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DOE OSTI2025

Atom Identification in Bilayer Moiré Materials with Gomb-Net

Moiré patterns in van der Waals bilayer materials complicate the analysis of atomic-resolution images, hindering the atomic-scale insight typically attainable with scanning transmission electron microscopy. Here, we report a method to detect the positions and identities of atoms in each of the individual layers that compose twisted bilayer heterostructures. We developed a deep learning model, Gomb-Net, which identifies the coordinates and atomic species in each layer, deconvoluting the moiré pattern. This enables layer-specific mapping of atomic positions and dopant distributions, unlike other commonly used segmentation models which struggle with moiré-induced complexity. Using this approach, we explored the Se atom substitutional site distribution in a twisted fractional Janus WS 2 -WS 2(1–x) Se 2x heterostructure and found that layer-specific implantation sites are unaffected by the moiré pattern’s local energetic or electronic modulation. In conclusion, this advancement enables atom identification within material regimes where it was not possible before, opening new insights into previously inaccessible material physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Unraveling Adsorbate-Induced Structural Evolution of Iron Carbide Nanoparticles

Iron carbide (Fe x C y ) nanoparticles (NPs) are promising candidates for replacing platinum group metals in industrial applications, such as high-temperature Fischer–Tropsch synthesis. However, due to their amorphous nature, characterization of the active sites has been challenging experimentally and computationally. Here, using a combined density functional theory (DFT), neural network interatomic potential-assisted global optimization, and ensemble learning study, we evaluate dynamic surface changes associated with syngas (H and CO) interactions. For this purpose, we have developed a general procedure that we use to model an experimentally relevant 270-atom Fe 182 C 88 NP using the neural network-assisted stochastic surface walk global optimization algorithm (SSW-NN). Once generated, the Fe 182 C 88 NP active sites and particle morphology are thoroughly characterized before the effects of syngas adsorbate interactions are explored by using DFT and molecular dynamics simulations. Lastly, we explore correlations between geometric and electronic features of the active sites and the adsorption of H (H ads ), using a regularized random forest machine learning algorithm. In doing so, we identified the Fe–C coordination number and p orbital occupancy as the most important descriptors affecting H ads . Furthermore, using a combined ML and quantum chemistry approach, our work demonstrates a general and efficient procedure for generating and probing complex surface phenomena on binary nanoparticles.

Adsorption↗

DOE OSTI2020

Crystal Structure and C–H Bond-Cleaving Reactivity of a Mononuclear Co IV –Dinitrate Complex

High-valent Fe IV =O intermediates with a terminal metal–oxo moiety are key oxidants in many enzymatic and synthetic C–H bond oxidation reactions. While generating stable metal–oxo species for late transition metals remains synthetically challenging, notably, a number of high-valent non-oxo–metal species of late transition metals have been recently described as strong oxidants that activate C–H bonds. In this work, we obtained an unprecedented mononuclear Co IV –dinitrate complex (2) upon one-electron oxidation of its Co(III) precursor supported by a tridentate dianionic N3 ligand. 2 was structurally characterized by X-ray crystallography, showing a square pyramidal geometry with two coordinated nitrate anions. Furthermore, characterization of 2 using combined spectroscopic and computational methods revealed that 2 is a low-spin (S = 1/2) Co(IV) species with the unpaired electron located on the cobalt d z2 orbital, which is well positioned for substrate oxidations. Indeed, while having a high thermal stability, 2 is able to cleave sp 3 C–H bonds up to 87 kcal/mol to afford rate constants and kinetic isotope effects (KIEs) of 2–6 that are comparable to other high-valent metal oxidants. The ability to oxidize strong C–H bonds has yet to be observed for Co IV –O and Co III =O species previously reported. Therefore, 2 represents the first high-valent Co(IV) species that is both structurally characterized by X-ray crystallography and capable of activating strong C–H bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

In Crystallo Snapshots of Rh 2 -Catalyzed C–H Amination

While X-ray crystallography routinely provides structural characterization of kinetically stable pre-catalysts and intermediates, elucidation of the structures of transient reactive intermediates, which are intimately engaged in bond-breaking and -making during catalysis, is generally not possible. Here, we demonstrate in crystallo synthesis of Rh 2 nitrenoids that participate in catalytic C-H amination, and characterize these transient intermediates as triplet adducts of Rh 2 . Further, we observe the impact of coordinating substrate, which is present in excess during catalysis, on the structure of transient Rh 2 nitrenoids. By providing structural characterization of authentic C-H functionali-zation intermediates, and not kinetically stabilized model complexes, these experiments provide the opportunity to define critical structure-activity relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Mining for Metal–Organic Systems: Chemistry Frontiers of Th-, U-, and Zr-Materials

The conceptual framework presented in this Perspective overviews the design principles of innovative thorium-based materials that could address urgent needs of the medicinal, nuclear energy, and waste remediation sectors from the lens of zirconium and uranium analogs. We survey the intersections of Zr, Th, and U chemistry with a focus on how the intrinsic behavior of each metal translates to broader material properties, including, but not limited to, structural and topological diversity, preferential metal–ligand binding, and reactivity. On the example of several classes of materials, including organometallic complexes, polyoxometalates, and the primary focus of this Perspective, metal–organic frameworks (MOFs), the design principles that govern the preparation of Zr-, Th-, and U-compounds, including oxophilicity, variation in oxidation states, and stable coordination environments have been considered. Further, we highlight how the impact of the mentioned variables may shift throughout the progression from discrete molecular systems to extended structures. We discuss the common assumption that zirconium-organic materials are typically considered a close analog of thorium-based congeners in areas such as material design and preparation. Through consideration of fundamental chemistry principles, we shed light on the relationships between Zr-, Th-, and U-based materials and highlight how a critical analysis of their distinct properties can be used to target a desired material performance. Finally, we provide a detailed understanding of Th-based materials chemistry by anchoring their fundamental properties between two well-studied reference points, zirconium- and uranium-containing analogs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

Abstract McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A Roadmap for the Future of Systems Biology in Cancer Research

Cancer systems biology seeks to understand how cancer arises as a system of interconnected molecules, cells, and tissues, with the goal of understanding, predicting, and controlling the disease. In the last decade, the field has rapidly grown as advances in experimental, computational, and analytic technologies have improved our ability to capture and recapitulate the complexities of cancer at multiple scales. However, the field’s promise to understand how specific molecular changes give rise to altered cancer outcomes remains incompletely fulfilled. Fortunately, an opportunity exists to accelerate progress by better coordinating modeling and data-gathering efforts across the cancer systems biology community. This will create the foundation for building accurate, multiscale cancer models that can better predict and identify improved therapeutic interventions. Here, in this study, we outline some of the current challenges in cancer systems biology research, how they can be addressed, and actions that the community can take to accelerate progress in the field.

Modeling & Simulation↗

DOE OSTI2022

Overview of the MOSAiC expedition—Atmosphere

With the Arctic rapidly changing, the needs to observe, understand, and model the changes are essential. To support these needs, an annual cycle of observations of atmospheric properties, processes, and interactions were made while drifting with the sea ice across the central Arctic during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition from October 2019 to September 2020. An international team designed and implemented the comprehensive program to document and characterize all aspects of the Arctic atmospheric system in unprecedented detail, using a variety of approaches, and across multiple scales. These measurements were coordinated with other observational teams to explore cross-cutting and coupled interactions with the Arctic Ocean, sea ice, and ecosystem through a variety of physical and biogeochemical processes. This overview outlines the breadth and complexity of the atmospheric research program, which was organized into 4 subgroups: atmospheric state, clouds and precipitation, gases and aerosols, and energy budgets. Atmospheric variability over the annual cycle revealed important influences from a persistent large-scale winter circulation pattern, leading to some storms with pressure and winds that were outside the interquartile range of past conditions suggested by long-term reanalysis. Similarly, the MOSAiC location was warmer and wetter in summer than the reanalysis climatology, in part due to its close proximity to the sea ice edge. The comprehensiveness of the observational program for characterizing and analyzing atmospheric phenomena is demonstrated via a winter case study examining air mass transitions and a summer case study examining vertical atmospheric evolution. Overall, the MOSAiC atmospheric program successfully met its objectives and was the most comprehensive atmospheric measurement program to date conducted over the Arctic sea ice. The obtained data will support a broad range of coupled-system scientific research and provide an important foundation for advancing multiscale modeling capabilities in the Arctic.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

DECOVALEX-2019 (Task E Final Report)

The DECOVALEX Project is an on-going international research collaboration, established in 1992, to advance the understanding and modeling of coupled Thermal (T), Hydrological (H), Mechanical (M) and Chemical (C) processes in geological in geological systems. DECOVALEX was initially motivated by the recognition that prediction of these coupled effects is an essential part of the performance and safety assessment of geologic disposal systems for radioactive waste and spent nuclear fuel. Later it was realized that these processes also play a critical role in other subsurface engineering activities, such as subsurface CO 2 storage, enhanced geothermal systems, and unconventional oil and gas production through hydraulic fracturing. Research teams from many countries (e.g., Canada, China, Czech Republic, Finland, France, Germany, Japan, Republic of Korea, Spain, Sweden, Switzerland, Taiwan, United Kingdom, and the United States) various institutions have participated in the DECOVALEX Project over the years, providing a wide range of perspectives and solutions to these complex problems. These institutions represent radioactive waste management organizations, national research institutes, regulatory agencies, universities, as well as industry and consulting groups. This document is the final report of Task E which was proposed and coordinated by Andra, the National Radioactive Waste Management Agency in France, presenting the technical definitions of the problems studied, approaches applied, achievements made and outstanding issues for future research. The purpose of Task E of the DECOVALEX-2019 project is to investigate upscaling THM modelling from small-scale experiments (some cubic meters) to full-scale experiments (some ten cubic meters) and finally to the scale of the waste repository (cubic kilometers). To achieve this aim, the data of two in-situ heating experiments performed by Andra (the French National Radioactive Waste Management Agency) in the Meuse/Haute-Marne Underground Research Laboratory (MHM URL) have formed the basis for the understanding of the THM behavior of the COx at different scales. The first experiment provided the reference values of the THM parameters by means of a calibration exercise and they were used for a blind prediction and an interpretative analysis of the second one.

58 GEOSCIENCES↗

NASA NTRS1975

Coordinate transformation and truncation for rotating spacecraft with flexible appendages

The analytical structures of alternative coordinate transformations for the variables that characterize the deformations of finite element models of flexible appendages on rotating spacecraft are examined. Particular emphasis is given to the truncation operations that are essential for efficient numerical simulations of flexible spacecraft, due to the necessarily large number of coordinates employed in a finite element description. A theorem is developed which establishes necessary conditions for the commutativity of the required truncation and inversion operations. The recommended alternative for the rotating elastic appendage is a complex transformation with previously published orthogonality properties, which permit the derivation in this paper of a relatively simple explicit set of transformed and truncated equations of modal vibration in real variables.

Likins, P.↗

NASA NTRS1981

Asymptotic form of the longitudinal correlation function for isotropic homogeneous turbulence

An asymptotic form is derived for the longitudinal correlation function for isotropic homogeneous turbulence in an incompressible fluid governed by the Navier-Stokes equation. The result is obtained from an analysis of the algebraic-differential structure of the two-point correlation tensor contained in the complex-valued Fourier transform of the probability measure over the turbulence ensemble, which reveals that the Hopf characteristic functional (the complex-valued Fourier transform of the probability measure) satisfies the Fourier interference inequality. Consequences of the expression obtained, in which the correlation function is a positive definite function of the inverse cube of the spatial coordinate as it approaches infinity, are shown to include the nonexistence of the Loitsianskii invariant, and the solution is shown to be consistent with empirical formulas.

Rosen, G.↗

NASA NTRS1982

Three dimensional flow computations in a turbine scroll

The compressible three dimensional inviscid flow in the scroll and vaneless nozzle of radial inflow turbines is analyzed. A FORTRAN computer program for the numerical solution of this complex flow field using the finite element method is presented. The program input consists of the mass flow rate and stagnation conditions at the scroll inlet and of the finite element discretization parameters and nodal coordinates. The output includes the pressure, Mach number and velocity magnitude and direction at all the nodal points.

Hamed, A.↗

NASA NTRS1986

A review of modelling techniques for the open and closed-loop dynamics of large space systems

This paper reviews the steps in the development of mathematical models that can be used to simulate the in-orbit dynamic behavior of large flexible systems. A general continuum formulation is compared with the hybrid coordinate formulation and also a finite element representation of the total system. A review of structural analysis routines emphasizes the use of computer generated graphics to help understand the different modal elastic shape functions of complex systems. Numerical techniques employed to synthesize shape and attitude control laws are summarized. Finally, the modeling of environmental disturbance torques due to the interaction of solar radiation pressure on vibrating and thermally deflected systems is discussed.

Bainum, Peter M.↗

NASA NTRS1996

Development of the command data system and ground software for the SEDSAT-1 microsatellite

SEDSAT-1 is designed to be a low cost scientific satellite which is to be used to perform a minimum of five tasks which include: (1) the acquisition of a number of important parameters associated with the tethering processes from the payloads perspective (such as accelerations incurred and imaging data of the tether during deployment), (2) to act as a remote sensing platform for making measurements of the Earth's Atmosphere (allowing research to be performed in such areas as vertical lightning observation, visible light spectrography, and cloud cover studies, (3) to act as a general purpose amateur radio communication satellite relaying information back to earth, (4) to demonstrate the feasibility of the deployment in low earth orbit of advanced technology such as the Gallium Arsenide Solar Cells, Nickel Metal Hydride batteries, and multi-chip module technology and, (5) to support student's active participation in applying the disciplines of engineering and science to space-based hardware platforms. The project includes the Three-axis Accelerometer System, TAS, Experiment which is designed to report the accelerations that the satellite undergoes during the tethering operations and during the second phase of the mission when the free floating satellite comes in contact with orbit debris. The SEASIS (SEDS Earth, Atmosphere, and Space Imaging System) is another SEDSAT experiment designed to provide images of the tether during its deployment and the earth during the second phase of the mission. To control these experiments and virtually all other satellite operations the Command Data System, CDS is employed. This system utilizes a moderate complexity micro-controller controlled by tasks operating under a real-time operating system to dynamically monitor and control the satellite. The scope of this researchers efforts has been in the general area of coordinating and assisting the student researchers with the development of the CDS and ground station interfaces. This included the low level CDS hardware design and the formulization of a general software plan and schedule for both the CDS and ground station portions of the project.

Wells, B. Earl↗

NASA NTRS2000

A Characterization of the Terrestrial Environment of Kodiak Island, Alaska for the Design, Development and Operation of Launch Vehicles

A quantitative characterization of the terrestrial environment is an important component in the success of a launch vehicle program. Environmental factors such as winds, atmospheric thermodynamics, precipitation, fog, and cloud characteristics are among many parameters that must be accurately defined for flight success. The National Aeronautics and Space Administration (NASA) is currently coordinating weather support and performing analysis for the launch of a NASA payload from a new facility located at Kodiak Island, Alaska in late 2001 (NASA, 1999). Following the first launch from the Kodiak Launch Complex, an Air Force intercontinental ballistic missile on November 5, 1999, the site's developer, the Alaska Aerospace Development Corporation (AADC), is hoping to acquire a sizable share of the many launches that will occur over the next decade. One such customer is NASA, which is planning to launch the Vegetation Canopy Lidar satellite aboard an Athena I rocket, the first planned mission to low earth orbit from the new facility. To support this launch, a statistical model of the atmospheric and surface environment for Kodiak Island, AK has been produced from rawinsonde and surface-based meteorological observations for use as an input to future launch vehicle design and/or operations. In this study, the creation of a "reference atmosphere" from rawinsonde observations is described along with comparisons between the reference atmosphere and existing model representations for Kodiak. Meteorological conditions that might result in a delay on launch day (cloud cover, visibility, precipitation, etc.) are also explored and described through probabilities of launch by month and hour of day. This atmospheric "mission analysis" is also useful during the early stages of a vehicle program, when consideration of the climatic characteristics of a location can be factored into vehicle designs. To be most beneficial, terrestrial environment definitions should a) be available at the inception of the program and based on the desired operational performance of the launch vehicle, b) be issued under the signature of the program manager and be part of the controlled program definition and requirements documentation, and c) specify the terrestrial environment for all phases of activity including prelaunch, launch, ascent, on-orbit, decent, and landing. Since the beginning of the space era, NASA has utilized some of the most detailed assessments of the terrestrial climatic environment in design, development, and operations of both expendable and reusable launch vehicles.

Rawlins, Michael A.↗

NASA NTRS2005

Physics-based Simulation of Human Posture Using 3D Whole Body Scanning Technology for Astronaut Space Suit Evaluation

Over the past few years high precision three-dimensional (3D) full body laser scanners have been developed to be used as a powerful anthropometry tool for quantification of the morphology of the human body. The full body scanner can quickly extract body characteristics in non-contact fashion. It is required for the Anthropometry and Biomechanics Facility (ABF) to have capabilities for kinematics simulation of a digital human at various postures whereas the laser scanner only allows capturing a single static posture at each time. During this summer fellowship period a theoretical study has been conducted to estimate an arbitrary posture with a series of example postures through finite element (FE) approximation and found that four-point isoparametric FE approximation would result in reasonable maximum position errors less than 5%. Subsequent pilot scan experiments demonstrated that a bead marker with a nominal size of 6 mm could be used as a marker for digitizing 3-D coordinates of anatomical landmarks for further kinematic analysis. Two sessions of human subject testing were conducted for reconstruction of an arbitrary postures from a set of example postures for each joint motion for the forearm/hand complex and the whole upper extremity.

Kim, Kyu-Jung↗

NASA NTRS2009

A Distributed Prognostic Health Management Architecture

This paper introduces a generic distributed prognostic health management (PHM) architecture with specific application to the electrical power systems domain. Current state-of-the-art PHM systems are mostly centralized in nature, where all the processing is reliant on a single processor. This can lead to loss of functionality in case of a crash of the central processor or monitor. Furthermore, with increases in the volume of sensor data as well as the complexity of algorithms, traditional centralized systems become unsuitable for successful deployment, and efficient distributed architectures are required. A distributed architecture though, is not effective unless there is an algorithmic framework to take advantage of its unique abilities. The health management paradigm envisaged here incorporates a heterogeneous set of system components monitored by a varied suite of sensors and a particle filtering (PF) framework that has the power and the flexibility to adapt to the different diagnostic and prognostic needs. Both the diagnostic and prognostic tasks are formulated as a particle filtering problem in order to explicitly represent and manage uncertainties; however, typically the complexity of the prognostic routine is higher than the computational power of one computational element ( CE). Individual CEs run diagnostic routines until the system variable being monitored crosses beyond a nominal threshold, upon which it coordinates with other networked CEs to run the prognostic routine in a distributed fashion. Implementation results from a network of distributed embedded devices monitoring a prototypical aircraft electrical power system are presented, where the CEs are Sun Microsystems Small Programmable Object Technology (SPOT) devices.

Bhaskar, Saha↗

DOE OSTI2020

Softwarized Federations of Science Instruments with Edge-Continuum Containers

Significant expansion of capabilities of DOE science complex of supercomputers, instruments and networks is expected as powerful experimental facilities, exascale computers and terabit networks are added. Combined with the advances in edge and cloud computing technologies, DOE science users now have the promise of unprecedented execution of complex, continuum workflows, namely, small and latency-sensitive computations at the edge and site, massive computations at remote HPC systems, and everything in between on the cloud. But, bringing this capability to the science user requires overcoming the overwhelming complexity of forming the federations of systems, and efficiently and effectively orchestrating the workflows while ensuring high utilization of the expensive facilities. Current manual configuration of the federated systems simply will not scale, since the coordination across sites may take weeks to months, often leading to under-utilized and hard-to-diagnose compositions. A powerful, composable software stack will be developed to (i) wrap the systems so that federations can be composed fast in software, and (ii) containerize computations to be orchestrated across the edge, site, cloud and HPC resources.

Rao, Nageswara S.↗