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DOE OSTI2020

Fundamental limitations on photoisomerization from thermodynamic resource theories

Small, out-of-equilibrium, and quantum systems defy simple thermodynamic expressions. Such systems are exemplified by molecular switches, which exchange heat with a bath. These molecules can photoisomerize, or change conformation, or switch, on absorbing light. The photoisomerization probability depends on kinetic details that couple the molecule’s energetics to its dissipation. Therefore, a simple, general, thermodynamic-style bound on the photoisomerization probability seems out of reach. We derive such a bound using a resource theory. The resource-theory framework is a set of mathematical tools, developed in quantum information theory, used to generalize thermodynamics to small and quantum settings. From this toolkit has been derived a generalization of the second law, the thermomajorization preorder. We use thermomajorization to upper-bound the photoisomerization probability. Then, we compare the bound with an equilibrium prediction and with a Lindbladian model. We identify a realistic parameter regime in which the Lindbladian evolution saturates the thermomajorization bound. We also quantify the energy coherence in the electronic degree of freedom, and we argue that this coherence cannot promote photoisomerization. Overall, this work illustrates how quantum-information-theoretic thermodynamics can elucidate complex quantum processes in nature, experiments, and synthetics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Combinatorial transcription factor binding encodes cis -regulatory wiring of mouse forebrain GABAergic neurogenesis

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays. We identified sets of putative regulatory elements with shared TF binding (TF-pRE modules) that orchestrate distinct processes of GABAergic neurogenesis and suppress other cell fates. The majority of pREs were bound by one or two TFs; however, a small proportion were extensively bound. These sequences had exceptional evolutionary conservation and motif density, complex chromosomal interactions, and activity as in vivo enhancers. Our results provide insights into the combinatorial TF-pRE interactions that activate and repress expression programs during telencephalon neurogenesis and demonstrate the value of TF binding toward modeling developmental transcriptional wiring.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Project Title: Demonstration High Temperature Superconducting NonPlanar Stellarator Magnet with Advanced Manufactured Assemblies

This is the final report for the project “Demonstration High Temperature Superconducting Non- Planar Stellarator Magnet with Advanced Manufactured Assemblies”, funded by DOE, and performed by Type One Energy from September, 2020, to March 2024 involving the Fusion Technology Institute at the University of Wisconsin–Madison, the Plasma Science and Fusion Center (PSFC) at the Massachusetts Institute of Technology (MIT) and Commonwealth Fusion Systems (CFS) to design and fabricate the first non-planar HTS (REBCO) coil for a high-field stellarator based on the SPARC tokamak’s VIPER cable concept. Stellarators at high fields make high-temperature superconducting magnets necessary for a compact fusion device. But the asymmetric and non-planar nature of its components, especially the magnets make it difficult for scalable producibility. To address these challenges, two promising technologies have emerged: advanced manufacturing (AM) for the supporting plates for forming the magnets, and high-temperature superconducting (HTS) cables inside the plates. AM has advanced enough to produce stellarator components with the necessary geometric complexity, size, and the precision, leading to potentially significant reductions in production time, cost, and waste. The cost of HTS tape has decreased dramatically, and progress in HTS planar magnet development has reached a point where it can be proposed for application to complex 3D non-planar magnets. The main objective of this project is to develop, demonstrate and pre-commercialize a novel, non-planar HTS coil shape that remains superconducting to achieve production scalable reductions in time and cost and performance. The proposed technology is based on the novel concept of a precision sub-scale HTS nonplanar coil assembly. This project focuses on the design, fabrication, material optimization of cable design, and validation and demonstration of the high current carrying capability of superconducting magnets and their support in a complex 3D shape needed for application to stellarator magnetic plasma confinement. The specific objectives of this research program include: (1) The successful application of metal AM to build a precision sub-scale HTS nonplanar coil, (2) An HTS cable and cross-section design that can conform to the required nonplanar coil shape (bend radii as tight as 10-cm) and remains superconducting at an engineering current density of 1.35 kA/cm 2 at 77 K and 1 tesla at the conductor (5 kA in the cable). To achieve the above challenging goals, we have formed a multidisciplinary research team consisting of members from Type One Energy and UW-Madison, MIT PSFC and CFS with complementary skills and strong facilities. The team worked collaboratively on fundamental and applied research on the following three major technical areas: (1) Design, fabrication, and optimization of non-planar HTS Cable The ultimate goal of the project is to determine if commercial REBCO tapes and additive manufacturing can be used to fabricate high field (≥ 10T) non-planar coils with tight bending radii (≃ 100mm) and with a degradation of the critical current (Ic) smaller than 20% with respect to the expected performance. We started with shorter length cable to evaluate the scalability of the production process and eventually reached multiple turns for higher magnetic fields. Our findings suggest that a stellarator coil system of a relevant size, characterized by its asymmetric and non-planar components, can be fabricated using a formed cable in plate method. This system can be simulated using a large-scale modeling approach. The use of hybrid modeling 3 techniques will be pivotal in reducing the complexity of the model and in assessing expected performance in designs. (2) Modeling and simulation of the non-planar HTS Cable Multiphysics simulations are performed using the commercial software and are carried out in self-field conditions, involving 2D and 3D models and twisted around one slot of twist-pitched VIPER cable. Multiphysics simulations are mainly focused on the coil for the critical current evaluation, the magnetic field map, self-Lorentz forces and mechanical, and magnetothermal behavior and the quench dynamics. The detailed model and prediction of the superconducting performance of a stellarator-relevant demonstration cable from numerical simulations supports the results from the actual testing backing the results. A detailed description and results are provided in the later sections. (3) Design, fabrication, and optimization of support for the non-planar HTS Cable The team developed an additive manufactured (AM) coil positioning plate that formed into the required non-planar geometry (with bend radii as tight as 10-cm) and to acceptable tolerances required for a stellarator magnet: (+0.25-mm from ideal on dimensions of coil positioning plates and up to +1-mm from ideal for position of wound coil). The plate materials is also included in this selection process from fabrication and 3D printing perspective and commensurate with eventual application to a fusion reactor. From the cost effectiveness point of view, the HTS coil and plate has the potential to cost less than that made in conventional methods with less waste (<75% waste) reducing time (<50%) and cost (<50%), especially as the AM field matures. The application of advanced manufacturing in the construction of the support plates will also lead to cost reduction, as the cables can be easily replaced, thereby making the assembly modular. With such high primary cost and time savings, high current densities and magnetic field, the funded R&D work has validated the designs, proven the feasibility, and characterized the performance of the HTS coil and plate assembly, paving the way for a relevant-size stellarator coil system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model

Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022

AoR↗
DOE OSTI2023

Use of Stable Mercury Isotopes to Assess Mercury and Methylmercury Transformation and Transport across Critical Interfaces from the Molecular to the Watershed Scale (Final Report)

This project titled “Use of Stable Mercury Isotopes to Assess Mercury and Methylmercury Transformation and Transport across Critical Interfaces from the Molecular to the Watershed Scale” represents a collaborative effort between the University of Michigan (Jason Demers, PI) and Oak Ridge National Laboratory (Scott Brooks, co-I). Much has been learned about mercury (Hg) cycling in stream ecosystems, and East Fork Poplar Creek (EFPC) in particular, through decades of previous research. Nevertheless, some of the most fundamental questions regarding the sources of bioavailable Hg and its transformation to toxic methylmercury (MeHg) have remained unanswered. These fundamental questions include: (1) what are the sources and biogeochemical processes that lead to the input of dissolved Hg to stream water across critical subsurface interfaces within stream ecosystems, and EFPC in particular? and (2) what are the sources and biogeochemical processes that control the production and fate of bioaccumulative MeHg within stream ecosystems, and in EFPC in particular? To address these fundamental questions, our project aimed to couple laboratory experiments and field observations, both utilizing natural abundance Hg stable isotope techniques, to identify the processes responsible for generating mobile, bioavailable dissolved Hg from recalcitrant legacy sources within critical subsurface zones (e.g., streambed hyporheic zone, riparian floodplain subsurface). We used the isotopic signature of this bioavailable dissolved Hg to track its mobilization across these critical interfaces in order to link diffuse subsurface sources of dissolved Hg with increases in surface water dissolved Hg flux measured at the watershed scale. Additionally, our research aimed to determine the isotopic composition of MeHg within these same critical subsurface zones. We directly assessed the isotopic composition of MeHg within biota in order to gain insight into which subsurface sources of inorganic Hg and toxic MeHg are available for bioaccumulation within the EFPC ecosystem. Net fluxes of dissolved Hg along the flow path of EFPC were shown to vary spatially and temporally. In the Upper EFPC, within the Y12 boundary, stream water flux of dissolved Hg consistently decreased between the outfall and the downstream boundary of Y12 (57% ± 29%, 1SD). Within the Upper EFPC, an assessment of Hg isotopic composition suggested that losses were strongly reaction-driven, although isotopic diagnostics did not conform to any known processes. Downstream of Y12, in the upper reach of the Lower EFPC, dissolved Hg fluxes tended to increase during the dormant season (net gain of 11-120%), and decrease during the growing season (net loss of 23% +/- 18%, 1SD). In the downstream-most reach of Lower EFPC, dissolved Hg fluxes increased by 12-108% in 9 out of 10 monthly assessments. Overall, diffuse fluxes from the non-Y12 watershed accounted for 34% (+/- 17%, 1SD) of all dissolved Hg exported during base flow. Within Lower EFPC, an assessment of Hg isotopic composition was consistent with the contribution of diffuse Hg inputs from high-concentration hotspots within riparian floodplains and streambed hyporheic pore water. To investigate remobilization of recalcitrant Hg from legacy sediment sources, we developed procedures that coupled isotopic analysis with sequential extractions of streambed sediment. We found that the proportion of weakly-bound Hg within EFPC streambed sediment was relatively small, but could still account for a large proportion of the annual flux of dissolved Hg from EFPC. These sequential extractions also showed that this weakly-bound Hg fraction could be replenished from the much larger fraction of recalcitrant Hg in sediment. The isotopic composition of these weakly-bound and remobilized recalcitrant Hg fractions within the sediment was consistent with high-concentration dissolved Hg hotspots within hyporheic pore water. Thus, this research provided novel evidence that legacy mercury sources within streambed sediment could provide an ongoing contribution of dissolved Hg to surface waters. Finally, we developed new methods for the direct determination of the MeHg isotopic composition of organisms, which allowed a more direct evaluation of inorganic Hg and MeHg sources accumulating in the food web. We found that fish and aquatic invertebrates in both EFPC and a regional background site obtained inorganic Hg and MeHg from multiple isotopically distinct sources, including sediment, suspended particulates, and periphyton. Photodemethylation was found to be an important reaction influencing MeHg dynamics at both sites. However, the balance of microbial methylation and demethylation processes differed between the two streams, with fractionation resulting from methylation and demethylation processes being relatively in balance within the regional background site, whereas microbial methylation appeared to be dominant over microbial demethylation within the EFPC ecosystem. Broadly, the application of Hg isotopic analysis in this study led to numerous novel insights regarding the biogeochemical cycling of Hg in stream ecosystems. This research project promoted the development of two new approaches, including the coupling of sequential extractions with Hg isotopic analysis to assess remobilization of recalcitrant Hg within sediments, and a new method for the isotopic analysis of MeHg isolated from environmental samples. Both of these efforts represent advances in capacity for the field of mercury isotopic analysis and environmental assessment. Overall, this study demonstrates that the application of Hg stable isotope techniques continues to provide new insights into the biogeochemical cycling of Hg in complex aquatic environments, both within the EFPC and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

A Cognitive-System Model for En Route Air Traffic Management

NASA Ames Research Center has been engaged in the development of advanced air traffic management technologies whose basic form is cognitive aiding systems for air traffic controller and flight deck operations. In the design and evaluation of such systems the dynamic interaction between the airborne aiding system and the ground-based aiding systems forms a critical coupling for control. The human operator is an integral control element in the system and the optimal integration of human decision and performance parameters with those of the automation aiding systems offers a significant challenge to cognitive engineering. This paper presents a study in full mission simulation and the development of a predictive computational model of human performance. We have found that this combination of methodologies provide a powerful design-aiding process. We have extended the computational model Man Machine Integrated Design and Analysis System (N13DAS) to include representation of multiple cognitive agents (both human operators and intelligent aiding systems), operating aircraft airline operations centers and air traffic control centers in the evolving airspace. The demands of this application require the representation of many intelligent agents sharing world-models, and coordinating action/intention with cooperative scheduling of goals and actions in a potentially unpredictable world of operations. The operator's activity structures have been developed to include prioritization and interruption of multiple parallel activities among multiple operators, to provide for anticipation (knowledge of the intention and action of remote operators), and to respond to failures of the system and other operators in the system in situation-specific paradigms. We have exercised this model in a multi-air traffic sector scenario with potential conflict among aircraft at and across sector boundaries. We have modeled the control situation as a multiple closed loop system. The inner and outer loop alerting structure of air traffic management has many implications that need to be investigated to assure adequate design. First, there are control and stability factors implicit in the design. As the inner loop response time approaches that of the outer loop, system stability may be compromised in that controllers may be solving a problem the nature of which has already been changed by pilot action. Second, information exchange and information presentation for both air and ground must be designed to complement as opposed to compete with each other. Third, the level of individual and shared awareness in trajectory modification and flight conformance needs to be defined. Fourth, the level of required awareness and performance impact of mixed fleet operations and failed-mode recovery must be explored.

Corker, Kevin M.↗
DOE OSTI2022

Non-Gaussianities in collider energy flux

The microscopic dynamics of particle collisions is imprinted into the statistical properties of asymptotic energy flux, much like the dynamics of inflation is imprinted into the cosmic microwave background. This energy flux is characterized by correlation functions < E(n → 1 )…E(n → k ) > of energy flow operators E(n → ). There has been significant recent progress in studying energy flux, including the calculation of multi-point correlation functions and their direct measurement inside high-energy jets at the Large Hadron Collider (LHC). In this paper, we build on these advances by defining a notion of “celestial non-gaussianity” as a ratio of the three-point function to a product of two-point functions. We show that this celestial non-gaussianity is under perturbative control within jets at the LHC, allowing us to cleanly access the non-gaussian interactions of quarks and gluons. We find good agreement between perturbative calculations of the non-gaussianity and a charged-particle-based analysis using CMS Open Data, and we observe a strong non-gaussianity peaked in the “flattened triangle” regime. The ability to robustly study three-point correlations is a significant step in advancing our understanding of jet substructure at the LHC. We anticipate that the celestial non-gaussianity, and its generalizations, will play an important role in the development of higher-order parton showers simulations and in the hunt for ever more subtle signals of potential new physics within jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in $γ$-Glu-(Pro) n -Met Peptides

The kinetics of intramolecular-contact formation between remote functional groups in peptides with restricted conformational flexibility were examined using designed peptides with variable-length proline bridges. As probes for this motion, free radicals were produced using the • OH-induced oxidation at the C-terminal methionine residue of γ-Glu-(Pro) n -Met peptides ( n = 0–3). The progress of the radicals’ motion along the proline bridges was monitored as the radicals underwent reactions along the peptides’ backbones. Of particular interest was the reaction between the sulfur atom located in the side chain of the oxidized Met residue and the unprotonated amino group of the glutamic acid moiety. Interactions between them were probed by the radiation-chemical yields (expressed as G values) of the formation of C-centered, α-aminoalkyl radicals (αN) on the Glu residue. These radicals were monitored directly or via their reaction with p -nitroacetophenone (PNAP) to generate the optically detected PNAP •– radical anions. The yields of these αN radicals were found to be linearly dependent on the number of Pro residues. A constant decrease by 0.09 μM J –1 per spacing Pro residue of the radiation-chemical yields of G (αN) was observed. Previous reports support the conclusion that the αN radicals in these cases would have to result from (S$\therefore$N) + -bonded cyclic radical cations that arose as a result from direct contact between the ends of the peptides. Furthermore, by analogy with the rate constants for the formation of intramolecularly (S$\therefore$S) + -bonded radical cations in Met-(Pro) n -Met peptides ( J. Phys. Chem. B 2016 , 120 , 9732), the rate constants for the formation of intramolecularly (S$\therefore$N) + -bonded radical cations are activated to the same extent for all of the γ-Glu-(Pro) n -Met peptides. Thus, the continuous decrease of G (αN) with the number of Pro residues (from 0 to 3) suggests that the formation of a contact between the S-atom in the C-terminal Met residue and the N-atom of a deprotonated N-terminal amino group of Glu is controlled in peptides with 0 to 3 Pro residues by the relative diffusion of the S •+ and unoxidized N-atom. The overall rate constants of cyclization to form the (S$\therefore$N)-bonded radical cations were estimated to be 3.8 × 10 6 , 1.8 × 10 6 , and 8.1 × 10 5 s –1 for peptides with n = 0, 1, and 2 Pro residues, respectively. If activation is the same for all of the peptides, then these rate constants are a direct indication for the end-to-end dynamics along the chain.

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

A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries

Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.

computational fluid dynamics (CFD)↗
DOE OSTI2025

Conformally coated scaffold design using water-tolerant Pr 1.8 Ba 0.2 NiO 4.1 for protonic ceramic electrochemical cells with 5,000-h electrolysis stability

Protonic ceramic electrochemical cells (PCECs) have potential as long-duration energy storage systems. However, their operational stability is limited under industrially relevant conditions due to the intrinsic chemical instability of doped barium cerate-based electrolytes and oxygen electrodes against H 2 O, as well as the poor electrode–electrolyte interfacial contact. Here, in this study, we present a conformally coated scaffold (CCS) design to comprehensively address these issues. A porous proton-conducting scaffold is constructed and conformally coated with Pr 1.8 Ba 0.2 NiO 4.1 electrocatalyst, which has high chemical stability against H 2 O, triple conductivity and hydration capability, and protects vulnerable electrolytes from H 2 O. The CCS structure consolidates the electrode–electrolyte interfacial bonding to enable fast proton transfer in the percolated network. This design enables PCECs to reach electrolysis stability for 5,000 h at −1.5 A cm−2 and 600 °C in 40% H 2 O. This work provides a general strategy to stabilize PCECs and offers guidance for designing resilient and stable solid-state energy storage systems.

Protonic ceramic electrochemical cell↗