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At least 127 records · Page 7

Evolution of Topography in Glaciated Mountain Ranges

This thesis examines the response of alpine landscapes to the onset of glaciation. The basic approach is to compare fluvial and glacial laudscapes, since it is the change from the former to the latter that accompanies climatic cooling. This allows a detailed evaluation of hypotheses relating climate change to tectonic processes in glaciated mountain belts. Fieldwork was carried out in the eastern Sierra Nevada, California, and the Sangre de Cristo Range, Colorado, alongside digital elevation model analyses in the western US, the Southern Alps of New Zealand, and the Himalaya of northwestern Pakistan. hypothesis is overstated in its appeal to glacial erosion as a major source of relief production and subsequent peak uplift. Glaciers in the eastern Sierra Nevada and the western Sangre de Cristos have redistributed relief, but have produced only modest relief by enlarging drainage basins at the expense of low-relief topography. Glaciers have lowered valley floors and ridgelines by similar amounts, limiting the amount of "missing mass' that can be generated, and causing a decrease in drainage basin relief. The principal response of glaciated landscapes to rapid rock uplift is the development of towering cirque headwalls. This represents considerable relief production, but is not caused by glacial erosion alone. Large valley glaciers can maintain their low gradient regardless of uplift rate, which supports the "glacial buzzsaw" hypothesis. However, the inability of glaciers to erode steep hillslopes as rapidly can cause mean elevations to rise. Cosmogenic isotope dating is used to show that (i) where plucking is active, the last major glaciation removed sufficient material to reset the cosmogenic clock; and (ii) former glacial valley floors now stranded near the crest of the Sierra Nevada are at varying stages of abandonment, suggesting a cycle of drainage reorganiszation and relief inversion due to glacial erosion similar to that observed in river networks. Glaciated landscapes are quite distinct from their fluvial counterparts in both landforms and processes. Given the scarcity of purely fluvial, active mountain ranges, it is essential that glacial erosion be considered amongst the processes sculpting active orogenic belts.

Brocklehurst, Simon H.↗

Preface: special issues on photosystem II

Here, the appearance of oxygenic photosynthesis 3–4 billion years ago is arguably one of the most important evolutionary developments which radically transformed both the biotic and abiotic landscapes of Earth. The presence of molecular oxygen enabled the evolution of complex lifeforms requiring large amounts of chemical energy which could only be produced by aerobic respiration. Additionally, molecular oxygen remodeled the geochemistry of the planet during its transition from a reducing to an oxidizing atmosphere during the Great Oxidation Event. Central to these processes is Photosystem II (PS II), the light energy-driven, water-plastoquinone oxidoreductase which initially evolved in cyanobacteria and subsequently was incorporated, along with Photosystem I (PS I), the cytochrome b 6 f complex and the Ndh complex, into all algae and higher plants by the process of endosymbiosis. This membrane protein complex releases molecular oxygen and protons as the byproducts of water splitting and produces plastoquinol, which provides reducing equivalents that are used sequentially by the cytochrome b 6 /f complex, PS I, and ultimately, as NADPH + H + , by the Calvin–Benson–Bassham cycle. Additionally, the protons released by PS II (and those pumped by the cytochrome b 6 /f complex and the NDH complex (during cyclic electron transfer)) form the proton motive force that drives ATP synthesis via the ATP Synthase, thus providing the chemical energy source for carbon fixation.

59 BASIC BIOLOGICAL SCIENCES↗

A large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (~ 38%), high recombination rates (ρ = 0.044), and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion may be controlled by frequent recombination. We additionally identified that within the ergoline biosynthetic cluster the lpsA1 and lpsA2 were the result of a recombination event. However, the high recombination rates observed in C. purpurea may be influencing an overall trend of purifying selection across the genome. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.

59 BASIC BIOLOGICAL SCIENCES↗

A reinforcement learning approach to long-horizon operations, health, and maintenance supervisory control of advanced energy systems

In this work, we develop a Reinforcement Learning (RL) approach to the supervisory control problem for advanced energy systems, such as novel nuclear reactors and other demand-driven, mission-critical, and component-health-sensitive energy plants. The inclusive problem landscape considered captures the stochastic confluence of plant performance, component health evolution, power demand from the grid, diverse maintenance actions, and operator-defined goals and constraints, all considered over meaningfully long-enough reasoning horizons. Key aspects of the proposed approach are a receding horizon control-inspired technique dictating time- or event-triggered supervisory policy (re-)constructions, as well as additional capability-enabling contributions such as timescale compression, to handle long reasoning horizons and uncertainty in parts of the problem, and practical yet demonstrably-effective handling of hybrid action spaces with continuous and discrete decision variables. The resulting algorithm consists of a simulation-based RL agent constructing stochastic supervisory control policies over nontrivial action spaces and for long horizons, applying the learned policy to the system for a much shorter interval, and perpetually repeating, to construct the next long-horizon policy. That next policy will only be applied, again, for a short interval, yet originally far-in-time events move progressively closer, their associated uncertainty decreases, and new events and aspects enter the reasoning horizon. The proposed methodology bridges fundamental receding horizon concepts with the unequivocally stronger and more scalable reasoning of contemporary RL. Numerical examples using Soft Actor–Critic Deep RL illustrate the operation and efficacy of the proposed technique for a power plant tasked with health-aware load following missions in a dynamic electricity market landscape.

97 MATHEMATICS AND COMPUTING↗

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn 2+ or Co 2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon due to loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

59 BASIC BIOLOGICAL SCIENCES↗

Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability

Snow plays a critical role in carbon cycling, vegetation dynamics, and permafrost hydrology at high latitudes by influencing surface energy exchange. Predicting snow distribution patterns is essential for understanding the evolution of Arctic ecosystems, yet scaling process-level knowledge to landscape predictions remains challenging. Here, we analyze snow depth (2019 and 2022), terrain elevation, and vegetation height from a watershed on the Seward Peninsula, Alaska, to examine how topography and shrubs shape snow redistribution across spatial scales. We find that snow depth is strongly coupled to terrain at scales below ∼60 m but becomes increasingly decoupled at larger scales. The topographic model of snow depth variation, which transforms terrain data to align with these scale-dependent snow patterns, is well correlated with local snow depth variations (linear fit R 2 > 0.5 for 85% of 100-m patches). A machine learning reconstruction of shrub canopy snow trapping reveals a simple exponential relationship between canopy structure and snow accumulation ( R 2 = 0.59), highlighting the combined influence of topography and vegetation on snow distribution. Together, these empirical relationships capture much of the observed snow variability in the watershed ( R 2 = 0.49, root mean square error (RMSE) = 30 cm), though systematic limitations persist in areas of strong scour and at coarser scales where wind-terrain interactions are more complex. These findings provide a framework for more efficient snow depth prediction and offer insights to improve snow-vegetation feedback representation in Earth System Models.

54 ENVIRONMENTAL SCIENCES↗

Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology

Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme’s conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme’s conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.

59 BASIC BIOLOGICAL SCIENCES↗

Impact cratering: A geologic process

The mechanisms involved in the formation of impact craters are examined theoretically, reviewing the results of recent investigations. Topics addressed include crater morphology, stress waves in solids, the contact and compression stage, the excavation stage, and ejecta deposits. Consideration is given to the scaling of crater dimensions, the crater modification stage, multiring basins, cratered landscapes, atmospheric interactions, and the implications of impact cratering for planetary evolution. Extensive diagrams, graphs, tables, and images of typical craters are provided.

Melosh, H. J.↗

Processes Modifying Cratered Terrains on Pluto

The July encounter with Pluto by the New Horizons spacecraft permitted imaging of its cratered terrains with scales as high as approximately 100 m/pixel, and in stereo. In the initial download of images, acquired at 2.2 km/pixel, widely distributed impact craters up to 260 km diameter are seen in the near-encounter hemisphere. Many of the craters appear to be significantly degraded or infilled. Some craters appear partially destroyed, perhaps by erosion such as associated with the retreat of scarps. Bright ice-rich deposits highlight some crater rims and/or floors. While the cratered terrains identified in the initial downloaded images are generally seen on high-to-intermediate albedo surfaces, the dark equatorial terrain informally known as Cthulhu Regio is also densely cratered. We will explore the range of possible processes that might have operated (or still be operating) to modify the landscape from that of an ancient pristinely cratered state to the present terrains revealed in New Horizons images. The sequence, intensity, and type of processes that have modified ancient landscapes are, among other things, the record of climate and volatile evolution throughout much of the Pluto's existence. The deciphering of this record will be discussed. This work was supported by NASA's New Horizons project.

New Horizons↗

A Survey of Earth Observation Data Needed by U.S. Federal Agencies

The Satellite Needs Working Group (SNWG), part of the U.S. Group on Earth Observations (USGEO), surveys U.S. Federal civil agencies every two years regarding the Earth observation data they need in order to accomplish their high-priority agency objectives. The 2020 SNWG survey marked the third assessment cycle (after 2016 and 2018). Information solicited by the survey includes the nature of the need, features and phenomena being observed, data measurement characteristics, satellites and data products the agency uses or plans to use, agency satisfaction with currently available data, and limitations to agency use of satellite data. For analysis purposes, agency needs are assigned to science Focus Areas such as atmospheric composition, carbon/ecosystems, solid Earth, water, etc. Analysis of the survey responses yields insights on the current landscape of Earth observation needs across the U.S. Government agencies. The evolution over multiple survey cycles has been analyzed by the SNWG Assessment team at the Interagency Implementation and Advanced Concepts Team (IMPACT) at Marshall Space Flight Center (MSFC). Key trends emerged in the agency-agnostic analysis that can be helpful to NASA decision-makers evaluating the ongoing, evolving, and emerging needs for NASA missions and instrument datasets expressed by participating agencies in the SNWG.

Katrina Virts↗

Characterizing Damage Accumulation in CMCs

Silicon carbide / silicon carbide ceramic matrix composites (SiC/SiC CMCs) are structural ceramics that are well-suited for the extreme environment conditions of aerospace applications largely due to their low weight, creep resistance, damage tolerance, and high specific strength. In CMCs, the initiation and evolution of damage is influenced by a number of factors including characteristics of the constituent landscape (porosity, interfacial properties, and geometric distribution of CMC constituents), thermo-mechanical loading parameters, and environmental conditions. However, much is still unknown about these factors and the interactions between them. In order to accurately predict the lifetimes of these advanced composites, it is critical to understand the evolution of damage and to characterize which early damage mechanisms (and their relationship to key microstructural features) subsequently lead to crack coalescence and macroscopic failure. This research focuses on the use of a multi-modal, experimental approach to examine the relative activity of surface and subsurface damage mechanisms in CMCs. The impact of fabrication choices on the evolution of damage to final failure, and the influence of constituent architecture on early damage mechanisms, are investigated. This approach combines acoustic emission (AE) with microscale deformation tracking via digital image correlation inside a scanning electron microscope (SEM-DIC). The potential application of this combined approach towards characterization of damage in SiC/SiC CMCs under more complex testing conditions is explored.

Swaminathan, Bhavana↗

A map of the rubisco biochemical landscape

Rubisco is the primary CO 2 -fixing enzyme of the biosphere, yet it has slow kinetics. The roles of evolution and chemical mechanism in constraining its biochemical function remain debated. Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed, although recent results indicate that the functional potential of rubisco has a wider scope than previously known. Here we developed a massively parallel assay, using an engineered Escherichia coli in which enzyme activity is coupled to growth, to systematically map the sequence–function landscape of rubisco. Composite assay of more than 99% of single-amino acid mutants versus CO 2 concentration enabled inference of enzyme velocity and apparent CO 2 affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO 2 affinity. These data indicate that non-trivial biochemical changes are readily accessible and that the functional distance between rubiscos from diverse organisms can be traversed, laying the groundwork for further enzyme engineering efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗

PanDA: Production and Distributed Analysis System

The Production and Distributed Analysis (PanDA) system is a data-driven workload management system engineered to operate at the LHC data processing scale. The PanDA system provides a solution for scientific experiments to fully leverage their distributed heterogeneous resources, showcasing scalability, usability, flexibility, and robustness. The system has successfully proven itself through nearly two decades of steady operation in the ATLAS experiment, addressing the intricate requirements such as diverse resources distributed worldwide at about 200 sites, thousands of scientists analyzing the data remotely, the volume of processed data beyond the exabyte scale, dozens of scientific applications to support, and data processing over several billion hours of computing usage per year. PanDA’s flexibility and scalability make it suitable for the High Energy Physics community and wider science domains at the Exascale. Beyond High Energy Physics, PanDA’s relevance extends to other big data sciences, as evidenced by its adoption in the Vera C. Rubin Observatory and the sPHENIX experiment. As the significance of advanced workflows continues to grow, PanDA has transformed into a comprehensive ecosystem, effectively tackling challenges associated with emerging workflows and evolving computing technologies. The paper discusses PanDA’s prominent role in the scientific landscape, detailing its architecture, functionality, deployment strategies, project management approaches, results, and evolution into an ecosystem.

97 MATHEMATICS AND COMPUTING↗

Towards High-Performance AI4NP Applications on Modern GPU Platforms

The evolution of modern heterogeneous accelerators, such as GPUs, has significantly advanced the landscape of artificial intelligence (AI). There is a notable surge to adopt AI within the nuclear physics domain (AI4NP). While most AI4NP studies focus on feasibility analysis, our attention is directed towards evaluating their performance on contemporary GPUs that integrate tensor cores. We first benchmark the throughput of hyperparameterized multi-layer perceptron (MLP) models. We then examine the performance of an AI4NP application: Hydra. We assess the performance gain and accuracy loss caused by the tensor cores for low-precision floating-point operations. Our experiments encompass the PyTorch and TensorFlow Keras frameworks on NVIDIA’s T4 and A100 GPUs. We explore the behavior of different GPU hardware platforms and AI software tools. This study can be a valuable resource for guiding the performance optimization of larger-scale deployments of AI4NP applications.

Mei, Xinxin↗

Impact processes and their implications for planetary formation and early evolution

Small impact craters dominate the geomorphology of small planetary bodies. Even Mars has extensive impact-dominated landscapes. The regoliths of the Moon and asteroids are created and maintained by impacts. It is now widely recognized that large impacts (craters 100-1000 km in diameter) are one of the major tectonic elements in the lithospheres of bodies like the Moon, Mercury, Mars and Callisto. The multiring basins these large impacts produce sometimes extend over an entire hemisphere. Such basins may have also affected tectonics during the Earth's hadean era. Although it has long been appreciated that low velocity collisions played a major role in the accretion of planetesimals into planets, recent work indicates a far more profound role for impacts. Studies of the interaction of planetary atmospheres with large impacts, begun in an effort to define the climatological effects of the K-T impactor, suggest that impacts may remove a significant fraction of a planet's atmosphere. Such removal now offers hope of explaining the puzzling systematics of the heavy noble gases in the atmospheres of the Earth, Venus, and Mars.

Melosh, H. J.↗

SMEFT ATLAS: The landscape beyond the Standard Model

The Standard Model Effective Field Theory (SMEFT) based on the unbroken gauge group SU(3) 𝐶 ⊗SU(2) 𝐿 ⊗U(1) 𝑌 and containing only particles of the Standard Model (SM) has developed in the last decade to a mature field. It is the framework to be used in the energy gap from scales sufficiently higher than the electroweak scale up to the lowest energy scale at which new particles show up. We summarize the present status of this theory with a particular emphasize on its role in the indirect search for new physics (NP). While flavour physics of both quarks and leptons is the main topic of our review, we also discuss electric dipole moments, anomalous magnetic moments (𝑔−2) 𝜇,𝑒 , 𝑍-pole observables, Higgs observables and high-𝑝𝑇 scattering processes within the SMEFT. We group the observables into ten classes and list for each class the most relevant operators and the corresponding renormalization group equations (RGEs). We exhibit the correlations between different classes implied both by the operator mixing and the SU(2) 𝐿 gauge symmetry. Our main goal is to provide an insight into the complicated operator structure of this framework which hopefully will facilitate the identification of valid ultraviolet completions behind possible anomalies observed in future data. Numerous colourful charts, and 85 tables, while representing rather complicated RG evolution from the NP scale down to the electroweak scale, beautify the involved SMEFT landscape. Over 1000 references to the literature underline the importance and the popularity of this field. We discuss both top-down and bottom-up approaches as well as their interplay. This allows us eventually to present an atlas of different landscapes beyond the SM that includes heavy gauge bosons and scalars, vector-like quarks and leptons and leptoquarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Formation of transfermium elements in reactions with Pb 208

Within the Langevin framework, we investigate the dynamics of the fusion process for production of transfermium elements in reactions of Ca 48 , Ti 50 , Cr 54 , and Fe 58 with Pb 208 . After the reacting nuclei have made contact, the early dynamical stage is dominated by the dissipation of the initial radial kinetic energy, while the subsequent shape evolution is diffusive. The probability for surmounting the inner barrier and forming a compound system is obtained by simulating the evolution as a Metropolis random walk in a five-dimensional potential-energy landscape. Good agreement with the available data is obtained, especially for the maximal formation probability. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗