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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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NASA NTRS2026

Hydrology Copilot: A Cloud-Native Ai System for Hydrological Data Analysis

The emergence of AI-driven Earth observation systems promises to broaden access to petabyte-scale geospatial data beyond domain specialists. However, translating this vision into operational scientific infrastructure requires addressing fundamental challenges in data virtualization, code transparency, and domain-specific reasoning. We present Hydrology Copilot, a cloud-native AI framework for natural-language-driven analysis of Earth observation data. To demonstrate operational capabilities at scale, we implement the system using NASA's North American Land Data Assimilation System version 3 (NLDAS-3), which provides surface meteorological forcing and land-surface model output across North and Central America at 1-km resolution, from which drought diagnostics are derived. The system integrates five core contributions: (1) scalable data virtualization using Kerchunk-based cloud optimized access, achieving a 1.5 to 4.6 times improvement in I/O latency across benchmark queries spanning regional single-day extractions (4.6 times speedup) to continental monthly aggregations (1.5 times speedup); (2) transparent code generation through Microsoft Azure AI Foundry agents that expose executable Python workflows for scientific verification; (3) persistent conversational memory enabling multi-turn analytical discourse across sessions; (4) intelligent query validation that enforces dataset boundaries and resolves ambiguous requests before execution; and (5) a multi-agent architecture coordinating query parsing, code generation, and visualization. We evaluate the system through drought-monitoring workflows, demonstrating reliable code generation, accurate results validated against reference computations and the operational U.S. Drought Monitor, and efficient operation across increasingly complex tasks. By bridging natural-language interfaces with rigorous hydrological analysis, Hydrology Copilot advances beyond proof-of-concept demonstrations to provide a deployable framework for operational Earth science applications.

Data virtualization↗
DOE OSTI2021

Characterizing Long COVID: Deep Phenotype of a Complex Condition

Background: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. Methods: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. Funding: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. Interpretation: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2026

Emergence of Diverse Failure Patterns in Weathering‐Induced Landslides: Insights From Particle Finite Element Simulations

Weathering is a fundamental driver of landslide evolution over geological timescales. Despite its ubiquity and importance, quantifying how weathering drives the progressive destabilization of rock slopes remains challenging. In this work, we develop a unified computational framework based on the particle finite element method to investigate the evolution of weathering‐induced landslides, from long‐term weathering to short‐term slope failure and runout dynamics. The framework integrates key processes, including weathering front propagation, time‐dependent strength degradation, rupture surface development, and post‐failure runout dynamics. Through numerical simulation experiments, we elucidate how interactions among weathering characteristics (type, intensity, and rate law), bedrock strength, fracture distribution, and slope geometry govern the failure modes and kinematics of weathering‐induced landslides. Simulations show that matrix‐dominated weathering leads to shallow translational failures, whereas fracture‐dominated weathering produces deep‐seated rotational and compound landslides. Pre‐existing fractures and slope morphology also strongly influence the movement of destabilized landmasses, affecting the failure pattern (e.g., kinematic mode and rupture surface geometry) and post‐failure behavior (e.g., runout velocity). We further demonstrate that the failure time and volume of weathered slopes are governed by the competition between gravitational driving forces and cohesive resisting forces during progressive destabilization. These findings provide new insights into the fundamental mechanisms that drive the emergence of diverse failure patterns of weathering‐induced landslides with important implications for landslide hazard assessment.

Wang, Liang [Eidgenoessische Technische Hochschule↗
DOE OSTI2020

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Classifying and analyzing small-angle scattering data using weighted k nearest neighbors machine learning techniques

A consistent challenge for both new and expert practitioners of small-angle scattering (SAS) lies in determining how to analyze the data, given the limited information content of said data and the large number of models that can be employed. Machine learning (ML) methods are powerful tools for classifying data that have found diverse applications in many fields of science. Here, ML methods are applied to the problem of classifying SAS data for the most appropriate model to use for data analysis. The approach employed is built around the method of weighted k nearest neighbors (wKNN), and utilizes a subset of the models implemented in the SasView package (https://www.sasview.org/) for generating a well defined set of training and testing data. The prediction rate of the wKNN method implemented here using a subset of SasView models is reasonably good for many of the models, but has difficulty with others, notably those based on spherical structures. A novel expansion of the wKNN method was also developed, which uses Gaussian processes to produce local surrogate models for the classification, and this significantly improves the classification accuracy. Further, by integrating a stochastic gradient descent method during post-processing, it is possible to leverage the local surrogate model both to classify the SAS data with high accuracy and to predict the structural parameters that best describe the data. The linking of data classification and model fitting has the potential to facilitate the translation of measured data into results for both novice and expert practitioners of SAS.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?

Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Using a computational approach, we quantified putative quadruplex-forming sequences (PQS) in 1359 genomes across the fungal kingdom and explored their presence in genes related to virulence, drug resistance and biological processes associated with pathogenicity in Aspergillus fumigatus. Here we present the largest analysis of PQS in fungi and identify significant heterogeneity of these sequences throughout phyla, genera and species. PQS were genetically conserved in Aspergillus spp. and frequently pathogenic species appeared to contain fewer PQS than their lesser/non-pathogenic counterparts. GO-term analysis identified that PQS-containing genes were involved in processes linked with virulence such as zinc ion binding, the biosynthesis of secondary metabolites and regulation of transcription in A. fumigatus. Although the genome frequency of PQS was lower in A. fumigatus, PQS could be found enriched in genes involved in virulence, and genes upregulated during germination and hypoxia. Moreover, PQS were found in genes involved in drug resistance. Quadruplexes could have important roles within fungal biology and virulence, but their roles require further elucidation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Clifford Circuit-Based Heuristic Optimization of Fermion-To-Qubit Mappings

Simulation of interacting Fermionic Hamiltonians is one of the most promising applications of quantum computers. However, the feasibility of analyzing Fermionic systems with a quantum computer hinges on the efficiency of Fermion-to-qubit mappings that encode nonlocal Fermionic degrees of freedom in local qubit degrees of freedom. While recent studies have highlighted the importance of designing Fermion-to-qubit mappings that are tailored to specific problem Hamiltonians, the methods proposed so far either are restricted to a narrow class of mappings or they use computationally expensive and unscalable brute-force search algorithms. Here, in this work, we address this challenge by designing a heuristic numerical optimization framework for Fermion-to-qubit mappings. To this end, we first translate the Fermion-to-qubit mapping problem to a Clifford circuit optimization problem and then use simulated annealing to optimize the average Pauli weight of the problem Hamiltonian. For all Fermionic Hamiltonians we have considered, the numerically optimized mappings outperform their conventional counterparts, including ternary-tree-based mappings that are known to be optimal for single creation and annihilation operators. We find that our optimized mappings yield between 15% and 40% improvements on the average Pauli weight when the simulation Hamiltonian has an intermediate level of complexity. Most remarkably, the optimized mappings improve the average Pauli weight for 6 × 6 nearest-neighbor hopping and Hubbard models by more than 40% and 20%, respectively. Surprisingly, we also find specific interaction Hamiltonians for which the optimized mapping outperforms any ternary-tree-based mapping. Our results establish heuristic numerical optimization as an effective method for obtaining mappings tailored for specific Fermionic Hamiltonian.

Hamiltonians↗
DOE OSTI2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Simulating the Effect of Space Vehicle Environments on Directional Solidification of a Binary Alloy

Space microgravity missions are designed to provide a microgravity environment for scientific experiments, but these missions cannot provide a perfect environment, due to vibrations caused by crew activity, on-board experiments, support systems (pumps, fans, etc.), periodic orbital maneuvers, and water dumps. Therefore, it is necessary to predict the impact of these vibrations on space experiments, prior to performing them. Simulations were conducted to study the effect of the vibrations on the directional solidification of a dendritic alloy. Finite element ca!cu!attie?ls were dme with a simd2titcr based on a continuum model of dendritic solidification, using the Fractional Step Method (FSM). The FSM splits the solution of the momentum equation into two steps: the viscous intermediate step, which does not enforce continuity; and the inviscid projection step, which calculates the pressure and enforces continuity. The FSM provides significant computational benefits for predicting flows in a directionally solidified alloy, compared to other methods presently employed, because of the efficiency gains in the uncoupled solution of velocity and pressure. finite differences, arises when the interdendritic liquid reaches the eutectic temperature and concentration. When a node reaches eutectic temperature, it is assumed that the solidification of the eutectic liquid continues at constant temperature until all the eutectic is solidified. With this approach, solidification is not achieved continuously across an element; rather, the element is not considered solidified until the eutectic isotherm overtakes the top nodes. For microgravity simulations, where the convection is driven by shrinkage, it introduces large variations in the fluid velocity. When the eutectic isotherm reaches a node, all the eutectic must be solidified in a short period, causing an abrupt increase in velocity. To overcome this difficulty, we employed a scheme to numerically predict a more accurate value for the rate of change of fraction of liquid as the liquid in an element solidifies. The new method enables us to contrast results of simulations in which the alloy is subjected to no gravity or a steady-state acceleration versus simulations when the alloy is subjected to vibration disturbances; therefore, the effect of vibration disturbances can be assessed more accurately. To assess the impact of these vibration-perturbations, transient accelerometer data from a space shuttle mission are used as inputs for the simulation model. These on-orbit acceleration data were obtained from the Microgravity Science Division at Glenn Research Center (GRC- MSD) and are applied to the buoyancy term of the momentum equation in a simulation of a Pb-5.8 wt. % Sb alloy that solidifies in a thermal gradient of 4000 K/m and a translation velocity of 3 p d s . Figure 2 shows the vertical velocity of a node that begins in the all-liquid region and subsequently solidifies; the vibrations are applied at 5000 seconds in this simulation. An important difficulty, common to all solidification models based on finite elements or 2 The magnitudes of the velocity oscillations that are vibration-induced are very small and acceptable. The biggest concern is whether the concentration of the liquid near the dendrite tips is distorted because of the vibration-induced perturbations. Results for this case show no concentration oscillations present in the all-liquid region.

Westra, D. G.↗
DOE OSTI2024

Universality of Collective Density Fluctuations in Liquids at and away from Equilibrium – An Integrated Neutron Scattering, Theoretical, and Computational Study (Final Technical Report)

Liquids, ubiquitous on earth, are prototypical disordered condensed matter. As the mediate phase between non-structured gases and ordered solids, liquids p ossess intriguing complexities that are absent on either extreme counter phase, especially when they are driven away from equilibrium. Despite decades of studies, the physics of liquids still keeps surprising us and challenges our understanding of condensed matter, emergent phenomena, and complex systems. Among the many interesting properties, the nature of collective dynamics in liquids remains elusive because of both the presence of strong interactions and the absence of translational invariance. This project studied the universal features of collective density fluctuations (or collective modes), which include both phonon-like excitations and collective relaxations, in the Q-dependent generalized hydrodynamic regime in liquids and liquid-like matter both at and away from equilibrium. We performed systematic studies of the fast collective dynamics (including both phonon-like excitations and collective relaxations) of four classes of liquids characterized by different fragilities and interactions using synergistically integrated coherent neutron scattering experiments (Inelastic Neutron Scattering (INS), Quasi-Elastic Neutron Scattering (QENS), and Neutron Spin Echo (NSE)), a ViscoElastic Hydrodynamics theory we have been developing, andMolecular Dynamics (MD) simulations and our analysis package LiquidLib. The transformative knowledge of the collective dynamics in liquids is important to understand and ultimately control the transport of mass, energy, and charge in liquids, both at and away from thermal equilibrium, which may will likely impact a wide range of disciplines.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Dynamical Signatures of Thermotoga maritima Maltose-Binding Proteins Affected by Ligand Binding

Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent differential binding of maltose and malto-oligomers while maintaining remarkable fold conservation. This differential behavior needs detailed characterization in native-like aqueous conditions to understand the effects of protein dynamics on ligand binding and recognition. Small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and dynamic light scattering (DLS) were used in conjunction with previously published computational molecular dynamics (MD) simulations to understand the dynamic behavior of tmMBPs experimentally. SANS provided information on the overall structure of the molecules, while NSE was used to determine the dynamics in the nanosecond time scale. Both tmMBP2 and tmMBP3 have a bidomain architecture linked with a flexible hinge, with the binding pocket sitting in the cleft between the two domains. tmMBP2 and tmMBP3 showed different solution dynamics, with the translational and rotational components dominating the dynamics of both systems, resulting in a clear differentiation of their diffusion pattern. A faster dynamics component was also observed and was attributed to segmental dynamics. Differences observed between the ligand-free (apo) and ligand-bound (holo) states of the two proteins are attributed to conformational entropy. Our results highlight the intricacies of how structure and dynamics can together shape binding to a repertoire of substrates in structurally similar proteins.

Diffusion↗
DOE OSTI2022

Snowmass2021 Computational Frontier White Paper: Cosmological Simulations and Modeling

Powerful new observational facilities will come online over the next decade, enabling a number of discovery opportunities in the "Cosmic Frontier", which targets understanding of the physics of the early universe, dark matter and dark energy, and cosmological probes of fundamental physics, such as neutrino masses and modifications of Einstein gravity. Synergies between different experiments will be leveraged to present new classes of cosmic probes as well as to minimize systematic biases present in individual surveys. Success of this observational program requires actively pairing it with a well-matched state-of-the-art simulation and modeling effort. Next-generation cosmological modeling will increasingly focus on physically rich simulations able to model outputs of sky surveys spanning multiple wavebands. These simulations will have unprecedented resolution, volume coverage, and must deliver guaranteed high-fidelity results for individual surveys as well as for the cross-correlations across different surveys. The needed advances are as follows: (1) Development of scientifically rich and broadly-scoped simulations, which capture the relevant physics and correlations between probes (2) Accurate translation of simulation results into realistic image or spectral data to be directly compared with observations (3) Improved emulators and/or data-driven methods serving as surrogates for expensive simulations, constructed from a finite set of full-physics simulations (4) Detailed and transparent verification and validation programs for both simulations and analysis tools. (Abridged)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Combined molecular and spin dynamics simulation of BCC iron with vacancy defects

Utilizing an atomistic computational model, which handles both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to investigate the effect of vacancy defects on spin wave excitations in ferromagnetic iron. Fourier transforms of space- and time-displaced correlation functions yield the dynamic structure factor, providing characteristic frequencies and lifetimes of the spin wave modes. A comparison of the system with a 5% vacancy concentration with pure lattice data shows a decrease in frequency and a decrease in lifetime for all transverse spin wave excitations observed. In addition, the clearly defined transverse spin wave excitations are distorted with the introduction of vacancy defects, and we observe reduced excitation lifetimes due to increased magnon–magnon scattering. We observe further evidence of increased magnon–magnon scattering, as the peaks in the longitudinal spin wave spectrum become less distinct. Finally, similar impacts are observed in the vibrational subsystem, with a decrease in characteristic phonon frequency and flattening of lattice excitation signals due to vacancy defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Nanostructures for Electrical Energy Storage (NEES) (2020 Final Technical Report)

Nanostructures for Electrical Energy Storage (NEES, www.efrc.umd.edu) was an Energy Frontier Research Center supported by the DOE Office of Science, Basic Energy Sciences, from 8/1/2009 to 7/31/2020. Led by the University of Maryland, NEES enjoyed extensive collaborations with its funded partners, including two DOE Laboratories and six universities. The NEES vision has been to reveal a set of scientific insights and design principles that can underpin a next-generation electrical energy storage approach, building on advances in nanoscale science and technology to achieve simultaneous high power and high energy over extended charge/discharge cycling. The vision is motivated by the recognition that scaling into the nano regime opens the door to new physical phenomena and that the tools enlisted in nanoscale research provide major new opportunities for the synthesis not only of materials at molecular scale but for structures at nano scale and above. NEES has translated this vision into its research program based on two observations. First, while the behavior of ions and electrons in electrolytes and in electrode materials is crucial to electrical energy storage (or more appropriately electrochemical energy storage), it is the transport of ion and electron charge between different structural components of a storage device that ultimately determine its performance. With it well recognized that the choice of electrode materials typically constrain ion transport kinetics as well as maximum ion concentration, the search for better electrode materials has been a primary driver of battery research. At the same time the synthesis of electrodes is typically based on aggregation of particles with varying size, shape, and orientation in the electrode. Together with the presence of additional materials to impart electrical conductivity and cohesion to the composite electrode, change in electrode materials is necessarily accompanied by structural changes at the nano/micro scale that are difficult to categorize and manage. From the beginning, NEES’ vision has been to create and study simpler, highly controlled spatial arrangements of known materials as battery components (electrodes, current collectors, and electrolyte) and to understand how design and structure above the molecular scale determines the energy storage performance available from known materials. Second, advances in nanoscience dramatically expanded the portfolio of synthesis methods, structural motifs, and new phenomena available for research. Some of these gave rapid access to new building blocks at the deep nanoscale (e.g., carbon nanotubes grown by self-assembly, nanoscale arrays formed by electrochemical self-alignment, monolayer films controlled by self-limiting reaction). Such advances served as the enabler for the NEES vision to be pursued experimentally through study of 3D structures created and controlled at the nano, micro, and meso scales. Here, we use meso as in the BES MESO Report, implying not only intermediate or varying length scales, but very much the way behavior is influenced by other factors including aggregation of nanocomponents at different densities and spatial configurations, statistical variations in the aggregates, hierarchical architectures in which they can be assembled, or local 3D configurations that result from the architectures. Over its life cycle, NEES has pursued two overarching goals: (1) to understand the scientific fundamentals of electrochemical storage from the nanoscale to the mesoscale; and (2) to create and learn from innovative, controlled, heterogeneous nanostructures, where such nanostructures can enable the first goal and serve as models for future paradigms in energy storage. Specific goals have included: Synthesize heterogeneous nanostructures comprised of multiple materials arranged in controlled fashion and characterize their behavior; Demonstrate and elucidate design principles for achieving simultaneous high power and high energy; Develop materials processes which enable precision control of thin layers and 3D structures; Investigate the impact of artificial interphases on electrode stability during ion insertion/deinsertion; Create dense arrays of nanostructures to understand how the architecture of these assemblies, along with nanostructure design, influences energy storage behavior at the mesoscale; Identify and understand the consequences of nanoconfinement and local inhomogeneities in 3D mesoscale arrays; Develop and apply computational models to stimulate, guide and interpret experiments.

25 ENERGY STORAGE↗
NASA NTRS2012

Wavefront Compensation Segmented Mirror Sensing and Control

The primary mirror of very large submillimeter-wave telescopes will necessarily be segmented into many separate mirror panels. These panels must be continuously co-phased to keep the telescope wavefront error less than a small fraction of a wavelength, to ten microns RMS (root mean square) or less. This performance must be maintained continuously across the full aperture of the telescope, in all pointing conditions, and in a variable thermal environment. A wavefront compensation segmented mirror sensing and control system, consisting of optical edge sensors, Wavefront Compensation Estimator/Controller Soft ware, and segment position actuators is proposed. Optical edge sensors are placed two per each segment-to-segment edge to continuously measure changes in segment state. Segment position actuators (three per segment) are used to move the panels. A computer control system uses the edge sensor measurements to estimate the state of all of the segments and to predict the wavefront error; segment actuator commands are computed that minimize the wavefront error. Translational or rotational motions of one segment relative to the other cause lateral displacement of the light beam, which is measured by the imaging sensor. For high accuracy, the collimator uses a shaped mask, such as one or more slits, so that the light beam forms a pattern on the sensor that permits sensing accuracy of better than 0.1 micron in two axes: in the z or local surface normal direction, and in the y direction parallel to the mirror surface and perpendicular to the beam direction. Using a co-aligned pair of sensors, with the location of the detector and collimated light source interchanged, four degrees of freedom can be sensed: transverse x and y displacements, as well as two bending angles (pitch and yaw). In this approach, each optical edge sensor head has a collimator and an imager, placing one sensor head on each side of a segment gap, with two parallel light beams crossing the gap. Two sets of optical edge sensors are used per segment-to-segment edge, separated by a finite distance along the segment edge, for four optical heads, each with an imager and a collimator. By orienting the beam direction of one edge sensor pair to be +45 away from the segment edge direction, and the other sensor pair to be oriented -45 away from the segment edge direction, all six degrees of freedom of relative motion between the segments can be measured with some redundancy. The software resides in a computer that receives each of the optical edge sensor signals, as well as telescope pointing commands. It feeds back the edge sensor signals to keep the primary mirror figure within specification. It uses a feed-forward control to compensate for global effects such as decollimation of the primary and secondary mirrors due to gravity sag as the telescope pointing changes to track science objects. Three segment position actuators will be provided per segment to enable controlled motions in the piston, tip, and tilt degrees of freedom. These actuators are driven by the software, providing the optical changes needed to keep the telescope phased.

Redding, David C.↗
DOE OSTI2020

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Discrete Fracture Network Modeling to Estimate Upscaled Parameters for the Topopah Spring, Lava Flow, and Tiva Canyon Aquifers at Pahute Mesa, Nevada National Security Site

This report describes the results of Discrete Fracture Network (DFN) simulations for the Topopah Spring Aquifer (TSA), Lava Flow Aquifer, and Tiva Canyon Aquifer (TCA), at Pahute Mesa on the Nevada National Security Site (NNSS), formerly the Nevada Test Site. The research focuses on calculating upscaled groundwater flow and contaminant transport parameters using DFNs generated according to fracture characteristics observed in the TSA, LFA and TCA at Pahute Mesa. The highly fractured and heterogeneous nature of these aquifers makes them candidates for stochastic DFN modeling of radionuclide transport on a small scale with subsequent upscaling. One hundred independent DFN realizations are generated for each aquifer, and the upscaled parameters for continuum simulations of subsurface flow and transport in fractured media at Pahute Mesa are calculated. Our goal is to implement a modeling approach that can translate parameters to larger-scale models that account for local-scale flow and transport processes, such as channelization of flow and transport along a few well connected, large fractures. Additionally, to simulate advective and advective-diffusive transport through the fracture networks, the Time Domain Random Walk (TDRW) approach is applied to account for matrix diffusion into a finite half-space. Moreover, a novel approach to calculate dynamic (active) fracture surface area to reflect flow channeling is implemented. This work will improve the representation of radionuclide transport processes in largescale, regulatory-focused models by providing estimates of hard-to-measure flow and contaminant transport parameters at large scales. In this report, we (1) show recent results of flow and transport simulations on multiple DFN realizations of the TSA, LFA, TCA; (2) discuss the resulting distributions of estimated upscaled parameters; (3) describe the estimation of upscaled parameters for an equivalent parallel-plate continuum model and (4) present a comparison between simulated transport from the equivalent continuum model and an actual DFN.

54 ENVIRONMENTAL SCIENCES↗