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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Autoregulation of the LIM kinases by their PDZ domain

LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the ‘x-Φ-G-Φ’ motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Choreographing root architecture and rhizosphere interactions through synthetic biology

Abstract Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A single-Pt-atom-on-Ru-nanoparticle electrocatalyst for CO-resilient methanol oxidation

Single Pt atom catalysts are key targets because a high exposure of Pt substantially enhances electrocatalytic activity. In addition, PtRu alloy nanoparticles are the most active catalysts for the methanol oxidation reaction. To combine the exceptional activity of single Pt atom catalysts with an active Ru support we must overcome the synthetic challenge of forming single Pt atoms on noble metal nanoparticles. In this report we demonstrate a process that grows and spreads Pt islands on Ru branched nanoparticles to create single-Pt-atom-on-Ru catalysts. By following the spreading process by in situ TEM, we found that the formation of a stable single atom structure is thermodynamically driven by the formation of strong Pt–Ru bonds and the lowering of the surface energy of the Pt islands. The stability of the single-Pt-atom-on-Ru structure and its resilience to CO poisoning result in a high current density and mass activity for the methanol oxidation reaction over time.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Effect of a redox-mediating ligand shell on photocatalysis by CdS quantum dots

Semiconductor quantum dots (QDs) are efficient organic photoredox catalysts due to their high extinction coefficients and easily tunable band edge potentials. Despite the majority of the surface being covered by ligands, our understanding of the effect of the ligand shell on organic photocatalysis is limited to steric effects. We hypothesize that we can increase the activity of QD photocatalysts by designing a ligand shell with targeted electronic properties, namely, redox-mediating ligands. Herein, we functionalize our QDs with hole-mediating ferrocene (Fc) derivative ligands and perform a reaction where the slow step is hole transfer from QD to substrate. Surprisingly, we find that a hole-shuttling Fc inhibits catalysis, but confers much greater stability to the catalyst by preventing a build-up of destructive holes. We also find that dynamically bound Fc ligands can promote catalysis by surface exchange and creation of a more permeable ligand shell. Finally, we find that trapping the electron on a ligand dramatically increases the rate of reaction. Furthermore, these results have major implications for understanding the rate-limiting processes for charge transfer from QDs and the role of the ligand shell in modulating it.

Chemistry↗
DOE OSTI2026

Decoupling plasma, catalyst, and gaseous mechanisms for non-oxidative methane conversion

Direct non-oxidative methane (CH 4 ) conversion to value-added hydrogen (H 2 ) and C 2 products remains hindered by fundamental catalytic scaling constraints and rapid surface deactivation at elevated temperatures. Plasma-enabled catalysis offers a promising route to overcome the thermodynamic and kinetic barriers of direct non-oxidative methane upgrading at mild conditions, yet control over C–C product selectivity and catalyst stability remains elusive. Here, we establish a unified mechanistic framework including Langmuir–Hinshelwood (L–H) and Langmuir–Rideal (L–R) mechanisms that disentangles the roles of plasma excitation (including vibrationally activated species and radicals), surface temperature (T sur ), and catalyst binding energy in steering CH 4 conversion to H 2 and C 2 hydrocarbons. Through a combination of density functional theory (DFT) informed microkinetic modeling, in situ and ex situ surface characterization, and product quantification under dielectric barrier discharge conditions, we show that vibrationally excited CH 4 lowers activation barriers selectively for dissociative chemisorption, enabling surface activation across a wide range of transition metal catalysts at low thermal energy input. We find that once CH 4 is dissociatively chemisorbed, the branching between C 2 H 2 , C 2 H 4 , and C 2 H 6 is governed by surface properties (carbon binding energy, T sur , etc), regardless of plasma excitation. The DFT informed microkinetic model decouples the effects of molecular activation from surface properties and indentifies operating windows that maximize target yields while suppressing carbon accumulation and subsequent catalytic inactivation. Experiments on polycrystalline Cu/Al 2 O 3 , Ni/Al 2 O 3 , and Pt/Al 2 O 3 validate these predictions, revealing catalyst-dependent branching toward ethane or ethylene and distinct deactivation profiles. We unify these trends into a generalized three-dimensional plasma-thermal-catalytic design space, from which reduced descriptors such as T vib /T sur in the limit of vibrationally excited L–H pathways emerge as predictive metrics. These results enable rational tuning of methane conversion pathways and unlock selective C 2 formation using earth-abundant metals under mild plasma conditions.

catalyst inactivation↗
DOE OSTI2024

Gut microbiota carbon and sulfur metabolisms support Salmonella infections

Abstract Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design

The Cas9 nuclease has become central to modern methods and technologies in synthetic biology, largely due to the ease with which it can be targeted to specific DNA loci via guide RNAs (gRNAs). Reports vary widely on the actual specificity of this targeting, with some studies observing 60% of gRNAs possessing no activity against the genome, yet an assumption persists within the E. coli community that inactive gRNAs are rare. To resolve these contradictions, we evaluated the activity of 463 000 unique gRNAs in the E. coli K12 MG1655 genome. We show that the overwhelming majority (at least 93%) of unique gRNAs are functional while only 0.3% are nonfunctional. These nonfunctional gRNAs exhibit strong spacer self-interaction, which can either be excluded using a simple design rule or “repaired” during library design. Finally, this work provides the greater microbial synthetic biology community both a set of nearly half a million empirically evaluated E. coli gRNAs as well as a thoroughly evaluated experimental procedure, complete with appropriate controls for Cas9 activity, for conducting Cas9 assays in E. coli specifically and bacteria more generally. Lastly, we have produced a webapp to allow users to easily browse and extract gRNA sequences from the E. coli genome, which can be accessed at https://grna.ornl.gov.

Kammerdiener, Elise K. [Oak Ridge National Laborat↗
DOE OSTI2020

Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes

In animals, several long-chain N-acylethanolamines (NAEs) have been identified as endocannabinoids and are autocrine signals that operate through cell surface G-protein coupled, cannabinoid receptors. Despite the occurrence of N-acylethanolamines in land plants, including non-vascular plants, their precise signaling properties and molecular targets are not well defined. Here we show that the activity of N-linolenoylethanolamine (NAE 18:3) requires an intact G-protein complex. Specifically, genetic ablation of the Gβγ dimer or loss of the full set of atypical Gα subunits strongly attenuates an NAE 18:3-induced de-greening of cotyledons in Arabidopsis seedlings. This effect involves, at least in part, transcriptional regulation of chlorophyll biosynthesis and catabolism genes. In addition, there is feedforward transcriptional control of G-protein signaling components and G-protein interactors. These results are consistent with NAE 18:3 being a lipid signaling molecule in plants with a requirement for G-proteins to mediate signal transduction, a situation similar, but not identical, to the action of NAE endocannabinoids in animal systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Materials Plasma Exposure eXperiment: Status of the Physics Basis Together With the Conceptual Design and Plans Forward

The Materials Plasma Exposure eXperiment (MPEX) is a linear plasma device that will address the plasma–material interaction (PMI) science for future fusion reactors and will enable testing of plasma-facing components (PFCs). It is designed as a steady-state device eventually delivering an ion fluence of up to 10 31 m -2 to the target. The device will be designed to handle neutron-activated materials. These capabilities should push the technical readiness level of PFCs up to six for some end-of-life aspects. In order to achieve the relevant plasma conditions, as they are expected in future fusion reactor divertors, MPEX will utilize a novel plasma source concept. This plasma source concept uses a high-power helicon (200 kW, 13.56 MHz), an electron cyclotron heating (ECH) system, which will heat electrons via electron Bernstein wave (EBW) heating (about 400 kW, 70 GHz), and an ion cyclotron heating (ICH) system (400 kW, 6–9 MHz). The physics basis for this plasma source concept including the heating physics and transport is based on experiments on Proto-MPEX. An overview of the experimental results and the physics basis will be given. The physics basis directly translates into functional requirements of MPEX and the conceptual design. The status of the conceptual design of MPEX will be shown.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Field Validation of Thermoelectric Generation System at Holcim Cement Plant in Alpena, Michigan

Executive Summary Project Background The Industrial Technology Validation (ITV) program aims to identify and demonstrate the performance of new, emerging, and underutilized energy-saving technologies in the industrial sector to help inform decisions to help accelerate their commercialization and deployment, as well as to help make industries more competitive. This ITV demonstration evaluated a thermoelectric generation (TEG) technology at a cement plant, aiming to reduce energy demand in the cement industry. A median cement plant consumes 5.73 million British thermal units per ton of clinker production (resulting in 0.838 metric tons of carbon dioxide [CO₂] emissions per ton of clinker) (Boyd and Zhang 2011, EPA 2021), equivalent to approximately 6.9 trillion British thermal units (TBtu) per year in energy consumption at a cement plant producing 3,300 tons of clinker per day.¹ Collaborating with Holcim, Advanced Thermovoltaic Systems (ATS) developed and deployed a pilot-scale thermoelectric power system to efficiently capture and convert waste heat to electricity. The system leverages the Seebeck effect to convert temperature differences on two sides of semiconductor cartridges into electrical power (ScienceDirect, n.d.). This generation is realized with minimal moving parts compared to existing waste-heat-to-generation solutions and allows capture from heat sources with temperatures as low as 150°C. This project aimed to validate a scalable solution applicable for capturing medium-temperature waste heat, including ambient losses from other high-temperature processes, and high-temperature sources less suitable for other waste-heat-to-power solutions. By recovering this otherwise wasted heat, this project intends to validate improvements to overall process efficiency through reduction in purchased electricity, thereby reducing operational costs while enhancing resiliency and competitiveness. Description and Scope This study evaluated the performance of a TEG system from ATS as a solution to convert waste heat into useful power at a Holcim cement plant in Alpena, Michigan. This plant is a fully integrated cement plant that has been operating since 1907. The facility operates continuously (24/7/365) with approximately 250 employees and five long dry kilns, yielding a total production capacity of 7,852 tons of cement per day (EPA 2023). Currently, the Alpena plant uses waste heat boilers to convert waste heat from the exhaust of each kiln into steam, which drives steam turbine generators. The ATS TEG is being evaluated for its potential to supplement the steam turbines by capturing the remaining lower grade heat. This technology is also being considered for other Holcim plants where steam turbines are not a viable option. ATS installed a pilot-scale TEG unit with an array of 582 individual thermoelectric semiconductor cartridges, of which 573 were operational. The cartridges are sandwiched between 48 hot plates and 49 cold plates. Each cartridge is designed to generate 20 watts (W) of gross power at a hot-side temperature of 240°C and cold-side temperature of 20°C. As such, the total gross generation capacity of the installed system is 11.5 kilowatts (kW) at design conditions. The system configuration for the evaluation was designed to prioritize convenience of installation and minimize disruption to production at the site, while ensuring that the heat required can be obtained for evaluating the TEG system at various operational conditions. To accomplish this, a portion of the steam supplied to Alpena’s steam turbine generation system was diverted to be used as the heat source for the TEG system, while water was supplied to the cold side of the system from nearby Lake Huron. This configuration was designed for the evaluation of the pilot-scale system to assess the performance at different conditions. A commercial-scale system will likely vary from the pilot system depending on typical configurations, including both scale and application. Future commercial applications of the ATS system would involve integrating the system into the exhaust from kiln preheaters, clinker coolers, or radiant heat capture from kiln shells for the heat source. For the cold source, a range of cooling solutions can be considered, including a mechanical cooling system, depending on the location and the application. To increase the generation capacity for commercial applications, the technology provider is working toward developing a commercial-scale TEG system, which would combine multiple TEG units (each similar in design to the pilot system) together. The scope of this evaluation includes the pilot-scale TEG system and all impacted equipment including pumps, controllers, and power handling equipment. Study Objectives The evaluation's goal was to assess the potential of the ATS TEG system to generate useful electrical power by capturing waste heat from cement production kilns. The objectives of this study are to evaluate and verify the following claims made by ATS regarding the pilot-scale system installed at the Holcim Alpena plant. The following design parameters and claims are also outlined in Table ES- 1 and Table ES- 2: • Gross Power: The thermoelectric system converts heat into power to create gross power, the total measured power generated by the system. The 573 active cartridge pilot-scale system is expected to generate 11.5 kW of gross power at the designed hot-side temperature of 240°C and cold-side temperature of 20°C. Power production is dependent on the temperature difference between the heat source (ultimately from the waste heat) and cold temperature supply source. • Net Power: The net power is the total usable power provided to the site by the TEG system after deducting parasitic power loads from the gross generated power. Supplementary equipment is required to operate the TEG system including pumps, controllers, and, in certain anticipated applications, mechanical cooling, which introduce parasitic loads to system operation. After deducting the parasitic loads from the gross power generation, ATS anticipates achieving a net power generation of 7.5 kW from the pilot-scale system. • Thermal Efficiency: The thermal efficiency is the percent of the total heat transferred to the TEG system that is converted to gross power. Historically, TEGs have a thermal efficiency of 2%–5% (DOE 2008). Prior industrial-scale TEG systems, such as the E1 TEG offered by Alphabet Energy, operated at an efficiency of 2.5% (Lamonica, 2014). ATS anticipates achieving an average efficiency of 4.8% or higher in converting heat energy to usable electricity. • Cartridge Performance: The TEG system comprises 573 active individual semiconductor cartridges, each of which generates a portion of the total power. Cartridge optimization and selection is an important design consideration for potential future TEG system design performance. Therefore, understanding the distribution of gross power and efficiency within the pilot system is vital to understanding what is achievable. At a design hot-side temperature of 240°C and cold-side temperature of 20°C, ATS anticipates a cartridge performance of 20 W of gross power per cartridge at an efficiency of 4.8% per cartridge. In addition to evaluating the claimed performance of the TEG pilot-scale unit, the study estimated the potential annual impacts of a scaled-up commercial system used to capture kiln waste heat over annual operations. The evaluation estimated the gross and net annual electric generation achievable by capturing heat from the two proposed tap-in points: the kiln exhaust and the clinker cooler exhaust; see Section 2.1 for details. Two use cases were examined: • Holcim Alpena: The Holcim Alpena site consists of long dry kilns with superheater boilers, which differs from the rest of Holcim’s cement plant portfolio and results in lower waste heat temperatures. The study estimates gross and net annual generation using the superheater boiler exhaust and clinker cooler exhaust, based on 2023 operational data. • Typical Installation: Common cement plants have preheater kilns with higher exhaust temperatures than Holcim Alpena across a range of production rates. The study estimates gross and net annual generation using the preheater exhaust and clinker cooler exhaust, with a sensitivity analysis to account for the typical range of preheater exhaust temperatures, clinker cooler exhaust temperatures, and clinker production rates. Methodology The evaluation methodology followed a measurement and verification (M&V) strategy based on the International Performance Measurement and Verification Protocol Option B through comprehensive measurements and analyses of the affected systems. Evaluation data was collected from March 9 to March 11, 2024, the test period of the pilot TEG system. During the test period, in coordination with the ITV team, the ATS team adjusted system operations to capture the range of variability expected for each of the variables pertinent to performance of the system. The methodology consisted of two parts: evaluating the performance of the pilot unit's TEG system and estimating the annual TEG impact in terms of gross and net power based on a given waste heat profile. First, the evaluation of the thermoelectric generation performance of the pilot unit relative to the claims was performed by analyzing the collected test data. Gross power of the pilot TEG system was directly measured. Net power was determined by deducting the measured parasitic power from the gross power. The gross power generation was compared to heat transferred to the system by the working fluid (which was heated by steam generated from the kiln waste heat) to calculate the thermal efficiency achieved by the system. Performance of individual semiconductor cartridges within the pilot array was also assessed in terms of measured gross cartridge power and calculated cartridge thermal efficiency. The second part of the evaluation estimated the annual TEG impacts in terms of gross power and net power (calculated from the difference between gross power and parasitic power). This analysis comprised development of mathematical regression models for gross power and parasitic power, with assessment of each model’s goodness-of-fit characteristics to ensure satisfaction of statistical requirements. The models predicted the gross power generation, the parasitic load based on the temperature difference between the hot working fluid and the cold-side fluid (cold water from Lake Huron) entering the system, the volumetric flow rate of the cold-side fluid at the inlet, and the volumetric flow rate of the hot working fluid at the inlet. The annual impact analysis considered a theoretical commercial-scale system sized to capture the available waste heat at a cement plant, consisting of linked pilot-scale units that receive heat from a theoretical gas-to-working-fluid heat exchanger. To estimate annual impacts at the Alpena plant, the gross power and parasitic power regression models were applied to the arrays in the theoretical commercial-scale system. The heat supplied to the unit was calculated based on the kiln run time, annual production, kiln exhaust waste heat, and clinker cooler waste heat derived from 2023 Holcim Alpena kiln operational data. Net power impacts were calculated by deducting the resulting parasitic power from the estimated gross power. Inputs for the model were generated from a combination of hourly data, assumed design considerations for TEG system scale-up from the pilot-scale unit, and assumptions regarding TEG system operations. This analysis was then used as the basis for estimating annual impacts of typical TEG installation at cement plants, by applying sensitivity analyses to key kiln operational characteristics including kiln preheater exhaust temperatures, cooler clinker exhaust temperatures, and plant daily production rates across a range of expected values. Project Results/Findings Table ES- 2 and Table ES- 2 provide a summary of the operating conditions and evaluation results compared to the stated claims from the technology provider. Key takeaways include: • Gross Power: The peak gross power achieved during the testing period was 10.0 kW, compared to the 11.5 kW expected for 573 active cartridges. The claimed gross power was associated with a target hot side of 240°C; however, the system only received a maximum hot-side mean plate temperature of 212°C during the testing period. • Net Power: The pilot-scale unit exceeded the claims for net power, achieving a peak of 7.7 kW net compared to a claim of 7.5 kW. One factor contributing to the higher achieved net power is the relatively high water pressure available through Lake Huron. The pilot TEG system did not require cold-side pumps during the test, whereas most installations would. This reduced the parasitic loads on the system, ultimately contributing to higher net power relative to the gross power. • Thermal Efficiency: The pilot-scale unit outperformed the claimed efficiency, achieving a peak system efficiency of 5.0% thermal efficiency compared to the stated 4.8%. • Cartridge Performance: To compare cartridge performance against claims, the study focused on the third day of testing, which aimed for conditions closest to the design specifications, with a hot side of 240°C and cold-side exit temperature of 6.4°–30°C. On this day, the mean gross power observed in the cartridges within the TEG array was 18.1 W/cartridge, and the peak performance was 34.7 W/cartridge. The estimated mean cartridge efficiency was 5.2%, and the estimated efficiency at peak gross cartridge power was 10%. The regression models developed for gross power generation and parasitic loads were used to estimate the generation impact for given heat input to the TEG from the working fluid (captured from the waste heat) and from the cold loop (Lake Huron) on an hourly basis for a year of operation. Based on this analysis, installation of a commercial-scale TEG system at the Holcim cement plant in Alpena, Michigan, with a waste heat exchanger of 0.85 effectiveness, would generate up to 391 kW of net power, translating to between 920,000 and 1,800,000 kilowatt-hours (kWh) in net electricity per year. Based on typical grid emissions for Alpena, this would avoid estimated net emissions by 752 metric tons of CO₂ annually.² The sensitivity analysis estimated that typical TEG system installations at cement plants could generate an average of 56–1,040 kW of net power, or between 488,000 and 9,110,000 kWh of net energy. This generation potential is most significantly affected by plant production rates and also influenced by preheater and clinker cooler exhaust temperatures. Applying the national average emission rate, typical commercial-scale installations at Holcim plants are projected to avoid between 182 and 3,401 metric tons of CO₂ annually per site. Table ES- 3 shows a summary of the estimated annual impacts.³ While parasitic loads are significant and vary by application, this analysis assumed the use of heating loop pumps and access to Lake Huron as a cold sink. This setup assumed no need for cooling loop pumps due to the available water pressure at the test site. Applications that require cooling towers or additional equipment are likely to experience higher parasitic loads. Therefore, the study’s estimates are most applicable to scenarios with similar parasitic load configurations—namely, access to a high-pressure cold sink. Applicability to other locations may be limited, as differing conditions could necessitate additional pumps and cooling systems, potentially impacting performance significantly.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Editorial: Nanotechnology for natural products

Humans around the globe have lived through an unprecedented time. The emergence and rapid spread of coronavirus disease 2019 (COVID-19) have resulted in the loss of millions of lives, and this number is still climbing every day and hour. As a consequence, there have been drastic changes over the past two years in how we live, communicate, and work, some of which may have changed forever: remote conferencing has become a new norm for businesses, schools, and academia; work-from-home and hybrid working is now more than just acceptable in many industries; most importantly, COVID-19 has raised global awareness of infectious diseases and pandemic responses to an exceptional level. Certainly, COVID-19 is not the only disease that is causing human suffering at this moment. Other highly contagious and lethal viruses, such as the human immunodeficiency virus (HIV), Ebola, and the recent addition to the list, Monkeypox, pose extraordinary challenges to modern civilizations. On the other hand, non-communicable diseases, such as heart disease, stroke, and cancer, are still claiming the majority of deaths on a global level (World Health Organization, 2020). Before the availability of synthetic drugs, civilizations worldwide relied on natural products extracted from the environment and various organisms for healthcare. Natural products and their derivatives continue to be critical components in the drug library available today. Indeed, almost a quarter of the new drugs approved by the US Food and Drug Administration (FDA) since 1981 are natural products, botanical mixtures, or their derivatives (Newman and Cragg, 2020). Recent developments in analytical characterization, genome mining, and engineering have further increased interest in drug discovery from the pool of natural products (Atanasov et al., 2021). This Research Topic celebrates a collection of studies at the intersection of natural product research and nanotechnological advances. As a successor and extension of the Research Topic in “Nanotechnology in Traditional Medicines and Natural Products” published last year (Zhang et al., 2021), the present collection focused more on recent developments in employing the synthesis and characterization of nanostructures for the delivery of functional natural products. Specifically, the use of carrier nanostructures to conjugate or encapsulate therapeutically active natural products with carrier nanostructures could enable their robust, targeted delivery tailored to either tackle a specific disease or unlock a drug administration pathway. Over the last decade, nanostructures such as liposomes (Pattni et al., 2015) and lipid nanoparticles (Hou et al., 2021) have been developed as versatile platforms for the inclusion and delivery of a wide range of therapeutical compounds; a significant advance in this aspect is the stabilization of mRNA strands for COVID-19 vaccination recently produced by Pfizer/BioNTech and Moderna (Tenchov et al., 2021). Such engineered nanomaterials are now widely used in the development of new drugs, while regulatory forces, such as the US FDA, remain cautious with the evaluation of each product on a case-by-case basis (Wang and Grainger, 2022). In this collection, Zeng et al. provided a timely review of natural products conjugated to and contained within nanomaterials for the ongoing COVID-19 pandemic. Natural products that are potentially useful in the mitigation of this disease, such as chloroquine and curcumin, supported in nanocarrier systems, have been discussed in detail. More broadly, Cheng et al. comprehensively reviewed the use of liposomes as a nanocarrier for natural products. This article provides a summary of natural product compounds and extracts used to form liposomal structures. Readers can further enjoy the practical aspects of these engineered drugs for the treatment of specific diseases as well as insights into future directions in this field.

peptides↗
DOE OSTI2021

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Using Domain Insertion to Create Sulfite Reductases That Present Chemical-Dependent Activities

Domain insertion can be used to create oxidoreductases whose activities are dependent upon analyte binding. To date, most domain insertion studies have targeted relatively small oxidoreductases of known structure, so it remains unclear how to apply this protein engineering approach to large hetero-oligomeric proteins that require dynamic conformational changes for catalysis. To address this question, we studied the effects of peptide and domain insertions on the activity of NADPH-dependent sulfite reductase (SiR) from Escherichia coli, a dodecameric oxidoreductase containing four hemoprotein and eight flavoprotein subunits. SiR mutational tolerance was first evaluated using systematic octapeptide insertion and a cellular selection, which identified regions across the hemoprotein structure that retain parent-like activity following insertion. When a ligand-binding domain was inserted at backbone locations tolerant to peptide insertion, including sites proximal and distal from the intersubunit interfaces, ∼90% retained catalytic activity, and >50% presented activity that is regulated by an endocrine disruptor. With one domain insertion variant, the conditional production of sulfide could be monitored electrochemically from cells using a bioelectrochemical reactor. These results show how systematic peptide insertion can be used to inform domain insertion in a large heterooligomeric protein complex, and they illustrate how SiR can be engineered to convert chemical information in the environment into a redox-active metabolite that diffuses across the cell membrane.

bacteria↗
DOE OSTI2023

Logical Activation Functions v.1.1

SAND2024-01501O Logical Activation Functions software is a PyTorch implementation from the paper, "Logical Activation Functions for Training Arbitrary Probabilistic Boolean Logic." The activation functions approximate logit-space marginalization of probabilistic truth tables from probabilistic interpretations of inputs. They also provide a general methodology to approximate logical relationships between abstract antecedents and consequents for machine learning architectures. They do not target any specific application or use-case. By training probabilistic truth tables, these activation functions can capture more expressive relationships in a neural network than typical elementwise activation functions. This code is only designed for a single compute node with a GPU and is limited to machine learning architectures than can fit within the memory of a single GPU. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Duersch, Jed↗
DOE OSTI2022

Controlling Structural, Electronic, and Energy Flow Dynamics of Catalytic Processes through Tailored Nanostructures

MoS 2 (molybdenum disulfide) is a highly-versatile catalyst material for support of numerous reactions from hydrodesulfurization and denitrogenation to the focus of this renewal proposal: hydrogenation of CO/CO 2 towards (higher) alcohols. At the same time, MoS 2 is a non-toxic, environmentally-benign and rather inert material- which under ambient conditions for some time has served as a lubricant and, more recently, as next-generation electronic material. The apparent contrast between inertness and stability in ambient, and catalytic activity under reactive conditions is puzzling and calls for a synergistic theoretical and experimental investigation with the long-term objective of enabling the rational design of MoS 2 -based catalysts for alcohol-formation reactions by providing a microscopic understanding of the environmental factors that determines site activity and selectivity. Our research project seeks answers to the questions (a) what conformation does MoS 2 adopt under reaction conditions (as opposed to that under ultrahigh vacuum and low temperatures)?; (b) what reaction pathways exist on such a material?; (c) how can the local environment of the active sites be manipulated so as to make MoS 2 an efficient catalyst for production of higher alcohol from syngas? In particular, research strategies will explore how the basal plane composed of sulfur atoms can be activated so as to exhibit a reactivity of its own, by addressing three research targets and building on extensive preliminary and enabling work: (1) vacancies and vacancy aggregates on the basal plane; (2) non-local catalyst transformation through alkali doping, hydrogenation and phase transition; (3) fabrication of a metal-nanoparticle-activated MoS 2 system, in which particle anchoring, reactive sites and pathways as well as selectivity are controlled by design, as an example of predictive development of a catalyst material,. All strategies are directed to improve the efficacy of the key reactive sites and selectivity of chemical pathways by design, to replace the inefficient methodology of trial and error in catalyst development. This research project represents a synergistic combination of computational guidance, foundational surface-science-based experiments and validation under reactive conditions that aims at transformative new insights into the working of MoS 2 -based hydrogenation-catalysts, a topic squarely at the center of the interest of DOE BES. Guided and led by Talat Rahman, a computational physicist, this project will apply density functional theory to understand structure, reaction pathways and chemical potentials associated with MoS 2 -based CO/CO 2 hydrogenation, augmented by kinetic Monte Carlo methods for reaction rates and prefactors as well as ab-initio molecular dynamics for evaluation of thermal stability. Complementary experimental input and validation will originate from co-PI Ludwig Bartels, a physical chemist and materials scientist, whose group focuses on local imaging and preparation of MoS 2 materials, from co-PI Peter Dowben, an experimental physicist, whose group is expert in the spectroscopy of occupied and unoccupied electronic states, and from senior collaborator Michael White of Brookhaven National Laboratory, whose group generates high-resolution electronic and activity information on size-selected well-defined metal chalcogenide clusters. This collaborative effort will enable a comprehensive understanding of the correlation of structural integrity and catalytic activity of MoS 2 in forms ranging from extended films to individual particles with known geometries and binding sites. Alcohol formation from syngas is a rapidly emerging application that has great potential through facile, economic, and decentralized biomass gasification. CO 2 activation is one of the most pressing concerns of our time: increasing CO 2 levels in the atmosphere change the climate and expose the globe to environmental transformations with the potential for enormous economic and societal impact. We will investigate CO/CO 2 hydrogenation via an interdisciplinary research collaboration with established synergy – one that, in accordance with the mission of the DOE, involves accredited Hispanic-Serving Institutions and that, through student exchange with international collaborators and National Labs, will directly benefit a broad spectrum of communities and generate human resources in sciences essential to their future.

2D materials↗
DOE OSTI2021

Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics

While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. Furthermore, this demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.

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

Vitrification of Hanford Tank 241-AP-107 with Recycled Condensate

During the vitrification of nuclear waste at the Hanford Waste Treatment and Immobilization Plant (WTP) – the primary mission of the U.S. Department of Energy Office of River Protection – the offgas condensate generated from the waste-to-glass conversion is currently planned to be concentrated by evaporation in the Effluent Management Facility (EMF). This concentrated condensate can then be recycled back to the incoming waste and vitrified. To test the recycle process, a test apparatus was designed to mimic the EMF evaporator and used to concentrate a volume of condensate that had been previously produced during the vitrification of Hanford tank 241-AP-107 (referred to herein as AP-107) waste in a continuous laboratory-scale melter (CLSM). The test apparatus successfully concentrated the AP-107 condensate by a factor of 10 while retaining over 90 % of the technetium-99 ( 99 Tc), Cs, and I inventory. A second portion of AP-107 waste was retrieved by Washington River Protection Solutions, LLC, given to Pacific Northwest National Laboratory, and combined with the AP-107 condensate concentrate after undergoing solids filtration and cesium removal by ion exchange. This combination served to approximate the recycling action to be performed at the WTP. After the addition of glass-forming chemicals (GFCs), the combined AP-107 waste and AP-107 condensate concentrate were processed in the CLSM to produce a glass, called AP-107-1R, that was designed to satisfy the WTP baseline requirements (Kim et al. 2012). During the 8.87 hours of processing, 7.27 kg of AP-107-1R glass were produced for an average glass production rate of 1739 kg m 2 d -1 . Compared to the previous run in the CLSM without recycled condensate, the run with the recycle had a greater average glass production rate, but the rate was within the potential range of variability when processing melter feeds with similar composition in the CLSM. The glass produced from the AP-107 recycle run in the CLSM was within 10 % of the target AP-107-1R glass composition with respect to the primary glass components. Analysis of the minor component impurities revealed that their content in the glass product had approached their nominal target after 2 turnovers of the glass inventory in the CLSM while the activity of the minor radionuclides was retained in the glass product. The 99 Tc and total cesium content in the combined AP-107 waste and recycled condensate were maintained at concentrations expected to be experienced at the WTP. During processing in the CLSM, at discrete sampling time periods, the target 99 Tc/Cs mass ratio in the glass formulation varied from 0.9 to 62.9. Across this range, the Cs retention in the glass ranged from 53 to 60 %, while the retention from the entire runtime totaled 68 %, values which align with Cs retention in other scaled melter systems while processing LAW melter feeds at 99 Tc/Cs mass ratios ranging from 1 to 100. The 99 Tc retention in the glass ranged from 22 to 32 %, primarily due to the cold-cap coverage on the glass melt surface, the area covered by reacting melter feed, varying from ~80 % to ~95 % during processing, demonstrating greater volatility of 99 Tc from the glass while more surface was exposed, as expected based on previous 99 Tc volatility studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗