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At least 145 records · Page 8

Space Synthetic Biology Project

Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the project in selecting the best approaches to the application of bioelectrochemical technologies to ECLS. Figure 1 shows results of simulation of charge transport in an experimental system. Figure 2 shows one of five conceptual designs for ECLS subsystems based on bioelectrochemical reactors. Also during the first 2 years, some work was undertaken to gather fundamental data (conductivities, overpotentials) relevant to the modeling efforts.

Howard, David↗

Evaluation of Synthetic Vision Display Concepts for Improved Awareness in Unusual Attitude Recovery Scenarios

A recent study conducted by the Commercial Aviation Safety Team (CAST) determined 40 percent of all fixed-wing fatal accidents, between 2001 and 2011, were caused by Loss-of-Control (LOC) in flight (National Transportation Safety Board, 2015). Based on their findings, CAST recommended manufacturers develop and implement virtual day-visual meteorological conditions (VMC) display systems, such as synthetic vision or equivalent systems (CAST, 2016). In a 2015 simulation study conducted at NASA Langley Research Center (LaRC), researchers gathered to test and evaluate virtual day-VMC displays under realistic flight operation scenarios capable of inducing reduced attention states in pilots. Each display concept was evaluated to determine its efficacy to improve attitude awareness. During the experiment, Evaluation Pilots (EPs) were shown the following three display concepts on the Primary Flight Display (PFD): Baseline, Synthetic Vision (SV) with color gradient, and SV with texture. The baseline configuration was a standard, conventional 'blue over brown' display. Experiment scenarios were simulated over water to evaluate Unusual Attitude (UA) recovery over 'featureless terrain' environments. Thus, the SV with color gradient configuration presented a 'blue over blue' display with a linear blue color progression, to differentiate attitude changes between sky and ocean. The SV with texture configuration presented a 'blue over blue' display with a black checkerboard texture atop a synthetic ocean. These displays were paired with a Background Attitude Indicator (BAI) concept. The BAI was presented across all four Head-Down Displays (HDDs), displaying a wide field-of-view blue-over-blue attitude indicator. The BAI aligned with the PFD and showed through the background of the navigation displays with opaque transparency. Each EP participated in a two-part experiment series with a total seventy-five trial runs: Part I included a set of twenty-five Unusual Attitude Recovery (UAR) scenarios; Part II included a set of fifty Attitude Memory Recall Tasks (AMRT). At the conclusion of each trial, EPs were asked to complete a set post-run questionnaires. Quantitative results showed that there were no significant statistical effects on UA recovery times when utilizing SV with or without the presence of a BAI. Qualitative results show the SV displays (color, texture) with BAI On are most preferred for both UA recognition and recovery when compared with the baseline display. When only comparing SV display concepts, EPs performed better when using the SV with texture, BAI On, than any other display configuration. This is an interesting find considering most EPs noted their preference towards the SV with color gradient when the BAI was on.

Nicholas, Stephanie↗

Quantifying the Relative Impact of Model Microphysics Parameterizations and Scattering Models in Simulating Synthetic Radar and Microwave Radiometer Observations

Output from numerical weather models is often used to simulate observations from remote sensing instruments, for purposes ranging from data assimilation, synthetic retrievals of geophysical quantities, and optimization of observing systems. However, when hydrometeors are present, the level of detail provided by the weather model is generally insufficient to fully constrain the input to the radiative transfer model (RTM), and further assumptions must be made by the RTM user in order to produce synthetic observations. Using a hierarchy of models including cloud-resolving, double-moment, bin microphysical, and ice-habit predicting models, along with scattering properties from the OpenSSP, Atmospheric Radiative Transfer Simulator (ARTS) databases, as well as relatively simple geometries (e.g., cylindrical plates and columns), we demonstrate the spread in synthetic observation output and the extent to which it is reduced when microphysics is more strongly constrained by the model. As an intermediate step, an error budget for the RTM simulations was derived and from that we developed and will describe best practices for observation simulation (e.g., optimal number of hydrometeor size bins, truncation of the particle size distribution, angular resolution of scattering phase function). Some statistical comparisons with observations will also be presented.

Munchak, S. Joseph↗

Tri-Frequency Synthetic Aperture Radar for the Measurements of Snow Water Equivalent

SWESARR (Snow Water Equivalent Synthetic Aperture Radar and Radiometer) is an airborne instrument developed at the NASA Goddard Space Flight Center for the retrieval of Snow Water Equivalent. SWESARR was specifically designed to measure co-located active and passive signals using a high resolution and multi-frequency Synthetic Aperture Radar (SAR) and a multifrequency radiometer. SWESARR’s Synthetic Aperture Radar (SAR) system is made up of three independent radar units that operate in the X, Ku-Low, and Ku-High bands with bandwidths up to 200 MHz, and acquires data in two polarizations (dual-polarization radar). The difference in sensitivity of the backscatter signals to snow microstructure, in conjunctions with radiometer measurements, permits an accurate estimation of the snow water equivalent (SWE).

Rincon, Rafael↗

Synthetic Tracking on a Small Telescope

Synthetic tracking uses high speed (up to 10 Hz) low noise (<2e-) large format sensors ~16 Mpix along with a multi-vector shift/add algorithm that coadds multiple image frames to increase the signal to noise ratio (SNR) needed to detect (if present) multiple moving objects in the field of view (FOV). We published the application of synthetic tracking to look for asteroids in 2014 (Shao 2014), but recently have applied it more as well to Earth orbiting objects. We have begun testing the data processing graphical processing unit (GPU) array with a small telescope, a 28 cm Celestron RASA telescope and a low cost low noise 16 Mpix CMOS camera at a dark site in California. This system is now operational with a 2 sqdeg FOV and a limiting magnitude between ~16-17.5 stellar magnitudes (mag) depending on a number of observational parameters for short integration times. The instrument can be used to search for NEOs, where we use much longer integration times to get sensitivity ~ 20.5 mag (at new moon). Synthetic tracking provides significant improvements in both sensitivity and astrometric accuracy.

Turyshev, Slava G.↗

Single-Crystal-to-Single-Crystal Post-Synthetic Modifications

Chalcogenides are the cornerstone of the semiconductor and thermoelectric industries and are up-and-coming materials for superconductors, catalysis, and battery applications. Challenges in synthesizing those materials emerge from the chalcogen's volatility and the tendencies of chalcogenides to react with even trace quantities of oxygen. Many techniques have been applied to the growth of chalcogenide single crystals, which are convenient for structure determinations and intrinsic property measurements. One of the recent advances in chalcogenide chemistry is the intriguing single-crystal-to-single-crystal (SCSC) transformation, leading to new metastable compositions. Post-synthetic transformations are well-known and studied for chalcogenide powders; however, examples of post-synthetic conversions that retain single crystallinity are rare. To date, the scope of SCSC reactions includes (de)intercalation in the layered compositions and ion exchange in open-framework materials, salt-inclusion chalcogenides, and layered structures. This poster will discuss the successful examples of SCSC modifications monitored by single-crystal X-ray diffraction (SC-XRD), emphasizing how post-synthetic transformations affect materials' properties.

chalcogenide↗

Data‐Efficient Generation of Synthetic Microstructures of Polymer‐Bonded Energetic Material With Fine‐Tuned Stable Diffusion

Among current deep learning approaches for synthetic image generation, diffusion-based models stand out in terms of algorithmic stability and ability to retain high-fidelity image features with detailed resolution. Here, in this work, we employ Dreambooth, a method for fine-tuning Stable Diffusion, on X-ray CT images of microstructure of the polymer-bonded form (PBX) of a commonly used high explosive, Pentaerythritol tetranitrate (PETN), which yields generative models for creating synthetic PBX images. The models developed here represent five classes (or ‘lots’) of microstructures and demonstrate successful generation of images of each class with high fidelity, as verified by computed classification accuracy of ∼ 94% or higher. Data augmentation afforded by such image synthesis can be used to more reliably decipher underlying statistics, build processing-structure correlations, recognize off-normal structural anomalies, and identify age-related changes. Ideas related to converting image data into appropriate density mapping and performing mesoscale simulation or surrogate modeling of detonation are also discussed.

Dreambooth↗

Validating automated resonance evaluation with synthetic data

The integrity and precision of nuclear data are crucial for a broad spectrum of applications, from national security and nuclear reactor design to medical diagnostics, where the associated uncertainties can significantly impact outcomes. A substantial portion of uncertainty in nuclear data originates from the subjective biases in the evaluation process, a crucial phase in the nuclear data production pipeline. Recent advancements indicate that automation of certain routines can mitigate these biases, thereby standardizing the evaluation process and enhancing reproducibility. This research aims to provide a methodology, framework, and metrics for the validation of automated nuclear data evaluation software leveraging high-quality synthetic data that closely mimic real experimental observables. An introduced error metric provides a scale and intuitive measure of the evaluation quality by quantifying the estimate’s accuracy and performance across the specified energy range. Synthetic data provides access to experimental observables and underlying resonance parameters, enabling comparison of different evaluations. The methodology is demonstrated using Ta-181 isotope data in the resolved resonance region. The Automated Resonance Identification Subroutine (ARIS), which operates without prior resonance information, was used to test and showcase the framework’s capabilities utilizing the proposed error metrics. The results demonstrate the effectiveness of the proposed approach and framework for optimizing software parameters and testing hypotheses through “what-if” controlled experiments, such as modifying assumptions about experimental conditions or average resonance parameters.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Light-Modulated Self-Assembly of Synthetic Nanotubes

Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.

DNA nanotechnology↗

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit

Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

Defined synthetic microbial communities colonize and benefit field-grown sorghum

The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, in this study, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.

60 APPLIED LIFE SCIENCES↗

DRDMannTurb: A Python package for scalable, data-driven synthetic turbulence

Synthetic turbulence models (STMs) are used in wind engineering to generate realistic flow fields and are employed as inputs to industrial wind simulations. Examples include prescribing inlet conditions in large eddy simulations that model loads on wind turbines and tall buildings. We are interested in STMs capable of generating fluctuations based on prescribed second-moment statistics since such models can simulate environmental conditions that closely resemble on-site observations. To this end, the widely used Mann model (see Mann, 1994, 1998) is the inspiration for DRDMannTurb. The Mann model is described by three physical parameters: a magnitude parameter influencing the global variance of the wind field and corresponding to the Kolmogorov constant multiplied by the rate of viscous dissipation of the turbulent kinetic energy to the two-thirds, αϵ 2/3 , a turbulence length scale parameter L, and a nondimensional parameter Γ related to the lifetime of the eddies. A number of studies, as well as international standards (e.g., those by the International Electrotechnical Commission (IEC)), include recommended values for these three parameters with the goal of standardizing wind simulations according to observed energy spectra. Yet, having only three parameters, the Mann model faces limitations in accurately representing the diversity of observable spectra. This Python package enables users to extend the Mann model and more accurately fit field measurements through flexible neural network models of the eddy lifetime function. Following Keith et al. (2021), we refer to this class of models as Deep Rapid Distortion (DRD) models. DRDMannTurb also includes a general module implementing an efficient method for synthetic turbulence generation based on a domain decomposition technique. This technique is also described in Keith et al. (2021).

17 WIND ENERGY↗

High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology (Final Technical Report)

Fatty acids can be produced biosynthetically in microbes and these compounds can serve as precursors to biodiesels and other high value oleochemicals. However, progress on engineering fatty acid biosynthesis, and biofuel synthesis more generally, has been hindered by current quantification methods that are either indirect or not amenable to high-throughput or single-cell resolution screening. In this project, we assembled an interdisciplinary team with complimentary expertise in synthetic biology and microscopy, metabolic engineering, and chemical imaging to address these challenges. We used chemical imaging to directly measure lipid biosynthesis in Escherichia coli engineered to produce fatty acids, obtaining detailed single-cell resolution measurements. We deployed stimulated Raman scattering (SRS) microscopy in concert with multiplexed genome engineering and gene circuit design strategies from synthetic biology to optimize production of fatty acids. These results provided novel insight into cell-to-cell heterogeneity present in biofuel production strains. In addition, we introduced new chemical imaging methods which are label-free and do not require fluorescent reporters. These efforts were complemented by other studied developing foundational tools for regulation and control, which offer excellent potential for advancing researchers’ ability to rapidly design, build, and test strains for enhanced biofuel synthesis.

09 BIOMASS FUELS↗

Catalytic Conversion of Biogenic and Synthetic Polymers into Carbon-Negative and -Neutral Chemicals and Fuels

We investigated a technology that enables the distributed decomposition of biogenic (lignin, cellulose) and synthetic (plastic) polymers into renewable or low-carbon-emission chemicals and fuel intermediates that can substitute fossil hydrocarbons for energy, chemical, and fuel production. The specific goal of this project is to (1) selectively convert biogenic polymers such as lignin and synthetic polymers such as polyethylene into hydrocarbons via electrocatalytic and thermocatalytic processes, and (2) optimize (electro)catalyst composition and reaction conditions to mitigate deactivation and control product selectivity.

09 BIOMASS FUELS↗

Height reconstruction techniques for synthetic aperture lidar systems

The data-processing techniques and acquisition modes of a synthetic aperture lidar (SAL) instrument operating at optical wavelengths are closely related to the analogous modes of a synthetic aperture radar (SAR) instrument operating at microwave frequencies. It is consequently natural to explore the applicability of SAR processing techniques to SAL sensors. In this paper, we examine the feasibility of adopting SAR height-reconstruction techniques with SAL sensors to obtain high-resolution 3-D imagery at optical wavelengths.

synthetic aperture lidar (SAL)↗

GeoSTAR - A Synthetic Aperture Microwave Sounder for Geostationary Missions

The Geostationary Synthetic Thinned Aperture Radiometer (GeoSTAR) is a new microwave atmospheric sounder under development. It will bring capabilities similar to those now available on low-earth orbiting environmental satellites to geostationary orbit - where such capabilities have not been available. GeoSTAR will synthesize the multimeter aperture needed to achieve the required spatial resolution, which will overcome the obstacle that has prevented a GEO microwave sounder from being implemented until now. The synthetic aperture approach has until recently not been feasible, due to the high power needed to operate the on-board high-speed massively parallel processing system required for 2D-synthesis, as well as a number of system and calibration obstacles. The development effort under way at JPL, with important contributions from the Goddard Space Flight Center and the University of Michigan, is intended to demonstrate the measurement concept and retire much of the technology risk.

geostationary↗

Microorganism Utilization for Synthetic Milk

A desired architecture for long duration spaceflight, like aboard the International Space Station or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of the Synthetic Biology project, Cow in a Column, was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel-through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) in order to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms were optimized in the laboratory and the desired end-products, sugars and lipids, were analyzed. Trichoderma reesei, a known cellulolytic fungus, was utilized to drive the production of glucose, with the intent that the produced glucose would serve as the carbon source for milk fat production and be a substitute for the milk sugar lactose. Lipid production would be carried out by Rhodosporidium toruloides, yeast known to accumulate those lipids that are typically found in milk fat. Results showed that glucose and total lipid content were below what was expected during this phase of experimentation. In addition, individual analysis of six fatty acids revealed that the percentage of each fatty acid was lower than naturally produced bovine milk. Overall, this research indicates that microorganisms could be utilized to breakdown inedible solid waste to produce useable products. For future work, the production of the casein protein for milk would require the development of a genetically modified organism, which was beyond the scope of the original project. Additional trials would be needed to further refine the required environment/organisms for the production of desired sugar and lipid end-products.

Microorganisms↗

Microbial Extremophiles for Earth and Beyond: Pushing the Boundaries with Synthetic Biology

All organisms live in a multi-dimensional physical and chemical niche space. Discoveries in the 20th century enormously expanded the range of what was considered "habitable." However, the current diversity of life on Earth begs the question of what terrestrial life - or indeed, another life form - would be capable of. With the needs of both modern laboratory science and the burgeoning field of biotechnology, as well as our deeply held desire to answer the question "are we alone in the universe?, we are exploiting the tools of synthetic biology to probe the question of whether we can create "synthetic extremophiles" or, as our lab has dubbed them, "Hell Cells."

synthetic extremophiles↗