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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Anomalies of coset non-invertible symmetries

Anomalies of global symmetries provide important information on the quantum dynamics. We show the dynamical constraints can be organized into three classes: genuine anomalies, fractional topological responses, and integer responses that can be realized in symmetry-protected topological (SPT) phases. Coset symmetry can be present in many physical systems including quantum spin liquids, and the coset symmetry can be a non-invertible symmetry. We introduce twists in coset symmetries, which modify the fusion rules and the generalized Frobenius-Schur indicators. We call such coset symmetries twisted coset symmetries, and they are labeled by the quadruple (G, K, ω D+1 , α D ) in D spacetime dimensions where G is a group and K ⊂ G is a discrete subgroup, ω D+1 is a (D + 1)-cocycle for group G, and α D is a D-cochain for group K. We present several examples with twisted coset symmetries using lattice models and field theory, including both gapped and gapless systems (such as gapless symmetry-protected topological phases). We investigate the anomalies of general twisted coset symmetry, which presents obstructions to realizing the coset symmetry in (gapped) symmetry-protected topological phases. We show that finite coset symmetry G/K becomes anomalous when G cannot be expressed as the bicrossed product G = H ⋈ K , and such anomalous coset symmetry leads to symmetry-enforced gaplessness in generic spacetime dimensions. We illustrate examples of anomalous coset symmetries with A 5 / \Z 2 symmetry, with realizations in lattice models.

Hsin, Po-Shen [King’s College London (United Kingd↗
DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗
DOE OSTI2021

De novo transcriptome in roots of switchgrass ( Panicum virgatum L. ) reveals gene expression dynamic and act network under alkaline salt stress

Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Play Fairway Analysis: Structurally Controlled Geothermal Systems in the Eastern Great Basin Extensional Regime, Utah

A research team with membership from the University of Utah/Energy & Geoscience Institute, the University of Utah/Dept. of Geology & Geophysics, and the Utah Geological Survey, undertook a play fairway analysis (PFA) for geothermal resources in the Eastern Great Basin (EGB) extensional tectonic regime of western Utah. This is a high-priority region for geothermal exploration because active Basin and Range (B&R) extension with volcanism having a N-S strike is superimposed upon pre-existing E-W belts of plutonic rocks and large-scale structural lineaments. Cumulative heat flow along the N-S strike of the state totals approximately 5 GWt above background stable interior. Three electricity producing power plants currently exist with substantial potential for increase. Succinctly, our PFA approach aims to resolve potential sources of heat and permeability in the region, which are the two principal criteria for establishing a geothermal resource. An initial Phase 1 was carried out using only existing geoscientific data in the area. Criteria selected for focusing heat potential include direct heat flow measurements in boreholes, magnetotelluric (MT) low resistivity anomalies, fluid/gas geochemistry, and proximity to recent volcanic eruptions. Permeability is established through geological structures (fault density, critically stressed areas, seismicity, gravity), and MT low resistivity anomalies. In Phase II of this PFA project, additional geological, geophysical and geochemical data were acquired and analysis carried out primarily over promising composite common risk (CCR) areas initially identified in Phase I in order to focus prospectivity and prepare for drilling recommendations. These prospects are near the Twin Peaks rhyolite field, high heat flow areas north of the producing Cove Fort system, and geophysical structure beneath the Crater Knoll area off the northeast flank of the Mineral Mountains. Additional data included MT site fill-in, structural mapping and analysis using high-resolution imagery, gravity and on-ground mapping, Nodal 3C passive seismic collection, and passive 3He surveying. Heat source and permeability potential are again expressed in terms of their individual common risk segment (CRS) maps, with a color scheme using green for most favorable (low risk) and red for least favorable (high risk). Diverse data types are united through the technique of probability kriging, which establishes prospectivity thresholds for each data type and then computes probability of exceeding that threshold over the PFA area. Modified CRS and CCRS maps are compared to those of Phase I to highlight tighter prospectivity focus. In doing so, the prospectivity threshold for heat was increased significantly to narrow the targeting. In the final Phase III of this project where a recommended deep thermal gradient hole was sited, additional geophysical, geochemical and geological field collection and analysis was carried out to refine drill hole targeting. This includes prospect-scale MT, gravity, structure, passive seismic deployment (Cove Fort area), and detailed 3He isotope profiling. It was the recommendation of the DOE Technical Monitoring Team (TMT) that one or more holes be sited in the north-ern Cove Fort area where legacy TG gradient holes showed high cumulative heat flow. These were to be of moderate depth, 2000-3000 feet, to reach the geothermal fluid table expected to start in excess of 1000 feet depth. The drilling organization stipulated by the DOE/GTO was that of the USGS Research Drilling Program (RDP) centered in Las Vegas, NV. A detailed well plan, appended to this report, was developed principally by Dr. Ben Barker consulting to University of Utah, Dr. Steve Pye on the DOE TMT, Mr. Steven Crawford of the USGS-RDP, and the project PI Phil Wannamaker. However, temperature and possible H 2 S at the systems lead to cancellation of the drilling last-minute as this appeared outside the experience base of the USGS-RDP. We hope to have the opportunity to revisit the test drilling and expand the Play Fairway Analysis of this region at some point in the future.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

X-ray Irradiance Distribution for an Interferometer with a Curved Biprism Array

The development of interferometry-based X-ray phase contrast imaging systems that provide highly resolved X-rays with spatially-modulated intensity is enabling the full potential of X-ray optics to image phase, attenuation, and small angle scatter properties of soft tissue. In this work we present analytical formulations of a new hardware concept for X-ray phase contrast imaging wherein the phase grating is replaced with an array of Fresnel biprisms. We derive expressions for the irradiance distribution pattern of a biprism interferometer composed of a curved biprism array with multiple biprisms and multiple point sources. These expressions are used to plot fringe patterns for X-ray design parameters, including 1) size, number, and period of X-ray point sources; 2) biprism parameters of material composition, angle, number, and period; and 3) biprism array to X-ray source and detector distances. Analytical results show that the biprism interferometer provides a longitudinally-nonperiodic pattern of spatially modulated intensity different from the Talbot longitudinally-periodic pattern common in grating interferometry. The curvature of the biprism array brings a sharper longitudinal fringe pattern. Experiments are being performed to verify the analytical calculations for a biprism plastic material of SU-8 using a synchrotron source. X-ray biprism material has widely varied indexes of refraction relative to wavelength and thus the separation of the virtual sources and resulting interference fringe period also varies with X-ray wavelength. Our aim is to develop biprism interferometry imaging systems with excellent polychromatic performance that produce high-contrast fringes with spatially incoherent X-ray illumination. Biprism interferometry will potentially provide higher fringe visibility with better image quality to that of diffraction grating interferometry.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme

Synthetic biology enables microbial hosts to produce complex molecules from organisms that are rare or difficult to cultivate, but the structures of these molecules are limited to those formed by reactions of natural enzymes. The integration of artificial metalloenzymes (ArMs) that catalyse unnatural reactions into metabolic networks could broaden the cache of molecules produced biosynthetically. Here, in this work, we report an engineered microbial cell expressing a heterologous biosynthetic pathway, containing both natural enzymes and ArMs, that produces an unnatural product with high diastereoselectivity. We engineered Escherichia coli with a heterologous terpene biosynthetic pathway and an ArM containing an iridium–porphyrin complex that was transported into the cell with a heterologous transport system. We improved the diastereoselectivity and product titre of the unnatural product by evolving the ArM and selecting the appropriate gene induction and cultivation conditions. This work shows that synthetic biology and synthetic chemistry can produce, by combining natural and artificial enzymes in whole cells, molecules that were previously inaccessible to nature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Report from the Inaugural Meeting on the Opportunities at the SEEMS Facility June 11-12, 2019

The Inaugural Meeting on the Opportunities at the Single Event Effects—Muon Spectroscopy (SEEMS) facility was held June 11–12, 2019, at Oak Ridge National Laboratory (ORNL). Capabilities of the SEEMS facility concept were reviewed, with emphasis on particle beams for single event effects (SEE) testing of electronic devices (integrated circuits) and systems—a topic of growing interest and concern in aerospace avionics, satellites, supercomputing, autonomous cars, unmanned aerial vehicles and more. Participants from these industries and their regulators attended. A clear consensus on the growing and urgent need for SEE test capabilities like those offered by SEEMS was expressed. Subsequent to the meeting, letters of support for SEEMS were sent by The Boeing Company and Honeywell to the ORNL Laboratory Director, Thomas Zacharia.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Development, Implementation, and Verification of Partially-Ionized Collisional Multifluid Plasma Models in Drekar

We consider the development of multifluid models for partially ionized multispecies plasmas. The models are composed of a standard set of five-moment fluid equations for each species plus a description of electromagnetics. The most general model considered utilizes a full set of fluid equations for each charge state of each atomic species, plus a set of fluid equations for electrons. The fluid equations are coupled through source terms describing electromagnetic coupling, ionization, recombination, charge exchange, and elastic scattering collisions in the low-density coronal limit. The form of each of these source terms is described in detail, and references for required rate coefficients are identified for a diverse range of atomic species. Initial efforts have been made to extend these models to incorporate some higher-density collisional effects, including ionization potential depression and three- body recombination. Some reductions of the general multifluid model are considered. First, a reduced multifluid model is derived which averages over all of the charge states (including neutrals) of each atomic species in the general multifluid model. The resulting model maintains full consistency with the general multifluid model from which it is derived by leveraging a quasi-steady-state collisional ionization equilibrium assumption to recover the ionization fractions required to make use of the general collision models. Further reductions are briefly considered to derive certain components of a single-fluid magnetohydrodynamics (MHD) model. In this case, a generalized Ohm's law is obtained, and the standard MHD resistivity is expressed in terms of the collisional models used in the general multifluid model. A number of numerical considerations required to obtain robust implementations of these multifluid models are discussed. First, an algebraic flux correction (AFC) stabilization approach for a continuous Galerkin finite element discretization of the multifluid system is described in which the characteristic speeds used in the stabilization of the fluid systems are synchronized across all species in the model. It is demonstrated that this synchronization is crucial in order to obtain a robust discretization of the multifluid system. Additionally, several different formulations are considered for describing the electromagnetics portion of the multifluid system using nodal continuous Galerkin finite element discretizations. The formulations considered include a parabolic divergence cleaning method and an implicit projection method for the traditional curl formulation of Maxwell's equations, a purely- hyperbolic potential-based formulation of Maxwell's equations, and a mixed hyperbolic-elliptic potential-based formulation of Maxwell's equations. Some advantages and disadvantages of each formulation are explored to compare solution robustness and the ease of use of each formulation. Numerical results are presented to demonstrate the accuracy and robustness of various components of our implementation. Analytic solutions for a spatially homogeneous damped plasma oscillation are derived in order to verify the implementation of the source terms for electromagnetic coupling and elastic collisions between fluid species. Ionization balance as a function of electron temperature is evaluated for several atomic species of interest by comparing to steady-state calculations using various sets of ionization and recombination rate coefficients. Several test problems in one and two spatial dimensions are used to demonstrate the accuracy and robustness of the discretization and stabilization approach for the fluid components of the multifluid system. This includes standard test problems for electrostatic and electromagnetic shock tubes in the two-fluid and ideal shock-MHD limits, a cylindrical diocotron instability, and the GEM challenge magnetic reconnection problem. A one-dimensional simplified prototype of an argon gas puff configuration as deployed on Sandia's Z-machine is used as a demonstration to exercise the full range of capabilities associated with the general multifluid model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

The Antioxidant Enzyme Methionine Sulfoxide Reductase A (MsrA) Interacts with Jab1/CSN5 and Regulates Its Function

Methionine sulfoxide (MetO) is an oxidative posttranslational modification that primarily occurs under oxidative stress conditions, leading to alteration of protein structure and function. This modification is regulated by MetO reduction through the evolutionarily conserved methionine sulfoxide reductase (Msr) system. The Msr type A enzyme (MsrA) plays an important role as a cellular antioxidant and promotes cell survival. The ubiquitin- (Ub) like neddylation pathway, which is controlled by the c-Jun activation domain-binding protein-1 (Jab1), also affects cell survival. Jab1 negatively regulates expression of the cell cycle inhibitor cyclin-dependent kinase inhibitor 1B (P27) through binding and targeting P27 for ubiquitination and degradation. Here we report the finding that MsrA interacts with Jab1 and enhances Jab1's deneddylase activity (removal of Nedd8). In turn, an increase is observed in the level of deneddylated Cullin-1 (Cul-1, a component of E3 Ub ligase complexes). Furthermore, the action of MsrA increases the binding affinity of Jab1 to P27, while MsrA ablation causes a dramatic increase in P27 expression. Thus, an interaction between MsrA and Jab1 is proposed to have a positive effect on the function of Jab1 and to serve as a means to regulate cellular resistance to oxidative stress and to enhance cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ultracentral Collisions of Small and Deformed Systems at RHIC

We study a range of collision systems involving deformed ions and compare the elliptic and triangular flow harmonics produced in a hydrodynamics scenario versus a color glass condensate (CGC) scenario. For the hydrodynamics scenario, we generate initial conditions using TRENTO and work within a linear response approximation to obtain the final flow harmonics. For the CGC scenario, we use the explicit calculation of two-gluon correlations taken in the high-p T “(semi)dilute-(semi)dilute” regime to express the flow harmonics in terms of the density profile of the collision. Here, we consider ultracentral collisions of deformed ions as a testbed for these comparisons because the difference between tip-on-tip and side-on-side collisions modifies the multiplicity dependence in both scenarios, even at zero impact parameter. We find significant qualitative differences in the multiplicity dependence obtained in the initial conditions+hydrodynamics scenario and the CGC scenario, allowing these collisions of deformed ions to be used as a powerful discriminator between models. We also find that sub-nucleonic fluctuations have a systematic effect on the elliptic and triangular flow harmonics which are most discriminating in 0–1% ultracentral symmetric collisions of small deformed ions and in 0–10% d197Au collisions. The collision systems we consider are 238 U 238 U, d 197 Au, 9 Be 197 Au, 9 Be 9 Be, 3 He 3 He, and 3 He 197 Au.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

CG-Kit: Code Generation Toolkit for performant and maintainable variants of source code applied to Flash-X hydrodynamics simulations

CG-Kit is a new Code Generation tool-Kit that we have developed as a part of the solution for portability and maintainability for multiphysics computing applications. The development of CG-Kit is rooted in the urgent need created by the shifting landscape of high-performance computing platforms and the algorithmic complexities of a particular large-scale multiphysics application: Flash-X. To efficiently use computing resources on a heterogeneous node, an application must have a map of computation to resources and a mechanism to move the data and computation to the resources according to the map. Most existing performance portability solutions are focussed on abstracting the expression of computations so that a unified source code can be specialized to run on different resources. However, such an approach is insufficient for a code like Flash-X, which has a multitude of code components that can be assembled in various permutations and combinations to form different instances of applications. Similar challenges apply to any code that has composability, where a single specified way of apportioning work among devices may not be optimal. Additionally, use cases arise where the optimal control flow of computation may differ for different devices while the underlying numerics remain identical. This combination leads to unique challenges including handling an existing large code base in Fortran and/or C/C++, subdivision of code into a great variety of units supporting a wide range of physics and numerical methods, different parallelization techniques for distributed and shared memory systems and accelerator devices, and heterogeneity of computing platforms requiring coexisting variants of parallel algorithms. All of these challenges demand that scientific software developers apply existing knowledge about domain applications, algorithms, and computing platforms to determine custom abstractions and granularity for code generation. There is a critical lack of tools to tackle those problems. CG-Kit is designed to fill this gap by providing a user with the ability to express their desired control flow and computation-to-resource map in the form a pseudocode-like recipe. It consists of standalone tools that can be combined into highly specific and, we argue, highly effective portability and maintainability toolchains. Here we present the design of our new tools: parametrized source trees, control flow graphs, and recipes. The tools are implemented in Python. They are agnostic to the programming language of the source code targeted for code generation. In conclusion, we demonstrate the capabilities of the toolkit with two examples, first, multithreaded variants of the basic AXPY operation, and second, variants of parallel algorithms within a hydrodynamics solver, called Spark, from Flash-X that operates on block-structured adaptive meshes.

Algorithmic portability↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Crosstalk between cyclophilins and T lymphocytes in coronary artery disease

Highlights: • CD147 receptor expression is elevated in T lymphocytes from CAD patients. • Intracellular CypA and B expression are augmented in T lymphocytes from CAD patients. • CypA, B and C, and IL-1β and IL-6 serum levels are increased in patients with CAD. • CypA and B levels in T lymphocytes are correlated with CypA and B serum levels, respectively. Cardiovascular diseases and atherosclerosis are currently some of the most widespread diseases of our time. Within cardiovascular disease, coronary artery disease and underlying atherosclerosis were recently linked with systemic and local inflammation. Cyclophilins participate in the initiation and progression of these inflammatory-related diseases. Cyclophilins are released into the extracellular space upon inflammatory stimuli and participate in the pathology of cardiovascular diseases. The cell surface receptor for extracellular cyclophilins, the CD147 receptor, also contributes to coronary artery disease pathogenesis. Nevertheless, the physiological relevance of cyclophilin's family and their receptor in cardiovascular diseases remains unclear. The present study aimed to better understand the role of cyclophilins in cardiovascular artery disease and their relationship with inflammation. Hence, cyclophilins and pro-inflammatory interleukins were measured in the serum of 30 subjects (divided into three groups according to coronary artery disease status: 10 patients with acute coronary syndrome, 10 patients with chronic coronary artery disease, and 10 control volunteers). In addition, cyclophilin levels and CD147 receptor expression were measured in T lymphocytes purified from these subjects. Cyclophilin A, B, and C, pro-inflammatory interleukins, and CD147 membrane expression were significantly elevated in patients with coronary artery disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Methane generation from low-maturity coals and shale source rocks at low temperatures (80–120 °C) over 14–38 months

This study contributes long-term (14 to 38 months) experimental evidence for geocatalytically mediated methanogenesis in immature to early mature shale and coal source rocks at temperatures from 80 to 120 °C. Borosilicate glass tubes with pre-outgassed coal and shale source rock chips and water were sealed under vacuum, sterilized, heated isothermally, and finally opened in connection with a vacuum line where headspace gases methane (CH 4 ) and carbon dioxide (CO 2 ) were collected. The possibility of admitting pre-existing CH 4 from closed pores into product gases during heating experiments was evaluated by comparative ball milling of original and heated rock chips, followed by quantitation of released gases with a novel closed-circuit laser-based SARAD RTM2200 gas detector system with sub-µmol sensitivity. The yields of produced CH 4 from individual source rocks were corrected by subtracting the amounts of pre-existing CH 4 from formerly closed pores in original source rocks that had leaked during long-term heating. Different shales and coals express contrasting propensities to geocatalytically generate CH 4 and CO 2 , with CH 4 yields ranging from 0.1 to 5.5 µmol g-1 total organic carbon (TOC). CH 4 yields from two petrographically different samples of Springfield Coal with comparable thermal maturity suggest that liptinite expresses a far higher propensity for methanogenesis, but liberates less CO 2 than vitrinite. Shale from the Second White Specks Formation generated approximately 10 times more CH 4 than New Albany Shale per g of TOC, further suggesting complex controls on CH 4 generation during catalytic methanogenesis. Higher temperature can enhance the activities of catalytic methanogenesis. Here, the extrapolation of laboratory-based reaction rates to natural conditions in organic-rich buried sediments suggests that geocatalytic methanogenesis can be fast enough in some source rocks to generate economically sizeable gas plays from immature to early mature source rocks over geologic time.

03 NATURAL GAS↗
DOE OSTI2023

Bayesian filtering for model predictive control of stochastic gene expression in single cells

This study describes a method for controlling the production of protein in individual cells using stochastic models of gene expression. By combining modern microscopy platforms with optogenetic gene expression, experimentalists are able to accurately apply light to individual cells, which can induce protein production. Here we use a finite state projection based stochastic model of gene expression, along with Bayesian state estimation to control protein copy numbers within individual cells. We compare this method to previous methods that use population based approaches. We also demonstrate the ability of this control strategy to ameliorate discrepancies between the predictions of a deterministic model and stochastic switching system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dimensionless parameters for cloudy Rayleigh-Bénard convection: Supersaturation, Damköhler, and Nusselt numbers

In steady-state Rayleigh-Bénard convection, heat is transported by turbulent thermal convection from the bottom, hot surface to the top, cold surface, leading to a height-independent sensible heat flux. When water vapor is present and cloud formation occurs, there is also an additional latent heat flux. Heat transport in cloudy Rayleigh-Bénard convection depends on turbulent flow as well as the microphysical state of the clouds: specifically, whether substantial supersaturations exist and whether cloud liquid water is removed through sedimentation/precipitation. In this article we bridge between the Rayleigh-Bénard convection literature and the atmospheric literature. We express the governing equations for cloudy convection in dimensionless form, thereby explicitly identifying the governing parameters relevant to the cloudy case, including Schmidt, Damköhler, supersaturation, and sedimentation numbers. We further connect to the atmospheric literature by obtaining a Nusselt number (dimensionless heat flux) for a cloud-convection system, directly from the conservation equations for temperature and water vapor. This flux has the same form as that identified by Zhang et al. [L. Zhang, K. L. Chong, and K.-Q. Xia, J. Fluid Mech. 874, 1041 (2019)] for convection with water vapor, but is extended to the cloudy case. For equal thermal and water vapor diffusivities, the flux corresponds to the widely used atmospheric quantities equivalent temperature and moist static energy. Using large eddy simulation (LES) of an idealized cloudy Rayleigh-Bénard convection system with fixed boundary conditions, we find that the equivalent heat flux (Nusselt number) is only weakly dependent on the microphysical details of the system, such as liquid water mixing ratio and cloud droplet number concentration. Finally, from the results, we show the vertical profiles of sensible and latent heat fluxes depend on the liquid water content, whereas the equivalent heat flux remains a constant throughout the height of the chamber.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Gravitational Self-force Errors of Poisson Solvers on Adaptively Refined Meshes

An error in the gravitational force that the source of gravity induces on itself (a self-force error) violates both the conservation of linear momentum and the conservation of energy. If such errors are present in a self-gravitating system and are not sufficiently random to average out, the obtained numerical solution will become progressively more unphysical with time: the system will acquire or lose momentum and energy due to numerical effects. In this paper, we demonstrate how self-force errors can arise in the case where self-gravity is solved on an adaptively refined mesh when the refinement is nonuniform. Here, we provide the analytical expression for the self-force error and numerical examples that demonstrate such self-force errors in idealized settings. We also show how these errors can be corrected to an arbitrary order by straightforward addition of correction terms at the refinement boundaries.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Effective viscosities in a hydrodynamically expanding boost-invariant QCD plasma

Background: The near-equilibrium properties of a QCD plasma can be encoded into transport coefficients such as bulk and shear viscosity. In QCD, the ratio of these transport coefficients to entropy density, ζ/$\textit{s}$ and η/$\textit{s}$, depends nontrivially on the plasma's temperature. This is unlike in conformal systems where they take constant values such as η/$\textit{s}$ = 1/(4π). Purpose: In this work, we show that in a (0 + 1)D boost-invariant fluid with no transverse expansion, a temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ can be described by an equivalent effective viscosity $\langleζ/s\rangle_{\text{eff}}$ or $\langleη/s\rangle_{\text{eff}}$. This effective viscosity combines the actual temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ with the temperature profile of the fluid. Further, we extend the concept of effective viscosity in systems with transverse expansion and discuss how effective viscosities can be used to identify families of ζ/$\textit{s(T)}$ and η /$\textit{s(T)}$ that lead to similar hydrodynamic evolution. Methods: The Navier-Stokes relativistic hydrodynamic equations are used to provide a first definition of effective viscosity, in (0 + 1)D and (1 + 1)D. In the (0 + 1)D case, the analysis is extended to Israel-Stewart-type second-order hydrodynamics to clarify the effect of higher-order hydrodynamics corrections on the effective viscosity. Results: In a boost-invariant fluid with no transverse expansion [(0 + 1)D], the effective viscosity is expressed as a simple integral of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ over temperature, with a weight determined by the speed of sound of the fluid. The result is general for any equation of state with a moderate temperature dependence of the speed of sound, including the QCD equation of state. This definition of effective viscosity can be used to identify infinite families of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ that produce essentially indistinguishable temperature profiles. In a boost-invariant cylindrical system [(1 + 1)D], a similar definition of effective viscosity is obtained in terms of characteristic trajectories in time and transverse direction. This leads to an infinite number of constraints on an infinite functional space for ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$. Realistic examples are presented by using a finite number of constraints on a finite functional space. Conclusions: The definition of effective viscosity in a (0 + 1)D system clarifies how infinite families of ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$ can result in nearly identical hydrodynamic temperature profiles. By extending the study to a boost-invariant cylindrical [(1 + 1)D] fluid, we identify an approximate but more general definition of effective viscosity that highlights the potential and limits of the concept of effective viscosity in fluids with limited symmetries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗