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DOE OSTI2021

Reconstruction of the Room D, B, G, and Q Closure Histories at the Waste Isolation Pilot Plant

Experimental measurements of room closure in salt repositories are valuable for understanding the evolution of the underground and for validating geomechanical models. Room closure was measured during a number of experiments at the Waste Isolation Pilot Plant (WIPP) during the 1980's and 1990's. Most rooms were excavated using a multi-pass mining sequence, where each pass necessarily destroyed some of the mining sequence closure measurement points. These destroyed points were promptly reinstalled to capture the closure after the mining pass. After the room was complete, the mining sequence closure measurement stations were supplemented with remotely read closure measurement stations. Although many aspects of these experiments were thoroughly documented, the digital copies of the closure data were inadvertently destroyed, the non-trivial process of zeroing and shifting the raw closure measurements after each mining pass was not precisely described, the various closure measurements within a given room were not directly compared on the same plot, and the measurements were collected for several years longer than previously reported. Consequently, the hand-written mining sequence closure measurements for Rooms D, B, G, and Q were located in the WIPP archives, digitized, and reanalyzed for this report. The process of reconstructing the mining sequence closure histories was documented in detail and the raw data can be found in the appendices. Within the mid-section of a given room, the reconstructed closure histories were largely consistent with other mining sequence and remotely read closure histories, which builds confidence in the experiments and suggests that plane strain is an appropriate modeling assumption. The reconstructed closure histories were also reasonably consistent with previously published results, except in one notable case: the reconstructed Room Q closure histories 30 days after excavation were about 45 % less than the corresponding closures reported in Munson's 1997 capstone paper.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2018

Experimental and FEM Study of Residual Stresses During Ultra-Precision Turning of Aluminum 2024-T3

Aluminum 2024-T3 is commonly used in ultra-precision turning. In this study, the residual stresses of aluminum 2024-T3 were investigated by the finite element method (FEM) and a series of cutting experiments. The effects of depth of cut, cutting speed, rake angle and tool edge radius on the residual stresses were discussed by FEM. Moreover, an orthogonal simulation experiment was also conducted. The order of the strong-to-weak sequence of factors on residual stresses in cutting direction is the rake angle, tool edge radius, depth of cut and cutting speed. The cutting experiments were conducted and the surface residual stresses in the cutting direction were measured by X-ray diffraction. The experimental results showed that increasing cutting speed and decreasing tool edge radius can reduce the surface residual stresses.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Relative Hausdorff distance for network analysis

Similarity measures are used extensively in machine learning and data science algorithms. The newly proposed graph Relative Hausdorff (RH) distance is a lightweight yet nuanced similarity measure for quantifying the closeness of two graphs. In this work we study the effectiveness of RH distance as a tool for detecting anomalies in time-evolving graph sequences. We apply RH to cyber data with given red team events, as well to synthetically generated sequences of graphs with planted attacks. In our experiments, the performance of RH distance is at times comparable, and sometimes superior, to graph edit distance in detecting anomalous phenomena. Furthermore, our results suggest that in appropriate contexts, RH distance has advantages over more computationally intensive similarity measures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Quantum eigenvalue estimation via time series analysis

We present an efficient method for estimating the eigenvalues of a Hamiltonian H from the expectation values of the evolution operator for various times. For a given quantum state ρ, our method outputs a list of eigenvalue estimates and approximate probabilities. Each probability depends on the support of ρ in those eigenstates of H associated with eigenvalues within an arbitrarily small range. The complexity of our method is polynomial in the inverse of a given precision parameter ε, which is the gap between eigenvalue estimates. Unlike the well-known quantum phase estimation algorithm that uses the quantum Fourier transform, our method does not require large ancillary systems, large sequences of controlled operations, or preserving coherence between experiments, and is therefore more attractive for near-term applications. The output of our method can be used to estimate spectral properties of H and other expectation values efficiently, within additive error proportional to ε.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

germs-lab/LAMPS-miscanthus-microbiome

Data and analysis to accompany our submitted paper characterizing the LAMPS Miscanthus Microbiome comparing 16S rRNA gene DNA sequencing of Miscanthus in a staggered-start experiment. Authors for this analysis include Fernando Igne Rocha, Lanying Ma, and Adina Howe.

Igne Rocha, Fernando↗

DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Validating Mixtures of 233 U, 235 U, and 239 Pu for the Sum-of-Fractions Method

The Sum-of-Fractions method is a technique used to assure that homogeneous mixtures of fissile and fissionable isotopes are below a minimum margin of k eff or reactivity. Current work by Pacific Northwest National Laboratory examines different mixtures of 233 U, 235 U, and 239 Pu to determine critical mass limits for mixtures of transuranic actinides lacking a validation basis. To provide a validation basis for these limits, the work presented here describes the results of a sensitivity and uncertainty analysis of various mixtures of these isotopes in various concentrations moderated and reflected by light water and polyethylene. The TSUNAMI-1D sequence in the SCALE code system was used to generate sensitivity coefficients for three different concentrations of mixtures of 233 U, 235 U, and 239 Pu. The TSUNAMI-IP sequence was then used for similarity assessment (c k ) with critical benchmark experiment sensitivity data files (SDFs) from the Oak Ridge National Laboratory Verified, Archived Library of Inputs and Data and the Nuclear Energy Agency SDF database. The VADER sequence in SCALE was used for statistical testing and to generate upper subcritical limits from the data to develop a basis for validating critical mass limits.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2024

Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition

Contact-dependent growth inhibition (CDI) is a widespread form of inter-bacterial competition mediated by CdiA effector proteins. CdiA is presented on the inhibitor cell surface and delivers its toxic C-terminal region (CdiA-CT) into neighboring bacteria upon contact. Inhibitor cells also produce CdiI immunity proteins, which neutralize CdiA-CT toxins to prevent auto-inhibition. Here, we describe a diverse group of CDI ionophore toxins that dissipate the transmembrane potential in target bacteria. These CdiA-CT toxins are composed of two distinct domains based on AlphaFold2 modeling. The C-terminal ionophore domains are all predicted to form five-helix bundles capable of spanning the cell membrane. The N-terminal "entry" domains are variable in structure and appear to hijack different integral membrane proteins to promote toxin assembly into the lipid bilayer. The CDI ionophores deployed by E. coli isolates partition into six major groups based on their entry domain structures. Comparative sequence analyses led to the identification of receptor proteins for ionophore toxins from groups 1 & 3 (AcrB), group 2 (SecY) and groups 4 (YciB). Using forward genetic approaches, we identify novel receptors for the group 5 and 6 ionophores. Group 5 exploits homologous putrescine import proteins encoded by puuP and plaP, and group 6 toxins recognize di/tripeptide transporters encoded by paralogous dtpA and dtpB genes. Finally, we find that the ionophore domains exhibit significant intra-group sequence variation, particularly at positions that are predicted to interact with CdiI. Accordingly, the corresponding immunity proteins are also highly polymorphic, typically sharing only ~30% sequence identity with members of the same group. Competition experiments confirm that the immunity proteins are specific for their cognate ionophores and provide no protection against other toxins from the same group. The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Processed Lab Data for Neural Network-Based Shear Stress Level Prediction

Machine learning can be used to predict fault properties such as shear stress, friction, and time to failure using continuous records of fault zone acoustic emissions. The files are extracted features and labels from lab data (experiment p4679). The features are extracted with a non-overlapping window from the original acoustic data. The first column is the time of the window. The second and third columns are the mean and the variance of the acoustic data in this window, respectively. The 4th-11th column is the the power spectrum density ranging from low to high frequency. And the last column is the corresponding label (shear stress level). The name of the file means which driving velocity the sequence is generated from. Data were generated from laboratory friction experiments conducted with a biaxial shear apparatus. Experiments were conducted in the double direct shear configuration in which two fault zones are sheared between three rigid forcing blocks. Our samples consisted of two 5-mm-thick layers of simulated fault gouge with a nominal contact area of 10 by 10 cm^2. Gouge material consisted of soda-lime glass beads with initial particle size between 105 and 149 micrometers. Prior to shearing, we impose a constant fault normal stress of 2 MPa using a servo-controlled load-feedback mechanism and allow the sample to compact. Once the sample has reached a constant layer thickness, the central block is driven down at constant rate of 10 micrometers per second. In tandem, we collect an AE signal continuously at 4 MHz from a piezoceramic sensor embedded in a steel forcing block about 22 mm from the gouge layer The data from this experiment can be used with the deep learning algorithm to train it for future fault property prediction.

15 GEOTHERMAL ENERGY↗

DOE OSTI2025

Divergent viral phosphodiesterases for immune signaling evasion

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase (PDE)-mediated oligonucleotide cleavage for immune evasion, a strategy whose diversity has not yet been explored. Here, we use a canonical 2H PDE (2H PDE) structure-based search of prokaryotic and eukaryotic viral sequences to identify an exceptional diversity of 2H PDEs across the virome, including enzymes not detectable with sequence search methods alone. Despite active site conservation, biochemical experiments reveal remarkable substrate specificity of these PDEs that corresponds to variations in the core 2H fold. This nuanced specificity allows 2H PDEs to selectively degrade oligonucleotide messengers to avoid interfering with host nucleotide signaling. Together, these findings nominate viral 2H PDEs as key regulators of CDN signaling across the tree of life.

CBASS↗

DOE OSTI2025

Inorganic Alterations in Unconventional Shale Reservoirs: Importance of Additive and Base Fluid Chemistry

The effective development of unconventional petroleum systems requires the use of significant water resources. In an effort to reduce the consumption of freshwater resources for hydraulic fracturing, highly saline produced waters are increasingly recycled for use as a base fluid. However, there are significant knowledge gaps regarding potential water–rock interactions resulting from the introduction of produced waters and associated additives into shale reservoirs such as formation and deposition of mineral scale, which can negatively affect hydrocarbon production through wellbore restriction and damage to hydraulically generated fractures. To assess the impacts of field stimulation practices in the subsurface, a series of laboratory experiments were completed using (a) three distinct sedimentary rock formations of the Midland Basin (Texas, USA) and (b) additives with two different base fluids: municipal fresh water and clean brine. The experimental approach used relevant injection sequences and mixing ratios in specialized reactors for 3 weeks. Static pressurized experiments and nonpressurized time-resolved experiments were undertaken. The resulting solids and liquids were analyzed by using a variety of laboratory- and synchrotron-based techniques. The use of an acid spearhead (15% HCl) resulted in texturing of both clay-rich and calcareous shales, which can temporarily enhance porosity but subsequently result in mineral scale deposition. The primary matrix scale was Fe(III)-bearing phases, which occurred in all experiments regardless of base fluid chemistry. Additionally, strontium sulfate (SrSO 4 ) precipitated on shale surfaces when clean brines were used. It was concluded that clean brine was the main source of Sr 2+ species, while persulfate breaker degradation and oxidation of pyrite were the sources of SO 4 2– . Sulfate scaling was more pronounced in clay-rich shales, suggesting that Sr sorption is important for promoting celestite formation. This work demonstrates that mineral scale deposition is a complex phenomenon, whereby the type and proportions of various mineral phases are determined from reservoir alteration processes and coprecipitation of constituents from injection fluids. In conclusion, the experimental results shown here should be considered when evaluating different base fluids and additives in order to mitigate mineral precipitation in unconventional shale reservoirs, which could result in reservoir degradation.

Jew, Adam D. [SLAC National Accelerator Laboratory↗

DOE OSTI2018

Unconventional and conventional quantum criticalities in CeRh 0.58 Ir 0.42 In 5

An appropriate description of the state of matter that appears as a second order phase transition is tuned toward zero temperature, viz. quantum-critical point (QCP), poses fundamental and still not fully answered questions. Experiments are needed both to test basic conclusions and to guide further refinement of theoretical models. Here, charge and entropy transport properties as well as AC specific heat of the heavy-fermion compound CeRh 0.58 Ir 0.42 In 5 , measured as a function of pressure, reveal two qualitatively different QCPs in a single material driven by a single non-symmetry-breaking tuning parameter. A discontinuous sign-change jump in thermopower suggests an unconventional QCP at p c1 accompanied by an abrupt Fermi-surface reconstruction that is followed by a conventional spin-density-wave critical point at p c2 across which the Fermi surface evolves smoothly to a heavy Fermi-liquid state. These experiments are consistent with some theoretical predictions, including the sequence of critical points and the temperature dependence of the thermopower in their vicinity.

36 MATERIALS SCIENCE↗

DOE OSTI2018

GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii

DeoR-type helix-turn-helix (HTH) domain proteins are transcriptional regulators of sugar and nucleoside metabolism in diverse bacteria and also occur in select archaea. In the model archaeon Haloferax volcanii , previous work implicated GlpR, a DeoR-type transcriptional regulator, in the transcriptional repression of glpR and the gene encoding the fructose-specific phosphofructokinase ( pfkB ) during growth on glycerol. However, the global regulon governed by GlpR remained unclear. Here, we compared transcriptomes of wild-type and ΔglpR mutant strains grown on glycerol and glucose to detect significant transcript level differences for nearly 50 new genes regulated by GlpR. By coupling computational prediction of GlpR binding sequences with in vivo and in vitro DNA binding experiments, we determined that GlpR directly controls genes encoding enzymes involved in fructose degradation, including fructose bisphosphate aldolase, a central control point in glycolysis. GlpR also directly controls other transcription factors. In contrast, other metabolic pathways appear to be under the indirect influence of GlpR. In vitro experiments demonstrated that GlpR purifies to function as a tetramer that binds the effector molecule fructose-1-phosphate (F1P). Furthermore, these results suggest that H. volcanii GlpR functions as a direct negative regulator of fructose degradation during growth on carbon sources other than fructose, such as glucose and glycerol, and that GlpR bears striking functional similarity to bacterial DeoR-type regulators.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome (Final Report for DE-SC0014395)

The specific project objectives were to: 1) Conduct deep census surveys of root microbiomes concurrent with phenotypic characterizations of a diverse panel of sorghum genotypes across multiple years to define the microbes associated with the most productive lines under drought and low nitrogen conditions. 2) Associate systems-level genotypic, microbial, and environmental factors with improved sorghum performance using robust statistical approaches. 3) Develop culture collections of sorghum root/leaf associated microbes that recapitulate root-enriched sequences defined in the census. 4) Perform controlled environment experiments for in-depth characterization and hypothesis testing of G sorghum x G microbe x E interactions . Validate physiological mechanisms, map genetic loci for stress tolerance, and determine the persistence of optimal microbial strains under greenhouse and field conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Universal Jaynes-Cummings Control of an Oscillator

The Jaynes-Cummings (JC) interaction-the coherent exchange of excitations between a two-level system and a harmonic oscillator-is one of the fundamental interactions of quantum optics, realized across platforms such as cavity quantum electrodynamics, trapped ions, mechanical resonators, and superconducting circuits. Although JC interactions and qubit rotations form a universal gate set for oscillator control, practical implementations have not been demonstrated. Here we develop and experimentally demonstrate universal JC-based oscillator control by compiling arbitrary unitary gates into sequences of JC interactions and qubit rotations. In our experiment, the oscillator is realized using a mode of a high quality factor microwave cavity and the ancilla qubit using a superconducting transmon circuit, with the JC interaction implemented by a sideband interaction enabled by the Josephson nonlinearity. The native gates are constructed to be closed below a chosen cutoff photon number, encoding a qudit with suppressed leakage errors, while ancilla relaxation errors are detectable. We further find that the dispersive shift serves as a compilation resource that reduces circuit depths. We demonstrate universal qudit control and implement a single-qutrit gate set with a mean post-selected process fidelity of 96%, as well as ququart and ququint shift gates. These results establish Jaynes-Cummings control as a practical route to universal oscillator control, enabling programmable bosonic processors across a variety of quantum platforms.

Huang, Jordan [Rutgers U., Piscataway]↗

DOE OSTI2024

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Folding and Assembly of Short α, β, γ -Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures

Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible, and peptides 2a and 2b adopt a noncanonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. As a result, the revealed systems offer ample opportunity for further structural optimization and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗