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DOE OSTI2014

Initial RattleSnake Calculations of the Hot Zero Power BEAVRS

The validation of the Idaho National Laboratory's next generation of reactor physics analysis codes is an essential and ongoing task. The validation process requires a large undertaking and includes detailed, realistic models that can accurately predict the behavior of an operational nuclear reactor. Over the past few years the INL has developed the RattleSnake application and supporting tools on the MOOSE framework to perform these reactor physics calculations. RattleSnake solves the linearized Boltzmann transport equation with a variety of solution meth ods. Various traditional reactor physics benchmarks have already been performed, but a more realistic light water reactor comparison was needed to solidify the status of the code and deter mine its fidelity. The INL team decided to use the Benchmark for Evaluation and Validation of Reactor Simulations, which was made available in early 2013. This benchmark is a one of-a-kind document assembled by the Massachusetts Institute of Technology, which includes two cycles of detailed, measured PWR operational data. The results from this initial study of the hot zero power conditions show the current INL analysis procedure with DRAGON4 cross section preparation and using the low order diffusion solver in RattleSnake for the whole core calculations yield very encouraging results for PWR analysis. The radial assembly power distributions, radial detector measurements and control rod worths were computed with good accuracy. The computation of the isothermal temperature coefficients of reactivity require further study.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2019

Bowles-Tatnall Wake Vortex Encounter Hazard Metric

Wake vortex spacing standards constrict the terminal area throughput and impose severe constraints on the overall capacity and efficiency of the National Airspace System. For more than two decades starting in the early 1990s, the National Aeronautics and Space Administration conducted extensive research on characterizing the formation and evolution of aircraft wakes. This multidisciplinary work included comprehensive field experiments (Pruis et al. 2016), flight tests (Vicroy et al. 1998), and wind tunnel tests (Rossow 1994; Chow et al. 1997). Parametric studies using large eddy simulations (Proctor 1998; Proctor et al. 2006) were conducted in order to develop fast-time models for the prediction of wake transport and decay (Ahmad et al. 2016). Substantial effort was spent on the formulation of acceptable vortex hazard metrics (Tatnall 1995; Hinton and Tatnall 1997). Several wake encounter severity metrics have been suggested in the past, which include the wake circulation strength, vortex-induced rolling moment coefficient (Clv), bank angle, and the roll control ratio (Tatnall 1995; Hinton and Tatnall 1997; Van der Geest 2012). The vortex-induced rolling moment coefficient introduced by Bowles and Tatnall (Tatnall 1995; Gloudemans et al. 2016) has been used extensively for risk and safety analysis of newly proposed air traffic management concepts and procedures. The original method of Bowles and Tatnall assumed a constant wing loading (the wing lift-curve slope, CL is constant), which resulted in an overestimation of the vortexinduced rolling moment coefficient. Bowles (2014) suggested a correction to the original method that provides more accurate values of Clv and which is also consistent with the underlying physics of the problem. The overestimation of Clv in the original method can be corrected by assuming an elliptical lift distribution. Figure 1.1 illustrates the correction in Clv achieved by the modified method.

Joel Malissa↗

NASA NTRSDate not supplied

NASA Langley FUN3D Analyses in Support of the 1st AIAA Stability and Control Prediction Workshop

This work summarizes the results of FUN3D analyses conducted for the 1st AIAA Stability and Control Workshop on behalf of participants from the NASA Langley Research Center. The workshop was created to establish best practices for the prediction of stability and control derivatives using computational fluid dynamics and assess the limitations of these methods when those best practices are applied. The inaugural workshop considered the ONERA version of the NASA/Boeing Common Research Model, which includes the wing, body, horizontal tail, and a vertical tail designed by ONERA. Wind tunnel data at small sideslip angles remain unpublished and served as ‘blind’ data for computational comparisons. The present research generated workshop test case data using the NASA FUN3D code, which is a parallelized, unstructured, node-based, finite-volume discretization, Reynolds-averaged Navier-Stokes flow solver. Steady- state numerical simulations were conducted for workshop test cases investigating the following: grid convergence, Mach number effect on static stability, wind tunnel sting increments, static stability-derivative calculations, and a sideslip angle sweep. Results were generated for two series of unstructured, mixed-element grids, one set provided by the workshop and another set created using the HeldenMesh grid generation software. The results provided include total- and component-level breakdowns of the force and moment coefficients, in addition to sectional pressure distributions for the wing and tail components for comparisons to wind tunnel data.

CFD↗

DOE OSTI2025

Three-Dimensional Pore Networks in Miocene Stevens Sandstone of California: Implications for CO 2 Geologic Storage

The Miocene Stevens Sandstone in the San Joaquin Basin of California is increasingly recognized as a promising candidate for CO 2 geological storage due to the enormous storage capacity, proven sealing, and existing infrastructure. In this study, computed microtomography imaging and pore network modeling were employed to investigate the influence of pore geometry and wettability on the CO 2 injectivity and residual trapping. Image analysis revealed that a significant fraction of the cement and matrix consists of microporous regions. The microporosity can substantially increase the overall pore space, yet its contribution to permeability remains modest, particularly in samples with low permeability. The intrinsic heterogeneity of turbidite reservoirs further complicates the reservoir properties among different layers. Two-phase flow simulations under varying wettability conditions (water-wet, weak water-wet, and neutral-wet) demonstrated that the CO 2 injection is predominantly controlled by macropores. CO 2 invades microporous regions only after these larger pores are filled. The presence of microporosity leads to a decrease in both initial and residual CO 2 saturations, with the magnitude of the reduction being influenced by wettability. Neutral-wet scenarios exhibit higher CO 2 mobility and thus lower residual trapping than water-wet scenarios. The results imply that heterogeneity in pore geometry and cement distribution across different layers can result in stratified CO 2 flow pathways, complicating efforts to predict injection performance. Overall, the Stevens Sandstone shows considerable promise for CO 2 geologic storage, but effective implementation will require detailed characterization of the pore structure as well as the integration of reactive fluid flow to account for potential mineral dissolution and fines migration.

fluids↗

DOE OSTI2023

Modelling galaxy cluster triaxiality in stacked cluster weak lensing analyses

Counts of galaxy clusters offer a high-precision probe of cosmology, but control of systematic errors will determine the accuracy of this measurement. Using Buzzard simulations, we quantify one such systematic, the triaxiality distribution of clusters identified with the redMaPPer optical cluster finding algorithm, which was used in the Dark Energy Survey Year-1 (DES Y1) cluster cosmology analysis. We test whether redMaPPer selection biases the clusters’ shape and orientation and find that it only biases orientation, preferentially selecting clusters with their major axes oriented along the line of sight. Modelling the richness–mass relation as log-linear, we find that the log-richness amplitude ln (A) is boosted from the lowest to highest orientation bin with a significance of 14σ, while the orientation dependence of the richness-mass slope and intrinsic scatter is minimal. We also find that the weak lensing shear-profile ratios of cluster-associated dark haloes in different orientation bins resemble a ‘bottleneck’ shape that can be quantified with a Cauchy function. We test the correlation of orientation with two other leading systematics in cluster cosmology – miscentering and projection – and find a null correlation. The resulting mass bias predicted from our templates confirms the DES Y1 finding that triaxiality is a leading source of bias in cluster cosmology. However, the richness-dependence of the bias confirms that triaxiality does not fully resolve the tension at low-richness between DES Y1 cluster cosmology and other probes. Our model can be used for quantifying the impact of triaxiality bias on cosmological constraints for upcoming weak lensing surveys of galaxy clusters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Initially Disordered, Reflectin Assembly Tunably and Reversibly Drives Biophotonic Color

Reflectin proteins are found in the reflective Bragg lamellae in skin cells of certain squids, where they tunably control color for camouflage and communication. Initially disordered in the monomeric form, the reflectins have unusual amino acid compositions and are block copolymers consisting of polyampholytic canonical repeats interspersed with cationic linkers. In vivo, phosphorylation of the cationic linkers induces condensation, secondary folding and hierarchical assembly of the reflectins with concomitant emergence of tunable iridescence. We analyzed the folding and assembly of recombinant phospho‐mimetic and deletion mutants of reflectin, using pH titration as a surrogate for in vivo phosphorylation. Results of dynamic light scattering, transmission electron microscopy, fluorescence, circular dichroism and x‐ray scattering reveal that neutralization of the cationic linkers progressively and reversibly drives the reflectins to form monodisperse spherical assemblies of reproducible size. These analyses reveal a strongly predictive relationship between net charge density and size of the assembled reflectin multimers, with the switch appearing to be equally distributed across the spatially segregated linkers. Accompanying the progressive neutralization of Coulombic repulsion of the linkers, assembly appears to be driven by entropically driven folding of the canonical repeats into amphiphilic secondary structures that are likely to enable hierarchical assembly. These results suggest a model for tunable reflectin assembly and provide insight into the behavior of this unique, initially disordered protein. Support or Funding Information This research was supported by the U.S. Department of Energy, U.S. Army Research Office, and Institute of Collaborative Biotechnologies. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Levenson, Robert↗

DOE OSTI2016

Characterization of 3D Cirrus Cloud and Radiation Fields Using ARS/AIRS/MODIS data and its Application to Climate Model

During the report period, we have made the following research accomplishments. First, we performed analysis for a number of MODIS scenes comprising of heavy dust events and ice clouds, covering regions of frequent dust outbreaks in East Asia, Middle East, and West Africa, as well as areas associated with long-range dust transports over the Equatorial Tropical Atlantic Ocean. These scenes contain both dust/aerosols and clouds. We collected suitable aerosol/ice-cloud data, correlated ice cloud and aerosol parameters by means of statistical analysis, and interpreted resulting correlation trends based on the physical principles governing cloud microphysics. Aerosol and cloud optical depths and cloud effective particle size inferred from MODIS for selected domains were analyzed from which the parameters including dust aerosol number concentration, ice cloud water path, and ice particle number concentration were subsequently derived. We illustrated that the Twomey (solar albedo) effect can be statistically quantified based on the slope of best-fit straight lines in the correlation study. Analysis of aerosol and cloud retrieval products revealed that for all cases, the region with a larger dust aerosol optical depth is always characterized by a smaller cloud particle size, consistent with the Twomey hypothesis for aerosol-cloud interactions. Second, we developed mean correlation curves with uncertainties associated with small ice-crystal concentration observations for the mean effective ice crystal size (De) and ice water content (IWC) by dividing the atmosphere into three characteristic regions: Tropics cirrus, Midlatitude cirrus, including a temperature classification to improve correlation, and Arctic ice clouds. We illustrated that De has a high correlation with IWC based on theoretical consideration and analysis of thousands of observed ice crystal data obtained from a number of ARM-DOE field campaigns and other experiments. The correlation has the form: ln(De) = a + b ln(IWC) + c ((ln(IWC))2, where a, b, and c are fitting coefficients and are functions of three regions. We demonstrated that this correlation can be effectively incorporated in GCMs and climate models that predict IWC - a significant advance in ice microphysics parameterization for interactive cloud-radiation analysis and feedback. Substantial July mean differences are shown in the OLR (W/m2) and precipitation (mm/day) patterns between UCLA GCM simulations based on Des determined from the De-IWC correlations and the control run using a fixed ice crystal size. Third, in order to improve the computation of spectral radiative transfer processes in the WRF model, we developed a consistent and efficient radiation scheme that can better resolve the spectral bands, determine the cloud optical properties, and provide more reliable and accurate radiative heating fields. In the newly developed radiation module, we have implemented in WRF a modified and improved version referred to as the Fu-Liou-Gu scheme, which includes a combination of delta-four-stream and delta-two-stream approximations for solar and IR flux calculations, respectively. This combination has been proven to be computationally efficient and at the same time to produce a high degree of accuracy. The incorporation of nongray gaseous absorption in multiple scattering atmospheres was based on the correlated k-distribution method. The solar and IR spectra are divided into 6 and 12 bands, respectively, according to the location of absorption bands of H2O, CO2, O3, CH4, N2O, and CFCs. We further included absorption by the water vapor continuum and a number of minor absorbers in the solar spectrum leading to an additional absorption of solar flux in a clear atmosphere on the order of 1-3 W/m2. Additionally, we incorporated the ice microphysics parameterization that includes an interactive mean effective ice crystal size in association with radiation parameterizations. The Fu-Liou-Gu scheme is an ideal tool for the simulation of radiative transfer and ice microphysics within the domain of WRF. It is particularly useful for studying direct and indirect aerosol radiative effects associated with ice cloud formation. The newly implemented radiation module has been demonstrated to work well in WRF and can be effectively used for studies related to cirrus cloud formation and evolution as well as aerosol-cloud-radiation interactions. With the newly implemented radiation scheme, the simulations of cloud cover and ice water path have been improved for cirrus clouds, with a more consistent comparison with the corresponding MODIS observations, especially for optically thin cirrus with an improvement of about 20% in the simulated mean ice water path.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2002

High-Efficiency High-Resolution Global Model Developments at the NASA Goddard Data Assimilation Office

The Data Assimilation Office (DAO) has been developing a new generation of ultra-high resolution General Circulation Model (GCM) that is suitable for 4-D data assimilation, numerical weather predictions, and climate simulations. These three applications have conflicting requirements. For 4-D data assimilation and weather predictions, it is highly desirable to run the model at the highest possible spatial resolution (e.g., 55 km or finer) so as to be able to resolve and predict socially and economically important weather phenomena such as tropical cyclones, hurricanes, and severe winter storms. For climate change applications, the model simulations need to be carried out for decades, if not centuries. To reduce uncertainty in climate change assessments, the next generation model would also need to be run at a fine enough spatial resolution that can at least marginally simulate the effects of intense tropical cyclones. Scientific problems (e.g., parameterization of subgrid scale moist processes) aside, all three areas of application require the model's computational performance to be dramatically improved as compared to the previous generation. In this talk, I will present the current and future developments of the "finite-volume dynamical core" at the Data Assimilation Office. This dynamical core applies modem monotonicity preserving algorithms and is genuinely conservative by construction, not by an ad hoc fixer. The "discretization" of the conservation laws is purely local, which is clearly advantageous for resolving sharp gradient flow features. In addition, the local nature of the finite-volume discretization also has a significant advantage on distributed memory parallel computers. Together with a unique vertically Lagrangian control volume discretization that essentially reduces the dimension of the computational problem from three to two, the finite-volume dynamical core is very efficient, particularly at high resolutions. I will also present the computational design of the dynamical core using a hybrid distributed-shared memory programming paradigm that is portable to virtually any of today's high-end parallel super-computing clusters.

Lin, Shian-Jiann↗

NASA NTRS2002

High-Efficiency High-Resolution Global Model Developments at the NASA Goddard Data Assimilation Office

The Data Assimilation Office (DAO) has been developing a new generation of ultra-high resolution General Circulation Model (GCM) that is suitable for 4-D data assimilation, numerical weather predictions, and climate simulations. These three applications have conflicting requirements. For 4-D data assimilation and weather predictions, it is highly desirable to run the model at the highest possible spatial resolution (e.g., 55 kin or finer) so as to be able to resolve and predict socially and economically important weather phenomena such as tropical cyclones, hurricanes, and severe winter storms. For climate change applications, the model simulations need to be carried out for decades, if not centuries. To reduce uncertainty in climate change assessments, the next generation model would also need to be run at a fine enough spatial resolution that can at least marginally simulate the effects of intense tropical cyclones. Scientific problems (e.g., parameterization of subgrid scale moist processes) aside, all three areas of application require the model's computational performance to be dramatically improved as compared to the previous generation. In this talk, I will present the current and future developments of the "finite-volume dynamical core" at the Data Assimilation Office. This dynamical core applies modem monotonicity preserving algorithms and is genuinely conservative by construction, not by an ad hoc fixer. The "discretization" of the conservation laws is purely local, which is clearly advantageous for resolving sharp gradient flow features. In addition, the local nature of the finite-volume discretization also has a significant advantage on distributed memory parallel computers. Together with a unique vertically Lagrangian control volume discretization that essentially reduces the dimension of the computational problem from three to two, the finite-volume dynamical core is very efficient, particularly at high resolutions. I will also present the computational design of the dynamical core using a hybrid distributed- shared memory programming paradigm that is portable to virtually any of today's high-end parallel super-computing clusters.

Lin, Shian-Jiann↗

NASA NTRSDate not supplied

Assimilation of Reconstructed Radiances from IASI Principal Component Scores into the GEOS-ADAS

Hyperspectral Infrared sounders such as IASI, AIRS, and CrIS have long been an integral part of radiance assimilation in numerical weather prediction (NWP), providing vertical profiles of water vapor and temperature information. Principal Component Scores (PCS) are a lossy form of compression that retains most information, such as temperature and moisture, by using a large training set of atmospheric profiles. However, PCS may not well represent profiles which are rare events, such as volcanic eruptions, and drops some sources of random noise. There has been an increased interest in the use of PCS as EUMETSAT plans to distribute future geostationary sounder radiances from MTG-IRS via PCS only. NWP centers use two approaches to deal with PCS: direct assimilation of the PCS by modifying the radiative transfer model to produce PCS and the associated Jacobians, or a simpler approach of decompressing the PCS and reconstructing the radiances back into channel space to allow assimilating radiances without modifications to the data assimilation system. EUMETSAT has developed a PCS product for IASI that has been operational since 2011. We utilize this product opting for the simpler approach, decompressing IASI PCS into channel space, and assimilating those radiances using the GEOS-ADAS. We then compare this with a control using the standard IASI radiance product. Resulting differences in global forecast statistics, differences in Forecast Sensitivity to Observation Impact, along with implications for implementation and quality control are discussed.

Bryan M. Karpowicz↗

DOE OSTI2017

Computed Tomography Radiomics Predicts HPV Status and Local Tumor Control After Definitive Radiochemotherapy in Head and Neck Squamous Cell Carcinoma

Purpose: This study aimed to predict local tumor control (LC) after radiochemotherapy of head and neck squamous cell carcinoma (HNSCC) and human papillomavirus (HPV) status using computed tomography (CT) radiomics. Methods and Materials: HNSCC patients treated with definitive radiochemotherapy were included in the retrospective study approved by the local ethical commission (93 and 56 patients in the training and validation cohorts, respectively). Three hundred seventeen CT radiomic features, including those based on shape, intensity, texture, and wavelet transform, were calculated in the primary tumor region. Cox and logistic regression models were built to predict LC and HPV status, respectively. The best-performing features in the univariable analysis were included in the multivariable analysis after the exclusion of redundant features. The quality of the models was assessed using the concordance index (CI) for modeling of LC and receiver operating characteristics area under the curve (AUC) for HPV status prediction. The radiomics LC model was compared to a model incorporating clinical parameters (tumor stage, volume, and HPV status) and a mixed model. Results: A radiomic signature comprising 3 features was significantly associated with LC (CI{sub training} = 0.75 and CI{sub validation} = 0.78), showing that tumors with a more heterogeneous CT density distribution are at risk for decreased LC. The addition of clinical parameters to the radiomics model slightly improved the model in the training cohort but not in the validation cohort. Another radiomic signature showed good performance in HPV status prediction (AUC{sub training} = 0.85 and AUC{sub validation} = 0.78) and indicated that HPV-positive tumors have a more homogenous CT density distribution. Conclusions: Heterogeneity of HNSCC tumor density, quantified by CT radiomics, is associated with LC after radiochemotherapy and HPV status.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

THE DEPENDENCE OF STELLAR MASS AND ANGULAR MOMENTUM LOSSES ON LATITUDE AND THE INTERACTION OF ACTIVE REGION AND DIPOLAR MAGNETIC FIELDS

Rotation evolution of late-type stars is dominated by magnetic braking and the underlying factors that control this angular momentum loss are important for the study of stellar spin-down. In this work, we study angular momentum loss as a function of two different aspects of magnetic activity using a calibrated Alfvén wave-driven magnetohydrodynamic wind model: the strengths of magnetic spots and their distribution in latitude. By driving the model using solar and modified solar surface magnetograms, we show that the topology of the field arising from the net interaction of both small-scale and large-scale field is important for spin-down rates and that angular momentum loss is not a simple function of large scale magnetic field strength. We find that changing the latitude of magnetic spots can modify mass and angular momentum loss rates by a factor of two. The general effect that causes these differences is the closing down of large-scale open field at mid- and high-latitudes by the addition of the small-scale field. These effects might give rise to modulation of mass and angular momentum loss through stellar cycles, and present a problem for ab initio attempts to predict stellar spin-down based on wind models. For all the magnetogram cases considered here, from dipoles to various spotted distributions, we find that angular momentum loss is dominated by the mass loss at mid-latitudes. The spin-down torque applied by magnetized winds therefore acts at specific latitudes and is not evenly distributed over the stellar surface, though this aspect is unlikely to be important for understanding spin-down and surface flows on stars.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1988

Part 1: Aspects of lithospheric evolution on Venus. Part 2: Thermal and collisional histories of chondrite parent bodies

The geological evolution of distinctly different kinds of solar system objects is addressed. Venus has been observed over the past decade by orbital radars on both American and Soviet spacecraft. These surface measurements provide clues to the structure and evolution of the lithosphere. The parent bodies of chondritic meteorites, thought to resemble asteroids, represent the other end of the size spectrum of terrestrial objects. Their early thermal and collisional histories may be constrained by the chemical and textural record preserved in meteorite samples. Impact craters on Venus have been observed by the Soviet Venera 15/16 spacecraft. A formalism is presented by which the size-frequency distribution of impact craters may be used to estimate upper bounds on the mean global rates of volcanic resurfacing and lithospheric recycling on that planet over the past several hundred million years. The impact crater density reported from Venera observations, if valid for the entire Venus surface, indicates a mean volcanic flux no greater than 2 cu km/y, corresponding to a maximum average rate of resurfacing of about 4 km/b.y. For the lowest estimated mean crater retention age of the surface of Venus imaged by Venera 15/16, the rate of lithospheric recycling on Venus does not exceed 1.5 sq km/y. Ordinary chondrite meteorites show textural and chemical patterns indicative of varying intensities of thermal metamorphism. The conventional onion-shell model, which envisions highly metamorphosed material in the core and less intensely heated rocks near the surface, predicts an inverse relation between peak temperature and cooking rate, but none has been observed. A metamorphosed-planetesimal model is devised to explain this discrepancy, whereby heating occurs in planetesimals a few kilometers in radius which then accrete to form 100-km-radius parent bodies. Cooling rates are then randomly controlled by burial depth. Thermal and collisional constraints are examined, and the model is found to be applicable only to highly insulating Al-26-rich planetesimals that remain closely aggregated upon accretion. An alternative model is presented, in which onion-shell parent bodies are collisionally fragmented during metamorphism and then gravitationally reassembled. If reassembly times are short, then cooling rates would be determined by burial depth in the reaccreted parent body. This model, unlike previous ones, can explain both coherent and incoherent cooling of Breccia clasts by collisions during or after metamorphism, respectively.

Grimm, Robert E.↗

DOE OSTI2015

SU-E-T-144: Bayesian Inference of Local Relapse Data Using a Poisson-Based Tumour Control Probability Model

Purpose: The purpose of this project is to develop a robust method of parameter estimation for a Poisson-based TCP model using Bayesian inference. Methods: Bayesian inference was performed using the PyMC3 probabilistic programming framework written in Python. A Poisson-based TCP regression model that accounts for clonogen proliferation was fit to observed rates of local relapse as a function of equivalent dose in 2 Gy fractions for a population of 623 stage-I non-small-cell lung cancer patients. The Slice Markov Chain Monte Carlo sampling algorithm was used to sample the posterior distributions, and was initiated using the maximum of the posterior distributions found by optimization. The calculation of TCP with each sample step required integration over the free parameter α, which was performed using an adaptive 24-point Gauss-Legendre quadrature. Convergence was verified via inspection of the trace plot and posterior distribution for each of the fit parameters, as well as with comparisons of the most probable parameter values with their respective maximum likelihood estimates. Results: Posterior distributions for α, the standard deviation of α (σ), the average tumour cell-doubling time (Td), and the repopulation delay time (Tk), were generated assuming α/β = 10 Gy, and a fixed clonogen density of 10{sup 7} cm−{sup 3}. Posterior predictive plots generated from samples from these posterior distributions are in excellent agreement with the observed rates of local relapse used in the Bayesian inference. The most probable values of the model parameters also agree well with maximum likelihood estimates. Conclusion: A robust method of performing Bayesian inference of TCP data using a complex TCP model has been established.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Internal Domains of Natural Porous Media Revealed: Critical Locations for Transport, Storage, and Chemical Reaction

Internal pore domains exist within rocks, lithic fragments, subsurface sediments and soil aggregates. These domains, which we term internal domains in porous media (IDPM), contain a significant fraction of their porosity as nanopores, dominate the reactive surface area of diverse porous media types, and are important locations for chemical reactivity and hydrocarbon storage. Traditionally difficult to interrogate, advances in instrumentation and imaging methods are providing new insights on the physical structures and chemical attributes of IDPM. In this review we: discuss analytical methods to characterize IDPM, evaluate what has been learned about their size distributions, connectivity, and extended structures; determine whether they exhibit unique chemical reactivity; and assess potential for their inclusion in reactive transport models. Three key findings are noteworthy. 1) A combination of methods now allows complete characterization of the porosity spectrum of natural materials and its connectivity; while imaging microscopies are providing three dimensional representations of the interconnected pore network. 2) Chemical reactivity in pores <10 nm is expected to be different from micro and macropores, yet research performed to date is inconclusive on the nature, direction, and magnitude of effect. 3) Existing continuum reactive transport models treat IDPM as a sub-grid feature with average, empirical, scale-dependent parameters; and are not formulated to include detailed information on pore networks. Overall we find that IDPM are key features controlling hydrocarbon release from shales in hydrofracking systems, organic matter stabilization and recalcitrance in soil, weathering and soil formation, and long term inorganic and organic contaminant behavior in the vadose zone and groundwater. We conclude with an assessment of impactful research opportunities to advance understanding of IDPM, and to incorporate their important effects in reactive transport models for improved environmental simulation and prediction.

58 GEOSCIENCES↗

DOE OSTI2016

The high-mass end of the red sequence at z ~ 0.55 from SDSS-III/BOSS: completeness, bimodality and luminosity function

The history of the expanding universe is encoded in the large-scale distribution of galaxies throughout space. By mapping out the three-dimensional locations of millions of galaxies with powerful telescopes, we can directly measure this expansion history. When interpreted using Einstein's theory of gravity, this expansion history lets us infer the contents of the universe, including the amount and nature of "dark energy", an as-yet unexplained energy density associated with the empty vacuum of space. However, to make these measurements and inferences accurately, we must understand and control for a large number of experimental effects. This paper develops a novel method for large cosmological galaxy surveys, and applies it to data from the "BOSS" experiment of the Third Sloan Digital Sky Survey. This method enables an accurate statistical characterization of the "completeness" of the BOSS experiment: the probability that a given galaxy at a given place in the universe is actually detected and successfully measured. It also enables the accurate determination of the underlying demographics of the galaxy population being studied by the experiment. These two ingredients can then be used to make a more accurate comparison between the results of the experiment and the theoretical models that predict the observable effects of dark energy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

60 APPLIED LIFE SCIENCES↗