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At least 1,027 records · Page 57

Towards a fully automated algorithm driven platform for biosystems design

Large-scale data acquisition and analysis are often required in the successful implementation of the design, build, test, and learn (DBTL) cycle in biosystems design. However, it has long been hindered by experimental cost, variability, biases, and missed insights from traditional analysis methods. Here, we report the application of an integrated robotic system coupled with machine learning algorithms to fully automate the DBTL process for biosystems design. As proof of concept, we have demonstrated its capacity by optimizing the lycopene biosynthetic pathway. This fully-automated robotic platform, BioAutomata, evaluates less than 1% of possible variants while outperforming random screening by 77%. A paired predictive model and Bayesian algorithm select experiments which are performed by Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB). BioAutomata excels with black-box optimization problems, where experiments are expensive and noisy and the success of the experiment is not dependent on extensive prior knowledge of biological mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

Freezing-in gravitational waves

The thermal plasma in the early Universe produced a stochastic gravitational wave (GW) background, which peaks today in the microwave regime and was dubbed the cosmic gravitational microwave background (CGMB). In previous works, only single graviton production processes that contribute to the CGMB have been considered. Here, we also investigate graviton pair production processes and show that these can lead to a significant contribution if the ratio between the maximum temperature and the Planck mass, T max / m p , divided by the internal coupling in the heat bath is large enough. As the dark matter freeze-in production mechanism is conceptually very similar to the GW production mechanism from the primordial thermal plasma, we refer to the latter as “GW freeze-in production.” We show that quantum gravity effects appear in single graviton production and are smaller by a factor ( T max / m p ) 2 than the leading order contribution. In our work, we explicitly compute the CGMB spectrum within a scalar model with quartic interaction. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Impact of Pressure Distribution and Magnitude on the Performance of Lithium Metal Anodes

Li metal anodes are a critical battery technology due to their ability to substantially increase the energy density of Li-based batteries. It is well known that pressure greatly impacts the performance of a Li-metal anode. However, precisely how the pressure value and distribution of pressure affect performance is unclear. Furthermore, the solid-electrolyte interphase composition that forms under varying pressure distributions remains a key parameter for practical lithium metal anodes. In this work, different pressure distributions were employed by using differently shaped and oriented mechanical springs in the coin cells, resulting in varying contact points. Pressure-sensitive films were used to spatially map the pressure and correlate it to the performance. It was found that higher average pressure does not necessarily have a positive effect on performance. When high pressure is paired with poor pressure uniformity, the performance is in fact worse likely due to the current focusing effect, rendering unsatisfied cycling stability. This work points to the importance of controlling the relationship between average pressure and pressure uniformity.

25 ENERGY STORAGE↗

Atmospheric-wake vortex interactions

The interactions of a vortex wake with a turbulent stratified atmosphere are investigated with the computer code WAKE. It is shown that atmospheric shear, turbulence, and stratification can provide the dominant mechanisms by which vortex wakes decay. Computations included the interaction of a vortex wake with a viscous ground plane. The observed phenomenon of vortex bounce is explained in terms of secondary vorticity produced on the ground. This vorticity is swept off the ground and advected about the vortex pair, thereby altering the classic hyperbolic trajectory. The phenomenon of the solitary vortex is explained as an interaction of a vortex with crosswind shear. Here, the vortex having the sign opposite that of the sign of the vorticity in the shear is dispersed by a convective instability. This instability results in the rapid production of turbulence which in turn disperses the smoke marking the vortex.

Bilanin, A. J.↗

Vortex generating flow passage design for increased film-cooling effectiveness and surface coverage

The fluid mechanics of the basic discrete hole film cooling process is described as an inclined jet in crossflow and a cusp shaped coolant flow channel contour that increases the efficiency of the film cooling process is hypothesized. The design concept requires the channel to generate a counter rotating vortex pair secondary flow within the jet stream by virture of flow passage geometry. The interaction of the vortex structures generated by both geometry and crossflow was examined in terms of film cooling effectiveness and surface coverage. Comparative data obtained with this vortex generating coolant passage showed up to factors of four increases in both effectiveness and surface coverage over that obtained with a standard round cross section flow passage. A streakline flow visualization technique was used to support the concept of the counter rotating vortex pair generating capability of the flow passage design.

Papell, S. S.↗

Microwelding of various metallic materials under ultravacuum (A0138-10)

In the space vacuum environment, the spacecraft mechanisms are liable to sustain damaging effects from microwelds due to molecular diffusion of the spacecraft constituent metals. Such microwelds result in a continuing increase in the friction factors and are even liable to jam the mechanisms altogether. The object of this experiment is to check the metal surfaces representative of the mechanism constituent metals (treated or untreated, lubricated or unlubricated) for microwelds afater an extended stay in the space environment. The experimental approach is to passively expose inert metal specimens to the space vacuum and to conduct end-of-mission verification of the significance of microwelds between various pairs of metal washers. The experiment will be located in one of the FRECOPA boxes in a 12-in. -deep peripheral tray that contains nine other experiments from France.

Assie, J. P.↗

Composite Material Property Nondestructive Characterization Using Obliquely Insonified Ultrasonic Waves

The analysis of reflected ultrasonic waves induced by oblique insonification of composite materials is a powerful tool for providing informations about defects and material properties. A device was developed to manipulate a pair of transmitting and receiving transducers at vrious angles of wave incidence and propagation with the fiber orientation.

Non-Destructive Evaluation Composites Mechanical P↗

Engagement of Metal Debris into a Gear Mesh

A series of bench top experiments was conducted to determine the effects of metallic debris being dragged through meshing gear teeth. A test rig that is typically used to conduct contact fatigue experiments was used for these tests. Several sizes of drill material, shim stock, and pieces of gear teeth were introduced and then driven through the meshing region. The level of torque required to drive the "chip" through the gear mesh was measured. From the data gathered, chip size sufficient to jam the mechanism can be determined. INTRODUCTION In some space mechanisms the loading can be so high that there is some possibility that a gear chip might be liberated while in operation of the mechanism [1-5]. Also, due to the closely packed nature of some space mechanisms and the fact that a space grease is used for lubrication, chips that are released can then be introduced to other gear meshes within this mechanism. In this instance, it is desirable to know the consequences of a gear chip entering in between meshing gear teeth. To help provide some understanding, a series of bench-top experiments was conducted to engage chips of simulated and gear material fragments into a meshing gear pair. One purpose of the experiments was to determine the relationship of chip size to the torque required to rotate the gear set through the mesh cycle. The second purpose was to determine the condition of the gear chip material after engagement by the meshing gears, primarily to determine if the chip would break into pieces and to observe the motion of the chip as the engagement was completed. This document also presents preliminary testing done with metal debris other than chips from gears, namely steel shim stock and drill bits of various sizes and diameters.

Handschuh, Robert F.↗

Structural Characterization of the Platinum Nanoparticle Hydrogen-Evolving Catalyst Assembled on Photosystem I by Light-Driven Chemistry

Directed assembly of abiotic catalysts onto biological redox protein frameworks is of interest as an approach for the synthesis of biohybrid catalysts that combine features of both synthetic and biological materials. In this report, we provide a multiscale characterization of the platinum nanoparticle (NP) hydrogen-evolving catalysts that are assembled by light-driven reductive precipitation of platinum from an aqueous salt solution onto the photosystem I protein (PSI), isolated from cyanobacteria as trimeric PSI. The resulting PSI-NP assemblies were analyzed using a combination of X-ray energy-dispersive spectroscopy (XEDS), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), small-angle X-ray scattering (SAXS), and high-energy X-ray scattering with atomic pair distribution function (PDF) analyses. The results show that the PSI-supported NPs are approximately 1.8 nm diameter disk-shaped particles that assemble at discrete sites with 145 Å separation. This separation is too large to be consistent with NP nucleation and growth at a site adjacent to the F B cofactor site. Instead, we suggest a mechanism for NP growth at hydrophobic sites on the PSI stromal surface. The NPs photoreductively assembled on the PSI stromal surface are found to be analogous to the nanostructures produced by successive cycles of atomic layer deposition (ALD) of platinum onto 40 nm porous anodic alumina oxide supports, although the mechanisms for nucleation appear to differ. In conclusion, this work establishes a foundation for the investigation of the reductive assembly of abiotic metal catalysts at sites connected to photochemically reducing equivalent production in PSI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum Ornstein-Zernike theory for two-temperature two-component plasmas

Laboratory plasma production almost always preferentially heats either the ions or electrons, leading to a two-temperature state. In this state, density functional theory molecular dynamic simulation is the state of the art for modeling bulk material properties. We construct a statistical mechanics model for the two temperature limit that is theoretically consistent with the molecular dynamics method. We proceed to derive the electron-ion multi-temperature quantum Ornstein-Zernike equations for the first time. This allows the construction of a two-temperature two-component plasma model using the average atom from which we can compute bulk material properties at a fraction of the computation time of the two-temperature density functional theory simulation. The accuracy of the model is benchmarked against ion pair correlation and self-diffusion results from ab initio simulation. Here, we proceed to compute the viscosity and ion thermal conductivity as a function of both ion and electron temperature.

Ab initio molecular dynamics↗

Experimental investigation of turbulent wake flows in a helically wrapped rod bundle in presence of localized blockages

In nuclear sodium fast reactors, bundles of rods are tightly packed into a triangular lattice, enclosed in a hexagonal duct, and each pin is spirally wrapped with a thin wire. Flow blockages can potentially impact the local flow characteristics and heat transfer mechanisms in the bundle due to its small subchannel size. The effects of the blockage on the flow structures and heat transfer mechanisms are important aspects that require an accurate investigation. In this study, the flow-field characteristics in the vicinity of a blockage located in the exterior subchannel of rod bundles with helically wrapped wires were experimentally investigated. The velocity fields in the exterior subchannel were acquired by applying matched-index-of-refraction and time-resolved particle image velocimetry (TR-PIV) techniques for Reynolds numbers of Re 1 = 4000 and Re 2 = 17 000, i.e., equivalent to Rew 1 = 19 600 and Rew 2 = 83 200, respectively, based on the blockage width. The results from the TR-PIV measurements revealed an arch-shaped vortex with a large flow recirculation and a pair of counter-rotating vortices in the wake region downstream of the blockage, which is commonly observed in the wake flow of bluff bodies. The relative lateral distance and angle between the two vortices decreased when the Reynolds numbers increased. Profiles of maximum turbulence intensity along the shear layers illustrated the transition process including the growth, peak, and decay along the flow direction. From the spectral analysis of the turbulent velocities extracted at points along the shear layer, the Strouhal numbers ( St ) representing the vortex shedding frequency were found to be St = 0.25 and St = 0.56 for the left and right shear layers, respectively. Characteristics of shear layers generated by the blockage in the exterior subchannel were investigated via the two-point cross correlation of fluctuating velocities. The patiotemporal cross correlations of turbulent velocities, computed at points in the region where the left shear layer exhibited rolling effects and vortex breakdowns, were considerably wider and longer. The convection velocity U c was estimated to be ~0.82 U m to 0.93 U m . Proper orthogonal decomposition (POD) analysis was applied to the instantaneous velocity fields to extract the statistically dominant flow structures. It was found that POD modes 2–3 and 4–5 formed the pair modes when the corresponding POD temporal coefficients depicted sinusoidal shapes and exhibited nearly circular orbits in the phase space. Spectral analysis of the POD temporal coefficients confirmed the vortex shedding frequencies detected in the analysis of turbulent velocities.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Methanol adsorption and dissociation on GaP(110) studied by ambient pressure X-ray photoelectron spectroscopy

Ambient pressure X-ray photoelectron spectroscopy (AP-XPS) was used to investigate methanol (CH 3 OH) adsorption and reaction on the GaP(110) surface. Exposure of CH 3 OH to GaP(110) at room temperature led to the formation of at least four different surface species as indicated by analysis of C 1s and O 1s XPS features. By combining AP-XPS data with density functional theory calculations, the surface species were identified as methoxy (CH 3 O*), formaldehyde (CH 2 O*), and paired methanol (p-CH 3 O*H) and methoxy (p-CH 3 O*) species, where “paired” means that they belong to a hydrogen-bonded methoxy-methanol complex. Asterisk * here indicates an adsite. The formation of CH 2 O* via the dehydrogenation of CH 3 O* was shown to be limited by the availability of vacant phosphorus (P) sites on GaP(110). With an increase in CH 3 OH pressure, the fractional coverage of CH 3 O* species reached 0.55, and the surface P sites were completely saturated with hydrogen. Under a constant CH 3 OH pressure of 0.5 Torr, the surface concentration of the paired species and of CH 2 O* remained constant until 400 K. At higher temperatures, thermally driven reactions led to a significant increase in the concentration of surface CH x * species, which suggests that C-O bond cleavage of the CH 3 O group is the dominant decomposition mechanism on GaP(110). In conclusion, based on the reactivity of GaP(110) toward CH 3 OH dehydrogenation, elevated temperatures and CH 3 OH pressures may be used to functionalize this surface.

36 MATERIALS SCIENCE↗

In crystallo observation of three metal ion promoted DNA polymerase misincorporation

Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗

An innovative air data system for the Space Shuttle Orbiter - Data analysis techniques

The Shuttle Entry Air Data System (SEADS) is an experimental system designed to supply research quality air data and to meet Orbiter operational air data requirements throughout entry. SEADS incorporates no mechanical devices but is based on the concept that the fuselage proper, whether symmetrical or not, can be instrumented so as to function both as a pitot-static probe and as a differential pressure flow direction sensor. Specifically SEADS consists of 20 flush orifices, each routed to a pair of absolute pressure transducers. A computational technique has been developed capable of extracting air data parameters solely from surface pressure measurements. The digital filtering algorithm implemented in SEADS is the natural adaptation to air data sensing of a technology widely used in navigation, guidance, and control systems.

Pruett, C. D.↗

Interactions of the C-terminal Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku(sub 70/80) complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The C-terminal domain of Ku70 (Ku70c, residues 559-609), contains an helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the Ku70c/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the subunit Ku70c and a 14 base pairs DNA duplex, whose starting structures are designed to be variable so as to mimic their different binding modes. By analyzing conformational changes and energetic properties of the complex during MD simulations, we found that interactions are preferred at DNA ends, and within the major groove, which is consistent with previous experimental investigations. In addition, the results indicate that cooperation of Ku70c with other subunits of Ku(sub 70/80) is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗

Astro2020 Science White Paper: Prospects for Pulsar Studies at MeV Energies

Enabled by the Fermi Large Area Telescope, we now know young and recycled pulsars fill the gamma-ray sky, and we are beginning to understand their emission mechanism and their distribution throughout the Galaxy. However, key questions remain: Is there a large population of pulsars near the Galactic center? Why do the most energetic pulsars shine so brightly in MeV gamma rays but not always at GeV energies? What is the source and nature of the pair plasma in pulsar magnetospheres, and what role does the polar cap accelerator play? Addressing these questions calls for a sensitive, wide-field MeV telescope, which can detect the population of MeV-peaked pulsars hinted at by Fermi and hard X-ray telescopes and characterize their spectral shape and polarization.

Harding, Alice K.↗