A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins
Abstract not provided
Kim, Hanseong↗
SEARCH · Engineering Papers
Results for “MODIS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Persistent impact of spring floods on crop loss in U.S. Midwest
Not Available
54 ENVIRONMENTAL SCIENCES↗
The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. In this work, five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.
60 APPLIED LIFE SCIENCES↗
Are Remote Sensing Evapotranspiration Models Reliable Across South American Ecoregions?
Many remote sensing-based evapotranspiration (RSBET) algorithms have been proposed in the past decades and evaluated using flux tower data, mainly over North America and Europe. Model evaluation across South America has been done locally or using only a single algorithm at a time. Here, in this work, we provide the first evaluation of multiple RSBET models, at a daily scale, across a wide variety of biomes, climate zones, and land uses in South America. We used meteorological data from 25 flux towers to force four RSBET models: Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), Global Land Evaporation Amsterdam Model (GLEAM), Penman–Monteith Mu model (PM-MOD), and Penman–Monteith Nagler model (PM-VI). ET was predicted satisfactorily by all four models, with correlations consistently higher (R 2 > 6) for GLEAM and PT-JPL, and PM-MOD and PM-VI presenting overall better responses in terms of percent bias (-10 < PBIAS < 10%). As for PM-VI, this outcome is expected, given that the model requires calibration with local data. Model skill seems to be unrelated to land-use but instead presented some dependency on biome and climate, with the models producing the best results for wet to moderately wet environments. Our findings show the suitability of individual models for a number of combinations of land cover types, biomes, and climates. At the same time, no model outperformed the others for all conditions, which emphasizes the need for adapting individual algorithms to take into account intrinsic characteristics of climates and ecosystems in South America.
54 ENVIRONMENTAL SCIENCES↗
Ground Heat Flux Reconstruction Using Bayesian Uncertainty Quantification Machinery and Surrogate Modeling
Ground heat flux (G 0 ) is a key component of the land-surface energy balance of high-latitude regions. Despite its crucial role in controlling permafrost degradation due to global warming, G 0 is sparsely measured and not well represented in the outputs of global scale model simulation. In this study, an analytical heat transfer model is tested to reconstruct G 0 across seasons using soil temperature series from field measurements, Global Climate Model, and climate reanalysis outputs. The probability density functions of ground heat flux and of model parameters are inferred using available G 0 data (measured or modeled) for snow-free period as a reference. When observed G 0 is not available, a numerical model is applied using estimates of surface heat flux (dependent on parameters) as the top boundary condition. These estimates (and thus the corresponding parameters) are verified by comparing the distributions of simulated and measured soil temperature at several depths. Aided by state-of-the-art uncertainty quantification methods, the developed G 0 reconstruction approach provides novel means for assessing the probabilistic structure of the ground heat flux for regional permafrost change studies.
54 ENVIRONMENTAL SCIENCES↗
A Novel Framework to Project the Permafrost Fate With Explicit Quantification of Soil Property and Future Climate Uncertainties
This study develops a novel general framework to project the permafrost fate with rigorous uncertainty quantification to assess dominant sources. Borehole temperature records from three sites in the Russian western Arctic are used to constrain the uncertainty of a high‐fidelity freeze‐thaw model. Projections from 9 Global Climate Models (GCM) are stochastically downscaled to generate future trajectories of surface ground heat flux. Under the two emission scenarios SSP2‐4.5 and SSP5‐8.5, the projected average thawing depths by 2100 vary from 0.4 to 14.4 m or 2.1 to 17.7 m, and the increase in the top 10 m average temperature from 2015 to 2100 is 1.2–2.7°C or 1.9–3.0°C. The results show that the freeze‐thaw model uncertainty can sometimes dominate over that of GCM outputs, calling for site‐specific information to improve model accuracy. The framework is applicable for understanding permafrost degradation and related uncertainties at larger scales.
Bayesian downscaling↗
TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control
The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits — TASOR, MPP8 and Periphilin — contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.
59 BASIC BIOLOGICAL SCIENCES↗
Opto-twistronic Hall effect in a three-dimensional spiral lattice
Studies of moire systems have elucidated the exquisite effect of quantum geometry on the electronic bands and their properties, leading to the discovery of new correlated phases. However, most experimental studies have been confined to a few layers in the 2D limit. The extension of twistronics to its 3D limit, where the twist is extended into the third dimension between adjacent layers, remains underexplored due to the challenges in precisely stacking layers. Here, in this study, we focus on 3D twistronics on a platform of self-assembled spiral superlattice of multilayered WS 2 . Our findings reveal an opto-twistronic Hall effect in the spiral superlattice. This mesoscopic response is an experimental manifestation of the noncommutative geometry that arises when translational symmetry is replaced by a non-symmorphic screw operation. We also discover signatures of altered laws of optical excitation, manifested as an unconventional photon momentum-lattice interaction owing to moire of moire modulations in the 3D twistronic system. Crucially, our findings mark the initial identification of higher-order quantum geometrical tensors in light-matter interactions. This breakthrough opens new avenues for designing quantum materials-based optical lattices with large nonlinearities, paving the way for the development of advanced quantum nanophotonic devices.
Ji, Zhurun↗
MFRED, 10 second interval real and reactive power for groups of 390 US apartments of varying size and vintage
Abstract Building electricity is a major component of global energy use and its environmental impacts. Detailed data on residential electricity use have many interrelated research applications, from energy conservation to non-intrusive load monitoring, energy storage, integration of renewables, and electric vs. fossil-based heating. The dataset presented here, Multifamily Residential Electricity Dataset (MFRED), contains the electricity use of 390 apartments, ranging from studios to four-bedroom units. All apartments are located in the Northeastern United States (IECC-climate-zone 4 A), but differ in their heating/cooling system and construction year (early to late 20 th century). To adhere to privacy guidelines, data were averaged across 15 apartments each, based on annual electricity use. MFRED includes real and reactive power, at 10-second resolution, for January to December 2019 (246 million data points). The annual average real power per apartment is 343 W (3.27 W/m 2 of floor area), with strong variation between seasons and apartment size. Considering its large number of apartments, high time resolution, real and reactive power, and 12-month duration, MFRED is currently unique for the multifamily-sector.
97 MATHEMATICS AND COMPUTING↗
Effect of electronic transitions on near edge optical properties of off-stoichiometric boron carbide thin films
In the present study, soft x-ray optical properties of off-stoichiometric boron carbide thin films are investigated, and the structure and chemical composition of the film is analyzed using angle dependent x-ray reflectivity and x-ray photoelectron spectroscopy techniques. Energy dependent soft x-ray reflectivity measured at a fixed grazing angle of 1.5° is used to determine the optical constants in the boron K edge region by applying the Kramers–Kronig technique. The measured optical constants show near edge fine features corresponding to σ* and π* resonances. Furthermore, the electronic transitions corresponding to σ* resonance cause a 40%–75% increase in the delta value in the above boron K edge region. The π* transitions corresponding to off-stoichiometric nature of the boron carbide are observed in the absorption spectra near ~ 192.7 eV. Details of the measured soft x-ray optical properties of the off-stoichiometric boron carbide thin film are discussed.
36 MATERIALS SCIENCE↗
A forward modeling approach to analyzing galaxy clustering with S IM BIG
We present cosmological constraints from a simulation-based inference (SBI) analysis of galaxy clustering from the SimBIG forward modeling framework. SimBIG leverages the predictive power of high-fidelity simulations and provides an inference framework that can extract cosmological information on small nonlinear scales. In this work, we apply SimBIG to the Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxy sample and analyze the power spectrum, P ℓ (k), to k max = 0.5 h/Mpc. We construct 20,000 simulated galaxy samples using our forward model, which is based on 2,000 high-resolution Quijote N -body simulations and includes detailed survey realism for a more complete treatment of observational systematics. We then conduct SBI by training normalizing flows using the simulated samples and infer the posterior distribution of ΛCDM cosmological parameters: Ω m , Ω b , h, n s , σ 8 . We derive significant constraints on Ω m and σ 8 , which are consistent with previous works. Our constraint on σ 8 is 27% more precise than standard P ℓ analyses because we exploit additional cosmological information on nonlinear scales beyond the limit of current analytic models, k > 0.25 h/Mpc. This improvement is equivalent to the statistical gain expected from a standard P ℓ analysis of galaxy sample ~ 60% larger than CMASS. While we focus on P ℓ in this work for validation and comparison to the literature, SimBIG provides a framework for analyzing galaxy clustering using any summary statistic. We expect further improvements on cosmological constraints from subsequent SimBIG analyses of summary statistics beyond P ℓ .
79 ASTRONOMY AND ASTROPHYSICS↗
High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity
High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.
36 MATERIALS SCIENCE↗
Mind the gap: the power of combining photometric surveys with intensity mapping
The long wavelength modes lost to bright foregrounds in the interferometric 21-cm surveys can partially be recovered using a forward modeling approach that exploits the non-linear coupling between small and large scales induced by gravitational evolution. In this work, we build upon this approach by considering how adding external galaxy distribution data can help to fill in these modes. We consider supplementing the 21-cm data at two different redshifts with a spectroscopic sample (good radial resolution but low number density) loosely modeled on DESI-ELG at z=1 and a photometric sample (high number density but poor radial resolution) similar to LSST sample at z=1 and z=4 respectively. We find that both the galaxy samples are able to reconstruct the largest modes better than only using 21-cm data, with the spectroscopic sample performing significantly better than the photometric sample despite much lower number density. Here, we demonstrate the synergies between surveys by showing that the primordial initial density field is reconstructed better with the combination of surveys than using either of them individually. Methodologically, we also explore the importance of smoothing the density field when using bias models to forward model these tracers for reconstruction.
79 ASTRONOMY AND ASTROPHYSICS↗
Joint velocity and density reconstruction of the Universe with nonlinear differentiable forward modeling
Reconstructing the initial conditions of the Universe from late-time observations has the potential to optimally extract cosmological information. Due to the high dimensionality of the parameter space, a differentiable forward model is needed for convergence, and recent advances have made it possible to perform reconstruction with nonlinear models based on galaxy (or halo) positions. In addition to positions, future surveys will provide measurements of galaxies' peculiar velocities through the kinematic Sunyaev-Zel'dovich effect (kSZ), type Ia supernovae, the fundamental plane relation, and the Tully-Fisher relation. Here we develop the formalism for including halo velocities, in addition to halo positions, to enhance the reconstruction of the initial conditions. We show that using velocity information can significantly improve the reconstruction accuracy compared to using only the halo density field. Here we study this improvement as a function of shot noise, velocity measurement noise, and angle to the line of sight. We also show how halo velocity data can be used to improve the reconstruction of the final nonlinear matter overdensity and velocity fields. We have built our pipeline into the differentiable Particle-Mesh FlowPM package, paving the way to perform field-level cosmological inference with joint velocity and density reconstruction. This is especially useful given the increased ability to measure peculiar velocities in the near future.
79 ASTRONOMY AND ASTROPHYSICS↗
Neural simulation-based inference of the neutron star equation of state directly from telescope spectra
Neutron stars provide a unique opportunity to study strongly interacting matter under extreme density conditions. The intricacies of matter inside neutron stars and their equation of state are not directly visible, but determine bulk properties, such as mass and radius, which affect the star's thermal X-ray emissions. However, the telescope spectra of these emissions are also affected by the stellar distance, hydrogen column, and effective surface temperature, which are not always well-constrained. Uncertainties on these nuisance parameters must be accounted for when making a robust estimation of the equation of state. In this study, we develop a novel methodology that, for the first time, can infer the full posterior distribution of both the equation of state and nuisance parameters directly from telescope observations. This method relies on the use of neural likelihood estimation, in which normalizing flows use samples of simulated telescope data to learn the likelihood of the neutron star spectra as a function of these parameters, coupled with Hamiltonian Monte Carlo methods to efficiently sample from the corresponding posterior distribution. Our approach surpasses the accuracy of previous methods, improves the interpretability of the results by providing access to the full posterior distribution, and naturally scales to a growing number of neutron star observations expected in the coming years.
79 ASTRONOMY AND ASTROPHYSICS↗
Overview of physics results from the ADITYA-U tokamak and future experiments
The ADITYA upgrade (ADITYA-U), a medium-sized (R 0 = 75 cm, a = 25 cm) conventional tokamak facility in India, has been consistently producing experiments findings by usingcircular and shaped-plasmas. Recognizing the plasma parameters aligning closely with the design parameters of circular limited plasmas, ADITYA-U shifted its focus toward exploring the operational regime for experimentation on saw-tooth and MHD phenomena. Moreover, ADITYA-U has made consistent advancements toward conducting preliminary plasma shaping experiments through the activation of top and bottom divertor coils utilizing hydrogen as well as deuterium fuels. Confinement is improved by a factor of ~1.5 in D 2 plasmas when compared to H 2 plasmas of ADITYA-U. Further, ADITYA-U operations emphasize preventing disruptions and runaway electrons (REs) to ensure safe operations for future fusion devices. Significant suppression of REs has been achieved in ADITYA-U with the application of pulsed localized vertical magnetic field (LVF) perturbation, thereby establishing the technique's independence from the tokamak device. The successful RE mitigation requires a critical threshold of LVF pulse magnitude, which is approximately 1% of the toroidal magnetic field, and a minimum duration of ~5 ms. Apart from this, several novel findings have been achieved in the ADITYA-U experiments, including the modification of sawtooth duration through gas-puff, the emergence of MHD-induced geodesic acoustic mode-like oscillations, the propagation of fast heat pulses induced by MHD activity, the control of RE dynamics through Gas-puffs, the propagation of pinch-driven cold-pulses, the transport and core accumulations of argon impurities, the mass dependency of plasma toroidal rotation and the detection of 'RICE' scaling, as well as the characterization of edge plasma using wall conditioning methods, such as glow discharge cleaning using a combination of Ar-H 2 mixture, localized wall cleaning by electron cyclotron resonant plasma, and the development of machine learning-based disruption predictions, will be discussed in this paper.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Simulations and symmetries
ABSTRACT We investigate the range of applicability of a model for the real-space power spectrum based on N-body dynamics and a (quadratic) Lagrangian bias expansion. This combination uses the highly accurate particle displacements that can be efficiently achieved by modern N-body methods with a symmetries-based bias expansion which describes the clustering of any tracer on large scales. We show that at low redshifts, and for moderately biased tracers, the substitution of N-body-determined dynamics improves over an equivalent model using perturbation theory by more than a factor of two in scale, while at high redshifts and for highly biased tracers the gains are more modest. This hybrid approach lends itself well to emulation. By removing the need to identify haloes and subhaloes, and by not requiring any galaxy-formation-related parameters to be included, the emulation task is significantly simplified at the cost of modelling a more limited range in scale.
79 ASTRONOMY AND ASTROPHYSICS↗
The DESI N -body Simulation Project – II. Suppressing sample variance with fast simulations
ABSTRACT Dark Energy Spectroscopic Instrument (DESI) will construct a large and precise three-dimensional map of our Universe. The survey effective volume reaches $\sim 20\, h^{-3}\, \mathrm{Gpc}^{3}$. It is a great challenge to prepare high-resolution simulations with a much larger volume for validating the DESI analysis pipelines. AbacusSummit is a suite of high-resolution dark-matter-only simulations designed for this purpose, with $200\, h^{-3}\, \mathrm{Gpc}^{3}$ (10 times DESI volume) for the base cosmology. However, further efforts need to be done to provide a more precise analysis of the data and to cover also other cosmologies. Recently, the CARPool method was proposed to use paired accurate and approximate simulations to achieve high statistical precision with a limited number of high-resolution simulations. Relying on this technique, we propose to use fast quasi-N-body solvers combined with accurate simulations to produce accurate summary statistics. This enables us to obtain 100 times smaller variance than the expected DESI statistical variance at the scales we are interested in, e.g. $k \lt 0.3\, h\, \mathrm{Mpc}^{-1}$ for the halo power spectrum. In addition, it can significantly suppress the sample variance of the halo bispectrum. We further generalize the method for other cosmologies with only one realization in AbacusSummit suite to extend the effective volume ∼20 times. In summary, our proposed strategy of combining high-fidelity simulations with fast approximate gravity solvers and a series of variance suppression techniques sets the path for a robust cosmological analysis of galaxy survey data.
cosmology: theory↗