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DOE OSTI2025

The impact of capillary heterogeneity on CO 2 flow and trapping across scales

Capillary heterogeneity has been identified over the last decade as a key control on subsurface CO 2 flow behavior during geological CO 2 sequestration. These heterogeneities can be formed in all sedimentary rocks, ranging from slight variations in the sand grain sizes to extensive sequences of interbedded sands, shales, and limestones. Capillary heterogeneity has been largely, although not entirely, overlooked in subsurface flow modeling because it is assumed to only directly influence fluid redistribution over scales of centimeters to meters. However, even small-scale fluid movements can result in dramatic impacts on the mobility and trapping of the CO 2 over kilometers. Therefore, neglecting capillary heterogeneity at multiple scales could potentially lead to errors in modeling and predicting field-scale plume migration. In this review paper, we aim to provide a consistent overview to (1) establish that capillary heterogeneity can have a major impact on CO 2 plume migration, (2) establish the respective length scales at which capillary heterogeneity matters, and (3) provide guidance for numerical modeling. This review covers pertinent literature and extracts key observations from the core to the field scales. Experimental studies have shown that millimeter-decimeter scale capillary heterogeneity can cause the so-called capillary heterogeneity trapping in addition to pore-scale residual trapping. Even at such a small scale, capillary heterogeneity can already lead to complex upscaled constitutive relationships, such as flow-rate dependent and anisotropic relative permeability, which affects field-scale CO 2 migration even when field-scale heterogeneities are present. Under gravity-dominated flow regimes, centimeter-meter scale capillary heterogeneity can entrap a significant amount of CO 2 at field scale, not just after imbibition but also during drainage. In certain cases, the presence of capillary heterogeneity can even completely stop the vertical movement of the CO 2 plume, hence greatly reducing leakage risks. At meter-kilometer scale, the influence of capillary heterogeneity is more pronounced and can hinder or redirect CO 2 migration in both lateral and vertical directions. The impact of capillary heterogeneity across multiple spatial scales poses a great challenge in modeling CO 2 migration at field scale, because it is practically impossible to build a field-scale earth model with grid blocks at millimeter scale. We recommend a hierarchical modeling approach to address this challenge. At field scale, earth models are built to capture geological features and heterogeneities in high but still practical grid resolutions. For each facies or rock type of the field-scale model, high- resolution meter-scale “conceptual” models are built with millimeter-scale grid blocks to capture representative fine-scale bedding geometries and heterogeneities in various environments of deposition, bridging the gap from subcore scale to the size of a field-scale simulation grid block. Upscaling is then used to preserve the smaller-scale flow dynamics of various rock types in field-scale simulations. Here, future work is needed to (1) refine, improve, and validate the hierarchical modeling approach; (2) build libraries of fine-scale bedding models for facies in various environments of deposition; (3) quantify multiscale capillary heterogeneity effects under subsurface uncertainties; (4) gain learning from different storage formations; and (5) establish best practices that balance accuracy and computational speed.

Capillary heterogeneity↗

DOE OSTI2025

High-throughput micro-scale bandgap mapping for perovskite-inspired materials with complex composition space

Abstract To realize the full promise of high-throughput experimental workflows, the rate of sample synthesis must be matched by that of characterization. Of growing interest are contactless optical techniques that can rapidly measure material homogeneity and properties. Here, we present a hyperspectral imaging method to measure local optical bandgap distributions within samples, utilizing spatially-resolved reflectance spectra coupled with automated data analysis. We collect approximately one million optical bandgap data across the compositional space of Cs 3 (Bi x Sb 1-x ) 2 (Br y I 1-y ) 9 perovskite-inspired materials. Our results show non-monotonic bandgap variations (i.e., bandgap bowing) along six composition gradient sequences, in addition to identifying samples with multiple bandgaps in statistics. High-throughput transient absorption spectroscopy reveals that within these compositions, the depletion of the ground state carriers to excited states occurred at discrete energy levels with independent carrier dynamics, consistent with the bandgap observation and indicative of phase separation. This work demonstrates the potential for rapid optical measurements to assess material quality and homogeneity in a high-throughput experimental setting, supporting screening and recipe optimization of optoelectronic material candidates with desired carrier dynamics and optical properties.

Science & Technology - Other Topics↗

DOE OSTI2022

CAPG: comprehensive allopolyploid genotyper

Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls. We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole-genome resequencing data. We demonstrate CAPG in allotetraploids, where it performs better than Genome Analysis Toolkit’s HaplotypeCaller applied to reads aligned to the combined subgenomic references.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Boundary Layer Controls on the Shallow-to-Deep Cumulus Transition (Final Technical Report)

This project advanced our understanding of the processes governing cumulus cloud formation and provides an improved observational basis for validating earth system models. To be specific, the project used laser- and radar-remote sensors to examine the physical properties of updrafts that rise from earth’s surface and initiate clouds deeper in the atmosphere. These updrafts comprise “thermals” and “plumes” and occur at small spatial and temporal scales (e.g., 10s of minutes, 100s of meters). These small scales preclude explicit representation in most earth system and climate models, and thus necessitate “sub-grid-scale” parameterization of updraft processes. The innovation of this project was to directly measure the size, shape, strength and water vapor content of these updrafts with Doppler and Raman lidars, respectively, and to link these updraft properties to cloud processes using vertically pointed weather radars. The resulting data sets comprise 100s of thousands of updrafts and thousands of clouds, which far exceeds previous efforts, and thereby provides a robust statistical and physical representation of these processes. From these large datasets the project produced a sequence of scientific analyses that: (1) Elucidate how variations in the turbulent structure of the convective boundary layer control shallow cumulus convection, (2) Quantify the upward transport of water vapor to cloud base via thermals and plumes, (3) Validate large-eddy simulations of updrafts and shallow convective clouds, (4) Demonstrate a size-to-strength relationship between updraft width and updraft speed, and (5) Demonstrate how updrafts interact with the stability at the top of the convective boundary layer to modulate the depth and vigor of convective clouds. These results have been disseminated via several published journal articles, academic theses, and conference presentations. Collectively these results contribute to the Atmospheric System Research (ASR) program’s goal to “improve understanding of the key cloud, aerosol, precipitation, and radiation processes that affect the Earth’s radiative balance and hydrological cycle, particularly processes that limit the predictive ability of regional and global earth system models”.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

6051R & 6051S Assembly and Annotation

We report the draft genomes of two morphologically distinct variants of Bacillus subtilis ATCC 6051 [NCBI3610]. The two isolates exhibit differences in not only morphology but also their genetics, despite identical 16S rRNA sequences. Investigating the genetic differences of colony morphology variation in this model organism can provide valuable insights.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Calculation procedure for transient heat transfer to a cooled plate in a heated stream whose temperature varies arbitrarily with time

Solutions for the surface temperature and surface heat flux are found for laminar, constant property, slug flow over a plate convectively cooled from below, when the temperature of the fluid over the plate varies arbitrarily with time at the plate leading edge. A simple technique is presented for handling arbitrary fluid temperature variation with time by approximating it by a sequence of ramps or steps for which exact analytical solutions are available.

Sucec, J.↗

NASA NTRS1976

Symmetries in laminated composite plates

The different types of symmetry exhibited by laminated anisotropic fibrous composite plates are identified and contrasted with the symmetries of isotropic and homogeneous orthotropic plates. The effects of variations in the fiber orientation and the stacking sequence of the layers on the symmetries exhibited by composite plates are discussed. Both the linear and geometrically nonlinear responses of the plates are considered. A simple procedure is presented for exploiting the symmetries in the finite element analysis. Examples are given of square, skew and polygonal plates where use of symmetry concepts can significantly reduce the scope and cost of analysis.

Noor, A. K.↗

NASA NTRS1982

On the variability of LSI+61 deg 303 (identical with GT 0236)

Out of six long and six short wavelength observations, one spectrum exhibits a significant photometric variation: or approximately 20%. Interpreting the continuum as due to superposition of an early B main sequence star plus a gaseous component contributing at lambda 2000 A, the wavelength dependence of the variation suggests that it derives from the latter component. The data indicate that if the observed variation is phase dependent, a minimum should occur between phases 0.8 and 0.2. However, since the variation is observed in only one spectrum, it may well be erratic.

Tanzi, E. G.↗

NASA NTRS1991

Event-scale relationships between surface velocity, temperature and chlorophyll in the coastal ocean, as seen by satellite

The overall goal of this project was to increase our understanding of processes which determine the temporally varying distributions of surface chlorophyll pigment concentration and surface temperature in the California Current System (CCS) on the time-scale of 'events', i.e., several days to several weeks. We also proposed to investigate seasonal and regional differences in these events. Additionally, we proposed to evaluate methods of estimating surface velocities and horizontal transport of pigment and heat from sequences of AVHRR and CZCS images. The four specific objectives stated in the original proposal were to: (1) test surface current estimates made from sequences of both SST and color images using variations of the statistical method of Emery et al. (1986) and estimate the uncertainties in these satellite-derived surface currents; (2) characterize the spatial and temporal relationships of chlorophyll and temperature in rapidly evolving features for which adequate imagery exist and evaluate the contribution of these events to monthly and seasonal averages; (3) use the methods tested in (1) to determine the nature of the velocity fields in the CCS; and (4) compare the currents, temperature, and currents in different seasons and in different geographic regions.

Strub, P. Ted↗

NASA NTRS2002

Solar Supergranulation Revealed as a Superposition of Traveling Waves

40 years ago two new solar phenomena were described: supergranulation and the five-minute solar oscillations. While the oscillations have since been explained and exploited to determine the properties of the solar interior, the supergranulation has remained unexplained. The supergranules, appearing as convective-like cellular patterns of horizontal outward flow with a characteristic diameter of 30 Mm and an apparent lifetime of 1 day, have puzzling properties, including their apparent superrotation and the minute temperature variations over the cells. Using a 60-day sequence of data from the MDI (Michelson-Doppler Imager) instrument onboard the SOHO (Solar and Heliospheric Observatory) spacecraft, we show that the supergranulation pattern is formed by a superposition of traveling waves with periods of 5-10 days. The wave power is anisotropic with excess power in the direction of rotation and toward the equator, leading to spurious rotation rates and north-south flows as derived from correlation analyses. These newly discovered waves could play an important role in maintaining differential rotation in the upper convection zone by transporting angular momentum towards the equator.

Gizon, L.↗

NASA NTRS2004

Central Stars of Planetary Nebulae in the LMC

In FUSE cycle 2's program B001 we studied Central Stars of Planetary Nebulae (CSPN) in the Large Magellanic Could. All FUSE observations have been successfully completed and have been reduced, analyzed and published. The analysis and the results are summarized below. The FUSE data were reduced using the latest available version of the FUSE calibration pipeline (CALFUSE v2.2.2). The flux of these LMC post-AGB objects is at the threshold of FUSE's sensitivity, and thus special care in the background subtraction was needed during the reduction. Because of their faintness, the targets required many orbit-long exposures, each of which typically had low (target) count-rates. Each calibrated extracted sequence was checked for unacceptable count-rate variations (a sign of detector drift), misplaced extraction windows, and other anomalies. All the good calibrated exposures were combined using FUSE pipeline routines. The default FUSE pipeline attempts to model the background measured off-target and subtracts it from the target spectrum. We found that, for these faint objects, the background appeared to be over-estimated by this method, particularly at shorter wavelengths (i.e., < 1000 A). We therefore tried two other reductions. In the first method, subtraction of the measured background is turned off and and the background is taken to be the model scattered-light scaled by the exposure time. In the second one, the first few steps of the pipeline were run on the individual exposures (correcting for effects unique to each exposure such as Doppler shift, grating motions, etc). Then the photon lists from the individual exposures were combined, and the remaining steps of the pipeline run on the combined file. Thus, more total counts for both the target and background allowed for a better extraction.

Bianchi, Luciana↗

NASA NTRS2010

Optimizing a Laser Process for Making Carbon Nanotubes

A systematic experimental study has been performed to determine the effects of each of the operating conditions in a double-pulse laser ablation process that is used to produce single-wall carbon nanotubes (SWCNTs). The comprehensive data compiled in this study have been analyzed to recommend conditions for optimizing the process and scaling up the process for mass production. The double-pulse laser ablation process for making SWCNTs was developed by Rice University researchers. Of all currently known nanotube-synthesizing processes (arc and chemical vapor deposition), this process yields the greatest proportion of SWCNTs in the product material. The aforementioned process conditions are important for optimizing the production of SWCNTs and scaling up production. Reports of previous research (mostly at Rice University) toward optimization of process conditions mention effects of oven temperature and briefly mention effects of flow conditions, but no systematic, comprehensive study of the effects of process conditions was done prior to the study described here. This was a parametric study, in which several production runs were carried out, changing one operating condition for each run. The study involved variation of a total of nine parameters: the sequence of the laser pulses, pulse-separation time, laser pulse energy density, buffer gas (helium or nitrogen instead of argon), oven temperature, pressure, flow speed, inner diameter of the flow tube, and flow-tube material.

Arepalli, Sivaram↗

NASA NTRS1995

Minimizing structural vibrations with Input Shaping (TM)

A new method for commanding machines to move with increased dynamic performance was developed. This method is an enhanced version of input shaping, a patented vibration suppression algorithm. This technique intercepts a command input to a system command that moves the mechanical system with increased performance and reduced residual vibration. This document describes many advanced methods for generating highly optimized shaping sequences which are tuned to particular systems. The shaping sequence is important because it determines the trade off between move/settle time of the system and the insensitivity of the input shaping algorithm to variations or uncertainties in the machine which can be controlled. For example, a system with a 5 Hz resonance that takes 1 second to settle can be improved to settle instantaneously using a 0.2 shaping sequence (thus improving settle time by a factor of 5). This system could vary by plus or minus 15% in its natural frequency and still have no apparent vibration. However, the same system shaped with a 0.3 second shaping sequence could tolerate plus or minus 40% or more variation in natural frequency. This document describes how to generate sequences that maximize performance, sequences that maximize insensitivity, and sequences that trade off between the two. Several software tools are documented and included.

Singhose, Bill↗

DOE OSTI2018

Using a meshless kernel-based method to solve the Black–Scholes variational inequality of American options

Under the Black–Scholes model, the value of an American option solves a free boundary problem which is equivalent to a variational inequality problem. Using positive definite kernels, we discretize the variational inequality problem in spatial direction and derive a sequence of linear complementarity problems (LCPs) in a finite-dimensional euclidean space. We use special kind of kernels to impose homogeneous boundary conditions and to obtain LCPs with positive definite coefficient matrices to guarantee the existence and uniqueness of the solution. The LCPs are then successfully solved iteratively by the projected SOR algorithm.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Exploring thermal equilibria of the Fermi-Hubbard model with variational quantum algorithms

Here, this study investigates the thermal properties of the repulsive Fermi-Hubbard model with chemical potential using variational quantum algorithms, crucial in comprehending particle behaviour within lattices at heightened temperatures in condensed matter systems. Conventional computational methods encounter challenges, especially in managing chemical potential, prompting exploration into Hamiltonian approaches. Despite the promise of quantum algorithms, their efficacy is hampered by coherence limitations when simulating extended imaginary time evolution sequences. To overcome these constraints, this research focuses on optimizing variational quantum algorithms to probe the thermal properties of the Fermi-Hubbard model. Physics-inspired circuit designs are tailored to alleviate coherence constraints, facilitating a more comprehensive exploration of materials at elevated temperatures. Our study demonstrates the potential of variational algorithms in simulating the thermal properties of the Fermi-Hubbard model while acknowledging limitations stemming from error sources in quantum devices and encountering barren plateaus.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. Moreover, we discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Multi-rate OCDMA system BER performance evaluations for different ML-code sequences

This paper analyzes Bit Error Rate (BER) of Optical Code Division Multiple Access (OCDMA) networks for different class of services which are data, voice, and video; whereas Multi-Length Weighted Modified Prime Code (ML-WMPC) sequences are utilized as a spreading code in with respect to previously used ML-Optical Orthogonal codes. Due to variations in bit rates between the mentioned services, each of them assigns a different WMPC sequence length. In addition, the shot noise, thermal noise, and the Multiple Access Interference (MAI) are included and considered as sources of noise in the BER performance analysis. Furthermore, Pulse Position Modulation, Manchester encoding and MAI cancellation (MAIC) technique are utilized to improve the network performance at a higher number of active users. For analysis, the BER performance calculations are investigated for three types of OCDMA receivers such as simple receiver, receiver with MAIC technique, and receiver with MAIC and Manchester encoding. Moreover, the BER mathematical models have been introduced for different bit rates according to the type of service in the presence of the ML-WMPC and the last of three mentioned OCDMA receivers. Finally, these models and their results are compared with the other existing models, where the results show an improvement in BER performance in the proposed approach.

42 ENGINEERING↗