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At least 1,135 records · Page 63

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DOE OSTI2018

Broom: application for non-redundant storage of high throughput sequencing data

Abstract Motivation The data generation capabilities of high throughput sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage strategies. Results We present Broom, a stand-alone application designed to select and store only high-quality sequencing reads at extremely high compression rates. Written in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompresses data in FASTA format. Availability and implementation C++ code available at https://scsb.utmb.edu/labgroups/fofanov/broom.asp. Supplementary information Supplementary data are available at Bioinformatics online.

Albayrak, Levent↗

DOE OSTI2022

Analysis of Compressibility Effects and Nonlinear Property Variations in a Supercritical CO2 Mixing Layer

Calculations are performed using the large eddy simulation technique to qualitatively assess the effects of fluid compressibility and thermodynamic nonlinearities on the dynamics of a supercritical flow field. Resulting data are also used to interrogate instantaneous subfilter-scale fields, as modeled by the mixed-dynamic Smagorinsky closure and gradient diffusion model. A three-dimensional wall-resolved calculation of a spatially evolving mixing layer composed solely of carbon dioxide is performed. This is followed by a coarse grid calculation to examine model performance as a function of resolution. Theoretical analysis indicates that the partial derivatives of density with respect to pressure and temperature are important modulators of the temperature and pressure field evolution, respectively. Results pertaining to subfilter velocity-velocity and velocity-temperature fields indicate that the models are most stressed in the regions where compressibility and thermo-fluid nonlinearities dominate the physics.

42 ENGINEERING↗

DOE OSTI2013

ENHANCED MAGNETIC COMPRESSIBILITY AND ISOTROPIC SCALE INVARIANCE AT SUB-ION LARMOR SCALES IN SOLAR WIND TURBULENCE

The anisotropic nature of solar wind magnetic turbulence fluctuations is investigated scale by scale using high cadence in situ magnetic field measurements from the Cluster and ACE spacecraft missions. The data span five decades in scales from the inertial range to the electron Larmor radius. In contrast to the inertial range, there is a successive increase toward isotropy between parallel and transverse power at scales below the ion Larmor radius, with isotropy being achieved at the electron Larmor radius. In the context of wave-mediated theories of turbulence, we show that this enhancement in magnetic fluctuations parallel to the local mean background field is qualitatively consistent with the magnetic compressibility signature of kinetic Alfven wave solutions of the linearized Vlasov equation. More generally, we discuss how these results may arise naturally due to the prominent role of the Hall term at sub-ion Larmor scales. Furthermore, computing higher-order statistics, we show that the full statistical signature of the fluctuations at scales below the ion Larmor radius is that of a single isotropic globally scale-invariant process distinct from the anisotropic statistics of the inertial range.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Computational optical physical unclonable function

A system or method for encryption of data includes a light source, a random optical element and a light detection element. The light source is arranged to transmit an input data signal to the random optical element. The light source is incident on the random optical element such that the input data signal is randomly scattered by the random optical element to generate an image at on the detector disposed at an output of the random optical element. The image received by the detector is applied to a compressive sensing algorithm to generate a transfer function. The transfer function defines a relationship between the input data signal and the image to enable estimation and reconstruction of the input data signal.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Computational optical physical unclonable function

Birch, Gabriel Carlisle↗

DOE OSTI2021

Flowback Test Analyses at the Utah Frontier Observatory for Research in Geothermal Energy (FORGE) Site

Abstract In 2017 and 2019, injection testing was carried out in three zones in a vertical well in granite at the Frontier Observatory for Research in Geothermal Energy site near Milford, Utah, USA. In several injection cycles, flowback was implemented rather than shut-in. The goal was to explore an alternative to prolonged shut-in periods for inferring closure stress, formation compressibility, and formation permeability (permeability thickness product). The flowback procedures involved a cyclic flowback/shut-in, while pressure decreased. The flowback data are presented, and analyses are shown. The inferred closure stress(es) from flowback analyses are lower than for equivalent injection cycles that were strictly shut-in. Relatively high formation compressibility obtained from the flowback analyses indicates an extensive, fractured system. This study also includes numerical simulation of the flowback events. The numerical model shows that the rebound pressure is not necessarily the lower bound of the minimum principal stress. The signature of stiffness change can be identified as the process when the depletion mainly transitions from hydraulic fracture to natural fractures from numerical analysis. Overall, flowback potentially has advantages over shut-in because of the reduced time to closure.

15 GEOTHERMAL ENERGY↗

DOE OSTI2022

Observations on the deformation of metal microspheres in shock-driven polymer flows

We report that solid particles can be fragmented by a fast-moving fluid if their velocity difference is great enough, such as during the atmospheric entry of meteoroids or the shock compression of engineered particulate composites. The extent of particle deformation and breakup in such systems is poorly understood because the necessary extreme conditions make observation difficult and data scarce. To meet this need, experiments combining ultrafast synchrotron-based radiography with plate impact loading were performed at the dynamic compression sector at the advanced photon source. Metal microspheres of several densities and strengths (Au, Ta, and W) were placed inside a polymer matrix. A planar shock wave was then produced in the polymer by the impact of a gun-launched flyer plate. X-ray images of the resulting flow were collected at ~150ns intervals. These images document the progression of particle deformation across a range of flow conditions and particle materials. They show that the extent of deformation is sensitive to the ratio of drag stress to particle strength. The deforming particle's shape is determined by the initial shock–particle interaction, fluid stagnation pressure, and vorticity, each acting on its own timescale. A set of scaling relationships is presented to capture these observations and enable comparison with prior hydrodynamic data. The result is a framework for predicting the conditions under which strong particles are severely deformed by a shock-driven flow.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Probing iron at Super-Earth core conditions

In this paper, we report on the quasi-isentropic compression of an iron sample using ramp shaped laser irradiation. This technique allows us to quasi-isentropically compress iron up to 700 GPa and 8500 K. To our knowledge, these data are the highest pressures reached on iron in off-Hugoniot conditions and the closest to the thermodynamic states thought to exist in Earth-like planetary cores. The experiment was performed on the Ligne d'Intégration laser facility at CESTA, Bordeaux, France.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Scaling of compressible magnetohydrodynamic turbulence in the fast solar wind

The role of compressible fluctuations in the energy cascade of fast solar wind turbulence is studied using a reduced form of an exact law derived recently for compressible isothermal magnetohydrodynamics and in situ observations from the THEMIS B/ARTEMIS P1 spacecraft. A statistical survey of the data revealed a turbulent energy cascade over a range of two decades of scales that is broader than the previous estimates made from an exact incompressible law. A term-by-term analysis of the compressible model reveals new insight into the role played by the compressible fluctuations in the energy cascade. The compressible fluctuations are shown to amplify by two to four times the turbulent cascade rate with respect to the incompressible model in ∼10% of the analyzed samples. This new estimated cascade rate is shown to provide the adequate energy dissipation required to account for the local heating of the non-adiabatic solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Quantifying the Agyrotropy of Proton and Electron Heating in Turbulent Plasmas

An important aspect of energy dissipation in weakly collisional plasmas is that of energy partitioning between different species (e.g., protons and electrons) and between different energy channels. Here we analyse pressure–strain interaction to quantify the fractions of isotropic compressive, gyrotropic, and nongyrotropic heating for each species. An analysis of kinetic turbulence simulations is compared and contrasted with corresponding observational results from Magnetospheric Multiscale Mission data in the magnetosheath. In assessing how protons and electrons respond to different ingredients of the pressure–strain interaction, we find that compressive heating is stronger than incompressive heating in the magnetosheath for both electrons and protons, while incompressive heating is stronger in kinetic plasma turbulence simulations. Concerning incompressive heating, the gyrotropic contribution for electrons is dominant over the nongyrotropic contribution, while for protons nongyrotropic heating is enhanced in both simulations and observations. Variations with plasma β are also discussed, and protons tend to gain more heating with increasing β.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Utah FORGE: 2024 Discrete Fracture Network Model Data

The Utah FORGE 2024 Discrete Fracture Network (DFN) Model dataset provides a set of files representing discrete fracture network modeling for the FORGE site near Milford, Utah. The dataset includes four distinct DFN model file sets, each corresponding to different time frames and modeling approaches in 2024. These models characterize both natural and induced fractures in the geothermal reservoir, which consists of crystalline granitic and metamorphic rock approximately 8,000 feet below the ground surface. The dataset includes a reference DFN model from February 2024 that incorporates planar fractures and well trajectories, as well as upscaled permeability, porosity, compressibility, and storage values on specified grids. Additionally, there are models based on new microseismic (MEQ) data from May and July 2024, including fracture planes fitted to the latest MEQ catalog datasets, tensile fractures from hydraulic stimulation, and an alternative connected DFN for modeling purposes. Coordinate data is provided in both global and local frames, with detailed instructions on the transformations used to align with principal stress orientations. The dataset also includes notes and calculation files for estimating fracture sizes and differences between various fracture sets. There are subfolders for Global Coordinates and Local Coordinates. To move from the global to the local coordinate frame, fractures and wells were a) rotated 20 degrees counterclockwise looking down about the global point (335376.400482041, 4263189.99998761, 250.093546450195) to better align with the principal stresses; and b) translated by (-335408.68, -4263010.9, 1150). Upscaled permeability values using the _XYZ suffix show directions with respect to the global XYZ coordinate frame, while those using the _IJK suffix are aligned with local coordinate frame.

15 GEOTHERMAL ENERGY↗

DOE OSTI2019

Thermal conductivity measurements and modeling of ceramic fiber insulation materials

Ceramic fiber insulation materials are used in numerous applications (e.g. aerospace, fire protection, and military) for their stability and performance in extreme environments. However, the thermal properties of these materials have not been thoroughly characterized for many of the conditions that they will be exposed to, such as high temperatures, pressures, and alternate gaseous atmospheres. The resulting uncertainty in the material properties can complicate the design of systems using these materials. In this study, the thermal conductivity of two ceramic fiber insulations, Fiberfrax T-30LR laminate and 970-H paper, was measured as a function of atmospheric temperature and compression in an air environment using the transient plane source technique. Furthermore, a model is introduced to account for changes in thermal conductivity with temperature, compression, and ambient gas. The model was tuned to the collected experimental data and results are compared. Lastly, the tuned model is also compared to published data sets taken in argon, helium, and hydrogen environments and agreement is discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Different site occupancies in substitution variants of Mo{sub 3}Sb{sub 7}

A series of samples with the initial formula Mo{sub 3–x}Fe{sub x}Sb{sub 7} and Mo{sub 3–x}Ni{sub x}Sb{sub 7} have been prepared by solid state reaction at 873 K, starting from the elements in the stoichiometric ratios. The materials were compressed via hot-pressing, and their thermoelectric properties determined. Single crystal data show that Ni atoms in part occupy the cubic voids of the Mo{sub 3}Sb{sub 7} structure, as well as replace some Mo atoms, in contrast to the Fe analogues, where we found no evidence for Fe in the cubic voids. Supported by electronic structure calculations, replacing Mo with Fe or Ni increases the valence-electron count, thus decreases the numbers of p-type carriers of Mo{sub 3}Sb{sub 7}. On the other hand, filling the holes with Ni atoms appears to have no such effect. As a consequence, the Ni containing samples exhibit higher electrical conductivity than the Fe analogues, and ultimately lower thermoelectric figure-of-merit, as the p-type carrier concentration remains too high. - Graphical abstract: Trying to substitute Ni atoms for Mo in Mo{sub 3}Sb{sub 7} resulted in partial filling of the cubic voids, in contrast to Mo{sub 3–x}Fe{sub x}Sb{sub 7}. Since the Ni atoms in the Sb{sub 8} cubes do not act as electron donors, the Ni-containing materials exhibit very high carrier concentration, and thus high electric conductivity and low Seebeck coefficient. - Highlights: • Various substitution variants of Mo{sub 3}Sb{sub 7} with Fe and Ni were characterized. • While the Fe atoms replace the Mo atoms, the Ni atoms also fill the cubic voids. • Higher Fe/Ni amount on the Mo sites causes a decrease of the charge carriers. • The Ni atoms on the cubic sites do not decrease the charge carriers. • The lower the carrier concentration, the better the thermoelectric properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Lattice Mismatch in Crystalline Nanoparticle Thin Films

For atomic thin films, lattice mismatch during heteroepitaxy leads to an accumulation of strain energy, generally causing the films to irreversibly deform and generate defects. In contrast, more elastically malleable building blocks should be better able to accommodate this mismatch and the resulting strain. In our work, that hypothesis is tested by utilizing DNA-modified nanoparticles as “soft,” programmable atom equivalents to grow a heteroepitaxial colloidal thin film. Calculations of interaction potentials, small-angle X-ray scattering data, and electron microscopy images show that the oligomer corona surrounding a particle core can deform and rearrange to store elastic strain up to ±7.7% lattice mismatch, substantially exceeding the ±1% mismatch tolerated by atomic thin films. Importantly, these DNA-coated particles dissipate strain both elastically through a gradual and coherent relaxation/ broadening of the mismatched lattice parameter and plastically (irreversibly) through the formation of dislocations or vacancies. These data also suggest that the DNA cannot be extended as readily as compressed, and thus the thin films exhibit distinctly different relaxation behavior in the positive and negative lattice mismatch regimes. These observations provide a more general understanding of how utilizing rigid building blocks coated with soft compressible polymeric materials can be used to control nano- and microstructure.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

The Hugoniot and chemistry of ablator plastic below 100 GPa

The equation of state of glow discharge polymer (GDP) was measured to high precision using the two-stage light gas gun at Lawrence Livermore National Laboratory at pressures up to 70 GPa. Both absolute measurements and impedance matching techniques were used to determine the principal and secondary Hugoniots. GDP likely reacts at about 30 GPa, demonstrated by specific emission at 450 nm coupled with changes to the Hugoniot and reshock points. As a result of these reactions, the shock pressure in GDP evolves in time, leading to a possible decrease in pressure as compression increases, or negative compressibility, and causing complex pressure profiles within the plastic. Velocity wave profile variation was observed as a function of position on each shot, suggesting some internal variation of GDP may be present, which would be consistent with previous observations. The complex temporal and possibly structural evolution of GDP under shock compression suggests that calculations of compression and pressure based upon bulk or mean measurements may lead to artificially low pressures and high compressions. Evidence for this includes a large shift in calculating reshock pressures based on the reflected Hugoniot. These changes also suggest other degradation mechanisms for inertial confinement fusion implosions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Development of an ab initio learned model of electron deposition range in deuterium-tritium plasmas through time-dependent density functional theory calculations and machine learning

Accurate hydrodynamic modeling for laser-direct-drive (LDD) inertial-confinement-fusion (ICF) relies on precise calculations of the electron thermal conduction in all target materials. The nonlocal stopping range of electrons in ICF plasmas directly influences thermal conduction; yet, no first principles model exists for the electron mean free path in the conduction-zone regime. This work utilized time-dependent stochastic density-functional theory (TD-sDFT) to calculate the electron stopping power in deuterium-tritium (DT) plasmas at (ρ, T) conditions relevant to the conduction zone and the compressed shell in ICF. Using a combination of our TD-sDFT data and already established analytical models, we developed and trained an artificial neural network to create a global model for the nonlocal electron deposition range, λ E . We compared our machine-learning (ML) based model for λ E to the currently-used modified-Lee-More model in LDD radiation-hydrodynamic codes, such as lilac, and saw an overall decrease in the deposition range. To understand the effects of λ E on LDD ICF implosion dynamics, we implemented the ML-based model into lilac; specifically, we looked at designs consistent with a current experiment on the OMEGA laser and for a newly designed LDD-ICF target for the future OMEGA-Next facility. In both cases, we saw an overall drop in predicted ablation pressure, peak areal density, and neutron yield due to the reduced thermal conduction (smaller λ E ) in DT plasmas. Comparisons with the experiment on OMEGA are also made.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

Molecular-Atomic Transition along the Deuterium Hugoniot Curve with Coupled Electron-Ion Monte Carlo Simulations

We have performed accurate simulations of the Deuterium Hugoniot using Coupled Electron Ion Monte Carlo (CEIMC). Using highly accurate quantum Monte Carlo methods for the electrons, we study the region of maximum compression along the principal Hugoniot, where the system undergoes a continuous transition from a molecular fluid to a monatomic fluid. We include all relevant physical corrections so that a direct comparison to experiment can be made. Around 50 GPa we found a maximum compression of 4.85, roughly 10% larger than previous theoretical predictions and experimental data but still compatible with the latter because of their large uncertainty.

74 ATOMIC AND MOLECULAR PHYSICS↗