapy improves the model fit. This risk of severe RE is underestimated by this model in patients receiving IMRT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2017

Optical and ultraviolet spectroscopic analysis of SN 2011fe at late times

This paper presents optical spectra of the nearby Type Ia supernova SN 2011fe at 100, 205, 311, 349 and 578 d post-maximum light, as well as an ultraviolet (UV) spectrum obtained with the Hubble Space Telescope at 360 d post-maximum light. We compare these observations with synthetic spectra produced with the radiative transfer code PHOENIX. The day +100 spectrum can be well fitted with models that neglect collisional and radiative data for forbidden lines. Curiously, including these data and recomputing the fit yields a quite similar spectrum, but with different combinations of lines forming some of the stronger features. At day +205 and later epochs, forbidden lines dominate much of the optical spectrum formation; however, our results indicate that recombination, not collisional excitation, is the most influential physical process driving spectrum formation at these late times. Consequently, our synthetic optical and UV spectra at all epochs presented here are formed almost exclusively through recombinationdriven fluorescence. Furthermore, our models suggest that the UV spectrum even as late as day +360 is optically thick and consists of permitted lines from several iron-peak species. These results indicate that the transition to the 'nebular' phase in Type Ia supernovae is complex and highly wavelength dependent.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2012

THE TRUNCATED DISK FROM SUZAKU DATA OF GX 339-4 IN THE EXTREME VERY HIGH STATE

We report on the geometry of accretion disk and high-energy coronae in the strong Comptonization state (the very high/steep power law/hard intermediate state) based on a Suzaku observation of the famous Galactic black hole GX 339-4. These data were taken just before the peak of the 2006-2007 outburst, and the average X-ray luminosity in the 0.7-200 keV band is estimated to be 2.9 Multiplication-Sign 10{sup 38} erg s{sup -1} for a distance of 8 kpc. We fit the spectrum with both simple (independent disk and corona) and sophisticated (energetically coupled disk and corona) models; all fits imply that the underlying optically thick disk is truncated significantly before the innermost stable circular orbit around the black hole. We show this directly by a comparison with similar broadband data from a disk-dominated spectrum at almost the same luminosity observed by XMM-Newton and RXTE 3 days after the Suzaku observation. During the Suzaku observation, the quasi-periodic oscillation (QPO) frequency changes from 4.3 Hz to 5.5 Hz, while the spectrum softens. The energetically coupled model gives a corresponding 5% {+-} 8% decrease in the derived inner radius of the disk. While this is not significant, it is consistent with the predicted change in QPO frequency from the Lense-Thirring precession of the hot flow interior to the disk and/or a deformation mode of this flow, as a higher QPO frequency implies a smaller size scale for the corona. This is consistent with the truncated disk extending further inward toward the black hole.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Gemini Planet Imager Spectroscopy of the Dusty Substellar Companion HD 206893 B

We present new near-infrared Gemini Planet Imager (GPI) spectroscopy of HD 206893 B, a substellar companion orbiting within the debris disk of its F5V star. The J, H, K1, and K2 spectra from GPI demonstrate the extraordinarily red colors of the object, confirming it as the reddest substellar object observed to date. The significant flux increase throughout the infrared presents a challenging atmosphere to model with existing grids. Best-fit values vary from 1200 to 1800 K for effective temperature and from 3.0 to 5.0 for log(g), depending on which individual wavelength band is fit and which model suite is applied. The extreme redness of the companion can be partially reconciled by invoking a high-altitude layer of submicron dust particles, similar to dereddening approaches applied to the peculiar red field L dwarf population. However, reconciling the HD 206893 B spectra with even those of the reddest low-gravity L dwarf spectra still requires the contribution of additional atmospheric dust, potentially due to the debris disk environment in which the companion resides. Orbit fitting from 4 yr of astrometric monitoring is consistent with a ∼30 yr period, an orbital inclination of 147°, and a semimajor axis of 10 au, well within the estimated disk inner radius of ∼50 au. As one of a very few substellar companions imaged interior to a circumstellar disk, the properties of this system offer important dynamical constraints on companion–disk interaction and provide a benchmark for substellar and planetary atmospheric study.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Kepler and TESS Observations of PG 1159-035

Abstract PG 1159-035 is the prototype of the PG 1159 hot (pre-)white dwarf pulsators. This important object was observed during the Kepler satellite K2 mission for 69 days in 59 s cadence mode and by the TESS satellite for 25 days in 20 s cadence mode. We present a detailed asteroseismic analysis of those data. We identify a total of 107 frequencies representing 32 ℓ = 1 modes, 27 frequencies representing 12 ℓ = 2 modes, and eight combination frequencies. The combination frequencies and the modes with very high k values represent new detections. The multiplet structure reveals an average splitting of 4.0 ± 0.4 μ Hz for ℓ = 1 and 6.8 ± 0.2 μ Hz for ℓ = 2, indicating a rotation period of 1.4 ± 0.1 days in the region of period formation. In the Fourier transform of the light curve, we find a significant peak at 8.904 ± 0.003 μ Hz suggesting a surface rotation period of 1.299 ± 0.002 days. We also present evidence that the observed periods change on timescales shorter than those predicted by current evolutionary models. Our asteroseismic analysis finds an average period spacing for ℓ = 1 of 21.28 ± 0.02 s. The ℓ = 2 modes have a mean spacing of 12.97 ± 0.4 s. We performed a detailed asteroseismic fit by comparing the observed periods with those of evolutionary models. The best-fit model has T eff = 129, 600 ± 11 100 K, M * = 0.565 ± 0.024 M ⊙ , and log g = 7.41 − 0.54 + 0.38 , within the uncertainties of the spectroscopic determinations. We argue for future improvements in the current models, e.g., on the overshooting in the He-burning stage, as the best-fit model does not predict excitation for all of the pulsations detected in PG 1159-035.

79 ASTRONOMY AND ASTROPHYSICS↗