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DOE OSTI2025

Directed self-assembly of block copolymers for high-precision patterning in the era of extreme ultraviolet lithography

Extreme ultraviolet (EUV) lithography enables unprecedented resolution in semiconductor patterning but faces critical challenges in developing resist materials that achieve high-precision at economically viable throughput. Directed self-assembly (DSA) of block copolymers (BCPs) offers a promising solution for pattern rectification by leveraging thermodynamically determined domain structures to decouple BCP pattern quality from the imperfect original lithographic pattern. This prospective presents an overview of recent progress on the EUV + DSA strategy, covering advances in BCP material design, processing, metrology, and pattern transfer. We highlight recent advances in high-χ BCPs with perpendicular orientation and domain spacings compatible with EUV dimensions, leveraging A-b-(B-r-C) architectures. We also discuss progress in chemical pre-pattern fabrication using both positive- and negative tone resists, along with processing strategies to minimize defects and roughness based on BCP thermodynamics and assembly kinetics. We further examine metrology platforms for characterizing the thermodynamics of BCP materials and quantifying the size and shape of BCP domains. Lastly, we review pattern transfer strategies for generating functional inorganic masks suitable for semiconductor manufacturing. Together, these advances highlight the potential of DSA to complement EUV lithography, offering a pathway to address critical challenges in achieving high-precision patterning for the semiconductor industry.

Lee, Kyunghyeon [Univ. of Chicago, IL (United Stat↗

DOE OSTI2024

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Particle size of several plutonium-238 oxide fuel samples from oxalate precipitation processes

Particle size of 238 PuO 2 powders is an important factor in determining the structural integrity of fuel pellets hot-pressed from the oxide powder. Understanding the evolution of particle size during aqueous processing is a first step in assuring control of particle size throughout the pellet formation process. Measured particle sizes are reported here, and discussed in terms of measured particle size changes occurring during calcining, observed aggregation of particulate, and particle morphology. Morphology and aggregation are related to surface energy, which governs granule formation and hot pressing behavior. Results are discussed in terms of reported dependence of oxide morphology on process temperatures and reagent concentrations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Fabricating Diamond-like Amorphous Carbon

Using a magnetically confined hot hollow cathode PE-CVD, hydrocarbon gas is decomposed under a diluent gas to deposit hydrogenated amorphous carbon onto a sample holder. During the fabrication of the hydrogenated amorphous carbon, the electric potential, electron temperature, and electron density of the plasma are measured with a Langmuir probe. Raman spectroscopy is used to determine the structural and electronic characterization of the final hydrogenated amorphous carbon solid.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Fast Particle-Wave Interactions and Alfvén Eigenmodes in JET Tokamak Plasmas

This document serves as the closeout report of DOE Grant Award No. DE-FG02-99ER54563 with project period 1 April 2015 through 31 March 2020. The project comprised the international collaboration between MIT and EU scientists on the JET facility to improve our understanding of the physics of energetic particle-wave interactions by measuring the damping rates of stable Alfvén Eigenmodes (AEs) and unstable energetic particle driven modes. More specifically, this project involved the continued participation of MIT, the Culham Centre for Fusion Energy, the Swiss Plasma Center, and theorists from various European laboratories and from UC Irvine. Past contributions from the University of São Paulo are gratefully acknowledged. The Alfvén Eigenmode Active Diagnostic (AEAD) on JET discharges was successfully upgraded in this period and has extracted physically useful information, in primarily deuterium plasma discharges. It is expected that such experiments would be continued during the DT campaign in CY 2021 to assess the damping rates of similar modes in the presence of alpha particles, a product of fusing burning plasma. Only JET would carry out such experiments in the near term in the world. It is important to note that this collaboration was continued under DOE Grant Award No. DE-SC0014264 from 1 April 2020 through the present. In this grant period, the AEAD was upgraded with a set of individual amplifiers for each of a set of six antennas in two toroidally opposite locations. These new amplifiers allowed targeted selection of the antennas’ toroidal spectrum for AEs of interest with toroidal mode number | n | ≤ 20. The resonant detection and measurement of the damping rates of AEs was obtained from magnetic probes that could be compared with theory and simulations. This is a key topic of investigation for ITER and all other next-step fusion experiments, where such modes will interact with energetic particles produced by fusion reactions (alpha particles), Neutral Beam Injection (NBI) and Ion Cyclotron Resonance Heating (ICRH). The majority of the observations during this period were of Toroidal Alfvén Eigenmodes (TAEs) as these are most commonly observed on JET; a number of measurements were made during dedicated TAE experiments. However, a new set of lower frequency band filters were procured with the goal of studying Geodesic Acoustic Modes (GAMs), Beta (Acoustic) AEs (BAE/BAAEs), and Reverse Shear AEs (RSAEs), also predicted by theory. Commissioning and optimizations were successfully completed in this period, and the diagnostic has been in operation during the more recent JET campaigns. Initial results have been obtained in dedicated TAE experiments and successfully compared to drift-kinetic theory. A wide range of theoretical studies have been undertaken in support of the upcoming JET campaigns experiments. To supplement the ongoing use of ideal MHD codes, such as MISHKA during the studies of TAEs, gyrokinetic simulations of low frequency AEs were performed in collaboration with UC Irvine. The Gyrokinetic Toroidal Code (GTC) was used to determine the structure, frequencies and stability of AEs in JET plasmas. Thus, a solid scientific foundation has been laid for future DT campaigns in JET in the 2021 operation period when the damping rates of relevant modes in the presence of alpha particles could be assessed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Emerging Functionality in Transition-Metal Compounds Driven by Spatial Confinement and Broken Symmetry

This research project investigates the emerging functionality in transition-metal-compounds (TMCs) driven by spatial confinement and broken symmetry. It combines advanced growth capabilities with cutting-edge characterization and first principles theory to probe and control the properties of TMC interfaces, including the utilization and development of state-of-the-art atomically resolved electron microscopy and spectroscopy to determine the structure, composition, and bonding at TMC interfaces. The proposed research will focus on four challenging areas: 1) manipulate interfaces to design new material phases such as magnetic metals with unique polar structure (net dipole) to achieve multiple functionality; 2) explore electronic mismatch or screening at interfaces of insulating/poor metal TMCs to produce novel electronic and magnetic properties; 3) elucidate and exploit the role of defects, both point and extended, on the functionality of interfaces; 4) develop advanced electron microscopy/spectroscopy techniques to explore temperature dependent phase transitions and couple these structural tools with new nonlinear optical probes of the electronic structure. The research team aims to close the materials-by-design loop of make, measure, model, and modify. The program promises to enhance our ability to engineer the desired physical properties at interfaces, superlattices (periodic arrays of films of different compounds), and heterostructures of TMCs.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The Scientific Case for Concurrent Neutron and X-ray Scattering and Spectroscopy

The interrogation of materials with X-rays or neutrons to determine the structure, energetics, and dynamics of materials is fundamental to advancing materials' physical and chemical science and developing innovative material technologies. A transcending challenge in developing novel materials is that progress hinges on understanding the structure and dynamics across multiple time and length scales in complex materials that feature multiple components, interfaces, and compositions. Despite the ever-growing demands on materials’ characterization, existing approaches are almost exclusively based on isolated X-ray or neutron scattering, i.e., an approach commensurate with the more narrowly defined needs of fifty years ago. A three-day workshop sponsored by the U.S. National Science Foundation (NSF) analyzed the demand for concurrent neutron and X-ray (NeX) experiments. It was held at the Spring Hill Suites, San Jose, California, from June 2 to 4, 2022. In this workshop, 70 national and international experts ascertained the crucial need to establish NeX capabilities to advance the science of complex materials and systems in the US. Here, we illustrate the need for NeX scattering and spectroscopy experiments by showcasing examples that span areas as diverse as biomaterials, energy science, soft matter, and nanomaterials. To provide NeX capability will require new instrumentation that enables concurrent experiments. Affected areas include chemistry, soft matter, quantum materials, pure and applied chemistry, bioscience, geoscience, and applied materials. NeX benefits research outcomes due to the complementarity of the two techniques, which is essential for better model refinement. While joint refinement of data from separate neutron and X-ray experiments is critical to avoid ambiguities, especially in multiphase-multicomponent materials, concurrent experiments overcome scientific and technical barriers associated with single measurements, separated by location and, thus, time. Among all the examples, these factors introduce uncertainties in the results that complicate data analysis. [1,2] [3] While models are strongly sample-dependent, the principles of joint refinement are generally applicable to these disciplines, including the development of advanced parameterization, modeling, and analysis techniques that also consider the temporal and spatial resolutions of the two methods, leading to unambiguous data interpretation. Solutions for technical barriers must be found to realize NeX experiments, including developing robust sample environments that meet the optical requirements of neutrons and X-rays.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Identifying the connections between grain growth and flux expulsion in low RRR niobium SRF cavities

The SRF community has shown that high temperature annealing can improve the flux expulsion of niobium cavities during cooldown. The required temperature will vary between cavities and different batches of material, typically around 800 C and up to 1000 C. However, for niobium with a low residual resistance ratio (RRR), even 1000 C is not enough to improve its poor flux expulsion. The purpose of this study is to observe the grain growth behavior of low RRR niobium coupons subjected to high temperature annealing to identify the mechanism for improving flux expulsion. We observe that low RRR material experiences less grain growth than high RRR when annealed at the same temperature. We search for the limitations to grain growth in low RRR material and develop a diagnostic based on grain structure to determine the appropriate recipe for good flux expulsion. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Identifying the Connections between Grain Growth and Flux Expulsion in Low RRR Niobium SRF Cavities

Howard, Katrina N. [Chicago U.] (ORCID:00000003256↗

DOE OSTI2025

Identifying the Connections between Grain Growth and Flux Expulsion in Low RRR Niobium SRF Cavities

Howard, Katrina [Chicago U.] (ORCID:00000003256133↗

DOE OSTI2026

Identifying the connections between grain growth and flux expulsion in low RRR niobium SRF cavities

Howard, K. [Chicago U.] (ORCID:0000000325613308)↗

DOE OSTI2026

Understanding the connections between grain growth and flux expulsion in low RRR niobium SRF cavities

The SRF community has shown that high temperature annealing can improve the flux expulsion of niobium cavities during cooldown. The required temperature will vary between cavities and different batches of material, typically around 800 C and up to 1000 C. However, for niobium with a low residual resistance ratio (RRR), even 1000 C is not enough to improve its poor flux expulsion. The purpose of this study is to observe the grain growth behavior of low RRR niobium coupons subjected to high temperature annealing to identify the mechanism for improving flux expulsion in low RRR cavities. We anneal the low RRR material up to 1200 C to understand the limits of flux expulsion performance. We observe that low RRR material experiences less grain growth than high RRR when annealed at the same temperature. We search for the limitations to grain growth in low RRR material and develop a diagnostic based on grain structure to determine the appropriate recipe for good flux expulsion. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

Howard, K. [Chicago U.]↗

DOE OSTI2020

Allometric Trophic Networks From Individuals to Socio-Ecosystems: Consumer–Resource Theory of the Ecological Elephant in the Room

A well-known parable is that of the blind men studying an elephant each of which assert the elephant is the part they first hold in their hands, e.g., “rope!” says the tail holder while the leg holder asserts “tree!” The various subdisciplines of ecology appear similar in that we each engage in our enthusiastic but at least somewhat myopic study with remarkably limited agreement or even discussion about the overall system which we all study. Allometric trophic network (ATN) theory offers a path out of this dilemma by integrating across scales, taxa, habitats and organizational levels from physiology to ecosystems based on consumer-resource interactions among co-existing organisms. The network architecture and the metabolic and behavioral processes that determine the structure and dynamics of these interactions form the first principles of ATN theory, which in turn provides a synthetic overview and powerfully predictive framework for ecology from organisms to ecosystems. Beyond ecology, ATN theory also synthesizes eco-evolutionary and socio-ecological research still largely based on consumer-resource mechanisms but respectively integrated with different processes including natural selection and market mechanisms. This paper briefly describes foundations, advances, and future directions of ATN theory including predicting an ecosystem’s phenotype from its community’s genotype in order to accelerate more predictive and unified understanding of the complex systems studied by ecologists and other environmental scientists.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Investigation of the Impact of Lipid Acyl Chain Saturation on Fusion Peptide Interactions with Lipid Bilayers

The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. Lipid bilayer vesicles composed of mixtures of lipids with two saturated acyl chains and lipids and one saturated and one unsaturated acyl chain, but identical head groups, were studied. The dependence of the peptide conformation on the unsaturated lipid content was probed by circular dichroism spectroscopy, while the impact of the peptide on the bilayer structure was determined by small-angle neutron scattering. The impact of the peptide on the lipid bilayer vesicle dynamics was investigated using neutron spin echo spectroscopy. Molecular dynamics simulations were used to characterize the behavior of the systems studied to determine if there were clear differences in their physical properties. The results reveal that the peptide–bilayer interaction is not a simple function of the unsaturated lipid acyl chain content of the bilayer. Instead, the peptide behavior is more consistent with that seen for the bilayer containing only unsaturated lipids, which is supported by lipid-specific interactions revealed by the simulations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Antarctic Soils Select Copiotroph-Dominated Bacteria

The life strategies of bacterial communities determine their structure and function and are an important driver of biogeochemical cycling. However, the variations in these strategies under different soil resource conditions remain largely unknown. We explored the bacterial life strategies and changes in structure and functions between Antarctic soils and forest (temperate, subtropical, and tropical) soils. The results showed that the weighted mean rRNA operon copy number in temperate soils was 19.5% lower than that in Antarctic soils, whereas no significant differences were observed among Antarctic, subtropical, and tropical soils. An unexpected result was that bacterial communities in Antarctic soils tended to be copiotrophs, such as Actinobacteriota and Bacteroidota, whereas those in temperate soils tended to be oligotrophs, such as Acidobacteriota and Chloroflexi. Functional predictions showed that in comparison to copiotrophs in Antarctic soils, temperate-inhabiting oligotrophic bacteria exhibited an 84.2–91.1% lower abundance of labile C decomposition genes (hemicellulose, cellulose, monosaccharides, and disaccharides), whereas a 74.4% higher abundance of stable C decomposition (lignin). Genes involved in N cycling (nitrogen fixation, assimilatory nitrate reduction, and denitrification) were 24.3–64.4% lower in temperate soils than in Antarctic soils. Collectively, our study provides a framework for describing the life strategies of soil bacteria, which are crucial to global biogeochemical cycles.

Microbiology↗

DOE OSTI2023

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Deep Learning Prediction of Interspecies Interactions from Self-organized Spatiotemporal Patterns of Co-evolving Organisms

Microorganisms colonizing natural habits such as soils co-evolve to form specific spatial patterns through interspecies interactions. These self-organized patterns are a key ecological phenotype, which provides critical information on their interaction mechanisms. However, conventional network inference techniques that analyze species population data in bulk have yet to be extended to account for such spatial heterogeneity. Here we proposed supervised deep learning as a new network inference tool for predicting interspecies interactions from spatiotemporal patterns of microbial evolution. Due to lack of biological imaging data that can be used for training deep learning networks, we used in silico data generated from high-fidelity agent-based models to determine model structure and parameters. Even though networks were trained under simple configurations where interaction coefficients are assumed to be spatially invariant, we demonstrated that the resulting model can be utilized to successfully predict spatial variation of interactions in more complex domains (i.e., configured with a context-dependent mixture of interaction coefficients) as well as in simple domains without further training. In the further test against real biological data obtained through imaging experiments of a binary consortium (Pseudomonas fluorescens and a mutant of Escherichia coli), our model also predicted the dramatic shifts in interactions of the two organisms across different environmental contexts. Through various successful demonstrations in this work, the combined use of the agent-based model and machine learning algorithm provides a means to use new type of data - microscopic images - for extracting microbial interactions, therefore presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Lee, Joon-Yong↗