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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 OSTI2020

Programming Amphiphilic Peptoid Oligomers for Hierarchical Assembly and Inorganic Crystallization

Natural organisms make a wide variety of exquisitely complex, nano-, micro-, and macroscale structured materials in an energy-efficient and highly reproducible manner. During these processes, the information-carrying biomolecules (e.g., proteins, peptides, and carbohydrates) enable (1) hierarchical organization to assemble scaffold materials and execute high-level functions and (2) exquisite control over inorganic materials synthesis, generating biominerals whose properties are optimized for their functions. Inspired by nature, significant efforts have been devoted to developing functional materials that can rival those natural molecules by mimicking in vivo functions using engineered proteins, peptides, DNAs, sequence-defined synthetic molecules (e.g., peptoids), and other biomimetic polymers. Among them, peptoids, a new type of synthetic mimetics of peptides and proteins, have received particular attention because they combine the merits of both synthetic polymers (e.g., high chemical stability and efficient synthesis) and biomolecules (e.g., sequence programmability and biocompatibility). The lack of both chirality and hydrogen bonds in their backbone results in a highly designable peptoid-based system with reduced structural complexity and side chain-chemistry-dominated properties. Here in this Account, we present our recent efforts in this field by programming amphiphilic peptoid sequences for (1) the controlled self-assembly into different hierarchically structured nanomaterials with favorable properties and (2) manipulating inorganic (nano)crystal nucleation, growth, and assembly into superstructures. First, we designed a series of amphiphilic peptoids with controlled side chain chemistries that self-assembled into 1D highly stiff and dynamic nanotubes, 2D membrane-mimetic nanosheets, hexagonally patterned nanoribbons, and 3D nanoflowers. These crystalline nanostructures exhibited sequence-dependent properties and showed promise for different applications. The corresponding peptoid self-assembly pathways and mechanisms were also investigated by leveraging in situ atomic force microscopy studies and molecular dynamics simulations, which showed precise sequence dependency. Second, inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, we developed peptoid-based biomimetic approaches for controlled synthesis of inorganic materials (e.g., noble metals and calcite), in which we took advantage of the substantial side chain chemistry of peptoids and investigated the relationship between the peptoid sequences and the morphology and growth kinetics of inorganic materials. For example, to overcome the challenges (e.g., complexity of protein- and peptide-folding, poor thermal and chemical stabilities) facing the area of protein- and peptide-controlled synthesis of inorganic materials, we recently reported the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. Moreover, we developed a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped gold nanoparticles (NPs). With this Account, we hope to stimulate the research interest of chemists and materials scientists and promote the predictive synthesis of functional and robust materials through the design of sequence-defined synthetic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Toward the Observation of Dimagnesocene

We have examined the electronic structure of C 5 H 5 MgMgC 5 H 5 , or dimagnesocene, using high-level coupled-cluster techniques. This research is suitable in light of the remarkable synthesis of the valence-isoelectronic diberyllocene by Boronski, Crumpton, Wales, and Aldridge. The Mg–Mg bond distance is predicted to be 2.758 Å, and the Mg–Mg bond dissociation energy is predicted to be 51.8 kcal/mol. Unique aspects to the present research is our characterization of the ionization energy and the electron affinity of this molecule, the energy of dissociation into two neutral cyclopentadienyl magnesium radicals, the determination of the neutral structure at the CCSD(T)/cc-pVTZ level, and the computation of the Raman intensities at the MP2/cc-pVDZ level. Apart from mass spectroscopy, the simplest means of experimental detection is gas-phase or matrix-isolated infrared spectroscopy, in which the A 2 ″ peak at 801 cm –1 should be the most prominent, with an intensity of 581 km/mol.

bond cleavage↗
DOE OSTI2025

Efficient and Selective Chemical Transformations in Highly Charged and Confined Nanodroplets

The acceleration of chemical reaction rates and the increased product selectivity in microdroplets compared to that in bulk solutions has become a topic of increasing interest that has been extensively characterized by electrospray ionization mass spectrometry (ESI-MS). However, the sources of this acceleration and the detailed relationships between droplet properties and resulting reaction rate acceleration are still under debate. Moreover, droplet properties are governed by multiple interrelated experimental parameters, i.e., electrospray voltage, solution flow rate, etc., which makes it difficult and time-consuming to explore this diverse parameter space using traditional manual experimental or computational approaches. In this work, we developed an automated experimental platform integrating reactions in controlled charged microdroplet environments with ESI-MS characterization and sequential hybrid Bayesian modeling, as well as an optimal experimental design framework, to achieve multidimensional parameter optimization for higher reaction turnover rates, based on a model reaction of tetraethylenepentamine (TEPA) with carbon dioxide. With the current platform, we have achieved automated scans with a range of electrospray voltages and solution flow rates, and determined and optimized parameter settings to achieve increased reaction turnovers. We have also linked this platform to the underlying properties of droplets via a hybrid model incorporating physics, high-level theoretical calculations, and machine learning (ML) approaches. The autonomous platform is broadly applicable to a range of chemical reactions relevant to DOE’s mission in chemical separations, catalysis, and materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Best practices in catalysis: A perspective

Catalysis, from its roots in petrochemical refining and conversion, has emerged as a transdisciplinary field that now encompasses synthesis of materials and molecules that enable applications in energy conversion and storage, environmental remediation, medicine, plastics, and fertilizer production, among numerous others. A handful of disciplines can claim relevance and success over such an extended period of time and continue to claim a preeminent role in defining the state-of-the-art in science and technology. Syncretic and rapid advancements in formulation and spectroscopic characterization of materials and molecules useful as catalysts, high-level density functional and molecular orbital theory calculations, and a strong foundation in concepts of physical chemistry, thermodynamics, and chemical kinetics offer new and abundant opportunities at the present day for addressing the grand challenge of controlling chemical transformations using catalysis. Here, we examine what we have learned of concepts that underpin heterogeneous catalysis but more importantly, how we learned to archive our knowledge in context of a set of best practices and standards that have emerged in the course of our learnings—ones we seek to highlight herein. Our perspective emphasizes concepts in synthesis, characterization, kinetics, and theory, because these four elements combined enable description of molecular acts that happen on surfaces and how fast they occur. In revisiting best practices in heterogeneous catalysis in these sub-fields and in authorship and peer review we aspire to augment clarity, reproducibility, and rigor in the science and practice of catalysis.

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

Implementation and Synthesis of Math Library Functions

Achieving speed and accuracy for math library functions like exp, sin, and log is difficult. This is because low-level implementation languages like C do not help math library developers catch mathematical errors, build implementations incrementally, or separate high-level and low-level decision making. This ultimately puts development of such functions out of reach for all but the most experienced experts. To address this, we introduce MegaLibm, a domain-specific language for implementing, testing, and tuning math library implementations. MegaLibm is safe, modular, and tunable. Implementations in MegaLibm can automatically detect mathematical mistakes like sign flips via semantic wellformedness checks, and components like range reductions can be implemented in a modular, composable way, simplifying implementations. Once the high-level algorithm is done, tuning parameters like working precisions and evaluation schemes can be adjusted through orthogonal tuning parameters to achieve the desired speed and accuracy. MegaLibm also enables math library developers to work interactively, compiling, testing, and tuning their implementations and invoking tools like Sollya and type-directed synthesis to complete components and synthesize entire implementations. MegaLibm can express 8 state-of-the-art math library implementations with comparable speed and accuracy to the original C code, and can synthesize 5 variations and 3 from-scratch implementations with minimal guidance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Interplay of Electronic and Geometric Structure Tunes Organic Biradical Character in Bimetallic Tetrathiafulvalene Tetrathiolate Complexes

The synthesis and design of organic biradicals with tunable singlet–triplet gaps have become the subject of significant research interest, owing to their possible photochemical applications and use in the development of molecular switches and conductors. Recently, tetrathiafulvalene tetrathiolate (TTFtt) has been demonstrated to exhibit such organic biradical character in doubly ionized bimetallic complexes. In this article we use high-level ab initio calculations to interrogate the electronic structure of a series of TTFtt-bridged metal complexes, resolving the factors governing their biradical character and singlet–triplet gaps. Here, we show that the degree of biradical character correlates with a readily measured experimental predictor, the central TTFtt C–C bond length, and that it may be described by a one-parameter model, providing valuable insight for the future rational design of TTFtt based biradical compounds and materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

ORCHA: A performance portability system for extreme heterogeneity

Heterogeneity is the prevalent trend in the rapidly evolving high-performance computing (HPC) landscape in both hardware and application software. The diversity in hardware platforms, currently comprising various accelerators and a future possibility of specializable chiplets, poses a significant challenge for scientific software developers aiming to harness optimal performance across different computing platforms while maintaining the quality of solutions when their applications are simultaneously growing more complex. Code synthesis and code generation can provide mechanisms to mitigate this challenge. We have developed a divide and conquer approach where different aspects of performance are handled by different stand-alone tools that are interfaced with the application through generated code. This portability system, ORCHA, enables users to configure and orchestrate their computations among available resources on a platform by specifying a high-level recipe, thereby permitting a many-to-many paradigm where each recipe results in a different variant of the application. The core design goal is to let users decide the application’s hardware mapping and orchestration by editing only the high-level recipe—without modifying the maintained source code or binding the application to a particular runtime system. Tools in ORCHA distribution are: CG-Kit for translating the recipe into an execution graph; Milhoja to execute the graph by orchestrating data and task movement among hardware resources; and Macroprocessor that enables users to define their own code-shorthand for higher composability and easier management of code variants. Additionally, the design of ORCHA permits tools to work in a plug-and-play mode where the application can build and run without CG-Kit and Milhoja, and either tool can be swapped out for other tools with similar capabilities by modifying the code generation portion of ORCHA. In this paper, we describe the design of ORCHA and the role that code-generation plays in isolating applications from tools. We demonstrate the breadth of configurations ORCHA enables with a case study in which an application configuration is realized on three distinct hardware mappings—a GPU-centric, a CPU/GPU balanced, and a CPU/GPU concurrent layouts by using different recipes.

Lee, Youngjun↗
DOE OSTI2026

Determining the Solubility Behavior of Kogarkoite in Simulated Nuclear Waste

Kogarkoite (Na 3 FSO 4 ) is a sparingly soluble fluoride–sulfate double salt that has been identified in high level nuclear waste sludge at the Hanford Site and, more recently, in sludge batch compilation samples at the Savannah River Site (SRS). Due to its complex dissolution behavior, which exhibits an inverse dependence on sodium ion activity, the presence of this mineral poses significant challenges to waste retrieval and processing. Incomplete dissolution during sludge washing can lead to the retention of fluoride and sulfate in the high-level waste feed, potentially causing the formation of corrosive, immiscible molten salt layers, known as "glass gall,” in vitrification melters. Current efforts to optimize flowsheet parameters and wash-water volumes are hindered by the absence of a commercially available, certified reference material, which prevents the accurate calibration of analytical methods and the verification of dissolution kinetics. To address this critical gap, this research focuses on the laboratory synthesis of pure Kogarkoite to serve as a standard for comprehensive solubility and washing performance testing. A coupled synthesis and simulant campaign was executed using an evaporative crystallization protocol designed to replicate the dynamic concentration effects observed in tank farm operations. Thirteen simulant matrices were prepared by dissolving systematically varied ratios of sodium fluoride (NaF) and sodium sulfate (Na 2 SO 4 ) in deionized water under three distinct caustic regimes: 0.0 g (control), 4.0 g (~1 M), and 12.0 g (~3 M) sodium hydroxide (NaOH). While thermodynamic equilibrium models suggest that high-caustic environments should favor the stability of the double salt7, results from this evaporative study at 25 0 C revealed a distinct kinetic divergence. Simulants with high hydroxide loading predominantly yielded large, blocky crystals of sodium sulfate decahydrate (Na 2 SO 4 .10H 2 O). Successful synthesis of pure Kogarkoite was achieved exclusively in specific NaOH-free compositional windows, where the precipitate manifested as fine, opaque granular aggregates. Ion chromatography (IC) analysis confirmed phase purity through the simultaneous stoichiometric depletion of both fluoride and sulfate from the supernatant. This successful synthesis establishes a reproducible route to generate bulk Kogarkoite, enabling the subsequent phase of quantitative dissolution testing using inhibited water to optimize sludge-batch assembly.

Sarker, Md Sharif [Florida International Univ. (FI↗
DOE OSTI2022

High-level co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol: Metabolic engineering and process optimization

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) are value-added chemicals with versatile applications in the chemical, pharmaceutical, and food industries. Nevertheless, sustainable production of 3-HP and 1,3-PDO is often limited by the lack of efficient strains and suitable fermentation configurations. We report attempts have been made to improve the co-production of both metabolites through metabolic engineering of Escherichia coli and process optimization. First, the 3-HP and 1,3-PDO co-biosynthetic pathways were recruited and optimized in E. coli, followed by coupling the pathways to the transhydrogenase-mediated cofactor regeneration systems that increased cofactor availability and product synthesis. Next, pathway rebalancing and block of by-product formation significantly improved 3-HP and 1,3-PDO net titer. Subsequently, glycerol flux toward 3-HP and 1,3-PDO synthesis was maximized by removing metabolic repression and fine-tuning the glycerol oxidation pathway. Lastly, the combined fermentation process optimization and two-stage pH-controlled fed-batch fermentation co-produced 140.50 g/L 3-HP and 1,3-PDO, with 0.85 mol/mol net yield.

1,3-propanediol↗
DOE OSTI2021

Bioorthogonal catalytic patch

The toxicity and complicated administration procedures of transition metal catalysts have hampered the applications of bioorthogonal catalysis in vivo. Here the authors fill the needles of a microneedle array patch with palladium nanoparticles deposited on titanium nanosheets and show that the device, applied locally on the skin of mouse models bearing melanoma, promotes intratumoural conversion of systemically injected caged doxorubicin into the active drug, reducing its toxicity and side effects. Bioorthogonal catalysis mediated by transition metals has inspired a new subfield of artificial chemistry complementary to enzymatic reactions, enabling the selective labelling of biomolecules or in situ synthesis of bioactive agents via non-natural processes. However, the effective deployment of bioorthogonal catalysis in vivo remains challenging, mired by the safety concerns of metal toxicity or complicated procedures to administer catalysts. Here, we describe a bioorthogonal catalytic device comprising a microneedle array patch integrated with Pd nanoparticles deposited on TiO 2 nanosheets. This device is robust and removable, and can mediate the local conversion of caged substrates into their active states in high-level living systems. In particular, we show that such a patch can promote the activation of a prodrug at subcutaneous tumour sites, restoring its parent drug's therapeutic anticancer properties. Finally, this in situ applied device potentiates local treatment efficacy and eliminates off-target prodrug activation and dose-dependent side effects in healthy organs or distant tissues.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Explainability and human intervention in autonomous scanning probe microscopy

The broad adoption of machine learning (ML)-based autonomous experiments (AEs) in material characterization and synthesis requires strategies development for understanding and intervention in the experimental workflow. Here, we introduce and realize a post-experimental analysis strategy for deep kernel learning-based autonomous scanning probe microscopy. This approach yields real-time and post-experimental indicators for the progression of an active learning process interacting with an experimental system. We further illustrate how this approach can be applied to human-in-the-loop AEs, where human operators make high-level decisions at high latencies setting the policies for AEs, and the ML algorithm performs low-level, fast decisions. The proposed approach is universal and can be extended to other techniques and applications such as combinatorial library analysis.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Towards Automatic and Agile AI/ML Accelerator Design with End-to-End Synthesis

Domain-specific designs offer greater energy efficiency and performance gain than general-purpose processors. For this reason, modern system-on-chips have a significant portion of their silicon area with custom accelerators. However, designing hardware by hand is laborious and time-consuming, given the large design space and the performance, power, and area constraints that are not realized in the software. Moreover, domain-specific algorithms (e.g., machine learning models) are evolving quickly, challenging the accelerator design further. To address these issues, this paper presents SODA Synthesizer, an automated open-source high-level ML framework to Verilog modular compiler targeting AI/ML Application-Specific Integrated Circuits (ASICs) accelerators. SODA tightly couples the Multi- Level Intermediate Representation (MLIR) compiler infrastructure [24] and open-source HLS approaches. Thus, SODA can support various ML frameworks and algorithms and can perform optimizations that combine specialized architecture templates and conventional HLS to generate the hardware modules. In addition, SODA’s closed-loop design space exploration (DSE) engine allows developers to perform end-to-end design space explorations on different metrics and technology nodes.

Zhang, Jeff↗
DOE OSTI2024

Non-classical crystallization in soft and organic materials

Classical nucleation and crystal growth theories describe how nuclei form, become stable after reaching a critical size and then enlarge through monomer attachment. More than two decades ago, non-classical pathways have been proposed for various types of (bio)molecules and materials, which can substantially alter the crystallization kinetics and outcomes. Direct observation of non-classical crystallization of inorganic nanomaterials, including metastable structure-mediated and particle attachment-based pathways that usually occur on the nanoscale, was enabled by in situ liquid-phase electron microscopy. However, it was not until recently that the crystallization dynamics of beam-sensitive soft materials were directly imaged with sufficient spatial resolution, and a level of microstructural understanding of defects and interfaces emerged. This article provides a high-level review of the non-classical crystallization pathways discovered in soft and organic materials and a forward-looking guide for future research. We first analyse how the characteristics of soft materials affect their crystallization pathways and kinetics. We then identify technical approaches to studying the crystallization trajectories of soft materials and discuss strategies to properly select and apply them to different systems. Breakthroughs made in understanding the crystallization of small organic molecules, (bio)macromolecules, colloids and reticular framework materials are examined. Lastly, we provide an outlook on the challenges in elucidating soft material crystallization pathways and the opportunities for assisting the design and synthesis of new materials and structures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The Los Angeles 100% Renewable Energy Study (LA100): Chapter 12. Synthesis

The City of Los Angeles has set ambitious goals to transform its electricity supply, aiming to achieve a 100% renewable energy power system by 2045, along with aggressive electrification targets for buildings and vehicles. To reach these goals, and assess the implications for jobs, electricity rates, the environment, and environmental justice, the Los Angeles City Council passed a series of motions directing the Los Angeles Department of Water and Power (LADWP) to determine the technical feasibility and investment pathways of a 100% renewable energy portfolio standard. The Los Angeles 100% Renewable Energy Study (LA100) is a first-of-its-kind objective, rigorous, and science-based power systems analysis to determine what investments could be made to achieve these goals. The LA100 final report is presented as a collection of 12 chapters and an executive summary, each of which is available as an individual download. This chapter reviews high-level findings, costs, benefits, and lessons learned from integrating this diverse suite of models and conducting a high-fidelity 100% renewable energy study.

100% Renewable↗
DOE OSTI2020

SQUARE: Strategic Quantum Ancilla Reuse for Modular Quantum Programs via Cost-Effective Uncomputation

Compiling high-level quantum programs to machines that are size constrained (i.e. limited number of quantum bits) and time constrained (i.e. limited number of quantum operations) is challenging. In this paper, we present SQUARE (Strategic QUantum Ancilla REuse), a compilation infrastructure that tackles allocation and reclamation of scratch qubits (called ancilla) in modular quantum programs. At its core, SQUARE strategically performs uncomputation to create opportunities for qubit reuse. Current Noisy Intermediate-Scale Quantum (NISQ) computers and forward-looking Fault-Tolerant (FT) quantum computers have fundamentally different constraints such as data locality, instruction parallelism, and communication overhead. Our heuristic-based ancilla-reuse algorithm balances these considerations and fits computations into resource-constrained NISQ or FT quantum machines, throttling parallelism when necessary. To precisely capture the workload of a program, we propose an improved metric, the "active quantum volume," and use this metric to evaluate the effectiveness of our algorithm. Furthermore, our results show that SQUARE improves the average success rate of NISQ applications by 1.47X. Surprisingly, the additional gates for uncomputation create ancilla with better locality, and result in substantially fewer swap gates and less gate noise overall. SQUARE also achieves an average reduction of 1.5X (and up to 9.6X) in active quantum volume for FT machines.

compiler optimization↗
DOE OSTI2020

Sulfonamide and Sulfonamido-phenol Ligands for Extraction of f-Elements from Alkaline High-Level Waste

Alkaline High Level Waste (HLW) has been accumulated at Hanford and Savannah River Sites as a result of reprocessing for nuclear weapons production during the cold war. A large volume (∼100 MGal) has been accumulated in carbon steel tanks at Savannah River (SRS) and Hanford. The tank waste contains three separate phases generated when NaOH was added to previously acidic Purex raffinates: 1-2 Supernatant liquid, salt-cake, and sludge. The sludge consists mainly of insoluble hydroxides of transition metals while the supernate and salt-cake contain caustic-soluble materials, including salts of highly radioactive fission products Cs(I) and Sr(II). Current treatment of alkaline HLW in SRS includes: i) The Actinide Removal Process (ARP), which is based on sorption of {sup 90}Sr and Actinides (An) on monosodium titanate (MST), also known as 'alpha-strike' process, followed by ii) Caustic Side Solvent Extraction (CSSX),4 which is used for the extraction of {sup 137}Cs by modified calixarenes in a hydrocarbon diluent. Residual actinides in some tanks are removed after CSSX by an additional ARP process commonly referred to as 'alpha-finishing'. Despite the success of ARP for Sr and An removal, as it is a sorption process, it represents the kinetic bottleneck of integrated salt waste processing. Hence potential introduction of additional organic ligands for actinide extraction (in a modified CSSX process) could simplify the overall integrated process, making it more efficient and economical, with less titanate needed and shorter sorption time, as some of the actinide component would be removed during CSSX. In this study tri-sulfonamide and o-sulfonamido-phenol (mono-sulfonamide) ligands have been studied as extractants for Sm(III), which is being used as an Am(III) surrogate. Our prior studies in the group using a tri-sulfonamide (iPr-tsa-B) showed favorable extraction for Sm(III) nitrate salts from alkaline solutions. Mono-sulfonamides possess similar orientation of binding sites to pyrocatechols, which have been found to be good ligands for Am(III) binding and extraction from alkaline media. Tri-sulfonamide of the type iPr-tsa-B6 (1 mM in CH{sub 2}Cl{sub 2} solution) was studied for Ln{sup 3+} extraction using Sm(NO{sub 3}){sub 3}.6H{sub 2}0 (10 and 25 μM) in alkaline solution of NaOH (0.05, 0.1, 0.2, 0.3 mM) / 0.1 M NaNO{sub 3}. Stripping of the organic phase was done using 0.1 M HNO{sub 3} and quantification of Sm{sup 3+} was done using ICP-OES at 359.3 nm. The need to improve stability of the complex led to synthesis of compounds with N-donor site closer to the central benzene ring to facilitate cation-π interactions. Synthesis of tri-sulfonamide type A: a) Chloromethyl methyl ether, SnCl{sub 4}, CH{sub 2}Cl{sub 2}, 0 deg. C, N{sub 2}, 4 h, 57%; b) NaN{sub 3}, reflux in H{sub 2}O/acetone for 22 h, 80%; c) PPh{sub 3}, THF/H{sub 2}O, 22 h, 79%; d) p-toluene sulfonyl chloride, Et{sub 3}N, 1,2-DCE, 22 h. Extraction: Sm(NO{sub 3}){sub 3}.6H{sub 2}O (2 mM) in 5 ml of aqueous NaOH (pH 10.5 - 14) + 6 ml of CH{sub 2}Cl{sub 2} solution of msa (20 mole equiv.) were rotated on a wheel (60 rpm; 20 h). Stripping: 5 ml of 0.1 M HNO{sub 3} + CH{sub 2}Cl{sub 2} solution of msa (after extraction, centrifugation and filtration) was rotated on the wheel (60 rpm; 20 h). Sm{sup 3+} was quantified using UV-Visible spectrophotometry.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga

Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle–regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle–regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis–dependent methylation following DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Accelerating accurate simulations of calorimeter showers with normalizing flows and probability density distillation

Recently, we introduced caloflow, a high-fidelity generative model for GEANT4 calorimeter shower emulation based on normalizing flows. Here, we present caloflow v2, an improvement on our original framework that speeds up shower generation by a further factor of 500 relative to the original. The improvement is based on a technique called probability density distillation, originally developed for speech synthesis in the machine learning literature, and which we develop further by introducing a set of powerful new loss terms. We demonstrate that caloflow v2 preserves the same high fidelity as the original using qualitative (average images, histograms of high-level features) and quantitative (classifier metric between geant4 and generated samples) measures. The result is a generative model for calorimeter showers that matches the state of the art in speed (a factor of 10 4 faster than GEANT4) and greatly surpasses the previous state of the art in fidelity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗