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DOE OSTI2025

Randomized Adiabatic Quantum Linear Solver Algorithm with Optimal Complexity Scaling and Detailed Running Costs

Solving linear systems of equations is a fundamental problem with a wide variety of applications across many fields of science, and there is increasing effort to develop quantum linear solver algorithms. Subaşı et al. [Phys. Rev. Lett. 122, 060504 (2019)] proposed a randomized algorithm inspired by adiabatic quantum computing, based on a sequence of random Hamiltonian simulation steps, with suboptimal scaling in the condition number 𝜅 of the linear system and the target error 𝜖. Here we go beyond these results in several ways. Firstly, using filtering [Lin and Tong, Quantum 4, 361 (2020)] and Poissonization techniques [Cunningham and Roland, ArXiv:2406.03972 (2024)], the algorithm complexity is improved to the optimal scaling 𝑂⁡(𝜅⁢log (1/𝜖))—an exponential improvement in 𝜖, and a shaving of a log 𝜅 scaling factor in 𝜅. Secondly, the algorithm is further modified to achieve constant factor improvements, which are vital as we progress towards hardware implementations on fault-tolerant devices. We introduce a cheaper randomized walk operator method replacing Hamiltonian simulation—which also removes the need for potentially challenging classical precomputations; randomized routines are sampled over optimized random variables; circuit constructions are improved. We obtain a closed formula rigorously upper bounding the expected number of times one needs to apply a block-encoding of the linear system matrix to output a quantum state encoding the solution to the linear system. The upper bound is 837⁢𝜅 at 𝜖 = 10 −10 for Hermitian matrices.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Development of a kinetic-thermodynamic model for lime-stabilization of Na-bentonite

This study presents the first kinetic model to predict the solid and pore solution composition of Na-bentonite clay reacting with slaked lime over a period of 720 days. The model successfully accounts for most experimental data using a single kinetic rate constant. The following sequence of reactions was predicted by the model: initial rapid dissolution of portlandite within the first 7 days, leading to a decrease in pH and dissolved calcium, and concurrent formation of calcium silicate hydrates (C-S-H: jennite), calcium aluminate hydrate (C-A-H: C₄AH₁₃), calcium aluminosilicate hydrates (stratlingite) and hydrotalcite. After 7 days, jennite and stratlingite are predicted to transform into tobermorite-II, contributing to strength development up to 28 days. From 28 to 90 days, continued montmorillonite dissolution is predicted, along with minor formation of ettringite, partial tobermorite-II dissolution, and precipitation of secondary phases such as albite and talc. Experimentally, portlandite dissolution was confirmed by TGA and XRD and found to be complete within 7 days, in agreement with model predictions. However, other predicted solid-phase transformations (e.g., tobermorite-II formation and dissolution, ettringite, albite, and talc formation) could not be conclusively verified through experimental techniques. Aqueous phase measurements confirmed that the pH and Ca trends in solution, and that equilibrium was reached by 90 days.

Chemical kinetics↗

DOE OSTI2026

Surface Reordering During Layer‐by‐Layer Growth on SrTiO 3

With the development of layer‐by‐layer growth techniques such as molecular beam epitaxy (MBE), it is now possible to construct materials with atomic‐level precision, with the layer sequence primarily determined by the growth recipe. However, materials can still restructure in the high‐temperature growth environment with surface thermodynamics strongly influencing growth behavior. Here, we demonstrate that growth on ${\rm SrTiO}_{3}$ (001), the principal platform for oxide electronics, does not occur in a layer‐by‐layer fashion but follows a more complex process in which a ${\rm TiO}_{2}$ plane continually diffuses toward the growth surface. Employing in situ synchrotron X‐ray scattering combined with ab initio thermodynamic calculations, we discover the existence of a stable ${\rm TiO}_{2}$ double‐layer structure on the pristine substrate and the occurrence of dynamic layer rearrangement during homoepitaxial growth by oxide MBE. Our findings suggest that the current methods used to precisely control ${\rm SrTiO}_{3}$ surfaces are limited, as well as our ability to dictate the composition of ultrathin films, resulting in important ramifications regarding the surface reactivity of perovskite materials grown on ${\rm SrTiO}_{3}$.

Coherent Bragg Rod Analysis↗

DOE OSTI1994

Nuclear Safety [Vol. 35, No. 2, July-December 1994]

Nuclear Safety is a journal that covers significant issues in the field of nuclear safety. Its primary scope is safety in the design, construction, operation, and decommissioning of nuclear power reactors worldwide and the research and analysis activities that promote this goal, but it also encompasses the safety aspects of the entire nuclear fuel cycle, including fuel fabrication, spent-fuel processing and handling, and nuclear waste disposal, the handling of fissionable materials and radioisotopes, and the environmental effects of all these activities. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 179 Consideration of Postaccident Consequences in the Determination of Safety Objectives for Future Nuclear Power Plants in France, D. Queniart, A. Sugier, and J. Lochard; ACCIDENT ANALYSIS: 187 Nuclear Safety Research: The Phebus FP Severe Accident Experimental Program, P. von der Hardt, A. V. Jones, C. Lecomte, and A. Tattegrain; 205 Containment Performance Analysis of the Advanced Neutron Source Reactor at the Oak Ridge National Laboratory, S. H. Kim, R. P. Taleyarkhan, and V. Georgevich; 213 Assessment of Fission Product Deposits in the Reactor Coolant System: The DEVAP Program, G. Le Marois and M. Megnin; 222 Erratum to “A Review of the Available Information on the Triggering Stage of a Steam Explosion," Vol. 35, No. 1, CONTROL AND INSTRUMENTATION: 223 Effects of Normal Aging on Calibration and Response Time of Nuclear Plant Resistance Temperature Detectors and Pressure Sensors, H. M. Hashemian; DESIGN FEATURES: 235 Defense in Depth Against the Hydrogen Risk—A European Research Program, F. Fineschi; ENVIRONMENTAL EFFECTS: 246 Technical Note: A Preliminary Analysis of the Risks to Hong Kong Resulting from Potential Accidents of Daya Bay Nuclear Power Plant, Z. Shi and X. Wei; OPERATING EXPERIENCES: 253 Reactor Shutdown Experience, Compiled by J. W. Cletcher; SPECIAL SECTION ON TMI-2 VESSEL INVESTIGATION PROJECT: 256 Three Mile Island—New Findings 15 Years After the Accident A. M. Rubin and E. Beckjord; 269 Relocation of Molten Material to the TMI-2 Lower Head, J. R. Wolf, D. W. Akers, and L. A. Neimark; 280 Insight Into the TMI-2 Core Material Relocation Through Examination of Instrument Tube Nozzles, L. A. Neimark; 288 Physical and Radiochemical Examinations of Debris from the TMI-2 Lower Head, D. W. Akers and B. K. Schuetz; 301 Results of Metallographic Examinations and Mechanical Tests of Pressure Vessel Samples from the TMI-2 Lower Head, D. R. Diercks and G. E. Korth; 313 Margin-to-Failure Calculations for the TMI-2 Vessel, J. Rempe, L. Stickler, S. Chavez, G. Thinnes, R. Witt, and M. Corradini; U.S. NUCLEAR REGULATORY COMMISSION INFORMATION AND ANALYSES: 328 1993 Accident Sequence Precursor (ASP) Program Results, L. N. Vanden Heuvel, J. W. Cletcher, D. A. Copinger, J. W. Minarick, B. W. Dolan, and P. D. O’Reilley; RECENT DEVELOPMENTS: 339 Reports, Standards, and Safety Guides, D. S. Queener; 345 Proposed Rule Changes as of June 30, 1994; ANNOUNCEMENTS: 234 Thirty-First Annual Meeting of the National Council on Radiation Protection and Measurements; 356 1995 International Incineration Conference; 358 Fifth International Controls and Instrumentation Conference; 359 ANS International Topical Meeting on Safety of Operating Reactors; 359 Fifth International Conference on Nuclear Criticality Safety; 360 International Conference on Probabilistic Safety Assessment Methodology and Applications; 351 The Authors; 357 Reviewers of Nuclear Safety, Vol. 35.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

The role of soil chemical properties and microbial communities on Dendrocalamus brandisii bamboo shoot quality, Yunnan Province, China

Objective To explore the effects of soil nutrients and microbial communities on the quality of Dendrocalamus brandisii shoots in different regions, providing a scientific basis for their development and utilization. Methods Using seven different geographic sources of D. brandisii from Yunnan Province as research subjects, this study employs chemical analysis and high-throughput sequencing to reveal the relationship between soil nutrients, microbial functional groups, and the nutritional quality of bamboo shoots. Results The results indicate that there are significant differences in soil nutrient content among the regions ( p < 0.05), with bamboo shoots from Baoshan Changning (CN) exhibiting the best overall nutritional quality. The key factors influencing bacterial community changes include pH, available phosphorus (AP), and available potassium (AK). In contrast, the main factors affecting fungal community changes are pH, soil organic matter (SOM), available potassium (AK), and total nitrogen (TN). This version maintains clarity and logical flow, making it easier for readers to understand the different factors influencing bacterial and fungal community changes. The diversity indices of soil microbial communities among different sources of Dendrocalamus brandisii show significant differences ( p < 0.05). The dominant groups in the seven regions include Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Ascomycota, and Basidiomycota. The soil microbial community in Baoshan Changning (CN) shows significant structural differences compared to the other six regions, with the highest relative abundances of Chloroflexi and Acidobacteriota. In contrast, the highest relative abundance of Proteobacteria is found in Honghe Shiping (SP), while Actinobacteriota has the highest relative abundance in Yuxi Xinping (XP). RDA analysis indicates that soil nutrients (SOM, pH, AP, TN) affect the water content, soluble sugar, and crude fat of bamboo shoots. Additionally, the bacterial communities including Actinobacteriota, Chloroflexi, Patescibacteria, GAL15, and Cyanobacteria influence the water content, soluble sugar, ash content, protein, and lignin of bamboo shoots. Discussion In the fungal community, Basidiomycota, Kickxellomycota, Mucoromycota, unclassified-k-Fungi, and Glomeromycota affect the water content and tannin levels in bamboo shoots. In summary, soil nutrients and soil microorganisms are interconnected and work together to influence the quality of bamboo shoots.

Chen, Qian↗

DOE OSTI2025

Catalytic Difunctionalization of Cyclic Dienes: Direct Entry to Novel ROMP Monomers

We developed a catalytic platform to convert simple hydrocarbon feedstocks into valuable, tunable materials by leveraging nickel-catalyzed difunctionalization of cyclic dienes to access a novel class of cyclic alkene monomers. These monomers undergo ring-opening metathesis polymerization (ROMP) to yield sequence-controlled polymers with defined stereochemistry. Through mechanistic studies and catalyst optimization, we established a scalable, gram-level synthesis for selective diarylation, and expanded the reaction scope to include arylalkylation through rationally tuning the organoboron coupling partner. The resulting polymers were systematically studied to understand how steric, electronic, and stereochemical features influence polymerization behavior and bulk material properties. Functionalized derivatives bearing sulfonated groups were explored as proton-exchange membranes, and chemical recycling pathways were developed to recover monomers from the final materials. This work bridges small-molecule catalysis and macromolecular design, enabling access to tunable, recyclable polymers from abundant hydrocarbon starting materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗

DOE OSTI2025

ARCADE Analysis Methods & Validation Pathway

The Advanced Reactor Cyber Analysis and Development Environment (ARCADE) provides an automated analysis system which supports risk-informed performance based (RIPB) evaluations of nuclear control systems. Every possible cyber threat which could lead to consequence is identified by simulating the unsafe control action sequences which transform digital harm into physical harm. Eliminating the simulation of complex digital cyber attack chains cuts out unnecessary computational overhead and focuses directly on the physics of cyber-physical attacks. This focus enables designers to make informed decisions which can entirely eliminate categories of cyber threats against advanced reactors through the physical nature of the plant design. This narrowing of cyber threat against nuclear power plants through the physics of the system is intended to make any remaining threat management and cost efficient. This is the goal of the Tiered Cyber Analysis (TCA) outlined in NRC Draft Regulation Guide (RG) 5.96, which provides a RIPB cybersecurity approach for new reactors. ARCADE has been custom developed to meet the demands of the rigorous analysis required in Tier 1 of the TCA, which forms the foundation of the TCA process. Currently, ARCADE is still under development, but has made significant leaps in capability. A pilot analysis on the opensource Asherah simulator was performed which demonstrated key functionality goals. The next stage of ARCADE development involves improvements to the applications which support the analysis system, and enabling the analysis system to utilize the full suite of unsafe control action simulations. Since the analysis method’s core functions are complete, validation of the analysis method will be started concurrent to the next development stages. The automated analysis ARCADE will provide can radically change the cybersecurity design process for advanced reactors, reducing the cost of security implementation while enhancing cyber resilience. The pathway for ARCADE’s development to this goal has become much clearer. The majority of technical hurdles have been cleared, and the remaining development needs have been solidified. ARCADE is now capable of assisting the advanced reactor design process and directly support advanced reactor industry RIPB practices.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Scale-up study of enhancing algal growth through bioaugmentation with the indole-3-acetic acid producing bacteria Azospirillum brasilense

Algae-based wastewater treatment technologies can recover nutrients while generating algal biomass with diverse application potentials. While numerous bacteria have demonstrated the ability to enhance algal growth through symbiotic relationships in laboratory settings, scaling this benefit to larger applications remains challenging due to complex wastewater conditions and microbe-algae dynamics. This study explores the effectiveness of bioaugmentation with Azospirillum brasilense, a plant growth-promoting bacterium known for producing the phytohormone indole-3-acetic acid (IAA), in boosting algal productivity within an Algaewheel wastewater treatment system. Through a series of experiments conducted at lab-, pilot-, and full-scale levels, we evaluated the impact of bioaugmentation on algal growth and developed a bioaugmentation strategy for an Algaewheel system. The results indicate that a biweekly dosing, achieving a final bioaugmenting cell density of 0.2–4 × 10 9 cells/L, effectively doubles the biomass productivity in a residential subdivision wastewater treatment plant in Northern Illinois. The bacterial production of IAA was the primary mechanism driving this enhancement, as demonstrated by the similar growth and yield improvements observed with chemically supplemented IAA and bioaugmentation across all experimental scales. High-throughput sequencing of 18S rRNA genes revealed that the algal community in the bioaugmented tank exhibited more stable biodiversity than the control. Additionally, bioaugmentation improved nutrient removal efficiency during winter, highlighting its potential to enhance the overall performance and sustainability of algae-based wastewater systems. The developed bioaugmentation and chemical treatment methods offer further operational solutions for managing yield, optimizing biochemical profiles, and enhancing biofuel production potential.

Algae-bacterial symbiotic relationship↗

DOE OSTI2025

Enhanced polymorph metastability drives glycine nucleation in aqueous salt solutions

Crystal nucleation from aqueous solutions influences countless geological, biochemical, astrophysical, environmental, and materials science–related phenomena, including ice formation, the manufacturing of active pharmaceutical ingredients, development of diseases such as Alzheimer’s and the origin of life itself. Understanding and controlling nucleation is essential for designing materials with specific properties, developing strategies to inhibit or promote crystallization in various contexts and preventing pathological aggregation in neurodegenerative diseases. Similar to the protein structure prediction problem—where a single amino acid sequence can in theory adopt one most stable conformation but in practice may sample multiple competing conformations—crystal nucleation faces a parallel challenge: the same chemical species can form diverse polymorphs under different environmental conditions (e.g., temperature, pressure, solvent). Each polymorph presents its own set of physical and chemical properties, highlighting the importance of understanding and controlling polymorph selection in fields ranging from pharmaceuticals to materials design. Despite advances in experimental and computational methods for studying phase transitions and polymorph stability, nucleation remains challenging due to its nanoscale nature. Furthermore, in practical settings, salts and impurities can further influence crystal nucleation in diverse contexts, from scaling in pipelines and desalination plants to the durability of concrete and the efficiency of battery materials. This can lead to the formation of polymorphs that may differ from the most stable phase in pure solutions. Or, even though the final structure might appear same irrespective of whether the environment contained impurities or not, the mechanism through which it was formed might be completely different and not intuitive.

Wang, Ruiyu [University of Maryland, College Park,↗

DOE OSTI2026

Methods for safely sharing dual-use genetic data

Background: Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.Results: Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.Conclusion: Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Viral Envelope Evolution in Simian–HIV-Infected Neonate and Adult-Dam Pairs of Rhesus Macaques

We recently demonstrated that Simian–HIV (SHIV)-infected neonate rhesus macaques (RMs) generated heterologous HIV-1 neutralizing antibodies (NAbs) with broadly-NAb (bNAb) characteristics at a higher frequency compared with their corresponding dam. Here, we characterized genetic diversity in Env sequences from four neonate or adult/dam RM pairs: in two pairs, neonate and dam RMs made heterologous HIV-1 NAbs; in one pair, neither the neonate nor the dam made heterologous HIV-1 NAbs; and in another pair, only the neonate made heterologous HIV-1 NAbs. Phylogenetic and sequence diversity analyses of longitudinal Envs revealed that a higher genetic diversity, within the host and away from the infecting SHIV strain, was correlated with heterologous HIV-1 NAb development. We identified 22 Env variable sites, of which 9 were associated with heterologous HIV-1 NAb development; 3/9 sites had mutations previously linked to HIV-1 Env bNAb development. These data suggested that viral diversity drives heterologous HIV-1 NAb development, and the faster accumulation of viral diversity in neonate RMs may be a potential mechanism underlying bNAb induction in pediatric populations. Moreover, these data may inform candidate Env immunogens to guide precursor B cells to bNAb status via vaccination by the Env-based selection of bNAb lineage members with the appropriate mutations associated with neutralization breadth.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Data for Engineering and Evolution of Yarrowia lipolytica for Producing Lipids from Lignocellulosic Hydrolysates

Yarrowia lipolytica , an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Hydrolysate↗

DOE OSTI2025

Structural Evolution of the Hogback Monocline and Its Tectonic Significance in the San Juan Basin

The San Juan Basin is recognized as a Laramide foreland basin. It is located within the Colorado Plateau, a broad tectonic province characterized by a thick sedimentary sequence that was segmented into smaller sub basins during the Late Cretaceous to Paleogene Laramide orogeny. The Hogback Monocline lies along the northwestern margin of the San Juan Basin and is considered a Laramide-age structure formed in response to compressional stress. In this study, we interpret surface and subsurface datasets to construct a structural geological model and evaluate its tectonic significance. Through seismic data, we identify key fault and fold geometries at depth. The seismic dataset used in this study was reprocessed in depth and constrained with well log velocity data to enhance seismic imaging quality. Additionally, we performed well log correlations to identify formation tops and assess variations in basin infill and thickness geometry. A series of structural cross-sections, constructed using seismic data and a high density of boreholes, are presented to evaluate geometric variations along the structure and its evolution during basin development. Furthermore, kinematic restoration and forward modeling analyses were conducted to validate our structural interpretation. This work suggests that the Hogback Monocline formed through fault-propagation folding and flexural slip affecting the pre-Laramide sedimentary sequence under compressional stresses associated with the Laramide orogeny. This structure is interpreted as a high-angle reverse fault that influenced the geometry of the late basin infill. Additionally, monocline bending along the structure may have been controlled by fault relay systems and, in some cases, influenced by strike-slip faulting.

Reyes, Martin [New Mexico Bureau o fGeology and Mi↗

DOE OSTI2024

Estimating Sparse Direct Effects in Multivariate Regression With the Spike-and-Slab LASSO

The multivariate regression interpretation of the Gaussian chain graph model simultaneously parametrizes (i) the direct effects of p predictors on q outcomes and (ii) the residual partial covariances between pairs of outcomes. We introduce a new method for fitting sparse versions of these models with spike-and-slab LASSO (SSL) priors. We develop an Expectation Conditional Maximization algorithm to obtain sparse estimates of the p × q matrix of direct effects and the q × q residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes individual model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior contraction rate for our model, buttressing our method’s excellent empirical performance with strong theoretical guarantees. Using our method, we estimated the direct effects of diet and residence type on the composition of the gut microbiome of elderly adults.

EM algorithm↗

DOE OSTI2026

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗

DOE OSTI2026

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗