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At least 145 records · Page 8

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DOE OSTI2022

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

Abstract Bacillus cereus strain CPT56D‐587‐MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF‐matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%–40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species—largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Constraints on Chondrule Generation, Disk Dynamics, and Asteroid Accretion from the Compositions of Carbonaceous Meteorites

The elemental and isotopic compositions of meteorites are expected to reflect several key processes that occurred in the early solar system, including the migration of gas and dust throughout the protoplanetary disk, the formation of chondrules, and the accretion of the first planetary bodies. However, the specific origins of the various compositions measured among these rocks are currently poorly constrained, limiting our understanding of these processes. Here, we use previously measured elemental and isotopic compositions of chondrites and iron meteorites to identify that carbonaceous (CC) meteorites are mixtures of noncarbonaceous (NC) material, calcium–aluminum-rich inclusion (CAI) material, and CI (Ivuna-like) material, in varying proportions. These trends indicate that chondrules in CO (Ornans-like), CM (Mighei-like), CV (Vigarano-like), and TL (Tagish Lake) chondrites share near-identical average proportions of CI material, arguing that they were generated through the remelting of preexisting NC chondrules all in the same disk environment. Because this proportion likely evolved over space and time throughout the disk, this similarity argues that these chondrules originate from a restricted spatial region and time interval, favoring their generation through a localized event. Moreover, the compositions of CR (Renazzo-like) chondrites indicate that their constituents formed through mechanisms different from those in CO, CM, CV, and TL chondrites. Furthermore, the recovered proportions of CI material in CC iron meteorites and chondrites together also argue for evolution in either the predominant direction of dust and gas motion in the first ~10 au of the disk or the radial distance of planetesimal accretion throughout the CC reservoir.

58 GEOSCIENCES↗

DOE OSTI2022

Smoothed boundary method for simulating incompressible flow in complex geometries

Simulating flow through porous media with explicit considerations of complex microstructures is very challenging using conventional sharp-interface methods because of the difficulties in generating meshes conformal to complex geometries. In this work, a diffuse interface embedded boundary method known as the Smoothed Boundary Method (SBM) is utilized to facilitate simulations of fluid dynamics involving complex geometries. In diffuse-interface methods, the geometry is described by a domain parameter. The SBM allows the straightforward reformulation of the time-dependent Navier-Stokes equations in terms of this domain parameter, using only algebraic identities. Thus, enforcing the appropriate boundary conditions at the irregular embedded boundary is greatly simplified. Adaptive mesh refinement is used to increase the accuracy of the diffuse interface method by allowing thinner interfacial thickness to be used in the domain parameter. Here, the SBM-formulated Navier-Stokes equations are solved with the Finite Difference Method on refined mesh systems. Sharp-interface Finite Element Method simulations using the commercial software COMSOL on body-conforming meshes are also provided for comparison. Favorable agreement between the two methods is observed. Since it is no longer necessary for the mesh to conform to the complex geometry, the grid system for the SBM simulations can be generated rapidly and without additional manual interventions, making the entire simulation process more expedient.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M . brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A Route to Molecular Quantum Technologies Using Endohedral Metallofullerenes

This project focused on fundamental studies of metal-organic hybrid molecules, including endohedral metallofullerenes (EMFs) and related cage-like structures in which quantum information can be encoded into the magnetic (spin) states associated with lanthanide (Ln) atoms that are encapsulated within a protective organic shell. This approach promises advantages over other current magnetic qubit targets based on inorganic molecules and solids. First and foremost, the organic cage provides a rigid environment devoid of elements that possess magnetic nuclei (the 12C nucleus is non-magnetic), thereby protecting the encapsulated atoms from well-known and stubborn noise sources – random vibrations and fluctuating magnetic fields due to nearby nuclei – that can easily erase fragile quantum information states. Equally important, this approach opens up the vast toolbox of organic molecular chemistry. This allows for large-scale synthesis of chemically identical species, with exquisite control over the quantum information states of the associated Ln atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Assembling a Cyber Range to Evaluate Artificial Intelligence / Machine Learning (AI/ML) Security Tools

In this case study, we will describe the design and assembly of a cyber security test range we have built at Oak Ridge National Laboratory in Oak Ridge, TN, USA. The range is designed to provide a flexible environment to evaluate cyber security tools—particularly those involving AI/ML—in a way that provides realistic environments and where we can control the experiments to determine the strengths and weaknesses of the tools. We have designed in the ability to repeat the evaluations, so additional tools can be evaluated and compared at a later time. The system is one that can be scaled up or down for experiment sizes. At the time of the conference we will have completed two full-scale, national, government challenges on this range. These challenges are evaluating the performance and operating costs for AI/ML-based cyber security tools for application into large, government-sized environments. These evaluations will be described, in order to provide motivation and context for various design decisions and adaptations we have made. The first challenge measured end-point security tools against 100K malware samples chosen across a range of types. The second is network detection of attempted penetration and exploitations with varying levels of covertness in a high-volume, business network. The scale of each of these challenges is requiring us to create automation systems to repeat the experiments identically for each tool. Preventing there being easy signs of malicious activity for the AI/ML tools to focus on has been a particularly interesting and challenging aspect of designing and executing these challenge events. After the events, the range continues to be used for other research such as adversarial machine learning where the repeatability, scale, and automation required for the national challenge events become essential elements for research.

Nichols, Jeff↗

DOE OSTI2020

Effect of Computational Schemes on Coupled Flow and Geo-Mechanical Modeling of CO 2 Leakage through a Compromised Well

Carbon capture, utilization, and storage (CCUS) describes a set of technically viable processes to separate carbon dioxide (CO 2 ) from industrial byproduct streams and inject it into deep geologic formations for long-term storage. Legacy wells located within the spatial domain of new injection and production activities represent potential pathways for fluids (i.e., CO 2 and aqueous phase) to leak through compromised components (e.g., through fractures or micro-annulus pathways). The finite element (FE) method is a well-established numerical approach to simulate the coupling between multi-phase fluid flow and solid phase deformation interactions that occur in a compromised well system. We assumed the spatial domain consists of a three-phases system: a solid, liquid, and gas phase. For flow in the two fluids phases, we considered two sets of primary variables: the first considering capillary pressure and gas pressure (PP) scheme, and the second considering liquid pressure and gas saturation (PS) scheme. Fluid phases were coupled with the solid phase using the full coupling (i.e., monolithic coupling) and iterative coupling (i.e., sequential coupling) approaches. The challenge of achieving numerical stability in the coupled formulation in heterogeneous media was addressed using the mass lumping and the upwinding techniques. Numerical results were compared with three benchmark problems to assess the performance of coupled FE solutions: 1D Terzaghi’s consolidation, Liakopoulos experiments, and the Kueper and Frind experiments. We found good agreement between our results and the three benchmark problems. For the Kueper and Frind test, the PP scheme successfully captured the observed experimental response of the non-aqueous phase infiltration, in contrast to the PS scheme. These exercises demonstrate the importance of fluid phase primary variable selection for heterogeneous porous media. We then applied the developed model to the hypothetical case of leakage along a compromised well representing a heterogeneous media. Considering the mass lumping and the upwinding techniques, both the monotonic and the sequential coupling provided identical results, but mass lumping was needed to avoid numerical instabilities in the sequential coupling. Additionally, in the monolithic coupling, the magnitude of primary variables in the coupled solution without mass lumping and the upwinding is higher, which is essential for the risk-based analyses.

deformation flow↗

DOE OSTI2021

Impacts of Anisotropic Porosity on Heat Transfer and Off-Gassing during Biomass Pyrolysis

The pore structure of biogenic materials imbues the ability to deliver water and nutrients through a plant from root to leaf. This anisotropic pore granularity can also play a significant role in processes such as biomass pyrolysis that are used to convert these materials into useful products like heat, fuel, and chemicals. Evolutions in modeling of biomass pyrolysis as well as imaging of pore structures allow for further insights into the concerted physics of phase change-induced off-gassing, heat transfer, and chemical reactions. In this work, we report a biomass single particle model which incorporates these physics to explore the impact of implementing anisotropic permeability and diffusivity on the conversion time and yields predicted for pyrolysis of oak and pine particles. Simulation results showed that anisotropic permeability impacts predicted conversion time more than 2 times when the Biot number is above 0.1 and pyrolysis numbers (Py 1 , Py 2 ) are less than 20. Pore structure significantly impacts predicted pyrolytic conversion time (>8 times) when the Biot number is above 1 and the pyrolysis number is below 1, i.e., the “conduction controlled” regime. Therefore, these nondimensional numbers reflect that when internal heat conduction limits pyrolysis performance, internal pyrolysis off-gassing further retards effective heat transfer rates as a closely coupled phenomenon. Overall, this study highlights physically meaningful opportunities to improve particle-scale pyrolysis modeling and experimental validation relevant to a variety of feedstock identities and preparations, guiding the future design of pyrolyzers for efficient biomass conversion.

09 BIOMASS FUELS↗

DOE OSTI2023

Exploring Plant Cis –Regulatory Elements at Single–Cell Resolution: Overcoming Biological and Computational Challenges to Advance Plant Research

Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall have limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Furthermore, advances in single cell epigenomics have revolutionized the field identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges and common pitfalls in analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Pseudoelastic deformation in Mo-based refractory multi-principal element alloys

Phase diagrams supported by density functional theory methods can be crucial for designing high-entropy alloys that are subset of multi-principal-element alloys. We present phase and property analysis of quinary (MoW) x Zr y (TaTi) 1-x-y refractory high-entropy alloys from combined Calculation of Phase Diagram (CALPHAD) and density-functional theory results, supplemented by molecular dynamics simulations. Both CALPHAD and density-functional theory analysis of phase stability indicates a Mo-W-rich region of this quinary has a stable single-phase body-centered-cubic structure. We report first quinary composition from Mo-W-Ta-Ti-Zr family of alloy with pseudo-elastic behavior, i.e., hysteresis in stress-strain. Our analysis shows that only Mo-W-rich compositions of Mo-W-Ta-Ti-Zr, i.e., Mo+W, show reproducible hysteresis in stress-strain responsible for pseudo-elastic behavior. The (MoW) 85 Zr 7.5 (TaTi) 7.5 was down-selected based on temperature-dependent phase diagram analysis and molecular dynamics simulations predicted elastic behavior that reveals twinning-assisted pseudoelastic behavior. While mostly unexplored in body-centered-cubic crystals, twinning is a fundamental deformation mechanism that competes against dislocation slip in crystalline solids. Furthermore, this alloy shows identical cyclic deformation characteristics during uniaxial < 100 > loading, i.e., the pseudoelasticity is isotropic in loading direction. Additionally, a temperature increase from 77 to 1,500 K enhances the elastic strain recovery in load-unload cycles, offering possibly control to tune the pseudoelastic behavior.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Understanding the Stabilization and Tunability of Divalent Europium 2.2.2B Cryptates

Lanthanides such as europium with more accessible divalent states are useful for studying redox stability afforded by macrocyclic organic ligands. Substituted cryptands, such as 2.2.2B cryptand, that increase the oxidative stability of divalent europium also provide coordination environments that support synthetic alterations of Eu(II) cryptate complexes. Two single crystal structures were obtained containing nine-coordinate Eu(II) 2.2.2B cryptate complexes that differ by a single coordination site, the occupation of which is dictated by changes in reaction conditions. A crystal structure containing a [Eu(2.2.2B)Cl] + complex is obtained from a methanol–THF solvent mixture, while a methanol–acetonitrile solvent mixture affords a [Eu(2.2.2B)(CH 3 OH)] 2+ complex. While both crystals exhibit the typical blue emission observed in most Eu(II) containing compounds as a result of 4f 6 5d 1 to 4f 7 transitions, computational results show that the substitution of a Cl– anion in the place of a methanol molecule causes mixing of the 5d excited states in the Eu(II) 2.2.2B cryptate complex. Additionally, magnetism studies reveal the identity of the capping ligand in the Eu(II) 2.2.2B cryptate complex may also lead to exchange between Eu(II) metal centers facilitated by π-stacking interactions within the structure, slightly altering the anticipated magnetic moment. Finally, the synthetic control present in these systems makes them interesting candidates for studying less stable divalent lanthanides and the effects of precise modifications of the electronic structures of low valent lanthanide elements.

Anions↗

DOE OSTI2023

First (p,n) reaction measurement in inverse kinematics with SECAR

Nucleosynthesis in the νp-process occurs in regions of slightly proton-rich nuclei in the neutrino-driven wind of core-collapse supernovae. The process proceeds via a sequence of (p,γ) and (n,p) reactions, and depending on the conditions, may produce elements between Ni and Sn. Recent studies show that a few key (n,p) reactions regulate the efficiency of the neutrino-p process (νp-process). We performed a study of one of such (n,p) reactions via the measurement of the reverse (p,n) in inverse kinematics with SECAR at NSCL/FRIB.Such proton-induced reaction measurements are particularly challenging, as the recoils and the unreacted projectiles have nearly identical masses. An appropriate separation level can be achieved with SECAR, and along with the incoincidence detection of neutrons these measurements become attainable. The preparation of the SECAR system for accommodating its first (p,n) reaction measurement, including the development of alternative ion beam optics, and the setup of the in-coincidence neutron detection, along with discussion on preliminary results from the p(58Fe,n)58Co reaction measurement are presented and discussed.

Tsintari, P↗

DOE OSTI2023

Transposon signatures of allopolyploid genome evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

amsession/Kmer-based-Subgenome-Mapping

Session, Adam↗

DOE OSTI2022

Duality and form factors in the thermally deformed two-dimensional tricritical Ising model

The thermal deformation of the critical point action of the 2D tricritical Ising model gives rise to an exact scattering theory with seven massive excitations based on the exceptional E_7 E 7 Lie algebra. The high and low temperature phases of this model are related by duality. This duality guarantees that the leading and sub-leading magnetisation operators, \sigma(x) σ ( x ) and \sigma'(x) σ ′ ( x ) , in either phase are accompanied by associated disorder operators, \mu(x) μ ( x ) and \mu'(x) μ ′ ( x ) . Working specifically in the high temperature phase, we write down the sets of bootstrap equations for these four operators. For \sigma(x) σ ( x ) and \sigma'(x) σ ′ ( x ) , the equations are identical in form and are parameterised by the values of the one-particle form factors of the two lightest \mathbb{Z}_2 ℤ 2 odd particles. Similarly, the equations for \mu(x) μ ( x ) and \mu'(x) μ ′ ( x ) have identical form and are parameterised by two elementary form factors. Using the clustering property, we show that these four sets of solutions are eventually not independent; instead, the parameters of the solutions for \sigma(x)/\sigma'(x) σ ( x ) / σ ′ ( x ) are fixed in terms of those for \mu(x)/\mu'(x) μ ( x ) / μ ′ ( x ) . We use the truncated conformal space approach to confirm numerically the derived expressions of the matrix elements as well as the validity of the \Delta Δ -sum rule as applied to the off-critical correlators. We employ the derived form factors of the order and disorder operators to compute the exact dynamical structure factors of the theory, a set of quantities with a rich spectroscopy which may be directly tested in future inelastic neutron or Raman scattering experiments.

Cortes Cubero, Axel↗

DOE OSTI2023

A technique for studying (n,p) reactions of astrophysical interest using radioactive beams with SECAR

The formation of nuclei in slightly proton-rich regions of the neutrino-driven wind of core-collapse supernovae could be attributed to the neutrino-p process (νp-process). As it proceeds via a sequence of (p,γ) and (n,p) reactions, it may produce elements in the range of Ni and Sn, considering adequate conditions. Recent studies identify a number of decisive (n,p) reactions that control the efficiency of the νp-process. The study of one such (n,p) reaction via the measurement of the reverse (p,n) in inverse kinematics was performed with SECAR at NSCL/FRIB. Proton-induced reaction measurements, especially at the mass region of interest, are notably difficult since the recoils have nearly identical masses as the unreacted projectiles. Such measurements are feasible with the adequate separation level achieved with SECAR, and the in-coincidence neutron detection. Adjustments of the SECAR system for the first (p,n) reaction measurement included the development of new ion beam optics, and the installation of the neutron detection system. The aforementioned developments along with a discussion on the preliminary results of the p(58Fe,n)58Co reaction measurement are presented.

Tsintari, P↗

DOE OSTI2025

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗