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At least 145 records · Page 8

Site Environmental Report for 2019

This report, prepared by Lawrence Berkeley National Laboratory (LBNL) for the U.S. Department of Energy, Bay Area Site Office (DOE!BASO), provides a comprehensive summary of the environmental program activities at LBNL for calendar year 2019. SERs are prepared annually for all DOE sites with significant environmental activities, and distributed to relevant external regulatory agencies and other interested organizations or individuals.

54 ENVIRONMENTAL SCIENCES↗

Advancing Enhanced Raman Spectroscopy to Detect and Measure NOW Pheromones (CPRB 2022 proposal)

Insect sex pheromones are chemical compounds that insects release to attract their partners over distances of hundreds of meters or even kilometers, in complete darkness and without any audible signals. Use of synthetic forms of key compounds have in some cases become an essential component of monitoring and/or managing key pests of agricultural crops, including navel orangeworm (Amyelois transitella) (NOW) in California tree nuts. These pheromone-based strategies can include monitoring, mating disruption, mass trapping, attract-and-kill and push-pull. There are currently multiple commercially available mating disruption products available for NOW and recent studies have demonstrated that they can be effectively used to reduce crop damage by this pest. Just how mating disruption works is not fully established and likely varies across products and target species. For instance, the extent to which synthetic pheromones compete with natural pheromone is not well understood, or in the case of monitoring, how efficaciously the insect follows the diffusing plumes, especially across large blocks and at plot borders. Furthermore, there may be specific conditions under which poor or impeded diffusion of synthetic pheromone diminishes the disruption effect, which could result in some males effectively locating females for reproduction. At the same time, many commercially available synthetic lures are also available, and growers have been effectively using them to track population development – although the attractive range of these lures remains unclear. That is, while pheromone lures can attract many moths, the relationship between trap capture and local populations, much less crop damage, remains unclear. Regardless of the emission source (aerosol puffers, meso emitters, lures etc.), we currently lack the ability to fully understand how these synthetic pheromone compounds diffuse away from their point-source of emission – and subsequently how this might affect the efficacy of mating disruption and/or the accuracy of monitoring efforts. Raman spectroscopy (RS) may offer a means to detect synthetic pheromone because of its analytical properties and recent technological advancements. In combination with nanostructured probes, RS has a demonstrated capability to detect volatiles at extremely low concentrations. While other methods for detecting pheromones have proven to be successful, such analytical methods like mass spectrometry (MS) gas chromatography (GC) require sampling in the fields and are not real-time. Other methods such as EAG/ EAD are also invasive (use antennas) but are of course valuable. Opto-electronic, micro and nano sensors just recently enticed interest. We fall in this latter category, proposing the use of optical spectroscopy (Raman) in a fiber aided by nanostructures to provide a chemical fingerprint without transductions and in real-time (i.e. no sampling). To date, we have been able to generate Raman signatures for the main chemicals in synthetic pheromones (a first for science, to the best of our knowledge), observe their trends at different concentrations, and also provide a clear distinction of such signatures in mixed samples via Principal Component Analysis (PCA) – all of which strengthens our conclusions on the ability of RS to detect emissions in more realistic conditions. We also established processes to enhance the detection sensitivity via preconcentration with Solid Phase Micro Extraction (SPME) fibers and Surface Enhanced Raman Spectroscopy (SERS) to increase the overall optical signals. Furthermore, we explored limitations and requirements for detecting from dispensers, lures, or live moths, including Dept. of Energy and CA State regulatory approvals. Finally, we setup some of our first “orchard in a box” experiments to measure pheromone diffusion along with developing appropriate models.

42 ENGINEERING↗

Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research

This final report summarizes the key accomplishments of the project entitled “Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research”. The goal of this project is aimed at developing innovative and improved imaging instrumentation for visualization and quantitative characterization of biomarkers related to molecular processes and cellular function in living plants. This project focused on three specific aims: 1) Development of Advanced Multimodal Optical Sensing And Imaging Combinatory (MOSAIC) System for SERS biosensing and bioimaging. 2) Evaluation of MOSAIC technologies for sensing and imaging gene expression in plant systems using plasmonic nanoprobes. 3) Application of MOSAIC techniques to bioenergy research.

47 OTHER INSTRUMENTATION↗

CORE-CM in The Greater Green River and Wind River Basins: Transforming and Advancing a National Coal Asset (Final Report)

The following document summarizes project results from “CORE-CM in the Greater Green River and Wind River Basins: Transforming and Advancing a National Coal Asset”. This project is part of the U.S. Department of Energy’s (“DOE”) National Energy Technology Laboratory’s (“NETL”) Carbon Ore, Rare Earth Elements, and Critical Minerals (CORE-CM) Initiative. This report concludes that the Greater Green River and Wind River Basins (GGRB-WRB) Area-of-Interest (AOI 9) is the ideal region for continued research and development in progressing the broader CORE-CM goals outlined by the DOE. Based upon the extensive analyses of technical, social, and community criteria, this report illustrates that the GGRB-WRB hosts numerous potential CORE-CM feedstocks (both coal- and non-coal based), diverse opportunities for utilizing existing industrial waste streams, ample infrastructure and industry to support new CORE-CM-focused technologies, and a highly motivated, well educated, and adaptable workforce to further develop the regional and national CORE-CM supply chain. Additionally, some potential solutions for technological gaps suggest that the GGRB-WRB's diverse resources can play a significant role in achieving the national goal of critical materials independence. With full community participation, meaningful involvement of regional Tribal Nations, and building upon the stakeholder engagement demonstrated here, the GGRB-WRB region presents a unique opportunity for advancing the CORE-CM Initiative. This project was designed to bring together coal-based communities and stakeholders from across the GGRB-WRB to advance new industries for CORE-CM resources. The University of Wyoming (UWyo) School of Energy Resources (SER) led a project team of experts from the Colorado Geological Survey (CGS), Colorado School of Mines (CSM), Los Alamos National Lab (LANL), and local community colleges. Input from basinal, regional, and national experts bolstered the coalition in order to advance the mission of DOE’s CORE-CM initiative and develop the domestic CORE-CM supply chain. Phase I of this project was designed to address the goal of developing and catalyzing economic growth, job creation, and technology innovation in the GGRB-WRB of Wyoming and Colorado, by increasing the supply of CORE-CM to manufacturers of non-fuel Carbon Based Products (CBP) and products reliant upon CM. The GGRB-WRB CORE-CM project worked toward providing benefit through several avenues of performance and research. • Develop a coalition team to achieve project objectives • Complete detailed assessments, including State-of-the-Art (SOTA) Data acquisition of potential CORE-CM materials across the AOI, and meaningfully contributes to DOE’s CORE-CM goals nationally. • Strategic planning for regional economic growth, job creation, and associated technology innovation around coal materials, including plans to maximize the development of potential CORE-CM resources and technology by creating regional public-private partnerships. • Define regional economic growth potential around existing strengths, energy infrastructure, business and industry, including planning for the leveraging of highly trained workforces, existing and novel coal technologies, and energy infrastructure in development of CORE-CM supply chains. • Develop a preliminary strategic plan for increasing the supply of CORE-CM materials to manufacturers of non-fuel Carbon Based Products (CBP) and products reliant upon CM, focusing on regional strengths that result in an emerging diversified CORE-CM economy. • Assemble a committed network of stakeholders and communities that learn about, accept, and grow new energy technologies within coal regions. Additionally, the project team significantly contributed to the CORE-CM Initiative’s national goals, through cross-regional scoping, collaborating with CORE-CM projects in other AOIs, and including parallel regional project experts. In addition to active inclusion and meaningful engagement and contribution to DOE-led working groups, the project team focused on engaging with regional communities including Tribal Nations, economic development groups, and regional government organizations. The project’s CORE-CM development and commercialization plan identified diverse CORECM feedstocks, potential routes towards integration with existing industries, methods for supply-chain development that leverage existing infrastructure and businesses considering the regional economy, identified entry barriers for incorporating traditional and new technologies in those supply chains, recognized opportunities for public-private partnerships to develop technology innovation centers, identified diverse workforces, and conducted stakeholder outreach and education to build a community of understanding on CORE-CM potential in the GGRB-WRB region. Detailed task descriptions can be found in each chapter.

01 COAL, LIGNITE, AND PEAT↗

PCOR partnership initiative to accelerate CCCUS deployment

The Plains CO 2 Reduction (PCOR) Partnership Initiative, led by the Energy & Environmental Research Center (EERC), was a 5-year collaborative effort under the U.S. Department of Energy’s Regional Initiative to Accelerate CCUS (carbon capture, utilization, and storage). With support from the University of Wyoming School of Energy Resources (UW SER), the University of Alaska Fairbanks Institute of Northern Engineering (UAF INE), and a broad network of public and private stakeholders, the program focused on overcoming regional challenges to CCUS across ten U.S. states and four Canadian provinces. This report summarizes the notable findings of the EERC and its collaborators through the 5-year PCOR Partnership Initiative phase. The EERC developed and demonstrated a risk-based area of review (AOR) workflow for U.S. Environmental Protection Agency Class VI carbon dioxide (CO 2 ) storage permitting.

01 COAL, LIGNITE, AND PEAT↗

The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11

SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019–2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11’s four heavy chain changes from the VH 3-53 germline sequence, $Thr^{28}_{FWRH1}$ to Ile and $Ser^{31}_{CDRH1}$ to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.

60 APPLIED LIFE SCIENCES↗

O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic pulmonary disease that is characterized by an excessive accumulation of extracellular matrix (ECM) proteins (e.g. collagens) in the parenchyma, which ultimately leads to respiratory failure and death. While current therapies exist to slow the progression, no therapies are available to resolve fibrosis. We characterized the O-linked N-Acetylglucosamine (O-GlcNAc) transferase (OGT)/O-GlcNAc axis in IPF using single-cell RNA-sequencing (scRNA-seq) data and human lung sections and isolated fibroblasts from IPF and non-IPF donors. The underlying mechanism(s) of IPF were further investigated using multiple experimental models to modulate collagen expression and accumulation by genetically and pharmacologically targeting OGT. Furthermore, we hone in on the transforming growth factor-beta (TGF-β) effector molecule, Smad3, by co-expressing it with OGT to determine if it is modified and its subsequent effect on Smad3 activation. We found that OGT and O-GlcNAc levels are upregulated in patients with IPF compared to non-IPF. We report that the OGT regulates collagen deposition and fibrosis resolution, which is an evolutionarily conserved process demonstrated across multiple species. Co-expression of OGT and Smad3 showed that Smad3 is O-GlcNAc modified. Blocking OGT activity resulted in decreased phosphorylation at Ser-423/425 of Smad3 attenuating the effects of TGF-β1 induced collagen expression/deposition. OGT inhibition or knockdown successfully blocked and reversed collagen expression and accumulation, respectively. Smad3 is discovered to be a substrate of OGT and its O-GlcNAc modification(s) directly affects its phosphorylation state. These data identify OGT as a potential target in pulmonary fibrosis resolution, as well as other diseases that might have aberrant ECM/collagen accumulation.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and Biochemical Characterization of a Novel Hormone-Sensitive Lipase Family Esterase Est19 from the Antarctic Bacterium Pseudomonas sp. E2-15

Esterases represent an important class of enzymes with a wide variety of industrial applications. A novel hormone-sensitive lipase (HSL) family esterase, Est19, from the Antarctic bacterium Pseudomonas sp. E2-15 is identified, cloned, and expressed. The enzyme possesses a GESAG motif containing an active serine (S) located within a highly conserved catalytic triad of Ser 155 , Asp 253 , and His 282 residues. The catalytic efficiency (k cat /K m ) of Est19 for the pNPC6 substrate is 148.68 s –1 mM –1 at 40 °C. Replacing Glu 154 juxtaposed to the critical catalytic serine with Asp (E154→D substitution) reduced the activity and catalytic efficiency of the enzyme two-fold, with little change in the substrate affinity. The wild-type enzyme retained near complete activity over a temperature range of 10–60 °C, while ~50% of its activity was retained at 0 °C. A phylogenetic analysis suggested that Est19 and its homologs may represent a new subfamily of HSL. The thermal stability and stereo-specificity suggest that the Est19 esterase may be useful for cold and chiral catalyses.

59 BASIC BIOLOGICAL SCIENCES↗

Arabinogalactan Structures of Repetitive Serine-Hydroxyproline Glycomodule Expressed by Arabidopsis Cell Suspension Cultures

Arabinogalactan-proteins (AGPs) are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily. They are heavily glycosylated with arabinogalactans, which are usually composed of a β-1,3-linked galactan backbone with 6-O-linked galactosyl, oligo-1,6-galactosyl, or 1,6-galactan side chains that are further decorated with arabinosyl, glucuronosyl, rhamnosyl, and/or fucosyl residues. Here, our work with Hyp-O-polysaccharides isolated from (Ser-Hyp)32-EGFP (enhanced green fluorescent protein) fusion glycoproteins overexpressed in transgenic Arabidopsis suspension culture is consistent with the common structural features of AGPs isolated from tobacco. In addition, this work confirms the presence of β-1,6-linkage on the galactan backbone identified previously in AGP fusion glycoproteins expressed in tobacco suspension culture. Furthermore, the AGPs expressed in Arabidopsis suspension culture lack terminal-rhamnosyl residues and have a much lower level of glucuronosylation compared with those expressed in tobacco suspension culture. These differences not only suggest the presence of distinct glycosyl transferases for AGP glycosylation in the two systems, but also indicate the existence of minimum AG structures for type II AG functional features.

59 BASIC BIOLOGICAL SCIENCES↗

The Heating and Pulsations of V386 Serpentis after Its 2019 Dwarf Nova Outburst

Following the pulsation spectrum of a white dwarf through the heating and cooling involved in a dwarf nova outburst cycle provides a unique view of the changes to convective driving that take place on timescales of months versus millennia for nonaccreting white dwarfs. In 2019 January the dwarf nova V386 Ser (one of a small number containing an accreting, pulsating white dwarf) underwent a large-amplitude outburst. Hubble Space Telescope ultraviolet spectra were obtained 7 and 13 months after outburst along with optical ground-based photometry during this interval and high-speed photometry at 5.5 and 17 months after outburst. The resulting spectral and pulsational analysis shows a cooling of the white dwarf from 21,020 to 18,750 K (with a gravity $\mathrm{log}(g)=8.1$) between the two UV observations, along with the presence of strong pulsations evident in both UV and optical at a much shorter period after outburst than at quiescence. The pulsation periods consistently lengthened during the year following outburst, in agreement with pulsation theory. However, it remains to be seen if the behavior at longer times past outburst will mimic the unusual nonmonotonic cooling and long periods evident in the similar system GW Lib.

79 ASTRONOMY AND ASTROPHYSICS↗

High efficiency active environmental sampling of chemical traces

A method of sample collection includes collecting an analyte from a sampling surface using a rapidly curable liquid gel comprising one or more metal particles; co-aggregating the one or more metal particles from the rapidly curable liquid gel and the analyte from the sampling surface; and rapidly curing the rapidly curable liquid gel. The composition and sample preparation conditions may facilitate improved collection efficiency of analytes during environmental and forensic evidence sampling. In addition, the composition and sample preparation conditions may facilitate enhanced detection and identification of the analyte using e.g., Surface Enhanced Raman Spectrometry (SERS).

Junghans, Ann↗

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗

Multi-Functional Applications of H-Glass Embedded with Stable Plasmonic Gold Nanoislands

Metal nanoparticles (MNPs) are synthesized using various techniques on diverse substrates that significantly impact their properties. However, among the substrate materials investigated, the major challenge is the stability of MNPs due to their poor adhesion to the substrate. Herein, it is demonstrated how a newly developed H-glass can concurrently stabilize plasmonic gold nanoislands (GNIs) and offer multifunctional applications. The GNIs on the H-glass are synthesized using a simple yet, robust thermal dewetting process. The H-glass embedded with GNIs demonstrates versatility in its applications, such as i) acting as a room temperature chemiresistive gas sensor (70% response for NO 2 gas); ii) serving as substrates for surface-enhanced Raman spectroscopy for the identifications of Nile blue (dye) and picric acid (explosive) analytes down to nanomolar concentrations with enhancement factors of 4.8 × 10 6 and 6.1 × 10 5 , respectively; and iii) functioning as a nonlinear optical saturable absorber with a saturation intensity of 18.36 × 10 15 W m -2 at 600 nm, and the performance characteristics are on par with those of materials reported in the existing literature. In conclusion, this work establishes a facile strategy to develop advanced materials by depositing metal nanoislands on glass for various functional applications.

36 MATERIALS SCIENCE↗

In-operando surface-sensitive probing of electrochemical reactions on nanoparticle electrocatalysts: Spectroscopic characterization of reaction intermediates and elementary steps of oxygen reduction reaction on Pt

In this paper we present an in-operando spectroscopic study of the reaction intermediates involved in ORR on electrified Pt nanoparticle electrocatalysts. To accomplish this, we have synthesized Ag-Pt core–shell nanoparticles, that contain a thin shell of Pt (~1 nm) uniformly deposited on a larger Ag core (~60 nm). We show that these nanostructures are ideal platforms for in-operando Plasmon Enhanced Raman Spectroscopy (PERS) of ORR on Pt. We combined these PERS studies with DFT calculations to assign the measured vibrational spectra to relevant surface intermediates as a function of electrocatalyst potential. Overall, these vibrational assignments were further verified and validated by performing PERS measurements using de-oxygenated and heavy oxygen (O 2 -18) saturated electrolyte. These studies allowed us to identity the presence of critical reaction intermediates (OH, O 2 , OOH, and H 2 O) as the function of operating voltage on the Pt surface and derive voltage-dependent elementary step mechanisms of the reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

El Agente: An autonomous agent for quantum chemistry

Computational chemistry tools are widely used to study the behavior of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El Agente Q, an LLM-based multi-agent system that dynamically generates and executes quantum chemistry workflows from natural language user prompts. The system is built on a novel cognitive architecture featuring a hierarchical memory framework that enables flexible task decomposition, adaptive tool selection, post-analysis, and autonomous file handling and submission. El Agente Q is benchmarked on six university-level course exercises and two case studies, demonstrating robust problem-solving performance (averaging >87% task success) and adaptive error handling through in situ debugging. It also supports longer-term, multi-step task execution for more complex workflows, while maintaining transparency through detailed action trace logs. Together, these capabilities lay the foundation for increasingly autonomous and accessible quantum chemistry.

agentic systems↗

Data-Driven Strategies for Accelerated Materials Design

The ongoing revolution of the natural sciences by the advent of machine learning and artificial intelligence sparked significant interest in the material science community in recent years. The intrinsically high dimensionality of the space of realizable materials makes traditional approaches ineffective for large-scale explorations. Modern data science and machine learning tools developed for increasingly complicated problems are an attractive alternative. An imminent climate catastrophe calls for a clean energy transformation by overhauling current technologies within only several years of possible action available. Tackling this crisis requires the development of new materials at an unprecedented pace and scale. For example, organic photovoltaics have the potential to replace existing silicon-based materials to a large extent and open up new fields of application. In recent years, organic light-emitting diodes have emerged as state-of-the-art technology for digital screens and portable devices and are enabling new applications with flexible displays. Reticular frameworks allow the atom-precise synthesis of nanomaterials and promise to revolutionize the field by the potential to realize multifunctional nanoparticles with applications from gas storage, gas separation, and electrochemical energy storage to nanomedicine. In the recent decade, significant advances in all these fields have been facilitated by the comprehensive application of simulation and machine learning for property prediction, property optimization, and chemical space exploration enabled by considerable advances in computing power and algorithmic efficiency. In this Account, we review the most recent contributions of our group in this thriving field of machine learning for material science. We start with a summary of the most important material classes our group has been involved in, focusing on small molecules as organic electronic materials and crystalline materials. Specifically, we highlight the data-driven approaches we employed to speed up discovery and derive material design strategies. Subsequently, our focus lies on the data-driven methodologies our group has developed and employed, elaborating on high-throughput virtual screening, inverse molecular design, Bayesian optimization, and supervised learning. We discuss the general ideas, their working principles, and their use cases with examples of successful implementations in data-driven material discovery and design efforts. Furthermore, we elaborate on potential pitfalls and remaining challenges of these methods. Finally, we provide a brief outlook for the field as we foresee increasing adaptation and implementation of large scale data-driven approaches in material discovery and design campaigns.

36 MATERIALS SCIENCE↗