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At least 19 records

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence

Programmed synthesis of mesoporous protein crystals in cellular reactors

Protein crystals are naturally derived mesoporous materials with versatile structures and physicochemical properties. Here we introduce an intracellular synthesis platform that enables controllable and programmable protein crystallization. In live cells, we show that, after initial nucleation, steady protein expression governs crystal growth, yielding predictable, tunable dynamics in live cells. Exploiting this feature, we combined HaloTag and click chemistries to achieve modular, programmable immobilization of diverse guest materials with spatial patterning down to ~100 nm resolution. We further demonstrated the sequential release of immobilized materials in physiologically relevant fluids. As a proof of concept, we programmed particles to carry human fibroblast growth factors in distinct layers, which elicited designed oscillatory Akt signalling patterns in cell culture. Finally, this work outlines a programmable method for producing mesoporous materials, with possible applications in catalysis and biomedicine.

Yang, Hongru [Johns Hopkins Univ., Baltimore, MD (

VISION: a modular AI assistant for natural human-instrument interaction at scientific user facilities

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an x-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instruments and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex—a synthetic extension to the cognition of scientists—may radically transform scientific practice and discovery.

36 MATERIALS SCIENCE

Development of a scalable, robust electrocatalytic technology for conversion of CO 2 to formic acid via microstructured materials

This project was funded by the Bioenergy Engineering for Product Synthesis (BEEPS) program under the Funding Opportunity Announcement (FOA) DE-FOA-0001916 Topic Area 5 “Rewiring Carbon Utilization”. This FOA sought projects that would electrocatalytically reduce CO 2 to a carbon intermediate and then upconvert to a multi-carbon product or fuel via non-photosynthetic biological system engineering. The project sought to combine the expertise of OCO Chem, whose chief scientist had previously developed an efficient electrocatalytic reactor for conversion of CO 2 to formate with potential to scale, Montana State University investigators who had recently patented a method for laterally grading membranes with the potential of improving reactant distribution and more uniform efficiency across membrane-based reactors, and University of South Florida which had recently discovered a novel C-C bond forming reaction not known to naturally occur in biological systems and which uses C1 substrates and circumvents the central microbial metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

CEERP SM3 Research, Monitoring, and Evaluation Workshop: Summary Report

The Columbia Estuary Ecosystem Restoration Program (CEERP) workshop, “CEERP Synthesis Memorandum (SM3): Research, Monitoring, and Evaluation,” was held in Portland, Oregon on June 24–25 2024. A diverse group of 26 domain experts with demonstrated knowledge and experience working in the Lower Columbia River Estuary (LCRE) participated. The workshop supported development of the forthcoming third Synthesis Memorandum for CEERP. The workshop furthered the collaborative understanding of the state of the science regarding the LCRE, helped to identify remaining knowledge gaps and uncertainties, and assisted in the prioritization of future restoration research and monitoring.

54 ENVIRONMENTAL SCIENCES

Carbon-Based Quantum Information Science with Symmetry Protected Topological States (Final Report, DOE-BES award DE-SC0023105)

This research program established the scientific foundation for the rational, bottom-up design, synthesis, isolation, and investigation of symmetry-protected topological (SPT) electron spin qubits embedded in graphene nanoribbons (GNRs). The work focused on integrating atomically precise low-dimensional carbon nanostructures with emerging quantum logic architectures, providing a pathway toward scalable quantum materials for next-generation computing and sensing technologies. A central component of the program was the elucidation of fundamental relationships between real-space molecular architecture, local spin density distributions, electronic band dispersion, and energy level alignment in atomically precise GNR systems. These correlations define key operational parameters of SPT qubits and were systematically investigated to establish quantitative benchmarks against established molecular and solid-state spin qubit platforms. Attention was given to properties critical for quantum device performance, e.g. decoherence times, spectral sharpness of energy transitions, and tunable exchange interactions between spin states. The research demonstrated that these parameters can be engineered with atomic precision through scalable bottom-up synthetic strategies. Theory-guided design played a central role in identifying candidate structures hosting topologically protected spin states. Experimental validation was performed using both ensemble measurements and single-molecule characterization. In addition to advances in quantum materials synthesis, the program developed and applied spin-sensitive scanning probe microscopy techniques capable of directly probing quantum states and dynamic processes with atomic-scale spatial resolution. These capabilities enabled direct observation and characterization of quantum structures at the single-atom level. While the research activities were primarily hypothesis-driven fundamental investigations, the program adopted a comprehensive materials-by-design framework aimed at translating scientific discoveries into technological concepts compatible with scalable and intelligent manufacturing approaches.

36 MATERIALS SCIENCE

Fundamental Studies of the Vibrational, Electronic, and Photophysical Properties of Tetrapyrrolic Architectures

The ability to capture and utilize light in the near-ultraviolet (NUV), visible and near-infrared (NIR-I and NIR-II) spectral regions (i.e., 320–400, 400–700, 700–1000, 1000–1700 nm) is essential for any solar-energy conversion scheme. Nature employs chlorophylls and bacteriochlorophylls in light-harvesting architectures to absorb light in the blue and red/NIR regions. Accessory pigments (carotenoids, bilins) augment absorption of the (bacterio)chlorophylls in the green region. The harvested energy is funneled to a reaction center protein, where charge separation occurs. Subsequent migration of the electron and the hole stabilizes and stores the energy from light via redox chemistry. The long-term objective of the Bocian/Holten&Kirmaier/Lindsey research program under this DOE grant has been to develop tetrapyrrole-based molecular architectures that absorb sunlight, funnel energy and separate charge with high efficiency. Integral to the program has been iterative cycles of design, synthesis and characterization that provided deep insights into the relationships between chemical composition, electronic structure, and key static and dynamic properties (vibrational, redox, photophysical, energy/charge transfer) of tetrapyrrolic systems. Such architectures included monomers, dyads, larger arrays, and complexes with accessory components. The objective was to develop molecular designs and guiding principles to enhance current and future energy-conversion schemes. Molecular arrays targeted to address one or more fundamental questions concerning light harvesting and energy/charge transfer were constructed from analogues of the naturally occurring hemes, chlorophylls and bacteriochlorophylls. Diverse, tunable synthetic building blocks were prepared that spanned the three respective tetrapyrrole families, which are the porphyrins, chlorins and bacteriochlorins. Thus, the research focused on porphyrins as well as synthetic surrogates for chlorophylls (chlorins, 13 1 -oxophorbines and chlorin-imides) and bacteriochlorophylls (bacteriochlorins, bacterio-13 1 -oxophorbines and bacteriochlorin-imides), generically termed hydroporphyrins. Although the three tetrapyrrole classes (porphyrins, chlorins and bacteriochlorins) absorb light strongly in the violet-blue spectral region, the long-wavelength absorption band typically lies in the green-orange, red, and NIR regions, respectively, with increasing intensity. Understanding the spectra, electronic structure, and energy/charge-transfer properties of such tetrapyrrolic macrocycles is of central importance for the rational design of molecular architectures for solar-energy conversion. Our integrated program of molecular design and synthesis coupled with a variety of spectroscopic, electrochemical, and computational studies have probed from first principles how structural and electronic properties of tetrapyrrolic macrocycles dictate spectral properties as well as the rates of ground-state hole/electron transfer and excited-state energy flow in multicomponent architectures. Individual molecules and multicomponent architectures were designed to test ideas of fundamental importance, often requiring the development of new synthetic methodology. The members of the collaborative team had almost daily discussions by phone and/or e-mail concerning design of molecules, flow of compounds between the labs, planning of physical characterization studies, discussing results and analysis and integrating into design of next generation architectures, and the preparation of manuscripts. Furthermore, students and postdocs in the different labs routinely communicated with one another to facilitate the advancement of the research activities. In short, a highly integrated and collaborative research program was well established among the groups. The research effort involved molecular design and synthesis of synthetic molecular architectures by the Lindsey group integrated with physicochemical and photophysical characterization by the Bocian group and the Holten&Kirmaier group (Figure 2). The Bocian group carried out electrochemical, electron paramagnetic resonance (EPR), resonance Raman (RR), and Fourier-transform infrared (FT-IR) studies, as well as density functional theory (DFT) calculations and the time-dependent extension (TDDFT) to gain insight into excited-state properties. The Holten&Kirmaier group carried out static and time-resolved absorption and fluorescence spectroscopy studies and simulated absorption spectra using molecular orbital (MO) energies from DFT as input to the four-orbital model to complement the TDDFT calculations. The combined measurements provided understanding of the vibrational/electronic properties of the individual molecules and the changes that occur upon incorporation into multicomponent architectures. This information underpinned elucidating the mechanisms and timescales of ground-state hole/electron transfer and excited-state energy and charge transfer.

14 SOLAR ENERGY

Shorter function summaries for finite state machine-based high consequence systems using logic synthesis and tautologies (Final Report LDRD 24-1302)

Computer programs are often viewed as collections of functions – each function has parameters (inputs) and computes a return value, and each has potential side effects that modify program state (outputs). In this research, a Sandia symbolic execution tool designed to support “human-in-the-loop” analysis was modified to automatically create “function summaries,” and a new tool, “diaboolical,” was created to support enhancing readability of the summary using a novel approach to bit-vector simplification that leverages logic synthesis and tautologies. For this effort, students at Auburn University created several finite state machines (FSMs) to serve as exemplars for high-consequence systems. Function summaries for each of the machines were obtained, and then portions of the summaries were simplified using both diaboolical and the simplification procedure of a popular SMT solver. A comparison of the results shows that diaboolical can often produce smaller function summaries, with expression length improvements over the unsimplified function summaries ranging from 0% to 90% for diaboolical and 0% to 65% for the SMT solver, though diaboolical had a significantly greater cost in time. Diaboolical was evaluated against a collection of “arbitrary” C-code as well as FSM exemplars, and for both datasets it achieved an approximately 10% improvement in expression length compared to simplifications that could be obtained using existing techniques. Function summaries can assist assurance efforts that evaluate existing systems and their executable code. A smaller function summary is likely easier for humans to understand and could thus increase the ability and efficacy of assurance practices centered around the analysis of executable artifacts.

97 MATHEMATICS AND COMPUTING

Robust Polymer Electrolytes For Flexible Energy Storage (CRADA Final Report)

As part of the Cyclotron Road program, Anthro Energy investigated the formulation, synthesis, and application of advanced supramolecular compounds for lithium-ion batteries. Anthro Energy developed and tested formulations and chemistries to create polymeric materials with improved mechanical strength, safety, and electrochemical performance. These materials were explored for use in next-generation batteries with a variety of form factors. Initially, Anthro Energy tested these materials to create flexible and deformable batteries, which are in high demand for the wearable/flexible electronics industry. In future work, Anthro Energy’s materials may be applied to create rigid structural batteries, or to enable novel chemistries such as silicon anodes or lithium metal anodes. In the process of testing the company’s unique lithium-ion cells, Anthro Energy explored the development and utilization of novel cell components, cell architectures, and testing protocols. These next-generation flexible and structural batteries may eventually enable new categories of electronic devices.

25 ENERGY STORAGE

Metamaterials as a Platform for the Development of Novel Materials for Energy Applications

To explore the fundamental properties of metamaterials (MMs) / metasurfaces and their potential for control of energy at the sub‐wavelength scale in support of the mission of the Department of Energy and the office of Basic Energy Sciences. Electromagnetic metamaterials provide a platform for the discovery and design of new materials with novel structures, functions, and properties. The PI proposes to advance the knowledge base of these materials through fundamental investigations of the experimental and theoretical properties of metamaterials for the discovery, prediction and design of new materials with novel structures, functions, and properties. The proposed research activities emphasize a complete basic research program including the conceptual / computational design, fabrication / synthesis of the materials, and the characterization and analysis of their electromagnetic properties. The proposed project explores the fundamental properties of metamaterials / metasurfaces and their potential for energy applications. There are three main topics which will be investigated: 1) Dispersion engineering with metamaterials and metasurfaces, 2) Epsilon near zero metamaterial absorbers and emitters, and 3) All dielectric metamaterials. The program implements a complete basic research program consisting of theory / design, modeling, characterization, and analysis, in order to fully characterize metamaterials and metasurfaces, while at the same time minimizing iterations necessary to achieve the proposal goals.

36 MATERIALS SCIENCE

A Novel Integrated Fermentation Process with Engineered Microbial Consortia for Butanol Production from Lignocellulose Sugars without CO 2 Emission

The goal of this project was to develop a synthetic microbial consortium consisting of a lactic acid bacterium, a carboxydotrophic acetogen, and a solventogenic clostridia for the production of n butanol, an advanced biofuel and industrial chemical, from lignocellulose sugars (mainly glucose and xylose) and formate (produced from CO 2 by electrochemical reduction) in an integrated bioprocess (biorefinery), which can provide an effective solution to the technical challenges in developing energy and carbon optimized synthesis for the bioeconomy and achieve the program objectives of ARPA-E. The project focused on the design, modeling and construction of synthetic microbial consortia consisting of three bacterial species to maximize carbon conversion and butanol production with a 100% theoretical product yield from glucose and zero or negative CO 2 emission.

09 BIOMASS FUELS

Molecular Programming of Diorganyl Dichalcogenides for Rational Nanocrystal Design

Soft-chemistry nanocrystal synthesis leverages low-temperature, solution-phase reactions to access materials that can be kinetically stabilized rather than thermodynamically favored. Under such mild conditions, reaction pathways are governed not only by precursor composition but also by the molecular details that dictate how reactive atomic species are generated and delivered. Furthermore, harnessing this kinetic sensitivity offers a powerful opportunity: by deliberately programming precursor reactivity, nanocrystal composition, structure, and morphology can be rationally designed rather than empirically discovered.

Chalcogenides

Steam-Assisted Ammonolysis of MoO2 as a Synthetic Pathway to Oxygenated δ-MoN

A common route for the synthesis of molybdenum nitrides is through the temperature-programmed reaction of molybdenum oxides with NH3, or ammonolysis. In this work, the role of precursor phase, gas phase chemistry (impact of H2O), and temperature profile on the reaction outcome (700 °C) was examined, which resulted in varying amounts of MoO2, H2MoO5, and the nitride phases—cubic γ (nominally Mo2N) and hexagonal δ (nominally MoN). The phase fraction of the δ phase increased with precursor in the sequence MoO2 > MoO3 > H2MoO5. Steam in the reaction gas also favored the production of δ over γ, but with too much steam, MoO2 was obtained in the product. Synthesis conditions for obtaining nearly phase-pure δ were identified: MoO2 as the precursor, 2% H2O in the gas stream, and a moderate heating rate (3 °C/min). In situ X-ray diffraction provided insights into the reaction pathway. Extensive physico-chemical analysis of the δ phase, including synchrotron X-ray and neutron diffraction, electron microscopy, thermogravimetric analysis, X-ray photoelectron spectroscopy, and prompt gamma activation analysis, revealed its stoichiometry to be MoO0.108(8)N0.892(8)H0.012(5), indicating non-trivial oxygen incorporation. The presence of N/O ordering and an impurity phase Mo5N6 were also revealed, detectable only by neutron diffraction. Notably, a computationally predicted MoON phase (doi: 10.1103/PhysRevLett.123.236402), of interest due to its potential to display a metal-insulator transition, did not appear under any reaction condition examined.

Pandey, Shobhit

Preliminary Design of Nuclear Reactor Heat Delivery Systems: Integration with Reference Oil Refinery, Methanol Synthesis, and Hydrogen Production

The Department of Energy’s (DOE) Integrated Energy Systems (IES) program is generating comprehensive analyses validating the opportunity for using nuclear energy in a variety of applications including future clean grids, providing heat for direct use, and providing heat to help reduce emissions in chemical commodities. This work focuses on the preliminary designs of thermal delivery systems that can integrate heat produced from a nuclear core to industrial processes. The key research question that needs to be answered is: what is the prospective method for integrating nuclear generated heat energy into non-electric applications that can facilitate combined heat and power operations by advanced nuclear reactor systems? This research is a composition of case studies showing preliminary conceptual designs for thermal delivery systems integrating advanced nuclear systems with a few industrial systems including high temperature steam electrolysis, a reference oil refinery, and potential future methanol systems that supplant some natural gas use with nuclear energy. Piping and instrumentation diagrams have been developed to show the conceptual integration of nuclear systems with representative industrial systems. Different features of the configurations are dependent on the specific integration requirements including energy source conditions, demand quantity, and require energy application conditions. Design concepts are validated using thermodynamic balance calculations to verify system performance including calculating system losses during transport. Key components: pumps and compressors, heat exchangers, and network piping are reported with key design information and sizing.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Fuel Salt Synthesis for the Molten Chloride Reactor Experiment: Scale-up, Operations, and Production Update

Over the previous 5 years, Idaho National Laboratory (INL) has been working with Southern Co. and TerraPower on the Advanced Reactor Demonstration Program (ARDP) funded Molten Chloride Reactor Experiment (MCRE) project. As part of this effort, INL has developed a fuel synthesis process to produce the NaCl-UCl3 fuel salt that MCRE will need for operation. Dr. Phillips will present on process development and scale-up testing and results, as well as provide an update on the current status of fuel production for MCRE. To date, the fuel synthesis process has been demonstrated at full scale using depleted uranium, and the equipment necessary for production of the fuel for MCRE has been installed in the Fuel Manufacturing Facility (FMF) at the INL’s Materials and Fuels Complex (MFC). The NaCl-UCl3 produced to-date has been shown to be of 99.99% purity or greater, and be within tolerance for all relevant parameters. Overall process efficiency in terms of uranium utilization has been demonstrated to be above 90%. The synthesis operation has also been shortened to allow for completion of the reaction within a single 10 hour working shift. Consequently, the process developed is expected to be capable of meeting all project objectives for efficiency, purity, scale, and scheduling. Production of NaCl-UCl3 fuel salt for MCRE is projected to begin during the Summer of 2025.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana . Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

59 BASIC BIOLOGICAL SCIENCES

Development of Metal Boride/Carbide Precursors for MOCVD Applications (Office of Naval Research Research Performance Progress Report)

Annual Report for Office of Naval Research (ONR) program office. Highlights the synthetic and corresponding computational efforts surrounding the synthesis and processing of chemical precursors and their subsequent processing for formation of metal carbide products. Focus of this annual report is largely directed toward the computational effort as that manuscript is being finalized for submission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

FEW questions, many answers: using machine learning to assess how students connect food–energy–water (FEW) concepts

There is growing support and interest in postsecondary interdisciplinary environmental education which integrate concepts and disciplines in addition to providing varied perspectives. There is a need to assess student learning in these programs as well as rigorous evaluation of educational practices, especially of complex synthesis concepts. This work tests a text classification machine learning model as a tool to assess student systems thinking capabilities using two questions anchored by the Food-Energy-Water (FEW) Nexus phenomena by answering two questions (1) Can machine learning models be used to identify instructor-determined important concepts in student responses? (2) What do college students know about the interconnections between food, energy and water, and how have students assimilated systems thinking into their constructed responses about FEW? Reported here are a broad range of model performances across 26 text classification models associated with two different assessment items, with model accuracy ranging from 0.755 to 0.992. Expert-like responses were infrequent in our dataset compared to responses providing simpler, incomplete explanations of the systems presented in the question. For those students moving from describing individual effects to multiple effects, their reasoning about the mechanism behind the system indicates advanced systems thinking ability. Specifically, students exhibit higher expertise for explaining changing water usage than discussing tradeoffs for such changing usage. This research represents one of the first attempts to assess the links between foundational, discipline-specific concepts and systems thinking ability. These text classification approaches to scoring student FEW Nexus Constructed Responses (CR) indicate how these approaches can be used, in addition to several future research priorities for interdisciplinary, practice-based education research. Development of further complex question items using machine learning would allow evaluation of the relationship between foundational concept understanding and integration of those concepts as well as more nuanced understanding of student comprehension of complex interdisciplinary concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION