SEARCH · Search NASA

Results for “base editing”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Design of Multicomponent Peptide Fibrils with Ordered and Programmable Compositional Patterns

Advanced applications of biomacromolecular assemblies require a stringent degree of control over molecular arrangement, which is a challenge to current synthetic methods. Here we used a neighbor-controlled patterning strategy to build multicomponent peptide fibrils with an unprecedented capacity to manipulate local composition and peptide positions. Eight peptides were designed to have regulable nearest neighbors upon co-assembly, which, by simulation, afforded 412 different patterns within fibrils, with varied compositions and/or peptide positions. The fibrils with six prescribed patterns were experimentally constructed with high accuracy. The controlled patterning also applies to functionalities appended to the peptides, as exemplified by arranging carbohydrate ligands at nanoscale precision for protein recognition. Importantly, this study offers a route to molecular editing of inner structures of peptide assemblies, prefiguring the uniqueness and richness of patterning-based material design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Tracking the Sun: Pricing and Design Trends for Distributed Photovoltaic Systems in the United States (2021 Edition) [Slides]

Berkeley Lab’s annual Tracking the Sun report describes trends among grid-connected, distributed solar photovoltaic (PV) systems in the United States. The latest edition of the report focuses on systems installed through year-end 2020, and is based on data from roughly 2.2 million systems, covering 79% of all distributed PV systems installed nationally through 2020. The report describes trends related to project characteristics, including system size, module efficiencies, prevalence of paired PV with storage, use of module-level power electronics, third-party ownership, mounting configurations, panel orientation, and non-residential customer segmentation ownership. Median installed-price trends, including both long-term and more recent temporal trends at the national and state levels, with comparisons to other recent PV cost and pricing benchmarks as well as to prices reported for other countries. Variability in pricing across individual projects based on system size, state, installer, module efficiency, inverter technology, and non-residential customer type. The report also includes an econometric analysis to estimate the effects of individual drivers on installed prices for host-owned residential systems installed in 2020.

14 SOLAR ENERGY↗

DOE OSTI2022

Tracking the Sun: Pricing and Design Trends for Distributed Photovoltaic Systems in the United States, 2022 Edition

Berkeley Lab’s annual Tracking the Sun report describes trends among grid-connected, distributed solar photovoltaic (PV) systems in the United States. The latest edition of the report focuses on systems installed through year-end 2021, and is based on data from roughly 2.5 million systems. New to the report this year is an expanded coverage of paired PV-plus-storage systems, including details on system design and pricing trends. The report describes trends related to: -Project characteristics, including system size, module efficiencies, prevalence of paired PV with storage, use of module-level power electronics, third-party ownership, mounting configurations, panel orientation, and non-residential customer segmentation ownership -Median installed-price trends, both nationally and by state, including preliminary data for first half of 2022 -Variability in pricing according to system size, state, installer, equipment type, and other factors, relying on both descriptive and econometric analysis

14 SOLAR ENERGY↗

NASA NTRS2009

R4SA for Controlling Robots

The R4SA GUI mentioned in the immediately preceding article is a userfriendly interface for controlling one or more robot(s). This GUI makes it possible to perform meaningful real-time field experiments and research in robotics at an unmatched level of fidelity, within minutes of setup. It provides such powerful graphing modes as that of a digitizing oscilloscope that displays up to 250 variables at rates between 1 and 200 Hz. This GUI can be configured as multiple intuitive interfaces for acquisition of data, command, and control to enable rapid testing of subsystems or an entire robot system while simultaneously performing analysis of data. The R4SA software establishes an intuitive component-based design environment that can be easily reconfigured for any robotic platform by creating or editing setup configuration files. The R4SA GUI enables event-driven and conditional sequencing similar to those of Mars Exploration Rover (MER) operations. It has been certified as part of the MER ground support equipment and, therefore, is allowed to be utilized in conjunction with MER flight hardware. The R4SA GUI could also be adapted to use in embedded computing systems, other than that of the MER, for commanding and real-time analysis of data.

Aghazarian, Hrand↗

NASA NTRS2004

Managing an Archive of Images

The SSC Multimedia Archive is an automated electronic system to manage images, acquired both by film and digital cameras, for the Public Affairs Office (PAO) at Stennis Space Center (SSC). Previously, the image archive was based on film photography and utilized a manual system that, by today s standards, had become inefficient and expensive. Now, the SSC Multimedia Archive, based on a server at SSC, contains both catalogs and images for pictures taken both digitally and with a traditional, film-based camera, along with metadata about each image. After a "shoot," a photographer downloads the images into the database. Members of the PAO can use a Web-based application to search, view and retrieve images, approve images for publication, and view and edit metadata associated with the images. Approved images are archived and cross-referenced with appropriate descriptions and information. Security is provided by allowing administrators to explicitly grant access privileges to personnel to only access components of the system that they need to (i.e., allow only photographers to upload images, only PAO designated employees may approve images).

Andres, Vince↗

DOE OSTI2024

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Transformation and gene editing in the bioenergy grass Miscanthus

Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.

09 BIOMASS FUELS↗

NASA NTRS2000

Developing CORBA-Based Distributed Scientific Applications from Legacy Fortran Programs

Recent progress in distributed object technology has enabled software applications to be developed and deployed easily such that objects or components can work together across the boundaries of the network, different operating systems, and different languages. A distributed object is not necessarily a complete application but rather a reusable, self-contained piece of software that co-operates with other objects in a plug-and-play fashion via a well-defined interface. The Common Object Request Broker Architecture (CORBA), a middleware standard defined by the Object Management Group (OMG), uses the Interface Definition Language (IDL) to specify such an interface for transparent communication between distributed objects. Since IDL can be mapped to any programming language, such as C++, Java, Smalltalk, etc., existing applications can be integrated into a new application and hence the tasks of code re-writing and software maintenance can be reduced. Many scientific applications in aerodynamics and solid mechanics are written in Fortran. Refitting these legacy Fortran codes with CORBA objects can increase the codes reusability. For example, scientists could link their scientific applications to vintage Fortran programs such as Partial Differential Equation(PDE) solvers in a plug-and-play fashion. Unfortunately, CORBA IDL to Fortran mapping has not been proposed and there seems to be no direct method of generating CORBA objects from Fortran without having to resort to manually writing C/C++ wrappers. In this paper, we present an efficient methodology to integrate Fortran legacy programs into a distributed object framework. Issues and strategies regarding the conversion and decomposition of Fortran codes into CORBA objects are discussed. The following diagram shows the conversion and decomposition mechanism we proposed. Our goal is to keep the Fortran codes unmodified. The conversion- aided tool takes the Fortran application program as input and helps programmers generate C/C++ header file and IDL file for wrapping the Fortran code. Programmers need to determine by themselves how to decompose the legacy application into several reusable components based on the cohesion and coupling factors among the functions and subroutines. However, programming effort still can be greatly reduced because function headings and types have been converted to C++ and IDL styles. Most Fortran applications use the COMMON block to facilitate the transfer of large amount of variables among several functions. The COMMON block plays the similar role of global variables used in C. In the CORBA-compliant programming environment, global variables can not be used to pass values between objects. One approach to dealing with this problem is to put the COMMON variables into the parameter list. We do not adopt this approach because it requires modification of the Fortran source code which violates our design consideration. Our approach is to extract the COMMON blocks and convert them into a structure-typed attribute in C++. Through attributes, each component can initialize the variables and return the computation result back to the client. We have tested successfully the proposed conversion methodology based on the f2c converter. Since f2c only translates Fortran to C, we still needed to edit the converted code to meet the C++ and IDL syntax. For example, C++/IDL requires a tag in the structure type, while C does not. In this paper, we identify the necessary changes to the f2c converter in order to directly generate the C++ header and the IDL file. Our future work is to add GUI interface to ease the decomposition task by simply dragging and dropping icons.

Sang, Janche↗

DOE OSTI2026

Flaw Tolerance Assessment for DOE Standard SNF Dry Storage Canisters - 26550

The U.S. DOE has designed four spent nuclear fuel (SNF) dry storage canisters for storing DOE standardized SNFs. The DOE standard canisters are cylindrical shells with a diameter of 24 inches (610 m) or 18 inches (457 m), a wall thickness of 0.5 inches (12.7 m) or 0.375 inches (9.53 m), and a length of 15 feet (4.57 m) or 10 feet (3.05 m). These DOE canister geometries are completely different from commercial canisters. The latter may experience chloride-induced stress cracking corrosion (CI-SCC) because they are stored near coastal regions. The former may not experience CI-SCC but face different challenges because they are stored in the SNF storage facilities. Because of large residual stresses, mechanical flaws may occur in the DOE canisters during long-distance transportation or lifting handling. To date, only limited structural integrity analyses were carried out through drop tests on the DOE canisters, but a more general flaw tolerance assessment has not been performed. Therefore, the failure assessment diagram (FAD)-based fracture mechanics method, as codified by the latest API 579-1/ASME FFS-1-2021 Edition, is adopted in this work to assess surface flaw tolerance for DOE canisters under operation loading and welding residual stresses (WRS), where the new code-recommended WRS distributions are used. To more adequately consider the transverse distribution of WRS, an equivalent WRS distribution is proposed to account for the WRS reduction with distance from the weld centerline. Moreover, the closed-form solutions of stress intensity factor K, which serves as the crack driving force during subcritical crack growth, are developed from the tabular data of the K factors provided in API 579-1/ASME FFS-1 and used to determine more accurate flaw sizes at flaw instability. Subsequently, the Level 2 assessment procedures with 12 assessment steps, as codified and detailed in API 579-1 and ASME FFS-1, are followed to assess the flaw tolerance for the surface flaws in the DOE standard canisters with consideration of normal or accident operation loads combined with WRS. The assessment results show that the four designs of DOE standard canisters can tolerate all surface flaws that meet the code permitted maximum sizes of a flaw length of 8 inches (i.e., 200 mm) and a flaw depth of 80% wall thickness. This demonstrates that all designs of DOE standard canisters are robust and reliable.

DOE standard canister↗

NASA NTRS2016

Laser Remote Sensing from ISS: CATS Cloud and Aerosol Level 2 Data Products (Heritage Edition)

With the recent launch of the Cloud-Aerosol Transport System (CATS) we have the opportunity to acquire a continuous record of space based lidar measurements spanning from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) era to the start of the EarthCARE mission. Utilizing existing well-validated science algorithms from the CALIPSO mission, we will ingest the CATS data stream and deliver high-quality lidar data sets to the user community at the earliest possible opportunity. In this paper we present an overview of procedures necessary to generate CALIPSO-like lidar level 2 data products from the CATS level 1 data products.

cloud-aerosol lidar↗

DOE OSTI2020

Development of Density Functional Tight-Binding Parameters Using Relative Energy Fitting and Particle Swarm Optimization

We provide a strategy to optimize density functional tight-binding (DFTB) parameterization for the calculation of the structures and properties of organic molecules consisting of hydrogen, carbon, nitrogen, and oxygen. We utilize an objective function based on similarity measurements and the Particle Swarm Optimization (PSO) method to find an optimal set of parameters. This objective function considers not only the common DFTB descriptors of binding energies and atomic forces but also incorporates relative energies of isomers into the fitting procedure for more chemistry-driven results. The quality in the description of the binding energies and atomic forces is measured based on the Ballester similarity index and relative energies through a similarity index induced by the Levenshtein edit distance to quantify the correct energetic order of isomers. Training and testing datasets were created to include all relevant chemical functional groups. Finally, the accuracy of this strategy is assessed, and its range of applicability is discussed by comparison against our previous parameterization. The improved performance of the new DFTB parameterization is validated with respect to the density functional theory large datasets QM-9 and ANI-1, where excellent agreement is found between the structures and properties available in these datasets, and the ones obtained with DFTB.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1983

Development INTERDATA 8/32 computer system

The capabilities of the Interdata 8/32 minicomputer were examined regarding data and word processing, editing, retrieval, and budgeting as well as data management demands of the user groups in the network. Based on four projected needs: (1) a hands on (open shop) computer for data analysis with large core and disc capability; (2) the expected requirements of the NASA data networks; (3) the need for intermittent large core capacity for theoretical modeling; (4) the ability to access data rapidly either directly from tape or from core onto hard copy, the system proved useful and adequate for the planned requirements.

Sonett, C. P.↗

NASA NTRS1993

Design strategies and functionality of the Visual Interface for Virtual Interaction Development (VIVID) tool

Development of interactive virtual environments (VE) has typically consisted of three primary activities: model (object) development, model relationship tree development, and environment behavior definition and coding. The model and relationship tree development activities are accomplished with a variety of well-established graphic library (GL) based programs - most utilizing graphical user interfaces (GUI) with point-and-click interactions. Because of this GUI format, little programming expertise on the part of the developer is necessary to create the 3D graphical models or to establish interrelationships between the models. However, the third VE development activity, environment behavior definition and coding, has generally required the greatest amount of time and programmer expertise. Behaviors, characteristics, and interactions between objects and the user within a VE must be defined via command line C coding prior to rendering the environment scenes. In an effort to simplify this environment behavior definition phase for non-programmers, and to provide easy access to model and tree tools, a graphical interface and development tool has been created. The principal thrust of this research is to effect rapid development and prototyping of virtual environments. This presentation will discuss the 'Visual Interface for Virtual Interaction Development' (VIVID) tool; an X-Windows based system employing drop-down menus for user selection of program access, models, and trees, behavior editing, and code generation. Examples of these selection will be highlighted in this presentation, as will the currently available program interfaces. The functionality of this tool allows non-programming users access to all facets of VE development while providing experienced programmers with a collection of pre-coded behaviors. In conjunction with its existing, interfaces and predefined suite of behaviors, future development plans for VIVID will be described. These include incorporation of dual user virtual environment enhancements, tool expansion, and additional behaviors.

Nguyen, Lac↗

NASA NTRS1999

Structured Course Objects in a Digital Library

We are developing an Undergraduate Digital Library Framework (UDLF) that will support creation/archiving of courses and reuse of existing course material to evolve courses. UDLF supports the publication of course materials for later instantiation for a specific offering and allows the addition of time-dependent and student-specific information and structures. Instructors and, depending on permissions, students can access the general course materials or the materials for a specific offering. We are building a reference implementation based on NCSTRL+, a digital library derived from NCSTRL. Digital objects in NCSTRL+ are called buckets, self-contained entities that carry their own methods for access and display. Current bucket implementations have a two level structure of packages and elements. This is not a rich enough structure for course objects in UDLF. Typically, courses can only be modeled as a multilevel hierarchy and among different courses, both the syntax and semantics of terms may vary. Therefore, we need a mechanism to define, within a particular library, course models, their constituent objects, and the associated semantics in a flexible, extensible way. In this paper, we describe our approach to define and implement these multilayered course objects. We use XML technology to emulate complex data structures within the NCSTRL+ buckets. We have developed authoring and browsing tools to manipulate these course objects. In our current implementation a user downloading an XML based course bucket also downloads the XML-aware tools: an applet that enables the user to edit or browse the bucket. We claim that XML provides an effective means to represent multi-level structure of a course bucket.

Maly, K.↗

DOE OSTI2020

Programming PAM antennae for efficient CRISPR-Cas9 DNA editing

Bacterial CRISPR-Cas9 nucleases have been repurposed as powerful genome editing tools. Whereas engineering guide RNAs or Cas nucleases have proven to improve the efficiency of CRISPR editing, modulation of protospacer-adjacent motif (PAM), indispensable for CRISPR, has been less explored. Here, we develop a DNA origami–based platform to program a PAM antenna microenvironment and address its performance at the single-molecule level with submolecular resolution. To mimic spatially controlled in vivo PAM distribution as may occur in chromatin, we investigate the effect of PAM antennae surrounding target DNA. We find that PAM antennae effectively sensitize the DNA cleavage by recruiting Cas9 molecules. Super-resolution tracking of single single-guide RNA/Cas9s reveals localized translocation of Cas9 among spatially proximal PAMs. We find that the introduction of the PAM antennae effectively modulates the microenvironment for enhanced target cleavage (up to ~50%). These results provide insight into factors that promote more efficient genome editing.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

CERES FluxByCldTyp NB2BB Fluxes Improvement based on Deep Neural Network

The NASA Clouds and the Earth's Radiant Energy System (CERES) product provides over 20 years of accurately observed top-of-the-atmosphere (TOA) and surface flux data record for climate monitoring and diagnostic studies. The interaction between clouds and radiation interaction is a key factor that dominate climate feedbacks but is not well understood. To further advance our understanding of the cloud-radiation interaction, a new CERES FluxByCldTyp (FBCT) product has been developed that contains radiative fluxes by cloud-type, which can provide more stringent constraints when validating models and reveal more insight into the interactions between clouds and climate. For CERES partly cloudy and multiple cloud-type footprints, the FBCT product utilizes Moderate Resolution Imaging Spectroradiometer (MODIS) narrow-band (NB) imager channel radiances partitioned by cloud-type within a CERES footprint to estimate the cloud-type broadband fluxes. The MODIS multi-channel derived broadband fluxes were compared with the CERES observed footprint fluxes and were found to be within 1% and 2.5% for LW and SW, respectively, as well as being mostly free of cloud property dependencies. The FBCT all-sky and clear-sky monthly averaged fluxes were found to be consistent with the CERES SSF1deg product. This study takes advantage of recent progress in machine learning (ML) field by applying deep neural network algorithm to improve fluxes based on MODIS NB radiances. The preliminary study shows ML produce are an improvement over the current FBCT Edition 4 NB2BB algorithm. Furthermore, unlike Ed4 NB2BB, the new ML method convert NB radiances directly to broadband fluxes. For future Ed5, new NB radiances are proposed and used by ML to improve fluxes calculation. Prelimary results show significant LW improvement.

Moguo Sun↗

NASA NTRSDate not supplied

Flux Improvement based on Machine Learning for the CERES FluxByCldTyp Data Product

Moguo Sun↗

NASA NTRSDate not supplied

Improvement of Radiative Fluxes for the CERES FluxByCldTyp Data Product Based on Machine Learning Technique

The NASA Clouds and the Earth's Radiant Energy System (CERES) product provides over 20 years of accurately observed top-of-the-atmosphere and surface flux data for climate studies. The interaction between clouds and radiation interaction is a key factor that dominate climate feedbacks but is not well understood. To further advance our understanding of the cloud-radiation interaction, a new CERES FluxByCldTyp (FBCT) product has been developed that contains radiative fluxes by cloud-type, which can provide more stringent constraints when validating models. The FBCT product utilizes Moderate Resolution Imaging Spectroradiometer (MODIS) narrow-band (NB) imager channel radiances partitioned by cloud-type within a CERES footprint to estimate their broadband fluxes. The MODIS multi-channel derived broadband fluxes were compared with the CERES observed footprint fluxes and were found to be within 1% and 2.5% for LW and SW, respectively, as well as being mostly free of cloud property dependencies. The FBCT all-sky and clear-sky monthly averaged fluxes were found to be consistent with the CERES SSF1deg product. This study takes advantage of recent progress in machine learning (ML) field by applying deep neural network algorithm to improve fluxes based on MODIS NB radiances. The preliminary study shows ML produce are an improvement over the current FBCT Edition 4 NB2BB algorithm. Furthermore, unlike Ed4 NB2BB, the new ML method convert NB radiances directly to broadband fluxes. For future Ed5, new NB radiances are proposed and used by ML to improve fluxes calculation. Preliminary results show significant LW improvement.

Sun, Moguo↗