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51 records · Page 3

OWD.2 TAG Expression

During the transformation of wild-type (WT) Arabidopsis thaliana, a T-DNA containing OLEOSIN-GFP (OLE1-GFP) was inserted by happenstance within the GBSS1 gene, resulting in significant reduction in amylose and increase in leaf oil content in the transgenic line (OG). The synergistic effect on oil accumulation of combining gbss1 with the expression of OLE1-GFP was confirmed by transforming an independent gbss1 mutant (GABI_914G01) with OLE1-GFP. The resulting OLE1-GFP/gbss1 transgenic lines showed higher leaf oil content than the individual OLE1-GFP/WT or single gbss1 mutant lines. Further stacking of the lipogenic factors WRINKLED1, Diacylglycerol O-Acyltransferase (DGAT1), and Cys-OLEOSIN1 (an engineered sesame OLEOSIN1) in OG significantly elevated its oil content in mature leaves to 2.3% of dry weight, which is 15 times higher than that in WT Arabidopsis. Inducible expression of the same lipogenic factors was shown to be an effective strategy for triacylglycerol (TAG) accumulation without incurring growth, development, and yield penalties.

Biomass Analytics↗

Initializing FLAG at Specified Density and Pressure

Five of the material-initialization nodes available in FLAG, stre, ptre, teofrp, reoftp, and ptofre , were studied as to their ability to initialize a material at a precise pressure and density. Using a fast, one-dimensional setup, initializations were attempted for each node at a pressure 1 bar and a density near ambient for six SESAME equations of state, 3720 (Al), 2024 (Be), 3337 (Cu), and 2705 (Au), and 7247 (LiD), and 2964 (Ti6Al4V). Only the teofrp node consistently reproduced the specified pressure and density to better than six significant figures.

36 MATERIALS SCIENCE↗

Simulations of Sweeping Wave Propagation in a Boron Carbide Plate

In February 2020, experiments were conducted at Los Alamos National Laboratory measuring the propagation of a sweeping wave through a plate of boron carbide which was induced by detonating an adjacent charge of high explosive. Six such shots were red and in each case progress of the wave along the exposed surface of the plate was tracked using photon doppler velocimetry (PDV). In this report we discuss calculations performed using the Lagrangian hydrocode FLAG to model data taken from these experiments. We discuss the models chosen for the different experimental components, the choice of mesh (focusing on, both, two- and three-dimensional geometries), and compare the results from these calculations to experimentally-extracted PDV traces. Notably, we find that the PDV traces for this experiment are most faithfully reproduced using the full three-dimensional geometry, even when the mesh resolution for the three-dimensional calculations was significantly lower than the resolution for the corresponding two-dimensional calculations. We attribute this to the geometry of the experimental setup. Moreover, we find only negligible differences for the PDV traces obtained using the sesame table equation of state for boron carbide and the Gruneisen equation of state.

36 MATERIALS SCIENCE↗

XCP- Computational Summer Workshop: Equation of State Overview [Slides]

An overview of Equation of State (EOS) theory, some relevant physics, experiments, computational methods, and the SESAME database will be presented. The goal will be to describe what types of data and modeling are required to make an EOS that typically spans up to ~10 9 GPa in pressure and 10 9 K in temperature.

42 ENGINEERING↗

A new equation of state for copper

A new copper equation of state is developed utilizing the available experimental data in addition to recent theoretical calculations. Semi-empirical models are fit to the data and the results are tabulated in the SNL SESAME format. Comparison to other copper EOS tables are given, along with recommendations of which tables provide the best accuracy.

36 MATERIALS SCIENCE↗

Path Integral Monte Carlo Simulations of Iron Plasmas (Final Technical Report)

This documents is the final technical report for our grant entitled "Path Integral Monte Carlo Simulations of Iron Plasmas" that focused on developing path integral Monte Carlo (PIMC) computer simulations. This techniques will be developed to study plasmas composed of heavier elements including iron and other third row elements. Equations of state (EOS) and transport properties will be derived in the regime of warm dense matter (WDM) and dense plasmas where existing first-principles methods cannot be applied. While standard density functional theory (DFT) has been used to accurately predict the structure of many solids and liquids up to temperatures on the order of 100,000 K, this method is not applicable at much higher temperature because the number of partially occupied electronic orbitals reaches intractably large numbers or the use of finite-temperature free energy functionals in orbital-free DFT introduces an uncontrolled approximation. Here we focus on PIMC methods that become more and more efficient with increasing temperatures and still include all electronic correlation effects. In this approach, electronic excitations increase the efficiency rather than reduce it. While it had commonly been assumed this method could only be applied to elements without core electrons, we showed that PIMC with free-particle nodes works well for first-row elements (PRL 108 (2012) 115502). Most recently, we extended the applicability range of all-electron PIMC to second-row elements by adopting localized nodal surfaces (PRL 115 (2015) 176403). To simulate third-row elements efficiently under WDM conditions, we propose a new method to remove core electrons by introducing pseudo-nodes. We explain our approach step by step and present preliminary results. We focus our method development on getting PIMC simulations of iron to work because of its fundamental importance for WDM and astrophysics. Then we move on to krypton and copper-doped beryllium, a ICF ablator material. We plan to continue working on key second-row material such as Na, Mg, MgO, Al, silica, and silicon-doped plastic ablators. Our collaborators at LLNL, will use our PIMC EOS data both as comparisons to existing semi-empirical, EOS-generating schemes, and as input for continuum radiation hydrodynamics simulations. We will establish an efficient pipeline from PIMC to macroscopic continuum studies of materials response. An emphasis will be placed on benchmarking such methods for plasmas of heavy elements at the very high temperatures (~100 eV) and low densities that are generated when Hohlraum radiation heats the ablator material in indirect drive laser experiments. Results from changes to the EOS will be of immeasurable importance to the designers at the National Ignition Facility (NIF) and at other facilities. Starting with our EOS of Cu-doped Be, our second collaborator at LLE, will perform real-time simulations of laser fusion experiments at the Omega laser and at the NIF to determine how sensitive the compression path depends on the ablator EOS. Since our collaborator also has experience in performing orbital-free DFT calculations, we propose to compare predictions from this method with PIMC results. In joint publications, we plan to analyze the accuracy of different free-energy functionals in order to understand why existing orbital-free DFT calculations do not predict compression peaks along the shock Hugoniot curve that we see with PIMC. The peaks are caused by the ionization of various electron shells. Their accurate characterization is important to compare with experimental results. We will break new ground by developing PIMC techniques that can simulate iron and all other third row elements in the plasma and WDM regimes. We introduce the concept of pseudo-nodes for the efficient treatment of the core-electrons. The EOS and transport properties will be derived and published online in the form of a new WDM database. Our PIMC EOS calculations will benchmark and possibly replace semi-analytical EOS tables like QEOS or SESAME, which will impact the hydrocode simulation community and will affect the design of NIF targets. Our PIMC results will help to improve the accuracy of orbital-free DFT simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spiner-EOSPAC Comparison: performance and accuracy on Power9 CPU and GPU

The goal of this report is to concisely compare EOSPAC to Spiner EOS for a selection of commonly-used materials over as much of their domain as is possible. Importantly, this comparison does not address the way that the Euler equations may amplify interpolation errors and we take as given that the rational function interpolator gives the best possible representation of the EOS represented by the Sesame data. Neither does the report address all, or even majority of, the capabilities of each code nor does it explore performance or accuracy over multiple compilers and platforms.

97 MATHEMATICS AND COMPUTING↗

Multiphase equation of state for Ta 2 O 5

A new equation of state for Ta 2 O 5 is presented. The EOS is constructed using the OpenSesame software and is referred to as SESAME 3530. The EOS uses a combination of density functional theory (DFT) calculations and experimental data. DFT calculations include cold curves and phonons of the solid phases, as well as DFT-based molecular dynamics simulations of the liquid phase. Experimental data includes isobaric, diamond anvil cell, and porous shock Hugoniot data. To fit the data, we create a multiphase EOS consisting of two solid phases and the liquid. Overall agreement with experimental data is shown, and we provide some suggestions for future experiments that could improve our knowledge of the phase diagram.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Atomic Mixing of Initially Separated Mixtures

We consider the atomic mixing of two materials, initially separated in space, at fixed temperature– pressure conditions [T, p], and zero mass-mean velocity. Each material is composed of a specified set of atomic species whose density corresponds to the specieswise real Equation of State (EOS) $\tilde{&#961}$ i [T, p]. Because there are no spatial gradients in the mean [T, p] state, the only mechanism for mixing is a specieswise nonequilibrium thermal velocity distribution. The recipe for nonequilibrium species mass fluxes is taken directly from Hirschfelder, Curtiss, and Bird, who express the diffusion velocities in terms of gradients in the molar concentrations and pairwise coefficients of diffusion. EOS data from the SESAME library is used for all species. Data for the specieswise self diffusion coefficients is adopted from the Orbital Free Molecular Dynamics (OFMD) simulations of Ticknor et al.; the so-called Darken approximation is used to express the mutual diffusion coefficients of a mixture in the manner used by White et al. A one-dimensional spatial domain is used; with the left half occupied by one multispecies material and the right half occupied by the other, and with zero–gradient boundary conditions at the ends of the domain. Hence the total mass in the domain is a constant. At time t = 0 the materials are separated. Accordingly, spatial gradients at the separation point are infinite and the species fluxes are also infinite. As t → $\textbf{∞}$ the spatial gradients approach zero and a uniform set of species concentrations is obtained; at this point the system is said to be at “thermodynamic equilibrium.” Analytic solution of the problem is not possible in general due to the nonlinear concentration dependence of the species fluxes. Hence we utilize the numerical solution apparatus in Mathematica for obtaining accurate time-dependent solutions for the mixing of various initial species masses for conditions of interest in laser-driven Inertial Confinement Fusion. Concentration profiles and the speed of propagation of the mixing fronts are discussed in light of the nonlinearity of the problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Parameter study of a Kinetic Phase Transition model

We investigate the ability of the two model parameters in the Kinetic Phase Transition (KPT) model of Carl Greeff to describe phase transitions of various types when combined with the tin Equation of states for the phases, SESAME 2162. While the two parameters are correlated, one combination can be associated with the nucleation process giving rise to the hysteresis seen in phase transition paths in pressure-temperature space and another can be associated with the overall timescale of the transition. We acknowledge the desire to have a model where the parameters are more independent of each other for easier model parameter determination.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Parameterization of the β and γ phases of Tin using the Vinet and Mie-Grüneisen Equations of State

When testing new phase aware materials models, it is often not possible to use tabulated Equations of States for the phases since the model might only be available in a smaller specialized research code without capability to read in tables. These EOS parameterizations for two of the solid phases of Tin were developed for testing the Kinetic Phase Transition model by Carl Greeff, LANL. They are based on two isotherms per phase obtained from work in progress by Carl Greeff, and their phase boundary corresponds fairly well to SESAME 2162. A full machinery is applied for the parameterization of the Vinet EOSs while the Mie-Grüneisen parameterizations are translated from the Vinet EOSs.

36 MATERIALS SCIENCE↗

Efficient and Accurate Pre-Inversion of Equation of State Data

In this report, we evaluate the trade-offs between accuracy and performance in three equation of state interpola- tion strategies- EOSPAC, SpinerEOSDependsRhoT, and SpinerEOSDependsRhoSie-using SESAME tabular data. We also investigate ways to reduce nonlinearity in the data through invertible transformations within the SpinerEOS- DependsRhoSie class with the goal of impacting interpolation accuracy. We include a variety of benchmarking tests that vary the grid densities and how memory is accessed.

36 MATERIALS SCIENCE↗

Ectopic Expression of OLEOSIN 1 and Inactivation of GBSS1 Have a Synergistic Effect on Oil Accumulation in Plant Leaves

During the transformation of wild-type (WT) Arabidopsis thaliana, a T-DNA containing OLEOSIN-GFP (OLE1-GFP) was inserted by happenstance within the GBSS1 gene, resulting in significant reduction in amylose and increase in leaf oil content in the transgenic line (OG). The synergistic effect on oil accumulation of combining gbss1 with the expression of OLE1-GFP was confirmed by transforming an independent gbss1 mutant (GABI_914G01) with OLE1-GFP. The resulting OLE1-GFP/gbss1 transgenic lines showed higher leaf oil content than the individual OLE1-GFP/WT or single gbss1 mutant lines. Further stacking of the lipogenic factors WRINKLED1, Diacylglycerol O-Acyltransferase (DGAT1), and Cys-OLEOSIN1 (an engineered sesame OLEOSIN1) in OG significantly elevated its oil content in mature leaves to 2.3% of dry weight, which is 15 times higher than that in WT Arabidopsis. Inducible expression of the same lipogenic factors was shown to be an effective strategy for triacylglycerol (TAG) accumulation without incurring growth, development, and yield penalties.

59 BASIC BIOLOGICAL SCIENCES↗

PRMI: A Dataset of Minirhizotron Images for Diverse Plant Root Study

Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA non-destructively by capturing root imagery over time. Precisely segmenting roots from the soil in MR imagery is a critical step in studying RSA features. In this paper, we introduce a large-scale dataset of plant root images captured by MR technology. In total, there are over 72K RGB root images across six different species including cotton, papaya, peanut, sesame, sunflower, and switchgrass in the dataset. The images span a variety of conditions including varied root age, root structures, soil types, and depths under the soil surface. All of the images have been annotated with weak image-level labels indicating whether each image contains roots or not. The image-level labels can be used to support weakly supervised learning in plant root segmentation tasks. In addition, 63K images have been manually annotated to generate pixel-level binary masks indicating whether each pixel corresponds to root or not. These pixel-level binary masks can be used as ground truth for supervised learning in semantic segmentation tasks. By introducing this dataset, we aim to facilitate the automatic segmentation of roots and the research of RSA with deep learning and other image analysis algorithms.

Xu, Weihuang↗

New equations of state for saturated tuff based on the CHEST model

The CHemical Equilibrium for Saturated Tuff (CHEST) model was originally presented in Ref. 1, with numerical results depicted in Figure 1 and tabulated in Appendix B of that work. The results consisted of specific internal energy as a function of pressure and specific volume, E(P, V), spanning the domain P = 10 –4 – 10 4 kbar and V = 0.17 – 752 cm 3 /g (ρ = 1.33 × 10 –3 – 5.9 g/cm 3 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗