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At least 379 records · Page 21

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.

59 BASIC BIOLOGICAL SCIENCES↗

Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation

Abstract Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis -muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O -demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.

09 BIOMASS FUELS↗

Missing baryons recovered: A measurement of the gas fraction in galaxies and groups with the kinematic Sunyaev-Zel’dovich effect and CMB lensing

We present new constraints on the halo masses and matter density profiles of DESI galaxy groups by cross-correlating samples of luminous red galaxies (LRGs) and bright galaxy survey (BGS) galaxies with the publicly available CMB lensing convergence map from ACT DR6. This provides an independent, lensing-based calibration of halo masses, complementary to methods relying on clustering or dynamics. We derive constraints on the mean halo mass for three DESI-selected samples, finding log⁡(𝑀 halo /(𝑀 ⊙ /ℎ)) ≈ 13.18, 13.03 and 13.02 for the main LRG, extended LRG, and BGS samples, respectively. Using a halo model approach, we also compare the projected galaxy-matter density profiles with previously reported gas profiles inferred from measurements of the kinematic Sunyaev-Zel’dovich (kSZ) effect. This work addresses one of the key uncertainties in interpreting kSZ signals—the unknown host halo mass distribution—by providing an independent and consistent mass calibration. The agreement between the gas and total mass profiles at large aperture suggests that sufficiently far from the group center (2–3 virial radii), we recover all the baryons, offering a resolution to the missing baryon problem. We further study the cumulative gas fractions for all galaxies as well as for the most massive galaxy groups in the sample [log⁡(𝑀 halo /(𝑀 ⊙ /ℎ)) ≈ 13.5], finding values that are physically sensible and in agreement with previous findings using kSZ and x-ray data: compared to the TNG300 simulation, the observed gas fractions are systematically lower at fixed radius by ≳ 4⁢𝜎, providing compelling, independent evidence for stronger baryonic feedback in the real Universe. These findings highlight the power of combining CMB lensing with galaxy surveys to probe the interplay between baryons and dark matter in group-sized halos.

Hadzhiyska, Boryana [Lawrence Berkeley National La↗

Fractional occupation numbers and self-interaction correction-scaling methods with the Fermi-Löwdin orbital self-interaction correction approach

In this work, we present a new assessment of the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) approach with an emphasis on its performance for predicting energies as a function of fractional occupation numbers (FONs) for various multielectron systems. Our approach is implemented in the massively parallelized NWChem quantum chemistry software package and has been benchmarked on the prediction of total energies, atomization energies, and ionization potentials of small molecules and relatively large aromatic systems. Within our study, we also derive an alternate expression for the FLO-SIC energy gradient expressed in terms of gradients of the Fermi-orbital eigenvalues and revisit how the FLO-SIC methodology can be seen as a constrained unitary transformation of the canonical Kohn–Sham orbitals. Finally, we conclude with calculations of energies as a function of FONs using various SIC-scaling methods to test the limits of the FLO-SIC formalism on a variety of multielectron systems. We find that these relatively simple scaling methods do improve the prediction of total energies of atomic systems as well as enhance the accuracy of energies as a function of FONs for other multielectron chemical species.

fractional occupation number↗

The impact of the $\text{WHIM}$ on the $\text{IGM}$ thermal state determined from the low- z Lyman $\alpha$ forest

At z ≲ 1, shock heating caused by large-scale velocity flows and possibly violent feedback from galaxy formation, converts a significant fraction of the cool gas (T ~ 10 4 K) in the intergalactic medium (IGM) into warm–hot phase (WHIM) with T > 10 5 K, resulting in a significant deviation from the previously tight power-law IGM temperature–density relationship, T = T 0 (P/$\bar{p}$) γ-1 ⁠. This study explores the impact of the WHIM on measurements of the low-z IGM thermal state, [T 0 , γ], based on the b–NH 1 distribution of the Ly α forest. Exploiting a machine learning-enabled simulation-based inference method trained on Nyx hydrodynamical simulations, we demonstrate that [T 0 , γ] can still be reliably measured from the b–NH 1 distribution at z = 0.1, notwithstanding the substantial WHIM in the IGM. To investigate the effects of different feedback, we apply this inference methodology to mock spectra derived from the IllustrisTNG and Illustris simulations at z = 0.1. The results suggest that the underlying [T 0 , γ] of both simulations can be recovered with biases as low as |Δlog(T 0 /K)| ≲ 0.05 dex, |Δγ| ≲ 0.1, smaller than the precision of a typical measurement. Given the large differences in the volume-weighted WHIM fractions between the three simulations (Illustris 38 percent, IllustrisTNG 10 percent, and Nyx 4 per cent), we conclude that the b–N H1 distribution is not sensitive to the WHIM under realistic conditions. Finally, we investigate the physical properties of the detectable Ly α absorbers, and discover that although their T and Δ distributions remain mostly unaffected by feedback, they are correlated with the photoionization rate used in the simulation.

79 ASTRONOMY AND ASTROPHYSICS↗

Search for dark matter production in association with bottom quarks and a lepton pair in proton-proton collisions at $\sqrt{s}=13$ TeV

A search is performed for dark matter produced in association with bottom quarks and a pair of electrons or muons in data collected with the CMS detector at the LHC, corresponding to 138 fb −1 of integrated luminosity of proton-proton collisions at a center-of-mass energy of 13 TeV. For the first time at the LHC, the associated production of a bottom quark-antiquark pair and a new heavy neutral Higgs boson (H) that subsequently decays into a leptonically decaying Z boson and a pseudoscalar (a) is explored. The latter acts as a dark matter mediator in the context of the two Higgs doublet model plus a pseudoscalar (2HDM+a). Multivariate techniques that target a wide range of mass configurations for the H and a particles are used. The observations are consistent with the expectations from standard model processes. Upper limits at 95% confidence level are set on the product of cross section and branching fraction of the new particles, ranging from 10 −2 pb for an H mass of 400 GeV to 10 −3 pb for an H mass of 2000 GeV. Constraints on the parameter space of a benchmark 2HDM+a model are derived and compared with expectations in the context of cosmological predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Distribution of Bound and Free Water in Anatomical Fractions of Pine Residues and Corn Stover as a Function of Biological Degradation

Biomass quality is influenced by water’s abundance, distribution, and status in relation to other chemical species within the polymer matrix. Water interacts with polymers that make up the cell walls, and these interactions govern the physical and chemical changes that occur during the storage and preprocessing of biomass feedstocks. Time-domain nuclear magnetic resonance (TD-NMR) was employed to explore variations in the physical constraints of water within the lignocellulosic microstructure in distinct anatomical fractions of biomass and as a function of biological degradation. The Carr–Purcell–Meiboom–Gill sequence, when combined with knowledge of the chemical composition and physical structure of pine residues and corn stover anatomical fractions, gives an accurate measurement of the bound and free water. In this work, the impacts of storage and biological degradation were investigated to elucidate changes in the status and distribution of water within distinct plant tissues. We also investigate how degradation during storage affects water interactions in different pine residues (e.g., bark, branch, and needle) and corn stover (e.g., cob, leaf, and stalk) anatomical fractions using transverse relaxation times (T2). As demonstrated herein, TD-NMR provides quantitative data on lignocellulosic biomass–water interactions within anatomical fractions, which can further aid in the investigation of preprocessing effects on feedstock quality. Our findings suggest that biological heating enhances biomass–water interactions at the cellular and macromolecular scale. In addition, analysis of three-dimensional scanning electron microscopy reconstructions indicates that surface roughness wavelengths align with microscale roughness, suggesting that pine forestry residue and corn stover particles have primarily hydrophobic exterior surfaces. Furthermore, this study offers multiscale insights into understanding the microstructure, wettability, and chemical environment that dictate diffusion, enzyme access, and recalcitrance of lignocellulosic biomass.

09 BIOMASS FUELS↗

Dissecting Anvil Cloud Response to Sea Surface Warming

Abstract We derive an anvil cloud diagnostic from the continuity equation of cloud ice and apply it to the output of convection‐permitting Energy Exascale Earth System Model (E3SM) simulations run in radiative‐convective equilibrium mode. This diagnostic shows that anvil cloud fraction can be reliably diagnosed as a product of cloud detrainment and lifetime. Detrainment is found to be approximated well by a product of clear sky convergence and cloud ice mixing ratio, while cloud lifetime is dominated by sedimentation. Taken together, this diagnostic expresses anvil cloud fraction as a function of five physically measurable quantities. Of these, clear‐sky convergence changes drive the anvil cloud reduction with warming while an increase in cloud ice mixing ratio buffers the decrease. Accordingly, this study provides a theoretical foundation upon which the Stability‐Iris hypothesis can be tested.

54 ENVIRONMENTAL SCIENCES↗

Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding Aitken Mode Aerosol Variability over the Southern Ocean and Antarctica: Insights from Cloud Condensation Nuclei Data

Aitken mode aerosol particles play an important role influencing cloud properties and sustenance, acting as a reservoir of potential cloud condensation nuclei against precipitation scavenging. However, there is limited data on Aitken mode aerosols. In this study, we develop a method to estimate Aitken mode aerosol concentrations and size distribution using cloud condensation nuclei measurements (CCN) and κ-Köhler theory. The performance of this method is evaluated using scanning mobility particle sizer (SMPS) data from recent field campaigns to demonstrate its skills and applicability. The method reasonably estimates Aitken- and accumulation-mode aerosol concentrations, achieving correlations of 0.7–0.9 with only modest biases (mean fractional bias within ±23% for Aitken mode and ±34% for accumulation-mode). This method is further applied to measurements collected over the Southern Ocean and Antarctica in recent years from multiple platforms, including ground sites, aircraft, and ships, to derive Aitken and accumulation-mode aerosol concentrations. Using the derived data, we examine the seasonal cycle, latitudinal variations, and vertical distribution of aerosols. Aitken mode aerosol concentrations are elevated over the Southern Ocean and Antarctica during the austral summer similar to the accumulation mode. In the austral summer, the free troposphere has more Aitken mode aerosols and fewer accumulation mode aerosols than the boundary layer, and thus likely serves as an important source of cloud-forming aerosol while also diluting the accumulation mode.

Kang, Litai [University of Washington] (ORCID:0000↗

Monochromation of pulsed electron beams with terahertz radiation at a planar mirror

Exquisite control of electron beam energy is required for many electron spectroscopy and imaging applications. For both continuous and pulsed beams, the beam energy spread is fundamentally limited by the electron source, and is typically a sizable fraction of an electron-volt. In this paper, we present a means to reduce electron beam energy spread after emission to the level of a few 10s of meV rms using femtosecond photoemission and an interaction with laser-derived single- to few-cycle terahertz (THz) radiation. We show analytically and in particle tracking simulations that this interaction can remove energy spread stored in both the transverse and longitudinal degrees of freedom. We analytically formulate the limit of energy spread that this technique can achieve, and map the non-ideal affects arising at high frequencies. The interaction is mediated by the beam's passage through a mirror which is reflective to terahertz radiation but allows transmission of the majority of the electron beam (e.g. a wire mesh). This method then only requires beam current losses of a few tens of percent, far smaller than what is achieved in prism and slit-based electron monochromators.

Accelerator Physics (physics.acc-ph)↗

Rational engineering to enhance C8-fatty acid biosynthesis in Picosynechococcus sp. PCC 7002

Medium-chain fatty acids (e.g., C8-C14) are important biofuel precursors that can be produced from CO2 by cyanobacteria and other photoautotrophs. However, cyanobacteria naturally direct a relatively small fraction of fixed carbon to lipid synthesis, primarily producing long-chain membrane-bound fatty acids. We investigated whether mitigating kinetic bottlenecks within the fatty acid biosynthesis (FAB) pathway could enhance flux to free fatty acid (FFA) production in Picosynechococcus sp. PCC 7002. Previous in vitro studies proposed that the FAB initiating enzyme FabH is the primary rate-controlling enzyme in PCC 7002. We hypothesized that enhancing fatty acid initiation could increase in vivo FFA production while shifting the kinetic bottleneck further downstream in the pathway. We enabled C8-FFA accumulation by knocking out the native acyl-acyl carrier protein synthetase gene (aas) and expressing the highly active Cuphea palustris-derived mutant thioesterase CpFatB1.2-M4-287 (CupTE), which selectively catalyzes C8 chain termination. We then expressed the diatom-derived Chaetoceros sp. GSL56 FabH ortholog (chKASIII), to enhance initiation, and a medium-chain selective E. coli ketosynthase ecFabF[I108F] (ecFabF∗), to enhance elongation. When expressed individually or in combination with ecFabF∗, chKASIII slowed growth and decreased net carbon fixation rates relative to the parental Δaas-CupTE strain. However, co-expression of chKASIII, ecFabF∗, and CupTE redirected a larger fraction of fixed carbon toward FFA production, increasing relative carbon flux to C8-FFA and decreasing the projected minimum selling price by four-fold. This work demonstrates how systems metabolic engineering can be applied to enhance C8-FFA production in cyanobacteria while highlighting the unpredictable physiological consequences of host metabolic burden.

09 BIOMASS FUELS↗

Paleotribological models using preserved fossil tissue properties reveal functional significance of Eurasian mammoth dental evolution

Eurasian mammoths (Mammuthus) underwent substantial modifications in molar morphology as later-diverging species evolved progressively thinner enamel and increased enamel crest complexity. These features have been hypothesized to reduce whole-tooth wear and extend dental longevity as increasingly graze-dominated diets evolved within the lineage. This hypothesis has yet to be directly tested. Here, in this study, we developed an in-silico wear model using experimentally derived wear rates from fossil and extant proboscidean dental tissues. The models revealed that shifts in tissue topology do not affect whole-tooth wear rate, as inverse trends in lamellar frequency and enamel thickness preserve a consistent surface enamel area fraction; the determining factor of wear. Rather, topological shifts produce a wear-emergent secondary occlusal surface with greater numbers of triturating crests that create a regular, low-relief, file-like shearing pavement. These changes in occlusal architecture likely directly impacted the mastication capacity of Mammuthus dentitions, facilitating their dietary expansion to incorporate fibrous, lower-nutrient graze.

Dental wear↗

Simulation of gas mixture dynamics in a pipeline network using explicit staggered-grid discretization

Here we develop an explicit staggered finite difference discretization scheme for simulating the transport of highly heterogeneous gas mixtures through pipeline networks. This study is motivated by the proposed blending of hydrogen into natural gas pipelines to reduce end use carbon emissions while using existing pipeline systems throughout their planned lifetimes. Our computational method accommodates an arbitrary number of constituent gases with very different physical properties that may be injected into a network with significant spatiotemporal variation. In this setting, the gas flow physics are highly location- and time- dependent, so that local composition and nodal mixing must be accounted for. The resulting conservation laws are formulated in terms of pressure, partial densities and flows, and volumetric and mass fractions of the constituents. We include non-ideal equations of state that employ linear approximations of gas compressibility factors, so that the pressure dynamics propagate locally according to a variable wave speed that depends on mixture composition and density. We derive compatibility relationships for network edge boundary values that are more complex than for a homogeneous gas. The simulation method is evaluated on initial boundary value problems for a single pipe and a small network, is cross-validated with a lumped element simulation, and used to demonstrate a local monitoring and control policy for maintaining allowable concentration levels.

97 MATHEMATICS AND COMPUTING↗

Light-Mediated Synthesis and Reprocessing of Dynamic Bottlebrush Elastomers under Ambient Conditions

We introduce a novel grafting-through polymerization strategy to synthesize dynamic bottlebrush polymers and elastomers in one step using light to construct a disulfide-containing backbone. The key starting material—α-lipoic acid (LA)—is commercially available, inexpensive, and biocompatible. When installed on the chain end(s) of poly(dimethylsiloxane) (PDMS), the cyclic disulfide unit derived from LA polymerizes under ultraviolet (UV) light in ambient conditions. Significantly, no additives such as initiator, solvent, or catalyst are required for efficient gelation. Formulations that include bis-LA-functionalized cross-linker yield bottlebrush elastomers with high gel fractions (83–98%) and tunable, supersoft shear moduli in the ~20–200 kPa range. An added advantage of these materials is the dynamic disulfide bonds along each bottlebrush backbone, which allow for light-mediated self-healing and on-demand chemical degradation. These results highlight the potential of simple and scalable synthetic routes to generate unique bottlebrush polymers and elastomers based on PDMS.

36 MATERIALS SCIENCE↗

A Machine Learning Assisted Development of a Model for the Populations of Convective and Stratiform Clouds

Abstract Traditional parameterizations of the interaction between convection and the environment have relied on an assumption that the slowly varying large‐scale environment is in statistical equilibrium with a large number of small and short‐lived convective clouds. They fail to capture nonequilibrium transitions such as the diurnal cycle and the formation of mesoscale convective systems as well as observed precipitation statistics and extremes. Informed by analysis of radar observations, cloud‐permitting model simulation, theory, and machine learning, this work presents a new stochastic cloud population dynamics model for characterizing the interactions between convective and stratiform clouds, with the goal of informing the representation of these interactions in global climate models. Fifteen wet seasons of precipitating cloud observations by a C‐band radar at Darwin, Australia are fed into a machine learning algorithm to obtain transition functions that close a set of coupled equations relating large‐scale forcing, mass flux, the convective cell size distribution, and the stratiform area. Under realistic large‐scale forcing, the derived transition functions show that, on the one hand, interactions with stratiform clouds act to dampen the variability in the size and number of convective cells and therefore in the convective mass flux. On the other, for a given convective area fraction, a larger number of smaller cells is more favorable for the growth of stratiform area than a smaller number of larger cells. The combination of these two factors gives rise to solutions with a few convective cells embedded in a large stratiform area, reminiscent of mesoscale convective systems.

54 ENVIRONMENTAL SCIENCES↗

A Multiwavelength Study of Active Galactic Nuclei in Post-merger Remnants

Here, we investigate the role of galaxy mergers in triggering active galactic nuclei (AGN) in the nearby universe. Our analysis is based on a sample of 79 post-merger remnant galaxies with deep X-ray observations from Chandra/XMM-Newton capable of detecting a low-luminosity AGN of ≥10 40.5 erg s -1 . This sample is derived from a visually classified, volume-limited sample of 807 post-mergers identified in the Sloan Digital Sky Survey Data Release 14 with log M * /M ⊙ ≥ 10.5 and 0.02 ≤ z ≤ 0.06. We find that the X-ray AGN fraction in this sample is 55.7% ± 5.6% compared to 23.6% ± 2.8% for a mass- and redshift-matched noninteracting control sample. The multiwavelength AGN fraction (identified as an AGN in one of X-ray, IR, radio or optical diagnostics) for post-mergers is 76.6% ± 4.8% compared to 39.1% ± 3.2% for controls. Thus post-mergers exhibit a high overall AGN fraction with an excess between 2 and 4 depending on the AGN diagnostics used. In addition, we find most optical, IR, and radio AGN are also identified as X-ray AGN while a large fraction of X-ray AGN are not identified in any other diagnostic. This highlights the importance of deep X-ray imaging to identify AGN. We find that the X-ray AGN fraction of post-mergers is independent of the stellar mass above log M * /M ⊙ ≥ 10.5 unlike the trend seen in control galaxies. Overall, our results show that post-merger galaxies are a good tracer of the merger–AGN connection and strongly support the theoretical expectations that mergers trigger AGN.

79 ASTRONOMY AND ASTROPHYSICS↗

Fast and Accurate Machine Learning Strategy for Calculating Partial Atomic Charges in Metal–Organic Frameworks

Computational high-throughput screening using molecular simulations is a powerful tool for identifying top-performing metal–organic frameworks (MOFs) for gas storage and separation applications. Accurate partial atomic charges are often required to model the electrostatic interactions between the MOF and the adsorbate, especially when the adsorption involves molecules with dipole or quadrupole moments such as water and CO 2 . Although ab initio methods can be used to calculate accurate partial atomic charges, these methods are impractical for screening large material databases because of the high computational cost. We developed a random forest machine learning model to predict the partial atomic charges in MOFs using a small yet meaningful set of features that represent both the elemental properties and the local environment of each atom. The model was trained and tested on a collection of about 320 000 density-derived electrostatic and chemical (DDEC) atomic charges calculated on a subset of the Computation-Ready Experimental Metal–Organic Framework (CoRE MOF-2019) database and separately on charge model 5 (CM5) charges. The model predicts accurate atomic charges for MOFs at a fraction of the computational cost of periodic density functional theory (DFT) and is found to be transferable to other porous molecular crystals and zeolites. In conclusion, a strong correlation is observed between the partial atomic charge and the average electronegativity difference between the central atom and its bonded neighbors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗