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At least 1,405 records · Page 78

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

59 BASIC BIOLOGICAL SCIENCES↗

Development of an ab initio learned model of electron deposition range in deuterium-tritium plasmas through time-dependent density functional theory calculations and machine learning

Accurate hydrodynamic modeling for laser-direct-drive (LDD) inertial-confinement-fusion (ICF) relies on precise calculations of the electron thermal conduction in all target materials. The nonlocal stopping range of electrons in ICF plasmas directly influences thermal conduction; yet, no first principles model exists for the electron mean free path in the conduction-zone regime. This work utilized time-dependent stochastic density-functional theory (TD-sDFT) to calculate the electron stopping power in deuterium-tritium (DT) plasmas at (ρ, T) conditions relevant to the conduction zone and the compressed shell in ICF. Using a combination of our TD-sDFT data and already established analytical models, we developed and trained an artificial neural network to create a global model for the nonlocal electron deposition range, λ E . We compared our machine-learning (ML) based model for λ E to the currently-used modified-Lee-More model in LDD radiation-hydrodynamic codes, such as lilac, and saw an overall decrease in the deposition range. To understand the effects of λ E on LDD ICF implosion dynamics, we implemented the ML-based model into lilac; specifically, we looked at designs consistent with a current experiment on the OMEGA laser and for a newly designed LDD-ICF target for the future OMEGA-Next facility. In both cases, we saw an overall drop in predicted ablation pressure, peak areal density, and neutron yield due to the reduced thermal conduction (smaller λ E ) in DT plasmas. Comparisons with the experiment on OMEGA are also made.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Transient Heat Transfer in Zero Gravity Environment

The objective is to provide computer codes and/or correlations for application in the design of transient heat transfer systems. The mathematical models in the computer codes are being tested by experimental data obtained in the laboratory using optical techniques. The elimination of natural convection (buoyancy) in the experimental data obtained in zero-g (KC-135) facilitates the study of thermal expansion effects which is of interest in the development and testing of the mathematical models of the transient heat transfer. Initial flight in the KC 135 (June 1983) suggested some modifications to the experimental apparatus and the data acquisition technique (high speed video will replace high speed movies for recording optical records generated during the experiments). A series of KC-135 flights with this experiment on board are scheduled for summer/fall 1984. The acquisition of the aforementioned data using interferometry and beam deflection optical techniques is anticipated. The measurements provide time dependent temperature fields above a horizontal heater surface submerged in a static fluid (Freon 13). The heater surface is electrically heated for a time interval approximately 0.100 sec. during which the data are optically recorded.

Giarratano, P. G.↗

Coupling Carbon Oxidation and Surface Recession in Direct-Simulation Monte Carlo Code, SPARTA

Ablative thermal protection system (TPS) materials for spacecraft are composites that are often made out of carbon-based reinforcement and a polymeric matrix. They endure high-temperature oxidation and surface recession when re-entering Earth’s atmosphere. Ablation is the result of many coupled and competing thermal, mechanical, and chemical phenomena, and it is difficult to isolate the role of each on the overall degradation of the TPS. Here we develop an ablation model for material recession coupled explicitly to finite rate carbon oxidation in complex microstructures. In this work, Stochastic PArallel Rarified-gas Time-accurate Analyzer (SPARTA), a direct-simulation Monte Carlo (DSMC) code, is modified to allow oxidation-driven ablation of implicitly defined carbon surfaces. In SPARTA, implicit surfaces are generated from the grid corner point values via a marching cubes algorithm, therefore creating a new set of surface elements every time ablation is performed. The finite-rate oxidation model developed by Gopalan et. al, was adapted to tally surface reactions and other surface data on a per-grid cell basis. The ablation functionality was also adjusted so once the reactions have occurred, the number of reactions leading to CO formation can be converted to corner point reduction values; therefore, carbon removal is directly proportional to surface recession. We also develop robust algorithms which handle the evolution of the flow cells and solid material regions, including split cells (flow cell divided in two by a solid surface). Finally, we demonstrate our implicit chemistry model for 2D and 3D geometries by producing reaction statistics and detailed visualization of oxidation-induced material recession at the microscale.

V Arias↗

Coupled Retrieval of Aerosol Properties and Surface Reflection Using the Airborne Multi-Angle SpectroPolarimetric Imager (AirMSPI)

The Airborne Multi-angle SpectroPolarimetric Imager (AirMSPI) has been flying aboard the NASA ER-2 high altitude aircraft since October 2010. In step-and-stare operation mode, AirMSPI acquires radiance and polarization data at 355, 380, 445, 470*, 555, 660*, 865*, and 935 nm (* denotes polarimetric bands). The imaged area covers about 10 km by 10 km and is observed from 9 view angles between ±67° off of nadir. We have developed an efficient and flexible code that uses the information content of AirMSPI data for a coupled retrieval of aerosol properties and surface reflection. The retrieval was built based on the multi-pixel optimization concept, with the use of a hybrid radiative transfer model that combines the Markov Chain and adding/doubling methods. The convergence and robustness of our algorithm is ensured by applying constraints on (a) the spectral variation of the Bidirectional Polarization Distribution Function (BPDF) and angular shape of the Bidirectional Reflectance Distribution Function (BRDF); (b) the spectral variation of aerosol optical properties; and (c) the spatial variation of aerosol parameters across neighboring image pixels. Our retrieval approach has been tested using over 20 AirMSPI datasets having low to moderately high aerosol loadings (~0.02<AOD550-nm<~0.45) and acquired during several field campaigns. Results are compared with AERONET aerosol reference data. We also explore the benefits of AirMSPI’s ultraviolet and polarimetric bands as well as the use of multiple view angles.

Xu, Feng↗

Acceleration of electrons and ions by strong lower-hybrid turbulence in solar flares

One of the outstanding problems in solar flare theory is how to explain the 10-20 keV and greater hard x-ray emissions by a thick target bremsstrahlung model. The model requires the acceleration mechanism to accelerate approximately 10(exp 35) electrons sec(exp -l) with comparable energies, without producing a large return current which persists for long time scales after the beam ceases to exist due to Lenz's law, thereby, producing a self-magnetic field of order a few mega-Gauss. In this paper, we investigate particle acceleration resulting from the relaxation of unstable ion ring distributions, producing strong wave activity at the lower hybrid frequency. It is shown that strong lower hybrid wave turbulence collapses in configuration space producing density cavities containing intense electrostatic lower hybrid wave activity. The collapse of these intense nonlinear wave packets saturate by particle acceleration producing energetic electron and ion tails. There are several mechanisms whereby unstable ion distributions could be formed in the solar atmosphere, including reflection at perpendicular shocks, tearing modes, and loss cone depletion. Numerical simulations of ion ring relaxation processes, obtained using a 2 1/2-D fully electromagnetic, relativistic particle in cell code are discussed. We apply the results to the problem of explaining energetic particle production in solar flares. The results show the simultaneous acceleration of both electrons and ions to very high energies: electrons are accelerated to energies in the range 10-500 keV, while ions are accelerated to energies of the order of MeVs, giving rise to x-ray emission and gamma-ray emission respectively. Our simulations also show wave generation at the electron cyclotron frequency. We suggest that these waves are the solar millisecond radio spikes. The strong turbulence collapse process leads to a highly filamented plasma producing many localized regions for particle acceleration and resulting in approximately 10(exp 17) electron 'beamlets' of width approximately equal to 10 lambda sub De which eliminates the production of large magnetic fields. In this paper, we demonstrate that the model produces an energetic electron spectrum with the right flux to account for the hard x-ray observations.

Spicer, D. S.↗

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Abstract Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

09 BIOMASS FUELS↗

Numerical Analysis of Temperature Gradients and Interface Shape During Directional Solidification of Al and Al-Cu Alloy Under Microgravity Conditions

Numerical modeling was undertaken to analyze the influence of radial thermal gradient on solid/liquid interface shape and convection patterns during solidification of pure Al and Al-4 wt. % Cu alloy. Steady state calculations were performed for different gravity levels and orientations. Furthermore, transient modeling was undertaken to investigate effect of the solidification velocity. The furnace configuration used in this analysis is the proposed International Space Station Furnace. Results from a thermal model of the furnace core were used as initial boundary conditions for solidification modeling. The Solidification model was adopted from previous work and was based on the finite element code FIDAP. Thermocouple data and quenched interface shape from a pure Al sample flown on the Life Sciences and Microgravity Spacelab (LMS) mission, July 1996 was used for model validation. Good agreement was obtained between the predicted interface shape and that measured from the quenched LMS sample. It was found that the imposed temperature boundary condition must be sufficiently smooth for the heat fluxes in the model to be self-consistent. The model predicted that alloy sample Al-Cu is more sensitive to variations in the gravity level compared to pure Al. For Al-Cu alloy, solute diffusivity is approximately 10(exp 4) times smaller than thermal diffusivity of pure Al. Hence, in a microgravity environment the weak convection has no measurable effect on the heat fluxes, but is still strong enough to affect concentration distribution. Since the alloy melting temperature is determined by concentration the interface shape depends on the level of convection. This was found not to be the case for pure metal.

Bune, Andris V.↗

Comparison of Models for Ball Bearing Dynamic Capacity and Life

Generalized formulations for dynamic capacity and life of ball bearings, based on the models introduced by Lundberg and Palmgren and Zaretsky, have been developed and implemented in the bearing dynamics computer code, ADORE. Unlike the original Lundberg-Palmgren dynamic capacity equation, where the elastic properties are part of the life constant, the generalized formulations permit variation of elastic properties of the interacting materials. The newly updated Lundberg-Palmgren model allows prediction of life as a function of elastic properties. For elastic properties similar to those of AISI 52100 bearing steel, both the original and updated Lundberg-Palmgren models provide identical results. A comparison between the Lundberg-Palmgren and the Zaretsky models shows that at relatively light loads the Zaretsky model predicts a much higher life than the Lundberg-Palmgren model. As the load increases, the Zaretsky model provides a much faster drop off in life. This is because the Zaretsky model is much more sensitive to load than the Lundberg-Palmgren model. The generalized implementation where all model parameters can be varied provides an effective tool for future model validation and enhancement in bearing life prediction capabilities.

Rolling-element Fatigue↗

Assessment of an Euler-Interacting Boundary Layer Method Using High Reynolds Number Transonic Flight Data

Flight-measured high Reynolds number turbulent-flow pressure distributions on a transport wing in transonic flow are compared to unstructured-grid calculations to assess the predictive ability of a three-dimensional Euler code (USM3D) coupled to an interacting boundary layer module. The two experimental pressure distributions selected for comparative analysis with the calculations are complex and turbulent but typical of an advanced technology laminar flow wing. An advancing front method (VGRID) was used to generate several tetrahedral grids for each test case. Initial calculations left considerable room for improvement in accuracy. Studies were then made of experimental errors, transition location, viscous effects, nacelle flow modeling, number and placement of spanwise boundary layer stations, and grid resolution. The most significant improvements in the accuracy of the calculations were gained by improvement of the nacelle flow model and by refinement of the computational grid. Final calculations yield results in close agreement with the experiment. Indications are that further grid refinement would produce additional improvement but would require more computer memory than is available. The appendix data compare the experimental attachment line location with calculations for different grid sizes. Good agreement is obtained between the experimental and calculated attachment line locations.

Bonhaus, Daryl L.↗

Statistical mechanics in biology: how ubiquitous are long-range correlations?

The purpose of this opening talk is to describe examples of recent progress in applying statistical mechanics to biological systems. We first briefly review several biological systems, and then focus on the fractal features characterized by the long-range correlations found recently in DNA sequences containing non-coding material. We discuss the evidence supporting the finding that for sequences containing only coding regions, there are no long-range correlations. We also discuss the recent finding that the exponent alpha characterizing the long-range correlations increases with evolution, and we discuss two related models, the insertion model and the insertion-deletion model, that may account for the presence of long-range correlations. Finally, we summarize the analysis of long-term data on human heartbeats (up to 10(4) heart beats) that supports the possibility that the successive increments in the cardiac beat-to-beat intervals of healthy subjects display scale-invariant, long-range "anti-correlations" (a tendency to beat faster is balanced by a tendency to beat slower later on). In contrast, for a group of subjects with severe heart disease, long-range correlations vanish. This finding suggests that the classical theory of homeostasis, according to which stable physiological processes seek to maintain "constancy," should be extended to account for this type of dynamical, far from equilibrium, behavior.

Non-NASA Center↗

Exploring the MeV Sky With A Combined Coded Mask and Compton Telescope: the Galactic Explorer With A Coded Aperture Mask Compton Telescope (GECCO)

The sky at MeV energies is currently poorly explored. Here we present an innovative mission concept that builds upon the heritage of past and current missions improving the sensitivity and, very importantly, the angular resolution. This consists in combining a Compton telescope and a coded-mask telescope. We delineate the motivation for such a concept and we define the scientific goals for such a mission. The Galactic Explorer with a Coded Aperture Mask Compton Telescope (GECCO) is a novel concept for a next-generation telescope covering hard X-ray and soft gamma-ray energies. The potential and importance of this approach that bridges the observational gap in the MeV energy range are presented. With the unprecedented angular resolution of the coded mask telescope combined with the sensitive Compton telescope, a mission such as GECCO can disentangle the discrete sources from the truly diffuse emission. Individual Galactic and extragalactic sources are detected. This also allows to understand the gamma-ray Galactic center excess and the Fermi Bubbles, and to trace the low-energy cosmic rays, and their propagation in the Galaxy. Nuclear and annihilation lines are spatially and spectrally resolved from the continuum emission and from sources, addressing the role of low-energy cosmic rays in star formation and galaxy evolution, the origin of the 511 keV positron line, fundamental physics, and the chemical enrichment in the Galaxy. Such an instrument also detects explosive transient gamma-ray sources, which, in turn, enables identifying and studying the astrophysical objects that produce gravitational waves and neutrinos in a multi-messenger context. By looking at a poorly explored energy band it also allows discoveries of new astrophysical phenomena.

Elena Orlando↗

Simulations of radiatively cooled magnetic reconnection driven by pulsed power

Magnetic reconnection is an important process in astrophysical environments, as it reconfigures magnetic field topology and converts magnetic energy into thermal and kinetic energy. In extreme astrophysical systems, such as black hole coronae and pulsar magnetospheres, radiative cooling modifies the energy partition by radiating away internal energy, which can lead to the radiative collapse of the reconnection layer. In this paper, we perform two- and three-dimensional simulations to model the MARZ (Magnetic Reconnection on Z) experiments, which are designed to access cooling rates in the laboratory necessary to investigate reconnection in a previously unexplored radiatively cooled regime. These simulations are performed in GORGON, an Eulerian two-temperature resistive magnetohydrodynamic code, which models the experimental geometry comprising two exploding wire arrays driven by 20 MA of current on the Z machine (Sandia National Laboratories). Radiative losses are implemented using non-local thermodynamic equilibrium tables computed using the atomic code Spk, and we probe the effects of radiation transport by implementing both a local radiation loss model and P 1/3 multi-group radiation transport. The load produces highly collisional, super-Alfvénic (Alfvén Mach number M A ≈ 1.5), supersonic (Sonic Mach number M S ≈ 4–5) strongly driven plasma flows which generate an elongated reconnection layer (Aspect Ratio L/δ≈100 , Lundquist number S L ≈ 400). The reconnection layer undergoes radiative collapse when the radiative losses exceed the rates of ohmic and compressional heating (cooling rate/hydrodynamic transit rate = τ$^{–1}_{cool}$/τ$^{–1}_{H}$ ≈100); this generates a cold strongly compressed current sheet, leading to an accelerated reconnection rate, consistent with theoretical predictions. Lastly, the current sheet is also unstable to the plasmoid instability, but the magnetic islands are extinguished by strong radiative cooling before ejection from the layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

African Swine Fever Virus Protein–Protein Interaction Prediction

The African swine fever virus (ASFV) is an often deadly disease in swine and poses a threat to swine livestock and swine producers. With its complex genome containing more than 150 coding regions, developing effective vaccines for this virus remains a challenge due to a lack of basic knowledge about viral protein function and protein–protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein–protein interactions (PPIs) using artificial intelligence-powered protein structure prediction tools. We benchmarked our PPI identification workflow on the Vaccinia virus, a widely studied nucleocytoplasmic large DNA virus, and found that it could identify gold-standard PPIs that have been validated in vitro in a genome-wide computational screening. We applied this workflow to more than 18,000 pairwise combinations of ASFV proteins and were able to identify seventeen novel PPIs, many of which have corroborating experimental or bioinformatic evidence for their protein–protein interactions, further validating their relevance. Two protein–protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring the MeV sky with a combined coded mask and Compton telescope: the Galactic Explorer with a Coded aperture mask Compton telescope (GECCO)

The sky at MeV energies is currently poorly explored. Here we present an innovative mission concept that builds upon the heritage of past and current missions improving the sensitivity and, very importantly, the angular resolution. This consists in combining a Compton telescope and a coded-mask telescope. We delineate the motivation for such a concept and we define the scientific goals for such a mission. The Galactic Explorer with a Coded Aperture Mask Compton Telescope (GECCO) is a novel concept for a next-generation telescope covering hard X-ray and soft gamma-ray energies. The potential and importance of this approach that bridges the observational gap in the MeV energy range are presented. With the unprecedented angular resolution of the coded mask telescope combined with the sensitive Compton telescope, a mission such as GECCO can disentangle the discrete sources from the truly diffuse emission. Individual Galactic and extragalactic sources are detected. This also allows to understand the gamma-ray Galactic center excess and the Fermi Bubbles, and to trace the low-energy cosmic rays, and their propagation in the Galaxy. Nuclear and annihilation lines are spatially and spectrally resolved from the continuum emission and from sources, addressing the role of low-energy cosmic rays in star formation and galaxy evolution, the origin of the 511 keV positron line, fundamental physics, and the chemical enrichment in the Galaxy. Such an instrument also detects explosive transient gamma-ray sources, which, in turn, enables identifying and studying the astrophysical objects that produce gravitational waves and neutrinos in a multi-messenger context. By looking at a poorly explored energy band it also allows discoveries of new astrophysical phenomena.

79 ASTRONOMY AND ASTROPHYSICS↗

Watershed Modeling with Remotely Sensed Big Data: MODIS Leaf Area Index Improves Hydrology and Water Quality Predictions

Traditional watershed modeling often overlooks the role of vegetation dynamics. There is also little quantitative evidence to suggest that increased physical realism of vegetation dynamics in process-based models improves hydrology and water quality predictions simultaneously. In this study, we applied a modified Soil and Water Assessment Tool (SWAT) to quantify the extent of improvements that the assimilation of remotely sensed Leaf Area Index (LAI) would convey to streamflow, soil moisture, and nitrate load simulations across a 16,860 km2 agricultural watershedin the midwestern United States. We modified the SWAT source code to automatically override the model’s built-in semiempirical LAI with spatially distributed and temporally continuous estimates from Moderate Resolution Imaging Spectroradiometer (MODIS). Compared to a “basic” traditional model with limited spatial information, our LAI assimilation model (i) significantly improved daily streamflow simulations during medium-to-low flow conditions, (ii) provided realistic spatial distributions of growing season soil moisture, and (iii) substantially reproduced the long-term observed variability of daily nitrate loads. Further analysis revealed that the overestimation or underestimation of LAI imparted a proportional cascading effect on how the model partitions hydrologic fluxes and nutrient pools. As such, assimilation of MODIS LAI data corrected the model’sLAI overestimation tendency, which led to a proportionally increased rootzone soil moisture and decreased plant nitrogen uptake. With these new findings, our study fills the existing knowledge gap regarding vegetation dynamics in watershed modeling and confirms that assimilation of MODIS LAI data in watershed models can effectively improve both hydrology and water quality predictions.

Adnan Rajib↗