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Agronomic performance of Populus deltoides trees engineered for biofuel production
Not Available
Economic impact of yield and compositions variation in bioenergy crops: Populus trichocarpa
Supplementary Data for Economic impact of yield and compositions variation in bioenergy crops: Populus trichocarpa manuscript
FLASSH 1.0: Full Law Analysis Scattering System Hub
Nuclear technologies, such as thermal reactors and critical systems, are driven by reaction rates which are directly dependent on thermal neutrons. The ability to calculate reaction rates is directly linked to the capability to predict and understand the cross sections. For atoms bound within a material structure, the available modes of energy exchange are captured in the Thermal Scattering Law (TSL, i.e. S(α,β)). The TSL is fundamentally a material property and can be defined explicitly to account for the excitation and deexcitation of the lattice energy states. This work describes the development of the Full Law Analysis Scattering System Hub (FLASSH) which calculates the TSL and cross sections. FLASSH is a modern code which has been designed to produce accurate TSL evaluations, remove historical approximations, and improve formulations while making advance physics accessible and simple to use.
Recent SCALE Activities Within the Nuclear Criticality Safety Program
The role of SCALE in the Department of Energy’s Nuclear Criticality Safety Program (NCSP) is defined according to the Five-Year Plan, and summarized as follows. 1. Sustain/improve SCALE NCS features through user driven enhancements, software quality assurance (SQA) and validation and verification (V&V). 2. Assure adaptability to various computing platforms and compilers. 3. Improve user interfaces/documentation consistent with modern engineering software. 4. Support responsive communication to SCALE criticality safety users through SCALE Newsletters, email notices, and updates on the SCALE website. 5. Modernize software infrastructure and capabilities to improve quality and reliability and to ensure long term sustainability of the NCS capabilities. This paper describes the specific activities which have been performed within each area above for the NCSP in the fiscal year (FY) 2018, from October 1, 2017, to September 30, 2018.
Measurement and control of optical nonlinearities in dispersive dielectric multilayers
Dispersive dielectric multilayer mirrors, high-dispersion chirped mirrors in particular, are widely used in modern ultrafast optics to manipulate spectral chirps of ultrashort laser pulses. Dispersive mirrors are routinely designed for dispersion compensation in ultrafast lasers and are assumed to be linear optical components. In this work, we report the experimental characterization of an unexpectedly strong nonlinear response in these chirped mirrors. At modest peak intensities <2 TW/cm 2 —well below the known laser-induced damage threshold of these dielectric structures—we observed a strong reflectivity decrease, local heating, transient spectral modifications, and time-dependent absorption of the incident pulse. Through computational analysis, we found that the incident laser field can be enhanced by an order of magnitude in the dielectric layers of the structure. The field enhancement leads to a wavelength-dependent nonlinear absorption, that shows no signs of cumulative damage before catastrophic failure. The nonlinear absorption is not a simply two-photon process but instead is likely mediated by defects that facilitate two-photon absorption. To mitigate this issue, we designed and fabricated a dispersive multilayer design that strategically suppresses the field enhancement in the high-index layers, shifting the high-field regions to the larger-bandgap, low-index layers. This strategy significantly increases the maximum peak intensity that the mirror can sustain. However, our finding of an onset of nonlinear absorption even at ‘modest’ fluence and peak intensity has significant implications for numerous past published experimental works employing dispersive mirrors. Additionally, our results will guide future ultrafast experimental work and ultrafast laser design.
Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain
Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP–chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low Tm downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.
Augmenting Epidemiological Models with Point-Of-Care Diagnostics Data
Not Available
Defining the genetic components of callus formation: A GWAS approach
A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide–log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.
Hard Rock Drilling Optimization Software
The main objective of the developed software is to reduce the cost per foot during drilling, in other words, optimize the drilling operational parameters in achieving optimum ROP while avoiding critical operational parameters due to either low ROP, drillstring vibration, accelerated cutter wear, or low MSE. The developed software can also be used for post-well analysis to provide insight and lessons learned for future drilling operations. Several functions are available in the software to help the user perform drilling analysis, optimization, and simulation.
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein
Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including Huntington’s and other neurological maladies. This suggests that the relative length of polyQ stretches is an important modulator of their function. Here, we report the identification of a Populus C-terminus binding protein (CtBP) ANGUSTIFOLIA (PtAN1) which contains a polyQ stretch whose functional relevance had not been established. Analysis of 917 resequenced Populus trichocarpa genotypes revealed three allelic variants at this locus encoding 11-, 13- and 15-glutamine residues. Transient expression assays using Populus leaf mesophyll protoplasts revealed that the 11Q variant exhibited strong nuclear localization whereas the 15Q variant was only found in the cytosol, with the 13Q variant exhibiting localization in both subcellular compartments. We assessed functional implications by evaluating expression changes of putative PtAN1 targets in response to overexpression of the three allelic variants and observed allele-specific differences in expression levels of putative targets. Our results provide evidence that variation in polyQ length modulates PtAN1 function by altering subcellular localization.
Equation of state and structural evolution of manganese dolomite (kutnohorite) under high pressures
Abstract Understanding the structural evolution of carbonate minerals with increasing pressure is essential to decoding the role of Earth’s mantle in the global carbon cycle and long-term climate change. Here, we carried out synchrotron single-crystal X-ray diffraction measurements on a natural sample of manganese dolomite [kutnohorite, Ca1.11Mn0.89(CO3)2] in a diamond-anvil cell up to 51.2 GPa at room temperature with neon as the pressure-transmitting medium. The manganese dolomite sample remains stable in the rhombohedral structure from 1 bar to ~13.3 GPa. The equation of state of Ca1.11Mn0.89(CO3)2 was determined: V0 = 334.06 ± 0.29 Å3, K0 = 99.9 ± 4.7 GPa, and K0′ = 4.3 ± 0.9; when K0′ is fixed at 4.0, V0 = 334.04 ± 0.24 Å3, and K0 = 101.4 ± 1.5 GPa. Upon further compression at room temperature, the split and disappearance of diffraction spots were observed. That is, the rhombohedral structure of manganese dolomite becomes highly distorted to lose its long-range order at 13.3–51.2 GPa at room temperature. Moreover, our single-crystal X-ray diffraction results reveal the mechanisms of the reported lattice and internal Raman mode splits of the same manganese dolomite sample approximately at 13 and 24 GPa, respectively. These results suggest manganese-bearing carbonates may play a distinct role in the deep carbon cycle.
FInal Technical Repot of the Project: Design and Implementation of Low-Power 10Gb/s/channel Laser/Silicon Photonics Modulator Drivers with SEU Tolerance for HL-LHC
During the funding period of this award from May 1, 2014 through March 30, 2016, we have accomplished the design, implementation and measurement results of two laser driver chips: LpGBLD10+ which is a low-power single-channel 10Gb/s laser driver IC, and LDQ10P, which is a 4x10Gb/s driver array chip for High Energy Physics (HEP) applications. With new circuit techniques, the driver consumes a record-low power consumption, 31 mW @10Gb/s/channel and occupies a small area of 400 µm × 1750 µm for the single-channel driver IC and 1900umx1700um for the LDQ10P chip. These characteristics allow for both the LpGBLD10+ ICs and LDQ10P suitable candidate for the Versatile Link PLUS (VL+) project, offering flexibility in configuring multiple Transmitters and receivers.
Graphical User Interface for Light Water Reactor Simulation
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Thermal-Mechanical Stress in Semiconductor Devices
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