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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS2026

Scientific Highlights and Status of the Mars Science Laboratory Mission, Years 9 through 12

We present the scientific highlights and status from years 9-12 of NASA’s Mars Science Laboratory mission, with its Curiosity rover. A thermochemolysis-based sample analysis revealed a variety of organic molecules preserved in clay mineral-rich lake/lake margin deposits of the Glen Torridon region. The stratigraphically higher clay-sulfate mineral transition on Aeolis Mons was found to be associated with a lithological change from lacustrine to dry aeolian depositional environments. Water intermittently returned to the surface after the increase in aridity, including during the deposition of wave ripple strata which indicate a climate capable of sustaining an ice-free lake in the early Hesperian. The overlying Mg sulfate-bearing unit has both poly- and monohydrated Mg sulfates and is also enriched in iron carbonate of a purity consistent with chemical sedimentation and therefore atmospheric sequestration. A channel-incised canyon within Gediz Vallis and distal alluvial deposits recorded numerous fluvial and debris flow events after the deposition, lithification, and erosion of the clay- and sulfate-bearing units. Bright clasts found in Gediz Vallis canyon are composed of native sulfur. The investigation of the modern atmosphere and environment focused on the influence of the crater and mountain topography and captured high-altitude noctilucent and iridescent clouds. Radiation monitoring now spans an 11-year solar cycle. Rover systems and science instruments remain capable of addressing mission scientific objectives. All ten scientific instruments continue to return high-value data despite degradation of the Chemistry and Camera instrument’s high-voltage system, loss of multispectral imaging capability, and loss of active neutron spectroscopy. The mission has mitigated the loss of redundant brakes on two arm joints, additional wheel wear, and highly reduced capability of the redundant flight computer. Efficiency improvements in rover energy utilization and operations staffing have allowed the mission team to maintain a high level of productivity despite declining rover power generation and funding.

Mars↗
NASA NTRSDate not supplied

Advances to a Global Agroclimatology Solar Insolation and Meteorological Parameter Data Base: Improved Solar Irradiance up to Hourly Temporal Resolution

A primary objective of NASA’s Prediction of Worldwide Energy Resource (POWER) project is to facilitate the use of NASA Earth Science data holdings within the energy, agricultural, and architectural industries. To this end daily averaged solar data from several NASA projects and metrological data from a NASA assimilation model have long been reformatted and via a user friendly web based data portal (https://power.larc.nasa.gov) at the native resolution of each data products. Potential users can access solar and metrological data in a column formatted DSSAT ASCII format by entering single site specific coordinates or from an area by entering the appropriate area coordinates. Upgrades to the POWER data portal have been implemented that result in a complete upgrade of the base solar insolation data products. From the years 1984 through 2000, a new version of the NASA/GEWEX Surface Radiation Budget (SRB) and Clouds is utilized that reduces the RMS relative to surface measurements. Additionally, Clouds and the Earth’s Radiant Energy System (CERES) SYNoptic 1x1 Degree (SYN1Deg) data products are utilized starting from January 1, 2001 through 3 months of real-time. The CERES Fast Longwave and SHortwave radiative Fluxes (FLASHFlux) is still used to provided daily data spanning from the end of SYN1Deg to within 7 days of real-time. Meteorological parameters now are taken from the NASA Modern Era Retrospective-analysis for Research and Applications (MERRA-2) data set which provides higher resolution data products (hourly and 0.5 x 625 degree) covering the entire globe. Besides updating the solar and meteorological data products, this new version features new data products such as photosynthetically active radiation (PAR), more cloud information, estimates of soil temperatures and improved options for long-term climatological data requests. More than 36+ years daily time slices are included in the combined solar and meteorological data sets. However, perhaps the most important innovation of the POWER GIS-enabled Web Services is the provision of hourly solar and meteorological data products beginning in Jan 1, 2001. The hourly values will enable more detailed modeling and crop analysis that incorporates the diurnal variability of these parameters. The new capability is made possible by utilizing both the CERES SYN1Deg and MERRA-2 data products that include parameters at these resolutions. An assessment of both the meteorological and the solar irradiance data are based upon comparisons with globally distributed surface observations. The meteorological observations from the National Center for Environmental Information’s “Integrated Surface Database” as well as the “Global Summary of the Day” (GSOD) data files. The estimates of solar insolation are compared to the Baseline Solar Radiation Network (BSRN) and other high quality surface measurement networks. Results from the uncertainty assessments demonstrates that the NASA’s meteorological and solar irradiance data can represent a viable alternative to surface observations, particularly in data sparse regions of the world.

solar irradiance↗
NASA NTRSDate not supplied

Biomass Harmonization and SAR Analysis with the Multi-mission Algorithm and Analysis Platform (MAAP)

The Multi‐mission Algorithm and Analysis Platform (MAAP) is a collaborative effort between NASA and the European Space Agency (ESA) to support above ground biomass (AGB) research in an open science framework. MAAP brings together relevant data, algorithms, and computing capabilities in a common cloud environment to address the challenges of sharing and processing data from field, airborne and satellite measurements. MAAP was publicly released in October 2021, providing computing capabilities co-located with the data, a collaborative coding and analysis environment, and a set of interoperable tools and algorithms developed to support the estimation and visualization of data. MAAP has allowed scientists from both North America and Europe to collaborate on the generation and analysis/visualization of data derived from multiple, discipline-adjacent missions in an open, collaborative environment that has reached beyond traditional scientific investigation. MAAP has been used to support multiple scientific activities. To date, existing LiDAR data from multiple platforms has been calibrated with field measurements and combined for more comprehensive and accurate estimates of above ground biomass AGB; these LiDAR platforms include airborne (e.g. LVIS), the International Space Station (NASA’s Global Ecosystem Dynamics Investigation (GEDI), and satellites (e.g. ICESat-2). The current challenge is to effectively and seamlessly combine the aforementioned LiDAR-based data with new data sources such as P-band RADAR from ESA’s upcoming BIOMASS mission, existing ESA Sentinel-1 C-band SAR, and the 30 PB/yr of high cadence global coverage L-band SAR data from the upcoming NASA-ISRO SAR (NISAR) mission. Recent analysis using MAAP merged ICESat-2 and optical data (Harmonized Landsat Sentinel) produced the most comprehensively precise estimate of boreal-wide AGB to date. Another effort using MAAP is the production and open distribution of global comparisons of AGB map estimates, including from ICESat-2 and GEDI, to bolster stakeholder uptake for policy applications. These map estimates will feed into the Intergovernmental Panel on Climate Change (IPCC) database, likely aiding the next Global Carbon Stocktake of the UNFCCC. Furthermore, the biomass retrieval intercomparison exercise BRIX-2 could benefit from the MAAP providing standardized test cases (based on airborne campaign and spaceborne data) allowing the community to develop and apply retrieval algorithms based on these test cases, while forthcoming SAR data training curricula could also use the MAAP as a teaching and learning platform. The MAAP is meeting the challenges inherent in international, open science collaboration and large scale computing with a platform that is entirely open source and cloud native, using open standards for data access, manipulation, protocols, and formats. The MAAP data system consists of a dedicated data store whose data is indexed in an online catalog conforming to established metadata, application programmatic interfaces (APIs), and service interface standards, using an implementation of the open sourced NASA Common Metadata Repository. Federation of user identities allows users from either NASA or ESA to access and consume services from the other using a unified metadata catalog for the data utilized across the ESA and NASA MAAP platforms. Similarly, we are exploring how to increase interoperability to achieve a common approach to packaging, orchestrating and executing algorithms, with interoperable access to data for subsetting, fast browse, and cloud-optimized access, all using interoperable standards such as those from the Open Geospatial Consortium (OGC). Designed for interoperability, ESA and NASA utilize a common architecture for the software platform. It provides a cloud-based algorithm development environment (ADE) that enables scientists to develop algorithms collaboratively with access to the MAAP data catalog as well as other data archives. MAAP provides an Eclipse Che-based ADE supporting both Python and R languages, popular in this biomass community. Algorithms developed and containerized within the ADE can be deployed to run to thousands of computational nodes in the MAAP’s data processing system (DPS), dramatically speeding up processing and giving scientists a rapid, iterative turnaround of results. NASA’s implementation of the DPS is based on the Hybrid Science Data System (HySDS) framework, used by NASA flight projects to produce Earth science standard products.

cloud computing↗
DOE OSTI2025

The Impact of Carotenoid Energy Levels on the Exciton Dynamics and Singlet–Triplet Annihilation in Isolated Bacterial Light-Harvesting 2 Complexes

The light-harvesting 2 (LH2) complex of purple phototrophic bacteria plays a critical role in absorbing solar energy and distributing the excitation energy. Exciton dynamics within LH2 complexes are controlled by the structural arrangement and energy levels of the bacteriochlorophyll (BChl) and carotenoid (Car) pigments. However, there is still debate over the competing light-harvesting versus energy-dissipation pathways. In this work, we compared five variants of the LH2 complex from genetically modified strains of Rhodobacter sphaeroides, all containing the same BChls but different Cars with increasing conjugation: zeta-carotene (N = 7; LH2 Zeta ), neurosporene (N = 9; LH2 Neu ), spheroidene (N = 10; LH2 Spher ), lycopene (N = 11; LH2 Lyco ), and spirilloxanthin (N = 13; LH2 Spir ). Absorption measurements confirmed that the Car excited-state energy decreased with increasing conjugation. Similarly, fluorescence spectra showed that the B850 BChl emission peak had an increasing red shift from LH2 Zeta →(LH2 Neu /LH2 Spher )→LH2 Lyco →LH2 Spir . In contrast, time-resolved fluorescence and ultrafast transient absorption (fs-TA) revealed similar excited-state lifetimes (∼1 ns) for all complexes except LH2 Spir (∼0.7 ns). From fs-TA analysis, an additional ∼7 ps nonradiative dissipation step from B850 BChl was observed for LH2 Zeta . Further, singlet− singlet and singlet−triplet annihilation studies showed a ∼50% average fluorescence lifetime reduction in LH2Zeta at high laser power and high repetition rate, compared to ∼10−15% reductions in LH2 Neu /LH2 Spher /LH2 Lyco and minimal lifetime change in LH2 Spir . In LH2 Zeta , the fastest decay component (<50 ps) became prominent at high repetition rates, consistent with strong singlet−triplet annihilation. Nanosecond TA measurements revealed long-lived (>40 μs) BChl triplet states in LH2 Zeta and signs of damage caused by singlet oxygen, whereas other LH2s showed faster triplet quenching (∼18 ns) by Cars. These findings highlight a key design principle of LH2 complexes: the Car triplet energy must be significantly lower than the BChl triplet energy to efficiently quench BChl triplets that otherwise act as potent “trap states,” causing exciton annihilation in laser-based experiments or photodamage in native membranes.

Absorption↗
DOE OSTI2022

Emerging wild virus of native grass bioenergy feedstock is well–established in the Midwestern USA and associated with premature stand senescence

The North American native prairie grass Panicum virgatum (switchgrass) is a primary bioenergy feedstock candidate. Its widespread distribution and genetic diversity enable the possibility of developing this perennial grass for high production in a variety of conditions, including on marginal lands. A critical concern in feedstock development and deployment is the risk of novel pathogen emergence. Here we investigate the landscape-scale prevalence and epidemiology of a little-studied North American virus first detected in switchgrass and other grasses in bioenergy trials in the US Midwest. Switchgrass mosaic virus (SwMV, Genus Marafivirus, Family Tymoviridae) is transmitted by leafhoppers and phylogenetically sister to Maize rayado fino virus, a significant pathogen of maize in parts of the Americas. Our goal was to determine whether SwMV is uniquely limited to specific bioenergy trials or well-established and circulating more broadly. We used molecular diagnostics to quantify naturally occurring SwMV infection in leafhoppers and switchgrass in naturalistic stands throughout a large Midwestern landscape, and quantified leafhopper abundances and stand performance. Our analysis revealed that this apparently wild virus is well-established and widespread. Infection was present at nearly all sites, across diverse landscape contexts, with prevalences ranging as high as 33%–60%. Infection appeared to accumulate and persist in stands over time. It was associated with increases in premature stand senescence but not with reductions in stand height. Although wild viruses are believed to evolve benign relationships with their natural hosts, these data suggest that SwMV has potential to impact yield components. Viruses are frequently overlooked in crop development efforts, but represent the majority of emerging plant pathogens. For SwMV, it is imperative to quantify its impact on host performance, to identify the extent of any host resistance, and to assess any risks of virus spillover to agricultural plantings of other Poaceae species, including maize and sorghum.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

Ikhana: A NASA UAS Supporting Long Duration Earth Science Missions

NASA's Ikhana unmanned aerial vehicle (UAV) is a General Atomics MQ-9 Predator-B modified to support the conduct of Earth science missions for the NASA Science Mission Directorate through partnerships, other government agencies and universities. Ikhana, a Native American word meaning 'intelligence', can carry over 2000 lbs of atmospheric and remote sensing instruments in the payload bay and external pods. The aircraft is capable of mission durations in excess of 24 hours at altitudes above 40,000 ft. Redundant flight control, avionics, power, and network systems increase the system reliability and allow easier access to public airspace. The aircraft is remotely piloted from a mobile ground control station (GCS) using both C-band line-of-sight and Ku-band over-the-horizon satellite datalinks. NASA's GCS has been modified to support on-site science monitoring, or the downlink data can be networked to remote sites. All ground support systems are designed to be deployable to support global Eart science investigations. On-board support capabilities include an instrumentation system and an Airborne Research Test System (ARTS). The ARTS can host research algorithms that will autonomously command and control on-board sensors, perform sensor health monitoring, conduct data analysis, and request changes to the flight plan to maximize data collection. The ARTS also has the ability to host algorithms that will autonomously control the aircraft trajectory based on sensor needs, (e.g. precision trajectory for repeat pass interferometry) or to optimize mission objectives (e.g. search for specific atmospheric conditions). Standard on-board networks will collect science data for recording and for inclusion in the aircraft's high bandwidth downlink. The Ikhana project will complete GCS development, science support systems integration, external pod integration and flight clearance, and operations crew training in early 2007. A large-area remote sensing mission is currently scheduled for the Summer 2007.

Cobleigh, Brent R.↗
DOE OSTI2023

A Search for Technosignatures Around 11,680 Stars with the Green Bank Telescope at 1.15–1.73 GHz

We conducted a search for narrowband radio signals over four observing sessions in 2020–2023 with the $L$-band receiver (1.15–1.73 GHz) of the 100 m diameter Green Bank Telescope. We pointed the telescope in the directions of 62 TESS Objects of Interest, capturing radio emissions from a total of ~11,680 stars and planetary systems in the ~9' beam of the telescope. All detections were either automatically rejected or visually inspected and confirmed to be of anthropogenic nature. We also quantified the end-to-end efficiency of radio SETI pipelines with a signal injection and recovery analysis. The UCLA SETI pipeline recovers 94.0% of the injected signals over the usable frequency range of the receiver and 98.7% of the injections when regions of dense radio frequency interference are excluded. In another pipeline that uses incoherent sums of 51 consecutive spectra, the recovery rate is ~15 times smaller at ~6%. The pipeline efficiency affects calculations of transmitter prevalence and SETI search volume. Accordingly, we developed an improved Drake figure of merit and a formalism to place upper limits on transmitter prevalence that take the pipeline efficiency and transmitter duty cycle into account. Based on our observations, we can state at the 95% confidence level that fewer than 6.6% of stars within 100 pc host a transmitter that is continuously transmitting a narrowband signal with an equivalent isotropic radiated power (EIRP) > 10 13 W. For stars within 20,000 ly, the fraction of stars with detectable transmitters (EIRP > 5 × 10 16 W) is at most 3 × 10 -4 . Finally, we showed that the UCLA SETI pipeline natively detects the signals detected with AI techniques by Ma et al.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Importance of Solution Studies for the Structural Characterization of the Enterovirus 5’ Cloverleaf

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5’ cloverleaf (5’CL). Here, we present a biophysical analysis of the 5’CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5’CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed a high propensity for dimerization, which was enhanced by the presence of salts. Enterovirus D70 was observed to be somewhat intermediate, with primarily a monomeric structure, but possessing some potential for dimerization. The equilibrium between the two monomeric and the dimeric conformations is also discussed. These results indicate that the 5’CL conformation may be more complex than the current literature suggests, thus underscoring the need for a combined crystal and solution approach for the accurate representation of the 5’CL conformation, and the conformation of other RNA structural elements, under native conditions.

Virology↗
NASA NTRS2010

Assessing Operational Total Lightning Visualization Products

In May 2003, NASA's Short-term Prediction Research and Transition (SPoRT) program successfully provided total lightning data from the North Alabama Lightning Mapping Array (NALMA) to the National Weather Service (NWS) office in Huntsville, Alabama. The major accomplishment was providing the observations in real-time to the NWS in the native Advanced Weather Interactive Processing System (AWIPS) decision support system. Within days, the NALMA data were used to issue a tornado warning initiating seven years of ongoing support to the NWS' severe weather and situational awareness operations. With this success, SPoRT now provides real-time NALMA data to five forecast offices as well as working to transition data from total lightning networks at Kennedy Space Center and the White Sands Missile Range to the surrounding NWS offices. The only NALMA product that has been transitioned to SPoRT's partner NWS offices is the source density product, available at a 2 km resolution in 2 min intervals. However, discussions with users of total lightning data from other networks have shown that other products are available, ranging from spatial and temporal variations of the source density product to the creation of a flash extent density. SPoRT and the Huntsville, Alabama NWS are evaluating the utility of these variations as this has not been addressed since the initial transition in 2003. This preliminary analysis will focus on what products will best support the operational warning decision process. Data from 19 April 2009 are analyzed. On this day, severe thunderstorms formed ahead of an approaching cold front. Widespread severe weather was observed, primarily south of the Tennessee River with multiple, weak tornadoes, numerous severe hail reports, and wind. This preliminary analysis is the first step in evaluation which product(s) are best suited for operations. The ultimate goal is selecting a single product for use with all total lightning networks to streamline training and science sharing.

Stano, Geoffrey T.↗
NASA NTRS1998

X-33 Environmental Impact Statement: A Fast Track Approach

NASA is required by the National Environmental Policy Act (NEPA) to prepare an appropriate level environmental analysis for its major projects. Development of the X-33 Technology Demonstrator and its associated flight test program required an environmental impact statement (EIS) under the NEPA. The EIS process is consists of four parts: the "Notice of Intent" to prepare an EIS and scoping; the draft EIS which is distributed for review and comment; the final ETS; and the "Record of Decision." Completion of this process normally takes from 2 - 3 years, depending on the complexity of the proposed action. Many of the agency's newest fast track, technology demonstration programs require NEPA documentation, but cannot sustain the lengthy time requirement between program concept development to implementation. Marshall Space Flight Center, in cooperation with Kennedy Space Center, accomplished the NEPA process for the X-33 Program in 13 months from Notice of Intent to Record of Decision. In addition, the environmental team implemented an extensive public involvement process, conducting a total of 23 public meetings for scoping and draft EIS comment along with numerous informal meetings with public officials, civic organizations, and Native American Indians. This paper will discuss the fast track approach used to successfully accomplish the NEPA process for X-33 on time.

McCaleb, Rebecca C.↗
DOE OSTI2024

Control And Optimization Modular Modeling Application For Nuclear Deployment

The purpose of the COMMAND code is to provide a flexible, scalable tool for use in developing, integrating, and testing the technologies necessary for achieving autonomous operations of advanced nuclear reactors. The code enables users to efficiently implement custom simulations and experiments by combining key methods from different software modules. These modules are focused on: modeling and simulation tools, such as nuclear simulation tools used for high-fidelity modeling (e.g., Reactor Excursion and Leak Analysis Program [RELAP5-3D] and Monte Carlo N-Particle [MCNP]); machine learning and optimization tools (e.g., anomaly detection and data-driven modeling techniques); advanced control in its digital, high-performance, and supervisory control forms (e.g., proportional integral derivative (PID) control and model predictive control (MPC); and integration with hardware through industrial communication protocols. To ensure flexibility and scalability, COMMAND was designed to be both modular—the software “pieces” all inherit from generic building blocks and can be combined and connected to create complicated simulations—and high performing—designed for parallel processing, enabling simulations and experiments to take advantage of multi-core computers, servers, and nodes. The code is written in the Python programming language due to the language's popularity, active community, and open-source and cross-platform nature. Maintaining consistency with other simulation tools used within the nuclear energy community, users implement simulations and experiments through text input files, which define components, parameters, connections, etc., through lines of text. Given that COMMAND is written in Python, these input files are native Python scripts, and so use the standard Python structure and formatting. This also enables users to take advantage of Python's extensive package library to develop custom capabilities for their specific use cases.

Faber, Jacob [Idaho National Laboratory (INL), Ida↗
DOE OSTI2021

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Catalyst: Fast and flexible modeling of reaction networks

We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

Spatiotemporal Monitoring of Hydrilla [Hydrilla verticillata (L. f.) Royle] to Aid Management Actions

Hydrilla is an invasive aquatic plant that has rapidly spread through many inland water bodies across the globe by outcompeting native aquatic plants. Drinking water supply, power generation, and recreational use of lakes are threatened by the spread of this invasive species. Moreover, hydrilla serves as a host for an epiphytic, toxic cyanobacteria known to be the causative agent of the neurodegenerative disease called avian vacuolar myelinopathy, which affects waterfowl, raptors, and amphibians. The early detection of hydrilla infestation is very important to reduce the costs associated with control and removal efforts of this invasive species. Therefore, this study was aimed at developing a rapid, frequent, and large-scale tool for monitoring and predicting spatial extent of hydrilla habitat. This was achieved by integrating in situ and Landsat 8 OLI satellite data for Lake J. Strom Thurmond, the largest US Army Corps of Engineers Lake east of the Mississippi River located on the Georgia/South Caroline border. The predictive model incorporated remote sensing reflectance, Secchi disk depth (SDD), light attenuation coefficient (Kd), maximum depth of colonization (Zc), and percentage of light available through water column (PLW). The model predicted ideal habitat for hydrilla featuring high SDD, low values of Kd, high Zc and PLW. Final analysis showed that hydrilla starts growing in April, reaches peak around October, begins retreating in the following months, and disappears in February. Additionally, physical meteorological factors were analyzed and were found to be closely associated with hydrilla extent. Management agencies can use these results to not only to plan future removal efforts, but also evaluate and adapt their current mitigation efforts.

Percentage of light available through the water co↗
NASA NTRS2015

Environment Modeling Using Runtime Values for JPF-Android

Software applications are developed to be executed in a specific environment. This environment includes external native libraries to add functionality to the application and drivers to fire the application execution. For testing and verification, the environment of an application is simplified abstracted using models or stubs. Empty stubs, returning default values, are simple to generate automatically, but they do not perform well when the application expects specific return values. Symbolic execution is used to find input parameters for drivers and return values for library stubs, but it struggles to detect the values of complex objects. In this work-in-progress paper, we explore an approach to generate drivers and stubs based on values collected during runtime instead of using default values. Entry-points and methods that need to be modeled are instrumented to log their parameters and return values. The instrumented applications are then executed using a driver and instrumented libraries. The values collected during runtime are used to generate driver and stub values on- the-fly that improve coverage during verification by enabling the execution of code that previously crashed or was missed. We are implementing this approach to improve the environment model of JPF-Android, our model checking and analysis tool for Android applications.

Verification↗
DOE OSTI2021

Chapter 4: What We Can Learn from Measuring Metabolic Fluxes in Cyanobacteria

Cyanobacteria with the capability of oxygen-evolving photosynthesis play a vital role in the global carbon, oxygen, and nitrogen cycles. From a biochemical perspective, all phenotypic traits and functions of cyanobacteria are derived from the potential of their metabolism and mirrored in metabolic fluxes through an integrated metabolic network. Metabolic flux, the rate of turnover of molecules through a metabolic pathway, is therefore of great importance for an in-depth understanding of the role of cyanobacteria in the biosphere. Recent interest in cyanobacteria metabolic fluxes is also motivated by the prospect to utilize their light-driven CO2 fixation for sustainable production of valuable chemicals and biofuels. Valorization of cyanobacterial metabolism will require engineering of the native metabolic network - a challenge that can benefit from a quantitative understanding of metabolic reactions taking place intracellularly. In this chapter, we will discuss some intriguing questions relevant to metabolic fluxes in cyanobacteria: How are metabolic fluxes predicted or measured? What do we know about the fluxome inside various cyanobacteria thus far? How are they different between strains as well as in different conditions? And how can we use fluxomics information to guide metabolic engineering and synthetic biology? This chapter will highlight updated knowledge on cyanobacterial metabolism. Specifically, we will focus on providing readers a quantitative vision to understand how this photosynthetic model works.

BASIC BIOLOGICAL SCIENCES,INORGANIC, ORGANIC, PHYS↗
DOE OSTI2025

Modeling neutral defects in III-V ternary alloys with a special quasirandom structure: Analysis of As- and III-site point defects in InGaAs

While first-principles density functional theory modeling has become a vital tool to investigate defect properties in semiconductors, the lack of crystalline periodicity in pseudobinary random composition alloys, such as In 1−𝑥 ⁢Ga 𝑥 ⁢As, complicates such analyses. We present a simulation strategy to systematically take into account the variability in the local defect environment in order to predict statistical properties of neutral intrinsic defects in In 1−𝑥⁢ Ga 𝑥 ⁢As. We use a comprehensive sampling from a modest-sized 64-atom special quasirandom structure (SQS) to define a statistically representative set of defects, and use a 512-atom hypercell, a 2 × 2 × 2 supercell of SQS supercells, to achieve cell-size convergence. We articulate an equivalent site principle and describe how it constrains atomic chemical reference energies in computation of defect formation energies in pseudobinary alloys. A simple protocol for estimating reference energies for the Ga and In atoms sharing the III site succeeds in obtaining the equivalence of defects at Ga-sites and In sites in the SQS supercell, (<30 meV differences in average formation energies). For III-site defects, such as the As antisite As III , the statistical variability in formation energies is modest, ≈ 0.1–0.2 eV. The variability in formation energy at As-site defects, such as the As vacancy 𝑣 As , can be much larger, >1 eV. The As antisite is shown to be a low-energy defect and the most likely to be present in as-grown materials, just as in GaAs. All other defects are higher-energy defects unlikely to be important in native material, but potentially important in radiation-damaged material. With a strong variability in defect energies, especially on the As-site, explicit consideration of statistical variability due to compositional randomness will be imperative for meaningful and quantitative comparisons to experiment.

Density functional theory↗