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Fully automatic characterization and data collection from crystals of biological macromolecules

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

CURRENT STATUS OF THE CHARACTERIZATION OF RPV MATERIALS HARVESTED FROM THE DECOMMISSIONED ZION UNIT 1 NUCLEAR POWER PLANT

The decommissioning of Units 1 and 2 of the Zion Nuclear Power Station in Zion, Illinois, after ~ 15 effective full-power years of service presents a unique opportunity to characterize the degradation of in-service reactor pressure vessel (RPV) materials and to assess currently available models for predicting radiation embrittlement of RPV steels [1-3]. Moreover, through-wall thickness attenuation and property distributions are being obtained and the results to be compared with surveillance specimen test data. It is anticipated that these efforts will provide a better understanding of materials degradation associated with extending the lifetime of existing nuclear power plants (NPPs) beyond 60 years of service and subsequent license renewal. In support of extended service and current operations of the US nuclear reactor fleet, the Oak Ridge National Laboratory (ORNL), through the U.S. Department of Energy, Light Water Reactor Sustainability (LWRS) Program, coordinated procurement of materials, components, and other items of interest from the decommissioned Zion NPPs. In this report, harvesting, cutting sample blocks, machining test specimens, test plans, and the current status of materials characterization of the RPV from the decommissioned Zion NPP Unit 1 will be discussed. The primary foci are the circumferential, Linde 80 flux, wire heat 72105 (WF-70) beltline weld and the A533B base metal from the intermediate shell harvested from a region of peak fluence (0.7 X 1019 n/cm2, E > 1.0 MeV) on the internal surface of the Zion Unit 1 vessel. Following the determination of the through-thickness chemical composition, Charpy impact, fracture toughness, tensile, and hardness testing are being performed to characterize the through-thickness mechanical properties of base metal and beltline-weld materials. In addition to mechanical properties, microstructural characterizations are being performed using various microstructural techniques, including Atom Probe Tomography, Small Angle Neutron Scattering, and Positron Annihilation Spectroscopy

Rosseel, T. M.↗

Characterization of scatter in digital mammography from physical measurements

Purpose: That scattered radiation negatively impacts the quality of medical radiographic imaging is well known. In mammography, even slight amounts of scatter reduce the high contrast required for subtle soft-tissue imaging. In current clinical mammography, image contrast is partially improved by use of an antiscatter grid. This form of scatter rejection comes with a sizeable dose penalty related to the concomitant elimination of valuable primary radiation. Digital mammography allows the use of image processing as a method of scatter correction that might avoid effects that negatively impact primary radiation, while potentially providing more contrast improvement than is currently possible with a grid. For this approach to be feasible, a detailed characterization of the scatter is needed. Previous research has modeled scatter as a constant background that serves as a DC bias across the imaging surface. The goal of this study was to provide a more substantive data set for characterizing the spatially-variant features of scatter radiation at the image detector of modern mammography units. Methods: This data set was acquired from a model of the radiation beam as a matrix of very narrow rays or pencil beams. As each pencil beam penetrates tissue, the pencil widens in a predictable manner due to the production of scatter. The resultant spreading of the pencil beam at the detector surface can be characterized by two parameters: mean radial extent (MRE) and scatter fraction (SF). The SF and MRE were calculated from measurements obtained using the beam stop method. Two digital mammography units were utilized, and the SF and MRE were found as functions of target, filter, tube potential, phantom thickness, and presence or absence of a grid. These values were then used to generate general equations allowing the SF and MRE to be calculated for any combination of the above parameters. Results: With a grid, the SF ranged from a minimum of about 0.05 to a maximum of about 0.16, and the MRE ranged from about 3 to 13 mm. Without a grid, the SF ranged from a minimum of 0.25 to a maximum of 0.52, and the MRE ranged from about 20 to 45 mm. The SF with a grid demonstrated a mild dependence on target/filter combination and kV, whereas the SF without a grid was independent of these factors. The MRE demonstrated a complex relationship as a function of kV, with notable difference among target/filter combinations. The primary source of change in both the SF and MRE was phantom thickness. Conclusions: Because breast tissue varies spatially in physical density and elemental content, the effective thickness of breast tissue varies spatially across the imaging field, resulting in a spatially-variant scatter distribution in the imaging field. The data generated in this study can be used to characterize the scatter contribution on a point-by-point basis, for a variety of different techniques.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

SU-D-19A-04: Parameter Characterization of Electron Beam Monte Carlo Phase Space of TrueBeam Linacs

Purpose: For TrueBeam Monte Carlo simulations, Varian does not distribute linac head geometry and material compositions, instead providing a phase space file (PSF) for the users. The PSF has a finite number of particle histories and can have very large file size, yet still contains inherent statistical noises. The purpose of this study is to characterize the electron beam PSF with parameters. Methods: The PSF is a snapshot of all particles' information at a given plane above jaws including type, energy, position, and directions. This study utilized a preliminary TrueBeam PSF, of which validation against measurement is presented in another study. To characterize the PSF, distributions of energy, position, and direction of all particles are analyzed as piece-wise parameterized functions of radius and polar angle. Subsequently, a pseudo PSF was generated based on this characterization. Validation was assessed by directly comparing the true and pseudo PSFs, and by using both PSFs in the down-stream MC simulations (BEAMnrc/DOSXYZnrc) and comparing dose distributions for 3 applicators at 15 MeV. Statistical uncertainty of 4% was limited by the number of histories in the original PSF. Percent depth dose (PDD) and orthogonal (PRF) profiles at various depths were evaluated. Results: Preliminary results showed that this PSF parameterization was accurate, with no visible differences between original and pseudo PSFs except at the edge (6 cm off axis), which did not impact dose distributions in phantom. PDD differences were within 1 mm for R{sub 7} {sub 0}, R{sub 5} {sub 0}, R{sub 3} {sub 0}, and R{sub 1} {sub 0}, and PRF field size and penumbras were within 2 mm. Conclusion: A PSF can be successfully characterized by distributions for energy, position, and direction as parameterized functions of radius and polar angles; this facilitates generating sufficient particles at any statistical precision. Analyses for all other electron energies are under way and results will be included in the presentation.

07 ISOTOPE AND RADIATION SOURCES↗

SU-E-T-160: Characterization and Monitoring of Linear Accelerator Gantry Radiation Isocenter Motion

Purpose: To characterize the motion of the radiation isocenter, over time, as a function of gantry rotation for multiple linear accelerators (linacs). Two semi-automated image-based quality control (QC) test workflows were designed to achieve this goal. Methods: The full QC-test workflow for motion characterization consisted of acquiring 16 megavoltage images at 8 gantry angles of a ball-bearing suspended off the end of the couch. Performance constancy was assessed using a shortened QC-test workflow which consisted of imaging a cube phantom placed on the couch (5 images at 4 gantry angles). Both workflows use an image processing algorithm to determine the field center and phantom position on each image and computed radiation isocenter motion as a function of gantry angle. Motion was characterized for 9 linacs of same model and performance monitored for 2 months on 3 linacs. Results: The maximum isocenter motion determined with the full-workflow for 9 linacs was within 0.38–0.79 mm. The shortened-workflow usually agreed within 0.1 mm with the full-workflow and the time required for these methods was about 4 and 15 min, respectively. For all linacs, the isocenter motion perpendicular to the gantry rotation plane followed a consistent pattern with maximum amplitude of 0.36–0.59 mm. In the gantry rotation plane, the variation among linacs was higher and the beam axis described a circle of up to 0.6 mm radius around the gantry axis of rotation (2 linacs). The radiation isocenter motion was stable as a function of time for the monitored linacs and was within ±0.1 mm of the average. Conclusion: Radiation isocenter motion parallel and perpendicular to the gantry rotation plane was characterized. In the gantry rotation plane, beam spot positioning adjustment might be used to reduce the observed radiation isocenter motion. A shortened-workflow was designed and enables performance monitoring over time.

60 APPLIED LIFE SCIENCES↗

SU-E-T-365: Estimation of Neutron Ambient Dose Equivalents for Radioprotection Exposed Workers in Radiotherapy Facilities Based On Characterization Patient Risk Estimation

Purpose: Previous measurements with Bonner spheres{sup 1} showed that normalized neutron spectra are equal for the majority of the existing linacs{sup 2}. This information, in addition to thermal neutron fluences obtained in the characterization procedure{sup 3}3, would allow to estimate neutron doses accidentally received by exposed workers, without the need of an extra experimental measurement. Methods: Monte Carlo (MC) simulations demonstrated that the thermal neutron fluence distribution inside the bunker is quite uniform, as a consequence of multiple scatter in the walls{sup 4}. Although inverse square law is approximately valid for the fast component, a more precise calculation could be obtained with a generic fast fluence distribution map around the linac, from MC simulations{sup 4}. Thus, measurements of thermal neutron fluences performed during the characterization procedure{sup 3}, together with a generic unitary spectra{sup 2}, would allow to estimate the total neutron fluences and H*(10) at any point{sup 5}. As an example, we compared estimations with Bonner sphere measurements{sup 1}, for two points in five facilities: 3 Siemens (15–23 MV), Elekta (15 MV) and Varian (15 MV). Results: Thermal neutron fluences obtained from characterization, are within (0.2–1.6×10{sup 6}) cm−{sup 2}•Gy{sup −1} for the five studied facilities. This implies ambient equivalent doses ranging from (0.27–2.01) mSv/Gy 50 cm far from the isocenter and (0.03–0.26) mSv/Gy at detector location with an average deviation of ±12.1% respect to Bonner measurements. Conclusion: The good results obtained demonstrate that neutron fluence and H*(10) can be estimated based on: (a) characterization procedure established for patient risk estimation in each facility, (b) generic unitary neutron spectrum and (c) generic MC map distribution of the fast component. [1] Radiat. Meas (2010) 45: 1391 – 1397; [2] Phys. Med. Biol (2012) 5 7:6167–6191; [3] Med. Phys (2015) 42:276 - 281. [4] IFMBE (2012) 39: 1245–1248. [5] ICRU Report 57 (1998)

60 APPLIED LIFE SCIENCES↗

Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough

ABSTRACT Due in large part to their ability to facilitate the diffusion of a diverse range of solutes across the outer membrane (OM) of Gram-negative bacteria, the porins represent one of the most prominent and important bacterial membrane protein superfamilies. Notably, for the Gram-negative bacterium Desulfovibrio vulgaris Hildenborough, a model organism for studies of sulfate-reducing bacteria, no genes for porins have been identified or proposed in its annotated genome. Results from initial biochemical studies suggested that the product of the DVU0799 gene, which is one of the most abundant proteins of the D. vulgaris Hildenborough OM and purified as a homotrimeric complex, was a strong porin candidate. To investigate this possibility, this protein was further characterized biochemically and biophysically. Structural analyses via electron microscopy of negatively stained protein identified trimeric particles with stain-filled depressions and structural modeling suggested a β-barrel structure for the monomer, motifs common among the known porins. Functional studies were performed in which crude OM preparations or purified DVU0799 was reconstituted into proteoliposomes and the proteoliposomes were examined for permeability against a series of test solutes. The results obtained establish DVU0799 to be a pore-forming protein with permeability properties similar to those observed for classical bacterial porins, such as those of Escherichia coli . Taken together, these findings identify this highly abundant OM protein to be the major porin of D. vulgaris Hildenborough. Classification of DVU0799 in this model organism expands the database of functionally characterized porins and may also extend the range over which sequence analysis strategies can be used to identify porins in other bacterial genomes. IMPORTANCE Porins are membrane proteins that form transmembrane pores for the passive transport of small molecules across the outer membranes of Gram-negative bacteria. The present study identified and characterized the major porin of the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, observing its preference for anionic sugars over neutral ones. Its predicted architecture appears to be novel for a classical porin, as its core β-barrel structure is of a type typically found in solute-specific channels. Broader use of the methods employed here, such as assays for channel permeability and electron microscopy of purified samples, is expected to help expand the database of confirmed porin sequences and improve the range over which sequence analysis-based strategies can be used to identify porins in other Gram-negative bacteria. Functional characterization of these critical gatekeeping proteins from divergent Desulfovibrio species should offer an improved understanding of the physiological features that determine their habitat range and supporting activities.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of Nanoscale Pores in Tight Gas Sandstones Using Complex Techniques: A Case Study of a Linxing Tight Gas Sandstone Reservoir

Pore structures with rich nanopores and permeability in tight gas reservoirs are poorly understood up to date. Advanced techniques are needed to be employed to accurately characterize pore structures, especially tiny pores which include micron and nanopores. In this study, various experimental techniques such as scanning electron microscopy (SEM), nuclear magnetic resonance (NMR) T 2 , nitrogen adsorption method, and NMR cryoporometry (NMRC) are combined to interrogate the complex pore systems of the tight gas reservoir in the Linxing formation, Ordos Basin, China. Results show that tight gas sandstones are primarily comprised of residual interparticle and clay-dominated pores. Clay and quartz are two dominate minerals while pyrite occupies a nontrivial amount as well. The permeability of tight gas sandstones is very low, exhibiting an extremely poor positive correlation with porosity. While pore types and relative pore contents are more influential factors on the permeability, accurate characterization of pore size distribution is critical for the permeability of tight gas sandstones. Therefore, complementary characterization methods are carried out, indicating that neither small pores with radii < 100 nm (around peak 1 in NMR T 2 distribution) nor large pores with radii > 5 μ m (around peak 3 in NMR T 2 distribution) control the permeability by analyzing the connectivity of the pores in various size ranges, but rather pores averaging approximately 350 ± X nm (around peak 2 in NMR T 2 distribution) have sufficient connectivity to host and transmit hydrocarbons. The pore size of tight gas sandstones is dominated by the clay-rich mineral assemblage. The study shows that the NMRC technique can be a very promising method, especially when referred to as a promising “roadmap” on how to interrogate tight formations such as the tight gas sands or even shale especially for the nanopore characterization.

15 GEOTHERMAL ENERGY↗

Application of DRIFTS, 13 C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic Matter Composition in a Mollic Xerofluvent

Chemical oxidations are routinely employed in soil science to study soil organic matter (SOM), and their interpretation could be improved by characterizing oxidation effects on SOM composition with spectroscopy. We investigated the effects of routinely employed oxidants on SOM composition in a Mollic Xerofluvent representative of intensively managed agricultural soils in the California Central Valley. Soil samples were subjected to oxidation by potassium permanganate (KMnO4), sodium hypochlorite (NaOCl), and hydrogen peroxide (H2O2). Additionally, non-oxidized and oxidized soils were treated with hydrofluoric acid (HF) to evaluate reduction of the mineral component to improve spectroscopy of oxidation effects. Oxidized non-HF and HF-treated soils were characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), 13C cross polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, and pyrolysis molecular beam mass spectrometry (py-MBMS), and for particle size distribution (PSD) using laser diffractometry (LD). Across the range of soil organic carbon (OC) removed by oxidations (14-72%), aliphatic C-H stretch at 3000-2800 cm-1 (DRIFTS) decreased with OC removal, and this trend was enhanced by HF treatment due to significant demineralization in this soil (70%). Analysis by NMR spectroscopy was feasible only after HF treatment, and did not reveal trends between OC removal and C functional groups. Pyrolysis-MBMS did not detect differences among oxidations, even after HF treatment of soils. Hydrofluoric acid entailed OC loss (13-39%), and for H2O2 oxidized soils increased C:N and substantially decreased mean particle size. This study demonstrates the feasibility of using HF to improve characterizations of SOM composition following oxidations as practiced in soil science, in particular for DRIFTS. Since OC removal by oxidants, mineral removal by HF, and the interaction of oxidants and HF observed for this soil may differ for soils with different mineralogies, future work should examine additional soil and land use types to optimize characterizations of oxidation effects on SOM composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

Zymomonas mobilis is a model bacterial ethanologen with many systems biology studies reported. Besides lignocellulosic ethanol production, Z. mobilis has been developed as a platform for biochemical production through metabolic engineering. However, identification and rigorous understanding of the genetic origins of cellular function, especially those based in non-coding region of DNA, such as promoters and ribosomal binding sites (RBSs), are still in its infancy. This knowledge is crucial for the effective application of Z. mobilis to new industrial applications of biotechnology for fuels and chemicals production. In this study, we explored the possibility to systematically predict the strength of promoters based on systems biology datasets. The promoter strength was clustered based on the expression values of downstream genes (or proteins) from systems biology studies including microarray, RNA-Seq and proteomics. Candidate promoters with different strengths were selected for further characterization, which include 19 strong, nine medium, and ten weak ones. A dual reporter-gene system was developed which included appropriate reporter genes. These are the opmCherry reporter gene driven by the constitutive PlacUV5 promoter for calibration, and EGFP reporter gene driven by candidate promoters for quantification. This dual reporter-gene system was confirmed using the inducible promoter, Ptet, which was used to determine the strength of these predicted promoters with different strengths. In addition, the dual reporter-gene system was applied to determine four synthetic RBSs with different translation initiation rates based on the prediction from bioinformatics server RBS calculator. Our results showed that the correlations between the prediction and experimental results for the promoter and RBS strength are relatively high, with R2 values more than 0.7 and 0.9, respectively. This study not only identified and characterized 38 promoters and four RBSs with different strengths for future metabolic engineering in Z. mobilis, but also established a flow cytometry-based dual reporter-gene system to characterize genetic elements including, but not limited to the promoters and RBSs studied in this work. This study also suggested the feasibility of predicting and selecting candidate genetic elements based on omics datasets and bioinformatics tools. Moreover, the dual reporter-gene system developed in this study can be utilized to characterize other genetic elements of Z. mobilis, which can also be applied to other microorganisms.

09 BIOMASS FUELS↗

Advancements in Life Cycle Human Exposure and Toxicity Characterization

The Life Cycle Initiative, hosted at the United Nations Environment Programme, selected human toxicity impacts from exposure to chemical substances as an impact category that requires global guidance to overcome current assessment challenges. The initiative leadership established the Human Toxicity Task Force to develop guidance on assessing human exposure and toxicity impacts. Based on input gathered at three workshops addressing the main current scientific challenges and questions, the task force built a roadmap for advancing human toxicity characterization, primarily for use in life cycle impact assessment (LCIA). The present paper aims at reporting on the outcomes of the task force workshops along with interpretation of how these outcomes will impact the practice and reliability of toxicity characterization. The task force thereby focuses on two major issues that emerged from the workshops, namely considering near-field exposures and improving dose–response modeling. The task force recommended approaches to improve the assessment of human exposure, including capturing missing exposure settings and human receptor pathways by coupling additional fate and exposure processes in consumer and occupational environments (near field) with existing processes in outdoor environments (far field). To quantify overall aggregate exposure, the task force suggested that environments be coupled using a consistent set of quantified chemical mass fractions transferred among environmental compartments. With respect to dose–response, the task force was concerned about the way LCIA currently characterizes human toxicity effects, and discussed several potential solutions. A specific concern is the use of a (linear) dose–response extrapolation to zero. Another concern addresses the challenge of identifying a metric for human toxicity impacts that is aligned with the spatiotemporal resolution of present LCIA methodology, yet is adequate to indicate health impact potential. Further research efforts are required based on our proposed set of recommendations for improving the characterization of human exposure and toxicity impacts in LCIA and other comparative assessment frameworks.

54 ENVIRONMENTAL SCIENCES↗

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion↗

Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

The protein family known as G-protein coupled receptors (GPCRs) comprises an important class of membrane-associated proteins, which remains a difficult family of proteins to characterize because their function requires a native-like lipid membrane environment. This paper focuses on applying a single step method leading to the formation of nanolipoprotein particles (NLPs) capable of solubilizing functional GPCRs for biophysical characterization. NLPs were used to demonstrate increased solubility for multiple GPCRs such as the Neurokinin 1 Receptor (NK1R), the Adrenergic Receptor aˆ2 (ADRB2) and the Dopamine Receptor D1 (DRD1). All three GPCRs showed affinity for their specific ligands using a simple dot blot assay. The NK1R was characterized in greater detail to demonstrate correct folding of the ligand pocket with nanomolar specificity. Electron paramagnetic resonance (EPR) spectroscopy validated the correct folding of the NK1R binding pocket for Substance P (SP). Fluorescence correlation spectroscopy (FCS) was used to identify SP-bound NK1R-containing NLPs and measure their dissociation rate in an aqueous environment. The dissociation constant was found to be 83 nM and was consistent with dot blot assays. This study represents a unique combinational approach involving the single step de novo production of a functional GPCR combined with biophysical techniques to demonstrate receptor association with the NLPs and binding affinity to specific ligands. Such a combined approach provides a novel path forward to screen and characterize GPCRs for drug discovery as well as structural studies outside of the complex cellular environment.

59 BASIC BIOLOGICAL SCIENCES↗

EVSE Characterization

NextGen Profiles' EVSE characterization efforts explored performance variability in production EVSE through the use of EV emulation equipment and assessed how different operational conditions influence charging behavior. Data were collected at a frequency of 10 Hz from both the EV emulator and EVSE during each charge session and stored in a time-series database for further analysis. As part of the NextGen Profiles project, characterization of high-power EVSE was performed on both conductive and wireless charging infrastructure; however, only conductive charging data are currently included in this repository. This EVSE characterization was performed over a range of DC output currents and voltages, covering both nominal and off-nominal test conditions. This EVSE characterization dataset includes high-power charging data from two types of 350-kW-capable EVSE using liquid-cooled Combined Charging System-1 (CCS1, North American version) cables and connectors. To protect confidentiality, all EVSE metadata are anonymized, and the publicly released datasets are metered at 10-Hz frequency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

New Insights on the Mechanical Characterization of Kerogen-Rich Shale, KRS

In the past decade, mechanical, physical, and chemical characterization of reservoir shale rocks, such as the Woodford shale, which is kerogen-rich shale (KRS), has moved toward micro- and nanoscale testing and analyses. Nanoindentation equipment is now widely used in many industrial and university laboratories to measure shale anisotropic Young’s moduli, kerogen stiffness, plastic yield parameters, and other isotropic and anisotropic poromechanical and viscoelastic properties. However, to date, failure analyses of KRS and the effects of organic components on the tensile strength have not been observed or measured at the micro- or nanoscales. In this study, preserved kerogen-rich Woodford shale samples manufactured in micro-beam and micro-pillar geometries were mechanically tested and brought to failure in tension and compression, respectively. These tests were conducted in situ using a nanoindenter inside a scanning electron microscope (SEM). The load versus displacement curves of prismatic micro-cantilever beams were analyzed in light of high-resolution images collected during tensile fracture initiation, propagation, and ultimately sample failure. The micro-pillar geometries were subjected to a uniaxial compressive load and were also brought to failure while capturing measurements of stress and strain. It was found that, within just a few hundred microns of the KRS microcantilever beams, both brittle and ductile failure modes were observed. In the ductile plastic domain, strain-softening and strain-hardening behaviors were identified and characterized. These were not due to confining stress variations, but due to the volume of the organic matter and the way it is interlaced with the shale minerals in and around the failure planes. The tensile strength characteristics and the large modulus of toughness of kerogen, which is a cross-linked polymer, definitely weigh heavily in our engineering field applications, such as hydraulic fracking, which is a Mode I tensile fracture opening and propagation phenomenon. This practice demands that, due to the complex composite nature of KRS, mechanical characterization be not only for unconfined compressive strength but also for unconfined tensile strength and moduli of ruptures. At the end of this study, the need for nanometer scale mechanical characterization of KRS will become apparent. These nano- and micro-scale shale failure tests reinforce our previous understanding of the heterogeneous composite nature of Woodford KRS and its complex behavior, as well as other source shale reservoir formations.

58 GEOSCIENCES↗

Characterization of Thermal, Hydraulic, and Gas Diffusion Properties in Variably Saturated Sand Grades

Core Ideas This study provides physical, hydraulic, and thermal properties of five sand grades. An extended three‐region thermal conductivity model is proposed. A gas diffusivity‐based variable tortuosity parameter is examined. Useful parametric functions and descriptive models were tested. Detailed characterization of partially saturated porous media is important for understanding and predicting vadose zone transport processes. While basic properties (e.g., particle‐ and pore‐size distributions and soil‐water retention) are, in general, essential prerequisites for characterizing most porous media transport properties, key transport parameters such as thermal conductivity and gas diffusivity are particularly important to describe temperature‐induced heat transport and diffusion‐controlled gas transport processes, respectively. Despite many experimental and numerical studies focusing on a specific porous media characteristic, a single study presenting a wide range of important characteristics, together with the best‐performing functional relationships, can seldom be found. This study characterized five differently textured sand grades (Accusand no. 12/20, 20/30, 30/40, 40/50, and 50/70) in relation to physical properties, water retention, hydraulic conductivity, thermal conductivity, and gas diffusivity. We used measured basic properties and transport data to accurately parameterize the characteristic functions (particle‐ and pore‐size distributions and water retention) and descriptive transport models (thermal conductivity, saturated hydraulic conductivity, and gas diffusivity). An existing thermal conductivity model was improved to describe the distinct three‐region behavior in observed thermal conductivity–water saturation relations. Applying widely used parametric models for saturated hydraulic conductivity and soil‐gas diffusivity, we characterized porous media tortuosity in relation to grain size. Strong relations among average particle diameter, characteristic pore diameter from soil‐water retention measurements, and saturated hydraulic conductivity were found. Thus, the results of this work are useful toward better describing, linking, and predicting mass transfer and pore network properties in variably saturated porous media.

Chamindu Deepagoda, T. K. K.↗

Improving Subsurface Stress Characterization for Carbon Dioxide Storage Projects

Researchers at New Mexico Tech, Los Alamos National Laboratory (LANL), Sandia National Laboratory (SNL), and other collaborators are developing a methodology to improve characterization of stress in the subsurface by means of a model-based inversion of reservoir engineering data, time lapse seismic measurements, and microseismicity. Historically, various geophysical techniques have been used in efforts to understand the state of stress in the subsurface through direct and indirect imaging of stress sensitive features (faults and fractures) and observations of transient stress related observations (time variant elastic moduli and microseismicity). Standard direct and indirect techniques for seismic fault and fracture imaging suffer from detectability limits due to reliance on high data quality and multiplicity. Variations in effective elastic properties from inversion of high quality seismic (Vertical Seismic Profile (VSP)) data may be used to infer stress near the wellbore through integration with independent experimental characterization of the stress-velocity relationship. Given a sufficiently robust observation network, microseismic emissions may be inverted to characterize focal mechanisms which, together with supporting assumptions and constraints, inform estimates of in-situ stress. While each of these techniques contributes in part to the characterization of stress within limited spatial and temporal domains, no one method provides an unambiguous stress measurement or a predictive capability over a site scale spatial extent. Challenges associated with solution non-uniqueness, measurement ambiguity, and irregular sampling may be greatly minimized through combination of one or more of independent measurements within a common framework in which realistic geological, hydrodynamic, geomechanical, and seismological constituent process models may act as constraints.

02 PETROLEUM↗

Real-time characterization of partially observed epidemics using surrogate models.

We present a statistical method, predicated on the use of surrogate models, for the 'real-time' characterization of partially observed epidemics. Observations consist of counts of symptomatic patients, diagnosed with the disease, that may be available in the early epoch of an ongoing outbreak. Characterization, in this context, refers to estimation of epidemiological parameters that can be used to provide short-term forecasts of the ongoing epidemic, as well as to provide gross information on the dynamics of the etiologic agent in the affected population e.g., the time-dependent infection rate. The characterization problem is formulated as a Bayesian inverse problem, and epidemiological parameters are estimated as distributions using a Markov chain Monte Carlo (MCMC) method, thus quantifying the uncertainty in the estimates. In some cases, the inverse problem can be computationally expensive, primarily due to the epidemic simulator used inside the inversion algorithm. We present a method, based on replacing the epidemiological model with computationally inexpensive surrogates, that can reduce the computational time to minutes, without a significant loss of accuracy. The surrogates are created by projecting the output of an epidemiological model on a set of polynomial chaos bases; thereafter, computations involving the surrogate model reduce to evaluations of a polynomial. We find that the epidemic characterizations obtained with the surrogate models is very close to that obtained with the original model. We also find that the number of projections required to construct a surrogate model is O(10)-O(10{sup 2}) less than the number of samples required by the MCMC to construct a stationary posterior distribution; thus, depending upon the epidemiological models in question, it may be possible to omit the offline creation and caching of surrogate models, prior to their use in an inverse problem. The technique is demonstrated on synthetic data as well as observations from the 1918 influenza pandemic collected at Camp Custer, Michigan.

59 BASIC BIOLOGICAL SCIENCES↗