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At least 343 records · Page 19

Divergence Reduction in Monte Carlo Neutron Transport with On-GPU Asynchronous Scheduling

While Monte Carlo Neutron Transport (MCNT) is near-embarrasingly parallel, the effectively unpredictable lifetime of neutrons can lead to divergence when MCNT is evaluated on GPUs. Divergence is the phenomenon of adjacent threads in a warp executing different control flow paths; on GPUS, it reduces performance because each work group may only execute one path at a time. The process of Thread Data Remapping (TDR) resolves these discrepancies by moving data across hardware such that data in the same warp will be processed through similar paths. A common issue among prior implementations of TDR is the synchronous nature of its remapping and processing cycles, which exhaustively sort data produced by prior processing passes and exhaustively evaluate the sorted data. In another work, we defined a method of remapping data through an asynchronous scheduler which allows for work to be stored in shared memory and deferred arbitrarily until that work is a viable option for low-divergence evaluation. This article surveys a wider set of cases, with the goal of characterizing performance trends across a more comprehensive set of parameters. These parameters include cross sections of scattering/capturing/fission, use of implicit capture, source neutron counts, simulation time spans, and tuned memory allocations. Across these cases, we have recorded minimum and average execution times, as well as a heuristically tuned near-optimal memory allocation size for both synchronous and asynchronous scheduling. Across the collected data, it is shown that the asynchronous method is faster and more memory efficient in the majority of cases, and that it requires less tuning to achieve competitive performance.

Computer Science↗

PcapDB: Search Optimized Packet Capture, Version 0.1.0.0

PcapDB is a packet capture system designed to optimize the captured data for fast search in the typical (network incident response) use case. The technology involved in this software has been submitted via the IDEAS system and has been filed as a provisional patent. It includes the following primary components: capture: The capture component utilizes existing capture libraries to retrieve packets from network interfaces. Once retrieved the packets are passed to additional threads for sorting into flows and indexing. The sorted flows and indexes are passed to other threads so that they can be written to disk. These components are written in the C programming language. search: The search components provide a means to find relevant flows and the associated packets. A search query is parsed and represented as a search tree. Various search commands, written in C, are then used resolve this tree into a set of search results. The tree generation and search execution management components are written in python. interface: The PcapDB web interface is written in Python on the Django framework. It provides a series of pages, API's, and asynchronous tasks that allow the user to manage the capture system, perform searches, and retrieve results. Web page components are written in HTML,CSS and Javascript.

Ferrell, Paul↗

Pretty Linter GrumPhP

This software takes JSON and YAML files, and after running them through a linter, sorts the keys of objects alphabetically. This helps prevent the following problems when checking these data/config files into repositories: Problems where the entire file looks like it was removed and added due to Indentation changes Key sorting differences Merging issues when 2 or more people add data to the same or similar locations

Williams, Thom↗

Cell Population–resolved Multiomics Atlas of the Developing Lung

The lung is a vital organ that undergoes extensive morphological and functional changes during postnatal development. To disambiguate how different cell populations contribute to organ development, we performed proteomic and transcriptomic analyses of four sorted cell populations from the lung of human subjects aged 0 to 8 years-old with a focus on early life. The cell populations analyzed included epithelial, endothelial, mesenchymal, and immune cells. Our results revealed distinct molecular signatures for each of the sorted cell populations that enable the description of molecular shifts occurring in these populations during post-natal development. Here, we confirmed that the proteome of the different cell populations was distinct regardless of age and identified functions specific to each population. We identified a series of cell population protein markers, including those located at the cell surface, that show differential expression and distribution on RNA in situ hybridization and immunofluorescence imaging. We validated the spatial distribution of AT1 and endothelial cell surface markers. Temporal analyses of the proteome of each of the four populations revealed processes modulated during postnatal development and disambiguating results obtained on whole tissue proteome. Finally, the proteome was compared to a transcriptomics survey performed on the same lung samples to evaluate processes under post-transcriptional control.

59 BASIC BIOLOGICAL SCIENCES↗

A Triple-Moment Representation of Ice in the Predicted Particle Properties (P3) Microphysics Scheme

In the original Predicted Particle Properties (P3) bulk microphysics scheme, all ice-phase hydrometeors are represented by one or more “free” ice categories, where the physical properties evolve smoothly through changes to the four prognostic variables (per category), and with a two-moment representation of the particle size distribution. As such, the spectral dispersion cannot evolve independently, which thus results in limitations in representation of ice—in particular, hail—due to necessary constraints in the scheme to prevent excessive gravitational size sorting. To overcome this, P3 has been modified to include a three-moment representation of the size distribution of each ice category through the addition of a fifth prognostic variable, the sixth moment of the size distribution. The details of the three-moment ice parameterization in P3 are provided. The behavior of the modified scheme, with the single-ice-category configuration, is illustrated through simulations in a simple 1D kinematic model framework as well as with near large-eddy-resolving (250-m grid spacing) 3D simulations of a hail-producing supercell. It is shown that the three-moment ice configuration controls size sorting in a physically based way and leads to an improved capacity to simulate large, heavily rimed ice (hail), including mean and maximum sizes and reflectivity, and thus an overall improvement in the representation of ice-phase particles in the P3 scheme.

54 ENVIRONMENTAL SCIENCES↗

Study of Microphysical Signatures Based on Spectral Polarimetry during the RELAMPAGO Field Experiment in Argentina

Weather radars with dual-polarization capabilities enable the study of various characteristics of hydrometeors, including their size, shape, and orientation. Radar polarimetric measurements, coupled with Doppler information, allow for analysis in the spectral domain. This analysis can be leveraged to reveal valuable insight into the microphysics and kinematics of hydrometeors in precipitation systems. This paper uses spectral polarimetry to investigate precipitation microphysics and kinematics in storm environments observed during the Remote Sensing of Electrification, Lightning, and Mesoscale/Microscale Processes with Adaptive Ground Observations (RELAMPAGO) field experiment in Argentina. This study uses range–height indicator scan measurements from a C-band polarimetric Doppler weather radar deployed during the field campaign. Here, in this work, the impact of storm dynamics on hydrometeors is studied, including the size sorting of hydrometeors due to vertical wind shear. In addition, particle microphysical processes because of aggregation and growth of ice crystals in anvil clouds, as well as graupel formation resulting from the riming of ice crystals and dendrites, are also analyzed here. The presence of different particle size distributions because of the mixing of hydrometeors in a sheared environment and resulting size sorting has been reported using spectral differential reflectivity (sZ dr ) slope. Spectral reflectivity sZ h and sZ dr have also been used to understand the signature of ice crystal aggregation in an anvil cloud. The regions of pristine ice crystals are identified from vertical profiles of spectral polarimetric variables in anvil cloud because of sZ h < 0 dB and sZ dr values around 2 dB. It is also found that the growth process of these ice crystals causes a skewed bimodal sZ h spectrum due to the presence of both pristine ice crystals and dry snow. Next, graupel formation due to riming has been studied, and it is found that the riming process produces sZ h values of about 10 dB and corresponding sZ dr values of 1 dB. This positive sZ dr indicates the presence of needle/columnar secondary ice particles formed by ice multiplication processes in the riming zones. Last, the temporal evolution of a storm is investigated by analyzing changes in hydrometeor types with time and their influence on the spectral polarimetric variables.

54 ENVIRONMENTAL SCIENCES↗

Polarimetric Signatures in Landfalling Tropical Cyclones

Polarimetric radar observations from the NEXRAD WSR-88D operational radar network in the contiguous United States, routinely available since 2013, are used to reveal three prominent microphysical signatures in landfalling tropical cyclones: 1) hydrometeor size sorting within the eyewall convection, 2) vertical displacement of the melting layer within the inner core, and 3) dendritic growth layers within stratiform regions of the inner core. Size sorting signatures within eyewall convection are observed with greater frequency and prominence in more intense hurricanes, and are observed predominantly within the deep-layer environmental wind shear vector-relative quadrants that harbor the greatest frequency of deep convection (i.e., downshear and left-of-shear). Melting-layer displacements are shown that exceed 1 km in altitude compared to melting-layer altitudes in outer rainbands and are complemented by analyses of archived dropsonde data. Dendritic growth and attendant snow aggregation signatures in the inner core are found to occur more often when echo-top altitudes are low (≤10 km MSL), nearer the -15°C isotherm commonly associated with dendritic growth. These signatures, uniquely observed by polarimetric radar, provide greater insight into the physical structure and thermodynamic characteristics of tropical cyclones, which are important for improving rainfall estimation and the representation of tropical cyclones in numerical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Severe Convective Storms in Limited Instability Organized by Pattern and Distribution

Abstract Severe convection occurring in high-shear, low-CAPE (HSLC) environments is a common cool-season threat in the southeastern United States. Previous studies of HSLC convection document the increased operational challenges that these environments present compared to their high-CAPE counterparts, corresponding to higher false-alarm ratios and lower probability of detection for severe watches and warnings. These environments can exhibit rapid destabilization in the hours prior to convection, sometimes associated with the release of potential instability. Here, we use self-organizing maps (SOMs) to objectively identify environmental patterns accompanying HSLC cool-season severe events and associate them with variations in severe weather frequency and distribution. Large-scale patterns exhibit modest variation within the HSLC subclass, featuring strong surface cyclones accompanied by vigorous upper-tropospheric troughs and northward-extending regions of instability, consistent with prior studies. In most patterns, severe weather occurs immediately ahead of a cold front. Other convective ingredients, such as lower-tropospheric vertical wind shear, near-surface equivalent potential temperature (θ e ) advection, and the release of potential instability, varied more significantly across patterns. No single variable used to train SOMs consistently demonstrated differences in the distribution of severe weather occurrence across patterns. Comparison of SOMs based on upper and lower quartiles of severe occurrence demonstrated that the release of potential instability was most consistently associated with higher-impact events in comparison to other convective ingredients. Overall, we find that previously developed HSLC composite parameters reasonably identify high-impact HSLC events. Significance Statement Even when atmospheric instability is not optimal for severe convective storms, in some situations they can still occur, presenting increased challenges to forecasters. These marginal environments may occur at night or during the cool season, when people are less attuned to severe weather threats. Here, we use a sorting algorithm to classify different weather patterns accompanying such storms, and we distinguish which specific patterns and weather system features are most strongly associated with severe storms. Our goals are to increase situational awareness for forecasters and to improve understanding of the processes leading to severe convection in marginal environments.

Meteorology & Atmospheric Sciences↗

The Fifth Adaptor Protein Complex

Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another. Four distinct AP complexes have been identified, which are present in most eukaryotes. We report the existence of a fifth AP complex, AP-5. Tagged AP-5 localises to a late endosomal compartment in HeLa cells. AP-5 does not associate with clathrin and is insensitive to brefeldin A. Knocking down AP-5 subunits interferes with the trafficking of the cationindependent mannose 6-phosphate receptor and causes the cell to form swollen endosomal structures with emanating tubules. AP-5 subunits can be found in all five eukaryotic supergroups, but they have been co-ordinately lost in many organisms. Concatenated phylogenetic analysis provides robust resolution, for the first time, into the evolutionary order of emergence of the adaptor subunit families, showing AP-3 as the basal complex, followed by AP-5, AP-4, and AP-1 and AP-2. Thus, AP-5 is an evolutionarily ancient complex, which is involved in endosomal sorting, and which has links with hereditary spastic paraplegia.

59 BASIC BIOLOGICAL SCIENCES↗

SOC Synthetic Microstructure Bank

QUICK START: Start with property_library.html (can be found by typing the filename into the query box) and use the interactive table to filter, sort, and select a microstructure with the desired properties. Search for the alphabetic code to obtain the corresponding dataset. Full description: This is a bank of 1,970 unique 3-phase electrode microstructure files. When you account for reassigning phase IDs (e.g. declare that 1=Ni and 2=pore, instead of 1=pore and 2=Ni), it actually represents 5,910 unique electrode microstructures, each of which could be considered to be either an air or a fuel electrode (e.g. declare that the phase IDs correspond to pore, Ni, and YSZ; or that they correspond to pore, LSCF, and GDC; or whatever electron-conductor and ion-conductor combination is being studied). The voxel size is 50 nm and each electrode file contains a 4x4 grid of (12.5 micron)^3 sub-volumes. If placed together in a grid, they comprise a 50x50x12.5 micron electrode (note that the interfaces between sub-volumes will be sharp; this can be mitigated via simulating annealing/relaxation). The sub-volumes can also be used individually for a reasonably sized 12.5 micron cubic region-of-interest. A user can simply consider the voxel size to be a different value to rescale the volumes (and all of their morphological features, including particle size) as desired. These microstructures were generated using DREAM3D. The general procedure is outlined in https://doi.org/10.1016/j.jpowsour.2018.03.025 The file names are an alphabetic code having to do with the input parameters used in DREAM3D when they were generated. Most users would be best served by starting with the file property_library.html or property_library_subvols.html (which lists properties for each individual subvolume). These files contain a catalogue of the actual, measured properties of every microstructure in the database. Any combination of property values can be filtered and sorted until a desired electrode is found, at which point the user can find the file corresponding to that alphabetic code. The properties in the catalogue include connected TPB density, and for each phase: phase fraction, average particle size, polydispersity of particle size, tortuosity, and connected pair-wise interfacial area. They also include what fraction of each property is connected through to the interfaces of the volume. If the desired combination of properties is not found at first, remember that the phase IDs can be re-assigned arbitrarily, e.g. swapping 1s and 2s. In fact, the database was generated with this in mind so as not to generate redundant microstructures. If the database does not contain the desired property combinations, try to search for the other possible permutations of those properties with re-assigned phase IDs. Please cite https://doi.org/10.1149/10301.0909ecst for use. Please contact the maintainer, William K. Epting, for additional information or assistance.

3D microstructure↗

Final technical report

Our overarching goals in this project were to: Develop and improve high-throughput sequencing methods and analytical approaches for quantitative analyses of microbial gene expression at the Hawaii Ocean Time Series Station and the Bermuda Atlantic Time Series Station; Conduct field analyses following gene expression patterns in picoplankton microbial communities in general, and Prochlorococcus flow sorted from that community, as they respond to different environmental variables (light, macronutrients, dissolved organic carbon), that are predicted to influence activity, productivity, and carbon cycling; Use the expression analyses of flow sorted Prochlorococcus to identify horizontally transferred genes and gene products, in particular those that are located in genomic islands and likely to confer habitat-specific fitness advantages; Use the microbial community gene expression data that we generate to gain insights, and test hypotheses, about the variability, genomic context, activity and function of as yet uncharacterized gene products, that appear highly expressed in the environment. We achieved the above goals, and even more over the course of the project. This includes a number of novel methodological developments, as well as the standardization of microbial community gene expression analyses in both field surveys, and experimental modalities. The availability of these methods, tools and approaches is changing current practice in microbial community analyses.

59 BASIC BIOLOGICAL SCIENCES↗

Heritable Genetic Changes in Cells Recovered from Irradiated 3D Tissue Contracts (Final report)

Combining contemporary cytogenetic methods with DNA CGH microarray technology and chromosome flow-sorting increases substantially the ability to resolve exchange breakpoints associated with interstitial deletions and translocations, allowing the consequences of radiation damage to be directly measured at low doses, while also providing valuable insights into molecular mechanisms of misrepair processes that, in turn, identify appropriate biophysical models of risk at low doses. The aims of this work apply to cells recovered from 3D tissue constructs of human skin and, for the purpose of comparison, the same cells irradiated in traditional 2D cultures. These aims are: to analyze by multi-flour fluorescence in situ hybridization (mFISH) the chromosomes in clonal descendents of individual human fibroblasts that were previously irradiated; to examine irradiated clones from Aim 1 for submicroscopic deletions by subjecting their DNA to comparative genomic hybridization (CGH) microarray analysis; and to flow-sort aberrant chromosomes from clones containing stable radiation-induced translocations and map the breakpoints to within an average resolution of 100 kb using the technique of 'array painting'.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Bridging the Divide: Linking Genomics to Ecosystem Responses to Climate Change: Final Report

Over the project period, we have addressed the following objectives: 1) assess the effects of altered precipitation patterns (i.e., increased variability in growing season precipitation) on genetic diversity of the dominant C4 grass species, Andropogon gerardii, and 2) experimentally assess the impacts of extreme climatic events (heat wave, drought) on responses of the dominant C4 grasses, A. gerardii and Sorghastrum nutans, and the consequences of these response for community and ecosystem structure and function. Below is a summary of how we have addressed these objectives. Objective 1 After ten years of altered precipitation, we found the number of genotypes of A. gerardii was significantly reduced compared to the ambient precipitation treatments (Avolio et al., 2013a). Although genotype number was reduced, the remaining genotypes were less related to one another indicating that the altered precipitation treatment was selecting for increasingly dissimilar genomes (based on mean pairwise Dice distance among individuals). For the four key genotypes that displayed differential abundances depending on the precipitation treatment (G1, G4, and G11 in the altered plots and G2 in the ambient plots), we identified phenotypic differences in the field that could account for ecological sorting (Avolio & Smith, 2013a). The three altered rainfall genotypes also have very different phenotypic traits in the greenhouse in response to different soil moisture availabilities (Avolio and Smith, 2013c). Two of the genotypes that increased in abundance in the altered precipitation plots had greater allocation to root biomass (G4 and G11), while G1 allocated more biomass aboveground. These phenotypic differences among genotypes suggests that changes in genotypic structure between the altered and the ambient treatments has likely occurred via niche differentiation, driven by changes in soil moisture dynamics (reduced mean, increased variability and changes in the depth distribution of soil moisture) under a more variable precipitation regime, rather than reduced population numbers (A. gerardii tiller densities did not differ between altered and ambient treatments; p = 0.505) or a priori differences in genotype richness (Avolio et al.2013a). This ecological sorting of genotypes, which accounts for 40% of all sampled individuals in the altered plots, is an important legacy of the press chronic climate changes in the RaMPs experiment. Objective 2 In May 2010, we established the Climate Extremes Experiment at the Konza Prairie Biological Station. For the experiment, a gradient of temperatures, ranging from ambient to extreme, were imposed in 2010 and 2011 as a mid-season heat wave under well-watered or severe drought conditions. This study allowed us for the first time to examine species-specific thresholds of responses to climate extremes and assess how these phenotypic responses may impact selection of particular genotypes, with the ultimate goal of linking alterations in individual performance and genetic diversity to ecosystem structure and functioning. We found that tallgrass prairie was resistant to heat waves, but it was not resistant to extreme drought, which reduced aboveground net primary productivity (ANPP) below the lowest level measured in this grassland in almost thirty years (Hoover et al. in press(a)). This extreme reduction in ecosystem function was a consequence of reduced productivity of both C4 grasses and C3 forbs. This reduction in biomass of the C4 grasses (Andropogon gerardii and Sorghastrum nutans) was, in part, due to significant reductions in photosynthesis, leaf water potential and productivity with drought in the dominant grasses species, with S. nutans was more sensitive than A. gerardii to drought (Hoover et al. in press(b)). However, the dominant forb was negatively impacted by the drought more than the dominant grasses, and this led to a reordering of species abundances within the plant community. Although this change in community composition persisted post-drought, ANPP recovered completely the year after drought due to rapid demographic responses by the dominant grass, compensating for loss of the dominant forb. Overall, our results show that an extreme reduction in ecosystem function attributable to a climate extreme (e.g., low resistance) does not preclude rapid ecosystem recovery. Given that dominance by a few species is characteristic of most ecosystems, knowledge of the traits of these species and their responses to climate extremes will be key for predicting future ecosystem dynamics and function. In addition, our research suggests that water stress will dominate photosynthetic and productivity responses caused by discrete drought and heat wave events, rather than direct or additive effects of heat stress, with differential sensitivity in these grasses altering future ecosystem function.

54 ENVIRONMENTAL SCIENCES↗

Smart Grid Information Clearinghouse (SGIC)

Since the Energy Independence and Security Act of 2007 was enacted, there has been a large number of websites that discusses smart grid and relevant information, including those from government, academia, industry, private sector and regulatory. These websites collect information independently. Therefore, smart grid information was quite scattered and dispersed. The objective of this work was to develop, populate, manage and maintain the public Smart Grid Information Clearinghouse (SGIC) web portal. The information in the SGIC website is comprehensive that includes smart grid information, research & development, demonstration projects, technical standards, costs & benefit analyses, business cases, legislation, policy & regulation, and other information on lesson learned and best practices. The content in the SGIC website is logically grouped to allow easily browse, search and sort. In addition to providing the browse and search feature, the SGIC web portal also allow users to share their smart grid information with others though our online content submission platform. The Clearinghouse web portal, therefore, serves as the first stop shop for smart grid information that collects smart grid information in a non-bias, non-promotional manner and can provide a missing link from information sources to end users and better serve users’ needs. The web portal is available at www.sgiclearinghouse.org. This report summarizes the work performed during the course of the project (September 2009 – August 2014). Section 2.0 lists SGIC Advisory Committee and User Group members. Section 3.0 discusses SGIC information architecture and web-based database application functionalities. Section 4.0 summarizes SGIC features and functionalities, including its search, browse and sort capabilities, web portal social networking, online content submission platform and security measures implemented. Section 5.0 discusses SGIC web portal contents, including smart grid 101, smart grid projects, deployment experience (i.e., use cases, lessons learned, cost-benefit analyses and business cases), in-depth information (i.e., standards, technology, cyber security, legislation, education and training and demand response), as well as international information. Section 6.0 summarizes SGIC statistics from the launch of the portal on July 07, 2010 to August 31, 2014. Section 7.0 summarizes publicly available information as a result of this work.

Rahman, Saifur↗

Rendering and Compositing Infrastructure Improvements to VisIt for Insitu Rendering

Compared to posthoc rendering, insitu rendering often generates larger numbers of images, as a result rendering performance and scalability are critical in the insitu setting. In this work we present improvements to VisIt's rendering and compositing infrastructure that deliver increased performance and scalability in both posthoc and insitu settings. We added the capability for alpha blend compositing and use it with ordered compositing when datasets have disjoint block domain decomposition to optimize the rendering of transparent geometry. We also made improvements that increase overall efficiency by reducing communication and data movement and have addressed a number of performance issues. We structured our code to take advantage of SIMD parallelization and use threads to overlap communication and compositing. We tested our improvements on a 20 core workstation using 8 cores to render geometry generated from a $256^3$ cosmology dataset and on a Cray XC31 using 512 cores to render geometry generated from a $2000^2 \times 800$ plasma dataset. Our results show that ordered compositing provides a speed up of up to $4 \times$ over the current sort first strategy. The other improvements resulted in modest speed up with one notable exception where we achieve up to $40 \times$ speed up of rendering and compositing of opaque geometry when both opaque and transparent geometry are rendered together. We also investigated the use of depth peeling, but found that the implementation provided by VTK is substantially slower,both with and without GPU acceleration, than a local camera order sort.

97 MATHEMATICS AND COMPUTING↗

A Compilation of Boiling Water Reactor Operational Experience for the United Kingdom's Office for Nuclear Regulation's Advanced Boiling Water Reactor Generic Design Assessment

United States nuclear power plant Licensee Event Reports (LERs), submitted to the United States Nuclear Regulatory Commission (NRC) under law as required by 10 CFR 50.72 and 50.73 were evaluated for reliance to the United Kingdom’s Health and Safety Executive – Office for Nuclear Regulation’s (ONR) general design assessment of the Advanced Boiling Water Reactor (ABWR) design. An NRC compendium of LERs, compiled by Idaho National Laboratory over the time period January 1, 2000 through March 31, 2014, were sorted by BWR safety system and sorted into two categories: those events leading to a SCRAM, and those events which constituted a safety system failure. The LERs were then evaluated as to the relevance of the operational experience to the ABWR design.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Experimental deformation in sandstone, carbonates and quartz aggregate

The first part of my thesis is mainly focused on the effect of grain size distribution on compaction localization in porous sandstone. To identify the microstructural parameters that influence compaction band formation, I conducted a systematic study of mechanical deformation, failure mode and microstructural evolution in Bleurswiller and Boise sandstones, of similar porosity (~25%) and mineralogy but different sorting. Discrete compaction bands were observed to develop over a wide range of pressure in the Bleurswiller sandstone that has a relatively uniform grain size distribution. In contrast, compaction localization was not observed in the poorly sorted Boise sandstone. My results demonstrate that grain size distribution exerts important influence on compaction band development, in agreement with recently published data from Valley of Fire and Buckskin Gulch, as well as numerical studies. The second part aimed to improve current knowledge on inelastic behavior, failure mode and brittle-ductile transition in another sedimentary rock, porous carbonates. A micritic Tavel (porosity of ~13%) and an allochemical Indiana (~18%) limestones were deformed under compaction in wet and dry conditions. At lower confining pressures, shear localization occurred in brittle faulting regime. Through transitional regime, the deformation switched to cataclastic flow regime at higher confining pressure. Specifically in the cataclastic regime, the (dry and wet) Tavel and dry Indiana failed by distributed cataclastic flow, while in contrast, wet Indiana failed as compaction localization. My results demonstrate that different failure modes and mechanical behaviors under different deformation regimes and water saturation are fundamental prior to any geophysical application in porous carbonates. The third part aimed to focus on investigating compaction on quartz aggregate starting at low (MPa) using X-ray diffraction. We report the diffraction peak evolution of quartz with increasing pressures. Through evaluating the unit cell lattice parameters and the volume of the quartz sample, macroscopic stress and strain were resolved. Moreover, we observed quartz peak broadened asymmetrically at low pressure, such extent is more prominent in axial than in radial direction. Our evaluation on peak [101] (highest intensity among peaks) demonstrated that full width at half maximum can be a good proxy for microscopic stress distribution. We observed deviations in the pressurevolume curves at P = ~0.4 GPa and speculated that it was the point of which onset of grain crushing and pore collapse occur in quartz. This is on the same order of which onset of grain crushing (commonly known as P*) is observed in sandstones in the rock mechanics literature. This demonstrated that there is potential in estimating grain crushing and pore collapse pressure with our technique.

58 GEOSCIENCES↗

Unravel lipid accumulation mechanism in oleaginous yeast through single cell systems biology study

Searching for alternative and clean energy is one of the most important tasks today. Our research aimed at finding the best living condition for certain types of oleaginous yeasts for efficient lipid production. We found that R. glutinis yeast cells has great variability in lipid production among cells while Y. lipolytica cells has similar oil production ability. We found some individual cells shows much higher level of oil production. In order to further study these cases, we employed a label-free chemical sensitive microscopy method call stimulated Raman scattering (SRS). With SRS, we could measure the lipid content in each cell. We combined SRS microscopy with microfluidic device so that we can isolate cells with high fat content. We also developed SRS imaging technique that has higher imaging speed, which is highly desirable for high throughput cell screening and sorting. Since these cells has similar genome, it must be the transcriptome caused their difference in oil production. We developed a single cell transcriptome sequencing method to study which genes are responsible for elevated oil production. These methods that are developed for this project can easily be applied for many other areas of research. For example, the single transcriptome can be used to study the transcriptomes of other cell types. The high-speed SRS microscopy techniques can be used to speed up chemical imaging for lablefree histology or imaging distribution of chemicals in tissues of live mice or in humans. The developed microfluidic platform can be used to sort other type of cells, e.g., white blood cells for diagnosis of cancer or other blood diseases.

09 BIOMASS FUELS↗