Atomic and micro-structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations
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Materials Science↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Electronic Structure Theories of Singlet Fission and Multiple Exciton Generation (Final Report)
This DOE grant supported the development of electronic structure theory, algorithms, and computer programs for simulating singlet fission and multiple excision generation processes from Sept. 2013 to Aug. 2018 (which was terminated due to the PI’s departure from Northwestern University to industry). One of the main achievements is the development of the so-called active space decomposition (ASD) method hat describes exciton dynamics in organic semiconductors and spin dynamics in strongly correlated materials. The resulting software was interfaced with the Brilliantly Advanced General Electronic-structure Library (BAGEL) package and widely disseminated to the research community.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Dissecting the structural heterogeneity of proteins by native mass spectrometry
Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
59 BASIC BIOLOGICAL SCIENCES↗
NASA LARC RAFTOR documentation version 1.0
The use of a preprocessor of the LaRC computer center that converts RAFTOR source into FORTRAN source code is described. The purpose of RAFTOR is to make FORTRAN a better programming language for both writing and structuring programs. It is concluded that RAFTOR can generate a well structured program with a source code that is easy to follow.
Dunn, H. J.↗
Generation of 3-D surface maps in waste storage silos using a structured light source
Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.
Burks, B. L.↗
Inverse design of cellular structures with the targeted nonlinear mechanical response
Advanced additive manufacturing capabilities have enabled a transformational ability to create sophisticated cellular structures using diverse materials. By altering the topology of the unit cell, the mechanical behavior, such as the stress-strain response during compression, can be modulated. Nevertheless, identifying a printable topology within an enormous design space that would precisely deliver the targeted nonlinear material response is challenging. We propose a data-driven generative framework based on a conditional variational autoencoder (cVAE) architecture that can inverse design the cellular structure based on the intended nonlinear stress-strain response. Trained on a dataset of structure-property pairs, the cVAE learns a compact and expressive latent space that enables efficient mapping from targets to feasible geometries. Two inference modes are explored: (1) decoder-only generation, which enables the exploration of diverse designs conditioned solely on the desired mechanical response, and (2) encoder-decoder generation, which further allows for the incorporation of desired topologies, ensuring the generated structure conforms to both mechanical properties and to desired-topology constraints. The results demonstrate that the model can generate structurally plausible and mechanically accurate designs, with the predicted stress-strain curves closely matching the targets. Even under joint conditioning, the model effectively balances geometric fidelity and functional performance.
36 MATERIALS SCIENCE↗
Impact of Forest Canopy Structure on Buoyant Plume Dynamics During Wildland Fires
Heterogeneous forest canopies can generate complex turbulent structures, but in the presence of a fire plume, these interactions are not fully understood. This study investigates the influence of forest canopy heterogeneity on buoyant plume dynamics resulting from surface thermal anomalies representing wildland fires, utilizing Large Eddy Simulation (LES). The Parallelized Large-Eddy Simulation Model (PALM) was employed to simulate six canopy configurations: no canopy, homogeneous canopy, external plume-edge canopy, internal plume-edge canopy, 100 m gap canopy, and 200 m gap canopy. Each configuration was analyzed with and without a static surface heat flux patch of 5000 W ∙ m -2 , resulting in a resting buoyant plume. Simulations were conducted under three crosswind speeds: 0, 5, and 10 m ∙ s -1 . Results show that canopy structure significantly modifies plume behavior, mean flow, and turbulent kinetic energy (TKE) budgets. Plume updraft speed and tilt varied with canopy configuration and crosswind speed. Horizontal pressure gradients associated with plume-atmosphere interaction were modified based on the canopy configuration, resulting in varying crosswind speed reductions at the plume region. Strong momentum absorption was observed above the canopy for the crosswind cases, with the greatest enhancement in the gap canopies. Momentum injection from below the canopy due to the heat source was also observed, resulting in plume structure modulation based on canopy configuration. TKE was found to be the largest in the gap canopy configurations. TKE budget analysis revealed that buoyant production dominated over shear production. At the center of the heat patch, the gap canopy configurations showed enhanced buoyancy within the gap. These results improve our knowledge of fire-canopy-atmosphere interactions that can inform fire models on the impacts of canopy heterogeneity on plume dynamics and ember ejections.
54 ENVIRONMENTAL SCIENCES↗
Test chip assembler and test program generator
One of the major problems in working at the geometry level for the generation of either test structure or functional circuit designs is the amount of labor involved in the design phase. To reduce the amount of labor involved in both the design and test of the structures used, JPL has developed a design and test program consisting of a Test Chip Assembler (TCA) and a Test Program Generator (TPG), which creates the geometrical description of the structures and generates the necessary test information using a high-level language. This system reduces the design time for a test chip by a factor of 30. To analyze the data obtained from wafer probing, a statistical package called STMJPL was developed. Some of the capabilities of the JPL software (STMJPL) are described.
Pina, C. A.↗
Large Composite Structures Processing Technologies for Reusable Launch Vehicles
Significant efforts have been devoted to establishing the technology foundation to enable the progression to large scale composite structures fabrication. We are not capable today of fabricating many of the composite structures envisioned for the second generation reusable launch vehicle (RLV). Conventional 'aerospace' manufacturing and processing methodologies (fiber placement, autoclave, tooling) will require substantial investment and lead time to scale-up. Out-of-autoclave process techniques will require aggressive efforts to mature the selected technologies and to scale up. Focused composite processing technology development and demonstration programs utilizing the building block approach are required to enable envisioned second generation RLV large composite structures applications. Government/industry partnerships have demonstrated success in this area and represent best combination of skills and capabilities to achieve this goal.
Clinton, R. G., Jr.↗
Structural characterization of a first-generation articulated-truss joint for space crane application
A first-generation space crane articulated-truss joint was statically and dynamically characterized in a configuration that approximated an operational environment. The articulated-truss joint was integrated into a test-bed for structural characterization. Static characterization was performed by applying known loads and measuring the corresponding deflections to obtain load-deflection curves. Dynamic characterization was performed using modal testing to experimentally determine the first six mode shapes, frequencies, and modal damping values. Static and dynamic characteristics were also determined for a reference truss that served as a characterization baseline. Load-deflection curves and experimental frequency response functions are presented for the reference truss and the articulated-truss joint mounted in the test-bed. The static and dynamic experimental results are compared with analytical predictions obtained from finite element analyses. Load-deflection response is also presented for one of the linear actuators used in the articulated-truss joint. Finally, an assessment is presented for the predictability of the truss hardware used in the reference truss and articulated-truss joint based upon hardware stiffness properties that were previously obtained during the Precision Segmented Reflector (PSR) Technology Development Program.
Sutter, Thomas R.↗
Mechanical adaptation of brachiopod shells via hydration-induced structural changes
The function-optimized properties of biominerals arise from the hierarchical organization of primary building blocks. Alteration of properties in response to environmental stresses generally involves time-intensive processes of resorption and reprecipitation of mineral in the underlying organic scaffold. Here, we report that the load-bearing shells of the brachiopod Discinisca tenuis are an exception to this process. These shells can dynamically modulate their mechanical properties in response to a change in environment, switching from hard and stiff when dry to malleable when hydrated within minutes. Using ptychographic X-ray tomography, electron microscopy and spectroscopy, we describe their hierarchical structure and composition as a function of hydration to understand the structural motifs that generate this adaptability. Key is a complementary set of structural modifications, starting with the swelling of an organic matrix on the micron level via nanocrystal reorganization and ending in an intercalation process on the molecular level in response to hydration.
36 MATERIALS SCIENCE↗
Generative Thermodynamic Computing
Here, we introduce a generative modeling framework for thermodynamic computing, in which structured data are synthesized from noise by the natural time evolution of a physical system governed by Langevin dynamics. While conventional diffusion models use neural networks to perform denoising, here the information needed to generate structure from noise is encoded by the dynamics of a thermodynamic system. Training proceeds by maximizing the probability with which the computer generates the reverse of a noising trajectory, which ensures that the computer generates data with minimal heat emission. We demonstrate this framework within a digital simulation of a thermodynamic computer. If realized in analog hardware, such a system would function as a generative model that produces structured samples without the need for artificially injected noise or active control of denoising.
Whitelam, Stephen [Lawrence Berkeley National Labo↗
Hyperbolic Methods for Surface and Field Grid Generation
This chapter describes the use of hyperbolic partial differential equation methods for structured surface grid generation and field grid generation. While the surface grid generation equations are inherently three dimensional, the field grid generation equations can be formulated in two or three dimensions. The governing equations are derived from orthogonality relations and cell area/volume constraints; and are solved numerically by marching from an initial curve or surface. The marching step size and marching distance can be prescribedly the user. Exact specifications of the side and outer boundaries are not possible with a one sweep marching scheme but limited control is achievable. Excellent orthogonality and grid clustering characteristics are provided by hyperbolic methods with one to two orders of magnitude savings in time over typical elliptic methods. Since hyperbolic grid generation methods do not require the exact specifications of the side and outer boundaries of a grid, these methods are particularly well suited for the overlapping grid approach for solving problems on complex configurations. Grid generation software based on hyperbolic methods and their applications on several complex configurations will be described.
Chan, William M.↗
Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL
Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.
59 BASIC BIOLOGICAL SCIENCES↗
Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model
We report two generative deep-learning models that predict amino acid sequences and 3D protein structures on the basis of secondary-structure design objectives via either the overall content or the per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity because they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary-structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in the conditional generative design of various biological or engineering systems. Future work could include additional conditioning and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1
The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.
Cross, James H., II↗
Coupling Noah-Multiparameterization land-surface Model with Energy Research and Forecasting Model
The Energy Research and Forecasting (ERF) model is a high-performance atmospheric model built on the AMReX adaptive mesh refinement (AMR) framework, enabling efficient simulations on heterogeneous computing platforms that combine multicore processors with hardware accelerators. To support land–atmosphere interactions within ERF’s AMR-based environment, a land-surface model must be capable of operating directly on hierarchically refined meshes. In this work, we present a methodology for coupling the Fortran-based Noah-Multiparameterization (Noah-MP) land-surface model with ERF’s C++ codebase. Rather than rewriting Noah-MP, we construct a Fortran–C interoperability layer using CodeScribe, a tool that leverages large language models (LLMs) to automate the generation of interface code. CodeScribe applies structured prompting techniques to generate bindings that support efficient data exchange and function calls between ERF and Noah-MP. The coupling framework also incorporates AMR-aware data handling strategies, allowing NoahMP to operate seamlessly within ERF’s hierarchical mesh structure. This work provides a structured approach for integrating legacy Fortran models into modern C++-based modeling systems using LLM-assisted code generation.
54 ENVIRONMENTAL SCIENCES↗
Structural Load Alleviation Applied to Next Generation Aircraft and Wind Turbines
Reducing the environmental impact of aviation is a goal of the Subsonic Fixed Wing Project under the Fundamental Aeronautics Program of NASAs Aeronautics Research Mission Directorate. Environmental impact of aviation is being addressed by novel aircraft configurations and materials that reduce aircraft weight and increase aerodynamic efficiency. NASA is developing tools to address the challenges of increased airframe flexibility created by wings constructed with reduced structural material and novel light-weight materials. This talk will present a framework and demonstration of a flight control system using optimal control allocation with structural load feedback and constraints to achieve safe aircraft operation. As wind turbines age, they become susceptible to many forms of blade degradation. Results will be presented on work in progress that uses adaptive contingency control for load mitigation in a wind turbine simulation with blade damage progression modeled.
adaptive control↗