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DOE OSTI2022

Design of quantum optical experiments with logic artificial intelligence

Logic Artificial Intelligence (AI) is a subfield of AI where variables can take two defined arguments, True or False, and are arranged in clauses that follow the rules of formal logic. Several problems that span from physical systems to mathematical conjectures can be encoded into these clauses and solved by checking their satisfiability (SAT). In contrast to machine learning approaches where the results can be approximations or local minima, Logic AI delivers formal and mathematically exact solutions to those problems. In this work, we propose the use of logic AI for the design of optical quantum experiments. We show how to map into a SAT problem the experimental preparation of an arbitrary quantum state and propose a logic-based algorithm, called Klaus, to find an interpretable representation of the photonic setup that generates it. We compare the performance of Klaus with the state-of-the-art algorithm for this purpose based on continuous optimization. We also combine both logic and numeric strategies to find that the use of logic AI significantly improves the resolution of this problem, paving the path to developing more formal-based approaches in the context of quantum physics experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Design Basis Document / Owner’s Technical Specification for Nitrate Salt Systems in CSP Projects (Final Technical Report)

The number of commercial coal, gas, and nuclear projects built over the past 100 years number in the thousands. As such, there is a large database, available to a wide range of commercial engineering contractors, on proven designs. In essence, unsuccessful designs have, through generations of iterations, been identified and then deleted from further consideration. In contrast, the number of commercial parabolic trough projects using nitrate salt for the thermal storage media is perhaps 60. Further, the number of commercial central receiver projects using nitrate salt as the working fluid is on the order of 20, including estimates for China. Given the relative immaturity of salt technology, and commercial pressures to successfully bid new solar projects into a mature electricity market, solar projects often promise more than has been delivered. The Design Basis Document / Owner’s Technical Specification is a first step in the iteration process. The report describes the successful features of commercial projects, outlines a range equipment and system failures in projects that didn’t operate as intended, and provides a draft set of design changes intended to correct the known problems. The product of the study is 3 volumes of technical material; one volume is on parabolic trough technologies; a second is on central receiver technologies, and the third is on potential design changes to parabolic trough and central receiver projects. The 3 volumes, which total some 590 pages, can be found at https://www.solardynllc.com/csp-plant-technologies. One of the principal topics in the report is the use of functional or prescriptive specifications. Functional specifications describe what the equipment needs to do, consistent with the minimum legal requirements of the local jurisdictions. The details of how this is to be accomplished is developed by the engineering contractor. Prescriptive specifications, which are developed by the Owner, prescribe to the engineering contractor how the functional requirements are to be met. This arrangement ensures that the favorable experience from a previous project is repeated. One example is the design code for the hot salt tank in central receiver projects. The closest design basis is API Standard 650 Welded Steel Tanks for Oil Storage. However, the maximum design temperature in API 650 is 260 °C. As such, solar projects have typically adopted a hybrid Code approach, in which allowable material stresses are taken from ASME Section II Materials. Further, since the tanks experience daily changes in temperature and in (static) pressure, and since portions of the tank can operate at stresses beyond the elastic range, the low cycle fatigue life of the tank is conducted using the rules of Section VIII Division 2. However, in a recent study by NREL, the principal damage mechanism was identified as creep rather than fatigue. Further, design stresses permitted under Section VIII Division 2, corresponding to a fatigue life of 30 years, result in projected creep lifetimes of only 2 to 5 years. An alternate design approach, prescribed by the Owner, would be based on Code sections intended for high temperature service in the creep regime. A candidate is Section III Division 5. Granted, this is a nuclear code section, and it’s use would not likely be mandated by local jurisdictions. However, the effects of creep have been deemed to be of sufficient importance that one nuclear project developer, and one central receiver project developer, have stipulated in the tank design specification that the equipment be designed to the requirements of Section III Division 5.

14 SOLAR ENERGY↗

DOE OSTI2023

Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization

Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed “activation” and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A WISER way for simulating the performance of gratings

Soft X-ray monochromators for synchrotron radiation sources have been continuously developed over the years, improving energy resolution and stability. Great effort has been made in improving the surface quality of the optics involved, reaching values permitting diffraction-limited images. Still, one problem has not been solved, nor fully understood, yet: groove placing errors. Nowadays, these are one of the major factors responsible for resolving the power reduction of diffraction-gratings-based X-ray monochromators. Despite decades of use of gratings, there is not yet a universally established method for predicting and simulating the effect of groove placing errors on monochromator performance. This is especially important in the new scenario of high-coherent X-ray sources, i.e. diffraction-limited storage rings and free-electron lasers. To address this problem, in this article an approach based on WISER (Wavefront propagatIon Simulation codE libRary) is presented. WISER is a physical optics simulation package, also available in the user-friendly Orange Synchrotron Radiation Suite – OASYS. Even though it was originally conceived to assess the focusing performance of X-ray mirrors in the presence of height defects, it perfectly simulates the performance of a periodic (or quasi-periodic) structure like a diffraction grating. In this article, the way to use WISER and its application to a specific case, e.g. the design of a monochromator for the upgrade of a beamline at the Advanced Light Source, are shown. A simple rule for estimating how well the grooves are placed on a grating, based on calculation of the Strehl ratio, is also presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Fabrication of 8-Strand Rutherford Cables Using Roped Strands Made from Ultrafine Wires

Conventional Rutherford cables are typically made from solid round wire. While multi-stage cables have been made elsewhere, the purpose was usually to achieve a higher strand count and therefore a higher current carrying capability. In this work, we attempt to use two-stage roped strands made from ultrafine wires to fabricate Rutherford cables. The ultimate goal of this work is to obtain a very flexible cable that can wind accelerator magnet coils with a very tight bend radius in both the “easy way” (along the broad face of the cable) and the “hard way” (along the edge of the cable) in the wind-and-react manner, or wind coils with a radius typically used today but in the react and-wind manner with a much reduced degradation in critical current. We report our experience fabricating such Rutherford cables at the Lawrence Berkeley National Laboratory, and the initial findings from the analysis of the experimental cables made. We will discuss how the conventional wisdom and some rules of thumb for making Rutherford cables are no longer applicable or relevant, and the new thinking required in designing these cables.

Pong, Ian↗

DOE OSTI2023

Application of multi-criteria decision analysis techniques and decision support framework for informing select agent designation for agricultural animal pathogens

The United States Department of Agriculture (USDA), Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents and toxins (Select Agent List) that potentially threaten agricultural health and safety, the procedures governing the transfer of those agents, and training requirements for entities working with them. Every 2 years the USDA DASAT reviews the Select Agent List, using subject matter experts (SMEs) to perform an assessment and rank the agents. To assist the USDA DASAT biennial review process, we explored the applicability of multi-criteria decision analysis (MCDA) techniques and a Decision Support Framework (DSF) in a logic tree format to identify pathogens for consideration as select agents, applying the approach broadly to include non-select agents to evaluate its robustness and generality. We conducted a literature review of 41 pathogens against 21 criteria for assessing agricultural threat, economic impact, and bioterrorism risk and documented the findings to support this assessment. The most prominent data gaps were those for aerosol stability and animal infectious dose by inhalation and ingestion routes. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for accuracy, particularly for pathogens with very few known cases, or where proxy data (e.g., from animal models or similar organisms) were used to address data gaps. The MCDA analysis supported the intuitive sense that select agents should rank high on the relative risk scale when considering agricultural health consequences of a bioterrorism attack. However, comparing select agents with non-select agents indicated that there was not a clean break in scores to suggest thresholds for designating select agents, requiring subject matter expertise collectively to establish which analytical results were in good agreement to support the intended purpose in designating select agents. The DSF utilized a logic tree approach to identify pathogens that are of sufficiently low concern that they can be ruled out from consideration as a select agent. In contrast to the MCDA approach, the DSF rules out a pathogen if it fails to meet even one criteria threshold. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Local rules for fabricating allosteric networks

Mechanical properties of disordered networks can be significantly tailored by modifying a small fraction of their bonds. This procedure has been used to design and build mechanical metamaterials with a variety of responses. A long-range “allosteric” response, where a localized input strain at one site gives rise to a localized output strain at a distant site, has been of particular interest. This work presents an approach to incorporating allosteric responses in experimental systems by pruning disordered networks in situ. Previous work has relied on computer simulations to design and predict the response of such systems using a cost function where the response of the entire network to each bond removal is used at each step to determine which bond to prune. It is not feasible to follow such a design protocol in experiments where one has access only to local response at each site. This paper presents design algorithms that allow determination of what bonds to prune based purely on the local forces in the network without employing a cost function; using only local information, allosteric networks are designed in simulations and then built out of real materials. The results show that some pruning strategies work better than others when translated into an experimental system. A method is presented to measure local stresses experimentally in disordered networks. This approach is then used to implement pruning methods to design desired responses in situ. Results from these experiments confirm that the pruning methods are robust and work in a real laboratory material.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Er Al :Al 2 ⁢O 3 for telecom-band photonics: Electronic structure and optical properties

Er-doped Al 2 ⁢O 3 is a promising host for telecom-band integrated photonics. Here, in this study, we combine ab initio calculations with a symmetry-resolved analysis to elucidate substitutional Er on the Al site (Er Al ) in 𝛼−Al 2 ⁢O 3 . First-principles relaxations confirm the structural stability of Er Al . We then use the local trigonal crystal-field symmetry to classify the Er-derived impurity levels by irreducible representations and to derive polarization-resolved electric-dipole selection rules, explicitly identifying the symmetry-allowed 𝑓−𝑑 hybridization channels. Kubo-Greenwood absorption spectra computed from Kohn-Sham states quantitatively corroborate these symmetry predictions. Furthermore, we connect the calculated intra-4⁢𝑓 line strengths to Judd-Ofelt theory, clarifying the role of 4⁢𝑓−5⁢𝑑 admixture in enabling optical activity. Notably, we predict a characteristic absorption near 1.47 µ⁢m (telecom band), relevant for on-chip amplification and emission. To our knowledge, a symmetry-resolved first-principles treatment of Er:Al 2 ⁢O 3 with an explicit Judd-Ofelt interpretation has not been reported, providing a transferable framework for tailoring rare-earth dopants in wide-band-gap oxides for integrated photonics. Our results for the optical spectra are in good agreement with experimental data. The resulting symmetry-based selection rules translate directly to polarization-dependent coupling in Al 2 ⁢O 3 integrated photonic waveguides and resonators, enabling device-level design of TE/TM-mode interaction with Er emitters in the 1.5-µ⁢m telecom band.

Er-doped Al2O3↗

DOE OSTI2024

Chemical Framework to Design Linear-like Relaxors toward Capacitive Energy Storage

ABO 3 -type perovskite relaxor ferroelectrics (RFEs) have emerged as the preferred option for dielectric capacitive energy storage. However, the compositional design of RFEs with high energy density and efficiency poses significant challenges owing to the vast compositional space and the absence of general rules. Here, we present an atomic-level chemical framework that captures inherent characteristics in terms of radius and ferroelectric activity of ions. By categorizing A/B-site ions as host framework, rattling, ferroelectrically active, and blocking ions and assembling these four types of ions with specific criteria, linear-like relaxors with weak locally correlated and highly extendable unit-cell polarization vectors can be constructed. As example, we demonstrate two new compositions of Bi 0.5 K 0.5 TiO 3- based and BaTiO 3- based relaxors, showing extremely high recoverable energy densities of 17.3 and 12.1 J cm –3 , respectively, both with a high efficiency of about 90%. Further, the role of different types of ions in forming heterogeneous polar structures is identified through element-specific local structure analysis using neutron total scattering combined with reverse Monte Carlo modeling. Further, our work not only opens up new avenues toward rational compositional design of high energy storage performance lead-free RFEs but also sheds light on atomic-level manipulation of functional properties in compositionally complex ferroelectrics.

25 ENERGY STORAGE↗

DOE OSTI2026

Enhanced Second and Third Harmonic Generations in Metasurfaces Enabled through Point Group Design and Accidental Bound States in the Continuum

Here, we investigate enhanced second‑ and third‑harmonic generation (SHG and THG) in GaAs metasurfaces by combining electromagnetic point‑group designs with accidental bound states in the continuum (BICs). Using group theory, we predict the existence, suppression, and polarization selection rules of SHG and THG for metasurfaces belonging to the D 2h and C 2v point groups. In D 2h metasurfaces, inversion symmetry suppresses SHG while enabling polarization‑selective THG, which is strongly enhanced near accidental BICs with ultrahigh Q‑factors approaching 107. By breaking inversion symmetry to form C 2v metasurfaces through the introduction of nanogaps, SHG is now allowed and is dramatically enhanced near accidental BICs. Importantly, accidental BICs preserve polarization selection rules while providing a robust parameter range for high‑Q resonances, in contrast to quasi‑BICs induced by symmetry breaking. Our results demonstrate that the combination of point‑group theory and accidental‑BIC engineering offers a predictive and robust route toward highly efficient nonlinear metasurfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

A rule-free workflow for the automated generation of databases from scientific literature

Abstract In recent times, transformer networks have achieved state-of-the-art performance in a wide range of natural language processing tasks. Here we present a workflow based on the fine-tuning of BERT models for different downstream tasks, which results in the automated extraction of structured information from unstructured natural language in scientific literature. Contrary to existing methods for the automated extraction of structured compound-property relations from similar sources, our workflow does not rely on the definition of intricate grammar rules. Hence, it can be adapted to a new task without requiring extensive implementation efforts and knowledge. We test our data-extraction workflow by automatically generating a database for Curie temperatures and one for band gaps. These are then compared with manually curated datasets and with those obtained with a state-of-the-art rule-based method. Furthermore, in order to showcase the practical utility of the automatically extracted data in a material-design workflow, we employ them to construct machine-learning models to predict Curie temperatures and band gaps. In general, we find that, although more noisy, automatically extracted datasets can grow fast in volume and that such volume partially compensates for the inaccuracy in downstream tasks.

36 MATERIALS SCIENCE↗

DOE OSTI2024

In Vitro Evolution and Computational Approaches to Predict, Prevent and Control Future Pandemics

The natural tendency of virus to mutate and the under-sampling of the environment makes it difficult to become aware of the emergence of new viral strains with pandemic potential. Being able to predict what mutations make a virus more infective might allow to spot such strains with minimal sampling and potentially allow to predict/prevent the next pandemic. The team attempted to mimic natural viral mutations and recombination through computational and experimental methods producing a variety of mutants of a SARS-COV-2 protein (receptor binding domain, RBD, of spike protein) responsible for viral entry in mammalian cells. The library of mutants was then interrogated for ability and lack-there-of to interact with the host cell receptor ushering viral entry, Angiotensin-converting enzyme 2 (ACE2). The negative and positive data set is intended to “teach the rules” of virus-host receptor interaction. Additionally, the positive clones were used to screen a set of antibody mutants designed to widen the breadth of viral mutants recognition, to demonstrate that this kind of libraries could also be a tool to produce antibody therapeutics impervious to viral mutation, even before a pandemic strain is discovered.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Phase Selection Rules of Multi‐Principal Element Alloys

Abstract Computational prediction of phase stability of multi‐principal element alloys (MPEAs) holds a lot of promise for rapid exploration of the enormous design space and autonomous discovery of superior structural and functional properties. Regardless of many plausible works that rely on phenomenological theory and machine learning, precise prediction is still limited by insufficient data and the lack of interpretability of some machine learning algorithms, e.g., convolutional neural network. In this work, a comprehensive approach is presented, encompassing the development of a complete dataset that contains 72 387 density functional theory calculations, as well as a predictive global phenomenological descriptor. The phase selection descriptor, based on atomic electronegativity and valence electron concentration, significantly outperforms the widely used valence electron concentration, excelling in both accuracy (with an f1 score of 63% compared to 47%) and its ability to predict the HCP phase (0.48 recall compared to 0). The comprehensive data mining on the global design space of 61 425 quaternary MPEAs made from 28 possible metals, together with the phenomenological theory and physical interpretation, will set up a solid computational science foundation for data‐driven exploration of MPEAs.

Chemistry↗

DOE OSTI2022

The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles

The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its “tensegrity” nature to its three rotationally-stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed [Z + 2/3] turn inter-junction segments, yielding right-handed, antiparallel, “J1” junctions. Here, we report here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one third of a helical turn. Here, we find that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction—the L1 junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. We identify a Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs Using Large Language Models

Abstract We evaluate the ability of machine learning to predict whether a hypothetical crystal structure can be synthesized and explain those predictions to scientists. Fine‐tuned large language models (LLMs) trained on a human‐readable text description of the target crystal structure perform comparably to previous bespoke convolutional graph neural network methods, but better prediction quality can be achieved by training a positive‐unlabeled learning model on a text‐embedding representation of the structure. An LLM‐based workflow can then be used to generate human‐readable explanations for the types of factors governing synthesizability, extract the underlying physical rules, and assess the veracity of those rules. These explanations can guide chemists in modifying or optimizing non‐synthesizable hypothetical structures to make them more feasible for materials design.

Kim, Seongmin [Department of Chemical and Biologic↗

DOE OSTI2025

Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs Using Large Language Models

Kim, Seongmin [Department of Chemical and Biologic↗

DOE OSTI2025

Linear Dichroism of the Optical Properties of SnS and SnSe Van der Waals Crystals

Abstract Tin monochalcogenides SnS and SnSe, belonging to a family of Van der Waals crystals isoelectronic to black phosphorus, are known as environmentally friendly materials promising for thermoelectric conversion applications. However, they exhibit other desired functionalities, such as intrinsic linear dichroism of the optical and electronic properties originating from strongly anisotropic orthorhombic crystal structures. This property makes them perfect candidates for polarization‐sensitive photodetectors working in near‐infrared spectral range. A comprehensive study of the SnS and SnSe crystals is presented, performed by means of optical spectroscopy and photoemission spectroscopy, supported by ab initio calculations. The studies reveal the high sensitivity of the optical response of both materials to the incident light polarization, which is interpreted in terms of the electronic band dispersion and orbital composition of the electronic bands, dictating the selection rules. From the photoemission investigation the ionization potential, electron affinity and work function are determined, which are parameters crucial for the design of devices based on semiconductor heterostructures.

Chemistry↗