Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Expression systems”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Arabidopsis bZIP11 Is a Susceptibility Factor During Pseudomonas syringae Infection

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2024

Charge Conservation beyond Uniformity: Spatially Inhomogeneous Electromagnetic Response in Periodic Solids

Nonlinear electromagnetic response functions have reemerged as a crucial tool for studying quantum materials, due to recently appreciated connections between optical response functions, quantum geometry, and band topology. Most attention has been paid to responses to spatially uniform electric fields, relevant to low-energy optical experiments in conventional solid state materials. However, magnetic and magnetoelectric phenomena are naturally connected by responses to spatially varying electric fields due to Maxwell’s equations. Furthermore, in the emerging field of moiré materials, characteristic lattice scales are much longer, allowing spatial variation of optical electric fields to potentially have a measurable effect in experiments. In order to address these issues, we develop a formalism for computing linear and nonlinear responses to spatially inhomogeneous electromagnetic fields. Starting with the continuity equation, we derive an expression for the second-quantized current operator that is manifestly conserved and model independent. Crucially, our formalism makes no assumptions on the form of the microscopic Hamiltonian and so is applicable to model Hamiltonians derived from tight-binding or calculations. We then develop a diagrammatic Kubo formalism for computing the wave vector dependence of linear and nonlinear conductivities, using Ward identities to fix the value of the diamagnetic current order by order in the vector potential. We apply our formula to compute the magnitude of the Kerr effect at oblique incidence for a model of a moiré-Chern insulator and demonstrate the experimental relevance of spatially inhomogeneous fields in these systems. We further show how our formalism allows us to compute the (orbital) magnetic multipole moments and magnetic susceptibilities in insulators. Turning to nonlinear response, we use our formalism to compute the second-order transverse response to spatially varying transverse electric fields in our moiré-Chern insulator model, with an eye toward the next generation of experiments in these systems. Published by the American Physical Society 2024

Physics↗
DOE OSTI2024

The RNA-binding protein Modulo promotes neural stem cell maintenance in Drosophila

A small population of stem cells in the developing Drosophila central nervous system generates the large number of different cell types that make up the adult brain. To achieve this, these neural stem cells (neuroblasts, NBs) divide asymmetrically to produce non-identical daughter cells. The balance between stem cell self-renewal and neural differentiation is regulated by various cellular machinery, including transcription factors, chromatin remodelers, and RNA-binding proteins. The list of these components remains incomplete, and the mechanisms regulating their function are not fully understood, however. Here, we identify a role for the RNA-binding protein Modulo (Mod; nucleolin in humans) in NB maintenance. We employ transcriptomic analyses to identify RNA targets of Mod and assess changes in global gene expression following its knockdown, results of which suggest a link with notable proneural genes and those essential for neurogenesis. Mod is expressed in larval brains and its loss leads to a significant decrease in the number of central brain NBs. Stem cells that remain lack expression of key NB identity factors and exhibit cell proliferation defects. Mechanistically, our analysis suggests these deficiencies arise at least in part from altered cell cycle progression, with a proportion of NBs arresting prior to mitosis. Overall, our data show that Mod function is essential for neural stem cell maintenance during neurogenesis.

Parra, Amalia S.↗
DOE OSTI2021

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

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

Influences of Mg Ions and Al Ions on Deposition Behavior of Supersaturated Silicic Acid - 20261

Silicic acid can change into various species such as deposit, colloidal, and soluble form under certain conditions: for example, gradual pH changes around geological disposal repositories. In particular, silicic acid deposits narrow groundwater flow paths, thereby restricting the flow of groundwater. Such effects may contribute to a delay in radionuclide migration. Previous studies have reported that silicic acid supersaturated in sodium and calcium ions can narrow the flow paths. This study examined the effect of magnesium (Mg) and aluminum (Al) ions on the deposition of supersaturated silicic acid on the solid phase. The deposition behavior of supersaturated silicic acid on the solid phase was investigated in a batch system while changing the initial supersaturation concentration, the coexisting ion concentration, and the amount of added solid phase. In the presence of Mg ions, silicic acid precipitation increased with increasing Mg ion concentration due to the influence of the electrolyte, and crosslinking reactions. The coexistence of Al ions significantly suppressed silicic acid deposition due to the formation of a covering on the solid surface during Al ion hydrolysis under conditions of high Al concentration (1.4 mM). On the basis of these experimental results, the apparent deposition rate constant of silicic acid was estimated to be in the range from 10{sup -11} to 10{sup -10} m/s. The Damkoehler number (the dimensionless number expressed by the ratio of the characteristic time of mass transfer and the chemical reaction constant) was sufficient to cause the clogging of the host rock by deposition. This suggests that supersaturated silicic acid deposition, regardless of the presence of Mg ions (and Al ions), contributes to improving barrier performance against radionuclide migration in the host rock. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi

SUMMARY The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant–fungal interactions today, it is hypothesized these kingdoms have a long‐standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free‐living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia , interact with P. patens in coculture. We also assess how Mollicute ‐related or Burkholderia ‐related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high‐throughput phenomics, microscopy, RNA‐sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high‐throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant–fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Global Market and Economic Welfare Implications of Changes in Agricultural Yields Due to Climate Change

The economic welfare effects of climate change on global agriculture will be mediated by several complex biophysical and economic processes. For a given emissions scenario, these include: (1) the response of the climate system to anthropogenic forcing, (2) the response of crop yields to climate system and carbon dioxide changes, given baseline improvements in crop yields, (3) the response of agricultural markets to crop yield changes, and (4) the economic welfare implications of such market responses. In this paper, we use information about the first two processes from available climate-crop model comparison studies to analyze implications for the third and fourth processes. Applying the range of crop yield changes in a Global Integrated Assessment Model (GCAM) highlights several important economic relationships. First, we find a consistent relationship between global cropland area and yield change that is approximately orthogonal to the relationship between regional cropland area and yield change. Second, we find that the change in economic welfare, expressed as total surplus change per unit economic output, peaks during the 21st century. Third, we find that, at the global level, changes in yield affect both producer surplus and consumer surplus. Specifically, surplus changes to producers and consumers are always opposite in sign, although which economic actors gain or lose varies with the sign of yield change for any given commodity. Taken together, these results contribute to a growing body of research on climate-induced changes on agriculture by highlighting several economic relationships that are robust to differences in the underlying biophysical responses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Ergothioneine alleviates senescence of fibroblasts induced by UVB damage of keratinocytes via activation of the Nrf2/HO-1 pathway and HSP70 in keratinocytes

Highlights: • EGT activated Nrf2/HO-1 pathway and HSP70 in UVB-irradiated keratinocytes. • EGT alleviated ROS production, apoptosis, and inflammation in UVB-irradiated keratinocytes. • EGT suppressed senescence and collagen imbalance in fibroblasts by inhibiting the keratinocyte-secreted factors. • EGT suppresses photoaging by UVB irradiation in a keratinocyte/fibroblast co-culture system. Ultraviolet B (UVB) irradiation induces skin damage and photoaging through several deleterious effects, including generation of reactive oxygen species (ROS), apoptosis of epidermal cells, inflammation, and collagen degradation in fibroblasts. Ergothioneine (EGT) is a naturally occurring amino acid with potential biological properties. We evaluated whether EGT protects against UVB-induced photoaging using a keratinocyte/fibroblast co-culture system. Keratinocytes were pretreated with EGT, irradiated with UVB, and co-cultured with fibroblasts. In keratinocytes, ROS production and apoptosis were assessed. We also analyzed the Nrf2/HO-1 pathway, HSP70, proapoptotic proteins, and paracrine cytokines by Western blotting and real-time PCR. Collagen degradation-related genes and senescence were also assessed in fibroblasts. EGT pretreatment of keratinocytes significantly inhibited downregulation of the Nrf2/HO-1 pathway and HSP70, and protected keratinocytes by suppressing production of ROS and cleavage of proapoptotic proteins, including caspase-8 and PARP. Furthermore, EGT significantly reduced the paracrine cytokines, including IL-1β, IL-6, and TNF-α. In co-cultures of fibroblasts with EGT-treated keratinocytes, the expression levels of collagen degradation-related genes and fibroblast senescence were significantly decreased; however, synthesis of procollagen type I was significantly increased. Our results confirm that EGT suppresses the modification of collagen homeostasis in fibroblasts by preventing downregulation of the Nrf2/HO-1 pathway and HSP70 in keratinocytes following UVB irradiation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Split selectable marker systems utilizing inteins facilitate gene stacking in plants

The ability to stack multiple genes in plants is of great importance in the development of crops with desirable traits but can be challenging due to limited selectable marker options. Here we establish split selectable marker systems using protein splicing elements called “inteins” for Agrobacterium-mediated co-transformation in plants. First, we show that such a split selectable marker system can be used effectively in plants to reconstitute a visible marker, RUBY, from two non-functional fragments through tobacco leaf infiltration. Next, to determine the general applicability of our split selectable marker systems, we demonstrate the utility of these systems in the model plants Arabidopsis and poplar by successfully stacking two reporters eYGFPuv and RUBY, using split Kanamycin or Hygromycin resistance markers. In conclusion, this method enables robust plant co-transformation, providing a valuable tool for the simultaneous insertion of multiple genes into both herbaceous and woody plants efficiently.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Time-resolved photoelectron imaging of complex resonances in molecular nitrogen

We have used the FERMI free-electron laser to perform time-resolved photoelectron imaging experiments on a complex group of resonances near 15.38 eV in the absorption spectrum of molecular nitrogen, N-2, under jet-cooled conditions. The new data complement and extend the earlier work of Fushitani et al. [Opt. Express 27, 19702-19711 (2019)], who recorded time-resolved photoelectron spectra for this same group of resonances. Time-dependent oscillations are observed in both the photoelectron yields and the photoelectron angular distributions, providing insight into the interactions among the resonant intermediate states. In addition, for most states, we observe an exponential decay of the photoelectron yield that depends on the ionic final state. This observation can be rationalized by the different lifetimes for the intermediate states contributing to a particular ionization channel. Finally, although there are nine resonances within the group, we show that by detecting individual photoelectron final states and their angular dependence, we can identify and differentiate quantum pathways within this complex system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Floquet-driven indirect exchange interaction mediated by topological insulator surface states

Light drives offer a potential tool for the dynamical control of magnetic interactions in matter. We theoretically investigate the indirect exchange coupling between two parallel chains of magnetic impurities on the surface of a topological insulator, driven by a time-periodic circularly polarized light field in the high-frequency, off-resonant regime. We derive a closed-form analytic expression for the spin susceptibility of the photon-dressed topological insulator surface states and obtain the irradiation dependence of the Ising, Heisenberg, and Dzyaloshinskii-Moriya exchange couplings between the impurity chains. Our results show a two-pronged modification of these exchange couplings by periodic drives. First, the Ruderman-Kittel-Kasuya-Yosida (RKKY) oscillation period of the exchange couplings can be extended by enhancing the driving strength. Second, increasing driving strength enhances the envelope of RKKY oscillations of the Ising type while suppressing those of the Heisenberg type and Dzyaloshinskii-Moriya type. Furthermore, our work provides useful insights for realizing Floquet engineering of collinear and noncollinear indirect exchange interactions in topological insulating systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Unraveling the Hsp70-ROS-autophagy axis in pentachlorophenol-challenged lung and liver epithelial cells

Pentachlorophenol (PCP) was extensively utilized as an organochlorine pesticide and wood preservative in the United States from the 1930s until the Environmental Protection Agency (EPA) imposed restrictions due to concerns about its toxicity and potential carcinogenic properties. Although it is no longer widely used, PCP remains a concern due to its environmental persistence and potential for long-term health effects. Significant occupational and environmental exposures have likely occurred, with the health and economic costs of PCP exposure potentially being substantial given its known toxicity. Notably, PCP exhibits rapid absorption through both the skin and respiratory system and has been shown to cause hepatotoxicity, developmental toxicity, immunotoxicity, irritation, and carcinogenicity in laboratory animal studies. PCP exposure induces oxidative stress, a key mechanism underlying its inflammatory and toxic effects, which can activate cellular stress responses including upregulation of heat shock protein 70 (Hsp70). Previous studies in lung and liver epithelial cells have shown that Hsp70 and oxidative stress play pivotal roles in triggering autophagy. This study establishes the critical role of the Hsp70-reactive oxygen species (ROS)-autophagy axis in regulating cellular responses to PCP exposure in human alveolar (A549) and liver carcinoma (HepG2) epithelial cells. Our research elucidated the molecular mechanisms underlying PCP's cellular effects, demonstrating that its exposure resulted in increased expression of autophagy-related proteins (Beclin-1, LC3B, ATG12, and ATG16), subunits of NADPH oxidase (NCF-1, NCF-2, NOX2, and Rac), and antioxidant proteins (SOD and GPx) in both lung and liver cell types. Notably, PCP augmented the interaction between Hsp70 and the autophagy regulator Beclin-1. Pretreatment with the ROS inhibitor N-acetylcysteine or Hsp70 knockdown markedly reversed PCP-induced responses. Our in-silico protein–protein docking analysis and molecular dynamics simulation studies revealed enhanced interactions and/or stable confirmations maintained throughout the simulations for TLR4-Hsp70 and Hsp70-Beclin-1 complexes in the presence of PCP. These findings provide a strong foundation for future studies, employing in vivo experimental models and human populations to identify promising targets for PCP-induced toxicity and cellular injury. As a result, these findings may have far-reaching implications for public health and environmental policy, ultimately leading to the identification of biomarkers and the development of more effective interventions for environmentally induced toxicity and diseases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Final Technical Report

The Department of Energy is interested in technologies that support the sustainable production of fuels, chemicals, and other bioproducts from plant biomass, to offset the nation’s reliance on fossil resources. The plant cell wall of energy crops provides the largest reservoir of raw materials for bioproducts. However, the widespread use of plant cell walls is hampered by their complexity and resistance to breakdown. To improve the productivity and cost-effectiveness of using energy crops to generate bioproducts, the fundamental problem of deconstructing plant cell walls must be addressed. This project developed and evaluated an innovative genetic modification technology to produce strategically designed enzymes that specifically accumulate in the plant cell wall. The resulting enzyme-engineered energy crops are expected to grow normally under natural conditions but break down more quickly and easily under high temperature during the production of biobased products. As such, this plant cell wall targeting enzyme engineering effort will reduce the cost of plant cell wall deconstruction and ultimately improve the economics of bioproducts. The overall objective of this project is to develop and evaluate the in-planta enzyme engineering technology to reduce lignocellulose deconstruction cost. The concept was first validated using tobacco plant, a model plant system that is typically used in lab testing for initial concept validation. Then the enzyme optimization was validated using switchgrass, the energy crop to be used to produce bioproducts. There are three specific objectives in this Phase I project: (1) validate the enzyme optimization concept using tobacco plant, a model plant system. (2) validate the enzyme optimization concept using switchgrass. (3) techno-economic analysis (TEA) for further scale-up application. By the end of this project, in-planta enzyme engineering was validated in both tobacco and switchgrass plants, with improved enzyme activity and saccharification efficiency. The in-planta enzyme engineering in Tabacco didn’t have a significant impact on plant growth and development. Transgenic tobacco plants with in-planta cellulose degrading enzymes showed higher biomass digestibility than wild type. Gene construction and transformation in switchgrass was much longer than expected, which delayed the research progress. Besides, in-planta engineering of lignin degrading enzyme is more challenging than cellulose degrading enzyme, in terms of expression detection. Expression of lignin degrading enzyme and cellulose degrading enzyme improved biomass yield and saccharification efficiency of switchgrass, respectively. It is promising to express both genes in switchgrass for optimized overall performance. According to the results of TEA, switchgrass biomass production cost is mainly attributed to by fertility and harvesting. Biomass production profit can increase up to 10-fold depending on biomass price. The PHA production profit is also sensitive to the biomass price. The proposed technology could potentially reduce the biomass deconstruction cost from 33% to 9% of PHA revenue, making the biomass-based PHA competitive to petroleum-based polymers even in case of relatively high biomass price of biomass. Therefore, cultivation of the genetically engineered self-deconstruction switchgrass for Polyhydroxyalkanoate (PHA) production could benefit switchgrass grower and PHA producer with attractive profits for both sectors. This new enzyme optimization approach will be beneficial for bioindustries that use energy crops as feedstocks. It will improve the economic viability of converting energy crops to renewable products that support a sustainable society and helps address the Nation’s long-term strategic needs for renewable products and reduction of reliance on fossil resources.

42 ENGINEERING↗
DOE OSTI2026

Gravity Well Commercial Economics Assessment: Potential Revenue and Cost: Cooperative Research and Development (Final Report)

In the Gravity Well Revenue Study, we evaluate the potential revenue from energy storage using historical energy-only electricity prices, forward-looking projections of hourly electricity prices, and actual reported revenue. This analysis examines the impact of storage duration and round-trip efficiency, as well as the location of the storage, on storage revenue within the current and projected U.S. power system. We also investigated the impact of round-trip efficiency on storage revenue. We found that the relationship between storage revenue and round-trip efficiency is nonlinear. The value of improved round-trip efficiency declines as round-trip efficiency increases. In the Gravity Well Future Cost Study, we applied learning curves to predict the future cost trajectory of Gravity Wells (GrWs). Two types of analysis were implemented. The first was a bottom-up analysis that used historical learning rates for cost components, such as motors and gearboxes, and cost categories (e.g., engineering and design, etc.) to determine the learning-by-doing based single-factor learning curve. The single factor learning curve expresses the relationship between the cost of GrW and the number of units deployed (or the cumulative capacity). In the second analysis, we predicted future GrW costs via a top-down approach. This approach accounts for historical cost trends in other renewable energy and storage technologies, which have similarities with GrWs. Using a multifactor learning curve that accounts for both intrinsic (cumulative capacity) and extrinsic (the elasticity in the price of steel) factors, we estimated the future cost of GrWs.

25 ENERGY STORAGE↗
DOE OSTI2024

Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration

The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The ATLAS experiment software on ARM

With an increased dataset obtained during the Run 3 of the LHC at CERN and the even larger expected increase of the dataset by more than one order of magnitude for the HL-LHC, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM architecture is becoming a competitive and energy efficient alternative. Some surveys indicate its increased presence in HPCs and commercial clouds, and some WLCG sites have expressed their interest. Chip makers are also developing their next generation solutions on ARM architectures, sometimes combining ARM and GPU processors in the same chip. Consequently it is important that the ATLAS software embraces the change and is able to successfully exploit this architecture. We report on the successful porting to ARM of the Athena software framework, which is used by ATLAS for both online and offline computing operations. Furthermore we report on the successful validation of simulation workflows running on ARM resources. For this we have set up an ATLAS Grid site using ARM compatible middleware and containers on Amazon Web Services (AWS) ARM resources. The ARM version of Athena is fully integrated in the regular software build system and distributed in the same way as other software releases. In addition, the workflows have been integrated into the HEPscore benchmark suite which is the planned WLCG wide replacement of the HepSpec06 benchmark used for Grid site pledges. In the overall porting process we have used resources on AWS, Google Cloud Platform (GCP) and CERN. A performance comparison of different architectures and resources will be discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Strong coupling expansion of free energy and BPS Wilson loop in $$ \mathcal{N} $$ = 2 superconformal models with fundamental hypermultiplets

As a continuation of the study (in arXiv:2102.07696 and arXiv:2104.12625 ) of strong-coupling expansion of non-planar corrections in \( \mathcal{N} \) = 2 4d superconformal models we consider two special theories with gauge groups SU( N ) and Sp(2 N ). They contain N -independent numbers of hypermultiplets in rank 2 antisymmetric and fundamental representations and are planar-equivalent to the corresponding \( \mathcal{N} \) = 4 SYM theories. These \( \mathcal{N} \) = 2 theories can be realised on a system of N D3-branes with a finite number of D7-branes and O7-plane; the dual string theories should be particular orientifolds of AdS 5 × S 5 superstring. Starting with the localization matrix model representation for the \( \mathcal{N} \) = 2 partition function on S 4 we find exact differential relations between the 1 /N terms in the corresponding free energy F and the \( \frac{1}{2} \) -BPS Wilson loop expectation value \( \left\langle \mathcal{W}\right\rangle \) and also compute their large ’t Hooft coupling ( λ » 1) expansions. The structure of these expansions is different from the previously studied models without fundamental hypermultiplets. In the more tractable Sp(2 N ) case we find an exact resummed expression for the leading strong coupling terms at each order in the 1 /N expansion. We also determine the exponentially suppressed at large λ contributions to the non-planar corrections to F and \( \left\langle \mathcal{W}\right\rangle \) and comment on their resurgence properties. We discuss dual string theory interpretation of these strong coupling expansions.

1/N expansion↗
DOE OSTI2022

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

09 BIOMASS FUELS↗