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Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

Bioelectrochemical System

From Extremophiles to Star Trek, The Use of Synthetic Biology in Astrobiology

Synthetic biology – the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes – has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as bio-mining, human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Life in Extreme Environments

Synthetic Astrobiology

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

synthetic biology

Where Synthetic Biology Meets ET

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

life in extreme environments

Improving microstructures segmentation via pretraining with synthetic data

Image analysis of material microstructures through microscopy is an integral capability in the field of materials science. The topological and chemical information obtained through microscopy allow us to draw vital connections between material microstructures, properties, and processing. While scanning electron microscopy (SEM) is able to yield a considerable wealth of information interpretable by the intuition of experts, there has been considerable interest in using machine learning, convolutional neural networks (CNNs) in particular, for such image analysis task. Training CNNs for an image analysis task requires a large annotated dataset. However, in many materials science applications, obtaining a large annotated dataset is cost and labor intensive. In this work, we study the use of synthetic data to enlarge the available annotated experimental data of uranium oxide. We utilize a modified Potts model to simulate uranium oxide particles with morphologies similar to those observed experimentally. We then leverage an image-to-image translation model to synthesize the simulated particles as if they are acquired with SEM. Through this process, we obtain pairs of particle images and their corresponding SEM representations, which corresponds to pairs of annotations and images. Unlike previous works, we leverage synthetic data for pretraining a CNN model prior, and finetune that model further with experimental data. We experimentally demonstrate that using synthetic data as incremental learning process benefits the overall performance compared to training a model on combined synthetic and experimental data.

36 MATERIALS SCIENCE

Updimensioning strategy derived from synthetic equiaxed grain structures for approximating 3D grain size distributions from 2D visualizations with 1D parameters

We generated synthetic equiaxed grain structures using computer graphics software to explore the relationship between various grain size determination methods and true three-dimensional (3D) grain diameters. Mirroring grain measurement techniques, the synthetic 3D grain structures are imaged as 2D micrographs which are measured to yield 1D grain size parameters. Synthetic grain structures provide data at a mass scale and permit exploration of both polished and fractured surface micrographs, revealing one-to-one correspondence between exposed 2D grain cross-sections and individual 3D grains. Analysis of this correspondence yielded a procedure to approximate 3D equiaxed grain size and volume distributions based on the mode of the 2D fractograph grain size distribution. The 3D approximation procedure is shown to be less susceptible to different imaging conditions that affect small, undiscernible grains compared to the standard planimetric and linear intercept methods, which by design also tend to underestimate the 3D grain diameter. The procedure requires larger sample sizes to lower variance and a deeper analysis which could become more practical with machine learning (ML) models for grain boundary segmentation, which synthetic grain structures can help train. This work lays the foundation for analyzing other grain distributions such as columnar and composite grains in similar depth.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Synthetic tensor gauge fields

Synthetic gauge fields have provided physicists with a unique tool to explore a wide range of fundamentally important phenomena. However, most experiments have focused on synthetic vector gauge fields. The very rich physics brought about by coupling tensor gauge fields to fracton phases of matter remains unexplored in laboratories. Here, we propose schemes to realize synthetic tensor gauge fields that address dipoles instead of single particles. A lattice tilted by a strong linear potential and a weak quadratic potential yields a rank-2 electric field for a dipole formed by a particle-hole pair. Such a rank-2 electric field leads to a new type of Bloch oscillations, which modulates the quadrupole moment and preserves the dipole moment of the system. In higher dimensions, the interplay between interactions and vector gauge potentials imprints a phase to the ring-exchange interaction and thus generates synthetic tensor gauge fields. Such tensor gauge fields make it possible to realize a dipolar Harper-Hofstadter model in laboratories. The resultant dipolar Chern insulators feature chiral edge currents of dipoles in the absence of net charge currents. Published by the American Physical Society 2025

Zhang, Shaoliang (ORCID:000000016635044X)

Producing High-fidelity Synthetic Population Ensembles at Scale

Used within social simulations, synthetic population ensembles enable uncertainty quantification (UQ) methods for obtaining more robust model inference and prediction. A synthetic population ensemble is a series of plausible virtual reconstructions of an area’s population at the granularity of people and residences, generated stochastically to preserve privacy of the source population survey’s respondents. In this paper, we demonstrate the production of large synthetic population ensembles for the US via Oak Ridge National Laboratory’s UrbanPop framework to support modeling of high spatial resolution energy affordability metrics from nationwide social surveys in collaboration with the fusionACS project. Our initial task involves creating ensembles for 17 US metropolitan areas, each consisting of 41 population instances (a base realization and 40 replicates). To accomplish this task at scale, we configured an integrated system comprised of a research cloud, virtual containerization, GPU-enhanced functionality, and a dual API/CLI to interact with UrbanPop’s maturing Likeness Python ecosystem. We observe a reduction in theoretical execution time while maintaining high-fidelity approximations of residential totals by metropolitan area and the demographic characteristics of neighborhoods. We discuss expansion of our approach to produce synthetic population ensembles for the entire US, particularly plans to establish automated workflows for job orchestration to increase computational efficiency, as well as provide outlook for broadening applications of the ensembles.

Gaboardi, James [ORNL] (ORCID:0000000247766826)

Studies of Cell-Mediated Immunity Against Immune Disorders Using Synthetic Peptides and Rotating Bioreactor System

Our proposed experiments included: (1) immunzing mice with synthetic peptides; (2) preparing spleen and lymph node cells; (3) growing them under conventional conditions as well as in the rotatory vessel in appropriate medium reconstituting with synthetic peptides and/or cytokines as needed; and (4) comparing at regular time intervals the specific CTL activity as well as helper T-cell activity (in terms of both proliferative responses and cytokine production) using established procedures in my laboratory. We further proposed that once we demonstrated the merit of rotatory vessel technology to achieve desired results, these studies would be expanded to include immune cells from non-human primates (rhesus monkeys and chimpanzees) and also humans. We conducted a number of experiments to determine CTL induction by the synthetic peptides corresponding to antigenic proteins in HIV and HPV in different mouse strains that express MHC haplotypes H-2b or H-2d. We immunized mice with 100 ug of the synthetic peptide, suspended in sterile water, and emulsified in CFA (1:1). The immune lymph node cells obtained after 7 days were restimulated by culturing in T25 flask, HARV-10, or STLV-50, in the presence of the peptide at 20 ug/ml. The results from the 5'Cr-release assay consistently revealed complete abrogation of CTL activity of cells grown in the bioreactors (both HARV and STLV), while significant antigen-specific CTL activity was observed with cells cultured in tissue culture flasks. Thus, overall the data we generated in this study proved the usefulness of the NASA-developed developed technology for understanding the known immune deficiency during space travel. Additionally, this ex vivo microgravity technology since it mimics effectively the in vivo situation, it is also useful in understanding immune disorders in general. Thus, our proposed studies in TMC-NASA contract round II application benefit from data generated in this TMC-NASA contract round I study.

Sastry, Jagannadha K.

Backus Effect on a Perpendicular Errors in Harmonic Models of Real vs. Synthetic Data

Measurements of geomagnetic scalar intensity on a thin spherical shell alone are not enough to separate internal from external source fields; moreover, such scalar data are not enough for accurate modeling of the vector field from internal sources because of unmodeled fields and small data errors. Spherical harmonic models of the geomagnetic potential fitted to scalar data alone therefore suffer from well-understood Backus effect and perpendicular errors. Curiously, errors in some models of simulated 'data' are very much less than those in models of real data. We analyze select Magsat vector and scalar measurements separately to illustrate Backus effect and perpendicular errors in models of real scalar data. By using a model to synthesize 'data' at the observation points, and by adding various types of 'noise', we illustrate such errors in models of synthetic 'data'. Perpendicular errors prove quite sensitive to the maximum degree in the spherical harmonic expansion of the potential field model fitted to the scalar data. Small errors in models of synthetic 'data' are found to be an artifact of matched truncation levels. For example, consider scalar synthetic 'data' computed from a degree 14 model. A degree 14 model fitted to such synthetic 'data' yields negligible error, but amplifies 4 nT (rmss) added noise into a 60 nT error (rmss); however, a degree 12 model fitted to the noisy 'data' suffers a 492 nT error (rmms through degree 12). Geomagnetic measurements remain unaware of model truncation, so the small errors indicated by some simulations cannot be realized in practice. Errors in models fitted to scalar data alone approach 1000 nT (rmss) and several thousand nT (maximum).

Voorhies, C. V.

Technical Challenges in the Development of a NASA Synthetic Vision System Concept

Within NASA's Aviation Safety Program, the Synthetic Vision Systems Project is developing display system concepts to improve pilot terrain/situation awareness by providing a perspective synthetic view of the outside world through an on-board database driven by precise aircraft positioning information updating via Global Positioning System-based data. This work is aimed at eliminating visibility-induced errors and low visibility conditions as a causal factor to civil aircraft accidents, as well as replicating the operational benefits of clear day flight operations regardless of the actual outside visibility condition. Synthetic vision research and development activities at NASA Langley Research Center are focused around a series of ground simulation and flight test experiments designed to evaluate, investigate, and assess the technology which can lead to operational and certified synthetic vision systems. The technical challenges that have been encountered and that are anticipated in this research and development activity are summarized.

Bailey, Randall E.

Synthetic Jets in Cross-flow: Round Jet - Part 1

Results of an experimental investigation on synthetic jets from round orifices with and without cross-flow are presented. Jet Reynolds number up to 46,000 with a fully turbulent approach boundary layer, and Stokes number up to 400. are covered. The threshold of stroke length for synthetic jet formation. in the absence of the cross-flow, is found to be Lo /D approximately 0.5. Above Lo /D is approximately 10, the profiles of normalized centerline mean velocity appear to become invariant. It is reasoned that the latter threshold may be related to the phenomenon of saturation of impulsively generated vortices. In the presence of the cross-flow, the penetration height of a synthetic jet is found to depend on the momentum- flux ratio . When this ratio is defined in terms of the maximum jet velocity and the cross-flow velocity. not only all data collapse but also the jet trajectory is predicted well by correlation equation available for steady jets-in-cross-flow. Distributions of mean velocity, streamwise vorticity as well as turbulence intensity for a synthetic jet in cross-flow are found to be similar to those of a steady jet-in-cross-flow. A pair of counter-rotating streamwise vortices, corresponding to the bound vortex pair of the steady case, is clearly observed. Mean velocity distribution exhibits a dome of low momentum fluid pulled up from the boundary layer, and the entire domain is characterized by high turbulence.

Zaman, K. B. M. Q.

Summary of the 2004 CFD Validation Workshop on Synthetic Jets and Turbulent Separation Control

A CFD validation workshop for synthetic jets and turbulent separation control (CFDVAL2004) was held in Williamsburg, Virginia in March 2004. Three cases were investigated: synthetic jet into quiescent air, synthetic jet into a turbulent boundary layer crossflow, and flow over a hump model with no-flow-control, steady suction, and oscillatory control. This paper is a summary of the CFD results from the workshop. Although some detailed results are shown, mostly a broad viewpoint is taken, and the CFD state-of-the-art for predicting these types of flows is evaluated from a general point of view. Overall, for synthetic jets, CFD can only qualitatively predict the flow physics, but there is some uncertainty regarding how to best model the unsteady boundary conditions from the experiment consistently. As a result. there is wide variation among CFD results. For the hump flow, CFD as a whole is capable of predicting many of the particulars of this flow provided that tunnel blockage is accounted for, but the length of the separated region compared to experimental results is consistently overpredicted.

Rumsey, C. L.

Synthetic Jet Flow Field Database for CFD Validation

An oscillatory zero net mass flow jet was generated by a cavity-pumping device, namely a synthetic jet actuator. This basic oscillating jet flow field was selected as the first of the three test cases for the Langley workshop on CFD Validation of Synthetic Jets and Turbulent Separation Control. The purpose of this workshop was to assess the current CFD capabilities to predict unsteady flow fields of synthetic jets and separation control. This paper describes the characteristics and flow field database of a synthetic jet in a quiescent fluid. In this experiment, Particle Image Velocimetry (PIV), Laser Doppler Velocimetry (LDV), and hot-wire anemometry were used to measure the jet velocity field. In addition, the actuator operating parameters including diaphragm displacement, internal cavity pressure, and internal cavity temperature were also documented to provide boundary conditions for CFD modeling.

Yao, Chung-Sheng

An Experimental Study Synthetic Jets from Rectangular Orifices

Results of an experimental investigation on isolated synthetic jets in crossflow from rectangular orifices of different aspect ratio and orientation are presented. Three aspect ratios, AR = 4, 8, and 16, with pitch a = 90deg., were investigated, Additionally, the AR = 8 case was pitched at 20 deg.. The yaw angle, , was varied through 0 deg., 10 deg., 45 deg. and 90 deg.. All orifices had same exit area and the data were compared with synthetic as well as steady jet from a circular orifice of same area. Hotwire measurements were performed to obtain all three components of mean velocity and turbulent stresses. Data were acquired for momentum-flux ratio up to J = 50. Distributions of time- and phase-averaged data were obtained on the cross sectional plane at x/D = 0.5, 5 and 10, as well as on the axial plane of the symmetry. Qualitative flowfield similarity between synthetic and steady jets is observed. However, high-momentum 'cap' above the low-momentum 'dome', characteristic of steady jets, does not necessarily appear in the synthetic jet. The position and shape of the high-momentum region depend on the distance from the orifice, pitch, yaw as well as momentum-flux ratio. Consequently, the location of the minimum velocity in the 'dome' measured at the plane of symmetry, y(submin), is adopted as a reference for penetration estimate and trajectory comparison. For AR = 16, the dome is the largest in area with maximum velocity deficit. However, the penetration is somewhat higher for AR = 4. Increase in yaw reduces the spatial extent of the dome and the penetration height but augments the velocity deficit. At low J the dome is connected to the boundary layer and traces of the cap of high momentum fluid are visible above it. Increase in J lifts the dome and reorganizes the high-momentum fluid around its perimeter, eventually bringing it underneath. Phase-averaged data document dynamic topological changes within the cycle. Phase-averaged streamwise velocity contours on the cross-sectional plane exhibit behavior commensurate with that seen in time-averaged data at various J.

Milanovic, Ivana M.

Flight Testing an Integrated Synthetic Vision System

NASA's Synthetic Vision Systems (SVS) project is developing technologies with practical applications to eliminate low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance for transport aircraft. The SVS concept being developed at NASA encompasses the integration of tactical and strategic Synthetic Vision Display Concepts (SVDC) with Runway Incursion Prevention System (RIPS) alerting and display concepts, real-time terrain database integrity monitoring equipment (DIME), and Enhanced Vision Systems (EVS) and/or improved Weather Radar for real-time object detection and database integrity monitoring. A flight test evaluation was jointly conducted (in July and August 2004) by NASA Langley Research Center and an industry partner team under NASA's Aviation Safety and Security, Synthetic Vision System project. A Gulfstream GV aircraft was flown over a 3-week period in the Reno/Tahoe International Airport (NV) local area and an additional 3-week period in the Wallops Flight Facility (VA) local area to evaluate integrated Synthetic Vision System concepts. The enabling technologies (RIPS, EVS and DIME) were integrated into the larger SVS concept design. This paper presents experimental methods and the high level results of this flight test.

Kramer, Lynda J.

Flight Test Evaluation of Situation Awareness Benefits of Integrated Synthetic Vision System Technology f or Commercial Aircraft

Research was conducted onboard a Gulfstream G-V aircraft to evaluate integrated Synthetic Vision System concepts during flight tests over a 6-week period at the Wallops Flight Facility and Reno/Tahoe International Airport. The NASA Synthetic Vision System incorporates database integrity monitoring, runway incursion prevention alerting, surface maps, enhanced vision sensors, and advanced pathway guidance and synthetic terrain presentation. The paper details the goals and objectives of the flight test with a focus on the situation awareness benefits of integrating synthetic vision system enabling technologies for commercial aircraft.

Prinzel, Lawrence J., III