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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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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Controlling Mineralization with Protein–Functionalized Peptoid Nanotubes

Sequence-defined foldamers that self-assemble into well-defined architectures are promising scaffolds to template inorganic mineralization. However, it has been challenging to achieve robust control of nucleation and growth without sequence redesign or extensive experimentation. Here, peptoid nanotubes functionalized with a panel of solid-binding proteins are used to mineralize homogeneously distributed and monodisperse anatase nanocrystals from the water-soluble TiBALDH precursor. Crystallite size is systematically tuned between 1.4 and 4.4 nm by changing protein coverage and the identity and valency of the genetically engineered solid-binding segments. The approach is extended to the synthesis of gold nanoparticles and, using a protein encoding both material-binding specificities, to the fabrication of titania/gold nanocomposites capable of photocatalysis under visible-light illumination. Here, beyond uncovering critical roles for hierarchical organization and denticity on solid-binding protein mineralization outcomes, the strategy described herein should prove valuable for the fabrication of hierarchical hybrid materials incorporating a broad range of inorganic components.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant

Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genomics of sorghum local adaptation to a parasitic plant

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multi-agent voltage control in distribution systems using GAN-DRL-based approach

Active distribution grids can experience voltage fluctuations and violations due to the high penetration of variable distributed energy resources (DERs). These problems might occur because of the uncertain and variable generation natures of these resources, especially solar photovoltaic resources, during panel shadowing scenarios. Volt-VAR control (VVC) is an efficient method that controls the reactive power set-points of the inverters to regulate the voltage of distribution grids. Although several VVC approaches have been proposed recently, the performance of these approaches degrades significantly if behind-the-meter solar generation data are unobservable/missing. Therefore, it is necessary to impute missing/unobservable PV data accurately to be utilized in VVC approaches. Further, this paper proposes a model-free, data-driven, centrally trained, and decentrally executed multi-agent deep reinforcement learning-based VVC architecture to regulate the voltage of distribution networks. A generative adversarial network (GAN) is incorporated to impute the unobservable PV data accurately, which improves the performance of the proposed control architecture. The proposed multi-agent-soft-actor–critic algorithm (MASAC)-based VVC technique utilizes the actual PV dataset as well as the imputed dataset from the GAN framework to learn the optimal coordinated control policy for controlling the optimal reactive power set-points of PV inverters. The effectiveness of the proposed approach is analyzed on a modified IEEE 34-bus test case with added PV inverters. The results are compared and analyzed with a base case model with no VVC and VVC with a local droop control approach, genetic algorithm optimization, and a centralized soft actor–critic-based approach. Moreover, the performance of the proposed approach is compared with that of a multi-agent VVC framework without using the PV generation data and load information as the system state. The results illustrate that the proposed method with more state input improves the voltage profile and reduces the power loss of the network across various loading and PV generation scenarios.

14 SOLAR ENERGY↗
DOE OSTI2023

3P Program: Phenotyping X Prediction = Productivity (Final Scientific/Technical Report)

The goal of the 3P Program was to establish integrated, real-time phenotyping and to analyze above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the Sorghum gene pool. There were two overarching themes: 1) the development of a new crop improvement approach utilizing advances in high-throughput phenotyping (HTP), computing, and genomics for public dissemination and 2) leveraging this platform for sorghum crop improvement and commercialization. The Clemson team worked on creating genomic resources and using both statistical learning and high-throughput phenotyping in genomics-assisted breeding. Research was broadly interested in the genetics of carbon partitioning, with the aim of improving crop performance and achieving sustainability. The technology and resources created can be readily found in the public domain and serve to advance scientific understanding of crop genomics and breeding. Genomic prediction was able to identify top crosses to be made, and a hybrid prediction pipeline is in place to drive year-over-year genetic gain. Roots have long been ignored by plant breeders and agronomists, not because they are unimportant but because they are hard to measure. This is an untapped white space of potential insight and innovation. To address this, Hi Fidelity Genetics developed the RootTracker to measure roots in the field on a continuous basis. A database system called RootTracker Tracker was developed to handle data coming from the RootTrackers. In using this device, valuable data was observed for plant breeding, hydrochemical development, and other agricultural biology applications. Carnegie Mellon’s goal was developing new techniques to generate high-resolution 3D models of plants from data collected in the field. The idea was that more useful and more informative phenotypes could be extracted by resolving small features, such as seeds and flowers, and that by modeling in 3D, the spatial structure of plants could be examined. To achieve this, multiple images collected by a new small format structured light stereo imager were fused together. A sorghum panicle modeling pipeline was developed to allow the collection and processing of data. Carolina Seed Systems is an agricultural technology company focused on decarbonizing the agricultural system. Their technology pipeline serves to drive fundamental progress towards creation and distribution of carbon negative crops. The genomic and the engineering technology developed through the 3P Program was leveraged to deliver both value and sustainability from the grower to the consumer. Promising sorghum hybrids were scaled up and commercialized. The overall goal of our research was to integrate, create, and deploy genetic and engineering concepts and technologies to enhance crop productivity in a sustainable fashion. The combination of public and private partners allowed the basic research and hypothesis testing to be quickly accelerated for commercial application by the companies yet maintained that the core framework and academic insights remain in the public domain for continued market disruption, competition, and innovation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Copernicus-LinCov (COPCOV) Software Integration in Support of Robust Trajectory Optimization

Robust trajectory optimization is the process of optimizing a trajectory while accounting for system uncertainty due to a variety of potential error sources. This work highlights the development and features of a novel tool known as CopCov to support robust trajectory optimization efforts. CopCov acts as an interface between Copernicus, a generalized trajectory design and optimization tool, and LinCov, a linear covariance analysis tool. By having a direct interface between these two software packages, Copernicus can receive covariance information from LinCov through a direct feedback loop, thus enabling optimization of a trajectory that is robust to trajectory dispersions and navigation errors. This paper details the architecture of CopCov and its flexibility to operate under varying configurations, including with both tools running locally or alternatively with the tools communicating via a remote connection. Additionally, the CopCov tool is demonstrated on a simple Hohmann transfer reference trajectory with varying numbers of Trajectory Correction Maneuvers (TCMs) and varying problem formulations. This example scenario is used to highlight how the inclusion of the CopCov interface affects burn placement of both major burns and minor burns (i.e., TCMs) in the optimized solution. Results are compared against analytical solutions and against a Genetic Algorithm (GA) optimizer for independent verification and validation.

Copernicus↗
DOE OSTI2025

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Computational design of mechanically coupled axle-rotor protein assemblies

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo–electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.

Science & Technology - Other Topics↗
DOE OSTI2023

Topologically associating domain boundaries are required for normal genome function

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1,2,3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deconstructing the root system of grasses through an exploration of development, anatomy and function

Abstract Well‐adapted root systems allow plants to grow under resource‐limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below‐ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts‐list of elements that function together in an integrated root system to promote survival and crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multinode Multi-GPU Two-Electron Integrals: Code Generation Using the Regent Language

The computation of two-electron repulsion integrals (ERIs) is often the most expensive step of integral-direct self-consistent field methods. Formally it scales as O(N 4 ), where N is the number of Gaussian basis functions used to represent the molecular wave function. In practice, this scaling can be reduced to O(N 2 ) or less by neglecting small integrals with screening methods. The contributions of the ERIs to the Fock matrix are of Coulomb (J) and exchange (K) type and require separate algorithms to compute matrix elements efficiently. We previously implemented highly efficient GPU-accelerated J-matrix and K-matrix algorithms in the electronic structure code TeraChem. Although these implementations supported the use of multiple GPUs on a node, they did not support the use of multiple nodes. This presents a key bottleneck to cutting-edge ab initio simulations of large systems, e.g., excited state dynamics of photoactive proteins. We present our implementation of multinode multi-GPU J- and K-matrix algorithms in TeraChem using the Regent programming language. Regent directly supports distributed computation in a task-based model and can generate code for a variety of architectures, including NVIDIA GPUs. We demonstrate multinode scaling up to 45 GPUs (3 nodes) and benchmark against hand-coded TeraChem integral code. Finally, we also outline our metaprogrammed Regent implementation, which enables flexible code generation for integrals of different angular momenta.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ensuring reliable connectivity to cellular-connected UAVs with up-tilted antennas and interference coordination

To integrate unmanned aerial vehicles (UAVs) in future large-scale deployments, a new wireless communication paradigm, namely, the cellular-connected UAV has recently attracted interest. However, the line-of-sight dominant air-to-ground channels along with the antenna pattern of the cellular ground base stations (GBSs) introduce critical interference issues in cellular-connected UAV communications. In particular, the complex antenna pattern and the ground reflection (GR) from the down-tilted antennas create both coverage holes and patchy coverage for the UAVs in the sky, which leads to unreliable connectivity from the underlying cellular network. To overcome these challenges, in this paper, we propose a new cellular architecture that employs an extra set of co-channel antennas oriented towards the sky to support UAVs on top of the existing down-tilted antennas for ground user equipment (GUE). To model the GR stemming from the down-tilted antennas, we propose a path-loss model, which takes both antenna radiation pattern and configuration into account. Next, we formulate an optimization problem to maximize the minimum signal-to-interference ratio (SIR) of the UAVs by tuning the up-tilt (UT) angles of the up-tilted antennas. Since this is an NP-hard problem, we propose a genetic algorithm (GA) based heuristic method to optimize the UT angles of these antennas. After obtaining the optimal UT angles, we integrate the 3GPP Release-10 specified enhanced inter-cell interference coordination (eICIC) to reduce the interference stemming from the down-tilted antennas. Our simulation results based on the hexagonal cell layout show that the proposed interference mitigation method can ensure higher minimum SIRs for the UAVs over baseline methods while creating minimal impact on the SIR of GUEs.

3GPP↗
DOE OSTI2020

Coral Gardens Reef, Belize: A refugium in the face of Caribbean-wide Acropora spp. coral decline

Caribbean Acropora spp. corals have undergone a decline in cover since the second half of the twentieth century. Loss of these architecturally complex and fast-growing corals has resulted in significant, cascading changes to the character, diversity, and available ecospaces of Caribbean reefs. Few thriving Acropora spp. populations exist today in the Caribbean and western North Atlantic seas, and our limited ability to access data from reefs assessed via long-term monitoring efforts means that reef scientists are challenged to determine resilience and longevity of existing Acropora spp. reefs. Here we used multiple dating methods to measure reef longevity and determine whether Coral Gardens Reef, Belize, is a refuge for Acropora cervicornis against the backdrop of wider Caribbean decline. We used a new genetic-aging technique to identify sample sites, and radiocarbon and high-precision uranium-thorium (U-Th) dating techniques to test whether one of the largest populations of extant A. cervicornis in the western Caribbean is newly established after the 1980s, or represents a longer-lived, stable population. We did so with respect for ethical sampling of a threatened species. Our data show corals ranging in age from 1910 ( 14 C) or 1915 ( 230 Th) to at least November 2019. While we cannot exclude the possibility of short gaps in the residence of A. cervicornis earlier in the record, the data show consistent and sustained living coral throughout the 1980s and up to at least 2019. We suggest that Coral Gardens has served as a refuge for A. cervicornis and that identifying other, similar sites may be critical to efforts to grow, preserve, conserve, and seed besieged Caribbean reefs.

58 GEOSCIENCES↗
DOE OSTI2020

Reflectin: Protein Driver of Dynamically Tunable Biophotonics; New Paradigm for Tunably Reconfigurable Materials

We discovered that the reflectins, with architecture and sequences unlike those of any other proteins known, exhibit a novel interplay between signal-controlled nucleation and growth of dynamically arrested liquid-liquid phase-segregated assemblies that uniquely enables the continuous and precise fine-tuning of physical properties governing the color and brightness of light reflected from the membrane-enclosed nanostructures that contain them. Our research included high-resolution structural analyses conducted at the DOE-BES user facilities of the Stanford Synchrotron Light Source and LBL National Laboratory’s Molecular Foundry, leveraging their capabilities for time-resolved SAXS and cryo-TEM with our ongoing genetic engineering, biophysical and computational analyses to identify the structural determinants and mechanisms governing the dynamic behaviors of the reflectins. We augmented these methods with EPR analyses that revealed for the first time the existence of a specific pathway of reflectin assembly. Using dynamic light scattering and continuously monitored circular dichroism and Raman microscopy, we elucidated the progression of structural changes underlying the mechanisms of signal-induced condensation, folding, assembly, liquefaction, dynamic arrest, regulation and reversal.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

A Boltzmann machine for the organization of intelligent machines

A three-tier structure consisting of organization, coordination, and execution levels forms the architecture of an intelligent machine using the principle of increasing precision with decreasing intelligence from a hierarchically intelligent control. This system has been formulated as a probabilistic model, where uncertainty and imprecision can be expressed in terms of entropies. The optimal strategy for decision planning and task execution can be found by minimizing the total entropy in the system. The focus is on the design of the organization level as a Boltzmann machine. Since this level is responsible for planning the actions of the machine, the Boltzmann machine is reformulated to use entropy as the cost function to be minimized. Simulated annealing, expanding subinterval random search, and the genetic algorithm are presented as search techniques to efficiently find the desired action sequence and illustrated with numerical examples.

Moed, Michael C.↗
DOE OSTI2026

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic “Toomer's Oak,” this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

Quercus virginiana↗
DOE OSTI2020

Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures

Molecular assemblies inside cells often undergo structural reconfiguration in response to stimuli to alter their function. Adaptive reconfiguration of cytoskeletal networks, for example, enables cellular shape change, movement, and cargo transport and plays a key role in driving complex processes such as division and differentiation. The cellular cytoskeleton is a self-assembling polymer network composed of simple filaments, so reconfiguration often occurs through the rearrangement of its component filaments’ connectivities. DNA nanotubes have emerged as promising building blocks for constructing programmable synthetic analogs of cytoskeletal networks. Nucleating seeds can control when and where nanotubes grow and capping structures can bind nanotube ends to stop growth. Such seeding and capping structure, collectively called termini, can organize nanotubes into larger architectures. However, these structures cannot be selectively activated or inactivated in response to specific stimuli to rearrange nanotube architectures, a key property of cytoskeletal networks. Here we demonstrate how selective regulation of the binding affinity of DNA nanotube termini for DNA nanotube monomers or nanotube ends can direct the reconfiguration of nanotube architectures. Using DNA hybridization and strand displacement reactions that specifically activate or inactivate four orthogonal nanotube termini, we demonstrate that nanotube architectures can be reconfigured by selective addition or removal of unique termini. Lastly, we show how terminus activation could be a sensitive detector and amplifier of a DNA sequence signal. These results could enable the development of adaptive and multifunctional materials or diagnostic tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 ( ZmCIPK15 )

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

59 BASIC BIOLOGICAL SCIENCES↗