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Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases

The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation that stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to phosphorylated immunoreceptor tyrosine-based activation motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen–deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the autoinhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.

59 BASIC BIOLOGICAL SCIENCES↗

Photon–photon chemical thermodynamics of frequency conversion processes in highly multimode systems

Abstract Frequency generation in highly multimode nonlinear optical systems is inherently a complex process, giving rise to an exceedingly convoluted landscape of evolution dynamics. While predicting and controlling the global conversion efficiencies in such nonlinear environments has long been considered impossible, here, we formally address this challenge even in scenarios involving a very large number of spatial modes. By utilizing fundamental notions from optical statistical mechanics, we develop a universal theoretical framework that effectively treats all frequency components as chemical reactants/products, capable of undergoing optical thermodynamic reactions facilitated by a variety of multi-wave mixing effects. These photon–photon reactions are governed by conservation laws that directly determine the optical temperatures and chemical potentials of the ensued chemical equilibria for each frequency species. In this context, we develop a comprehensive stoichiometric model and formally derive an expression that relates the chemical potentials to the optical stoichiometric coefficients, in a manner akin to atomic/molecular chemical reactions. This advancement unlocks new predictive capabilities that can facilitate the optimization of frequency generation in highly multimode photonic arrangements, surpassing the limitations of conventional schemes that rely exclusively on nonlinear optical dynamics. Notably, we identify a universal regime of Rayleigh–Jeans thermalization where an optical reaction at near-zero optical temperatures can promote the complete and entropically irreversible conversion of light to the fundamental mode at a target frequency. Our theoretical results are corroborated by numerical simulations in settings where second-harmonic generation, sum-frequency generation and four-wave mixing processes can manifest.

Optics↗

Historic climate, cosmogenic 10Be, denudation-rate, and geospatial datasets from the Pikes Peak region, Colorado, USA

This data package contains geographic information system (GIS) layers and tabular datasets associated with the study of elevation-dependent denudation rates on Pikes Peak in the Front Range of the Rocky Mountains, Colorado, USA. The package includes GIS layers used to produce the study-area map, including sample locations, sample watershed boundaries, the Pikes Peak batholith, Pleistocene glacier extent, weather station locations, and elevation and hillshade rasters, together with comma-separated value (CSV) tables and matching CSV data dictionaries. These mapped layers provide the geographic framework for interpreting denudation patterns across the Pikes Peak region and for relating sample locations to watershed geometry, bedrock setting, glacial history, and nearby climate stations. The first group of tables reports climate and geospatial context for the study area. These files include station-based temperature and precipitation data used to characterize elevational gradients in mean annual climate and monthly climate seasonality, sample locations, denudation-rate and topographic metrics, fixed frost-cracking model parameters, frost-cracking intensity and precipitation-frequency metrics, and stream-power inversion results. Together, these data provide the basis for evaluating how denudation varies with elevation, climate, and landscape form across sampled catchments on Pikes Peak. The second group of tables reports cosmogenic nuclide and erosion-model results used in the denudation analysis. Included files contain accelerator mass spectrometry (AMS) measurements for in situ-produced cosmogenic beryllium-10 (10Be), including sample identifiers, measured 10Be:9Be ratios, analytical uncertainties, carrier mass, quartz mass, blank corrections, blank-group statistics, and calculated 10Be concentrations and uncertainties. Additional tables summarize stream-power-law inversion results for sampled catchments, including optimized model parameters, predicted erosion rates, residual metrics, channel-pixel counts, and convergence status, as well as regression equations and summary statistics used to evaluate relationships among elevation, climate, frost cracking, precipitation forcing, and denudation rate. The package contains GIS files, comma-separated value files (.csv), Microsoft Excel files (.xlsx), CSV data dictionaries, a file-level metadata table, and a readme text file.

10Be cosmogenic nuclides↗

Climate change drives convergent evolution of root traits on Sky Island climate relicts

Roots are essential to the strategies plants use to survive in variable environments, yet we know little of how they vary within species. Experimental conditions demonstrate that intraspecific plant root traits respond strongly to variation in the environment; however, it is unclear when these responses can be characterized as evolution in response to selective pressures of climate change over many generations. Sky Islands are model, natural climate relict ecosystems to examine climate-change driven evolution. Utilizing a common garden with replicate genotypes of Populus angustifolia (Narrowleaf cottonwood) from six Sky Island (SI) populations and nine adjacent Mountain Chain (MC) populations across three genetic provenances, we hypothesized that SI root traits have diverged due to historical isolation in warmer, drier climates. When grown in common conditions, populations originating on SI’s showed convergent evolution across three distinct genetic provenances, which was characterized by 44.16% decreased total root length, 42.64% decreased average root volume, 43.31% decreased root surface area, and significantly less root trait variation, relative to adjacent mountain chains. Convergent evolution of root traits from trees originating on SI’s is correlated with changes in mean annual precipitation and potential evapotranspiration in the field over the past ~ 125 years. These results demonstrate a consistent pattern in root trait evolution at the landscape scale and the role of climate on the evolution of root traits in a genetic and geographic context relevant to climate change.

Convergent evolution↗

High Entropy Alloys: Irradiation

High entropy alloys (HEAs) have been considered as structural materials for nuclear applications due to their promising mechanical properties and radiation resistance. For this purpose, irradiation-induced defect evolution and microstructure change have been characterized to evaluate the irradiation performance of different HEAs. This article reviews recent advances in understanding the irradiation response of HEAs, including the effect of disordered states on the defect energy landscape and defect evolution, irradiation-induced microstructure changes, void swelling, phase stability, mechanical properties under irradiation, as well as the He irradiation effects.

Zhao, Shijun↗

A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Abstract Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer, potentially explaining ∼40% of relapses. If other mechanisms underlie the evolution of hormone-dependent breast cancer under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CRE) to cancer evolution by focusing on 12 megabases of noncoding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of noncoding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies trigger the emergence of transient features which could ultimately be exploited to hinder the adaptive process. Significance: This study shows that cells adapting to endocrine therapies undergo changes in the usage or regulatory regions. Dormant cells are less vulnerable to regulatory perturbation but gain transient dependencies which can be exploited to decrease the formation of dormant persisters.

Oncology↗

NGEE Arctic LANL Overview [Slides]

The Next-Generation Ecosystem Experiments (NGEE Arctic) project has a goal to "deliver a process-rich ecosystem model, extending from bedrock to the top of the vegetative canopy/atmospheric interface, in which the evolution of Arctic ecosystems in a changing climate can be modeled at the scale of a high resolution Earth System Model (ESM) grid cell." LANL works across multiple NGEE Arctic science questions, such as: Q1. How does the structure and organization of the landscape control permafrost evolution and associated carbon and nutrient fluxes in a changing climate? Q5. Where, when, and why will the Arctic become wetter or drier, and what are the implications for climate forcing? and Q6. What controls the vulnerability of Arctic ecosystems to disturbance, and how do disturbances alter the structure and function of these ecosystems? This report features LANL's research summaries.

54 ENVIRONMENTAL SCIENCES↗

Dating fractures using luminescence

Rock fracturing (cracking) is a universal process that drives and limits chemical degradation, sediment production and erosion, and deterioration of infrastructure. Despite extensive research gains in rock mechanics on one hand and geochronology on the other, there remains a glaring gap in our ability to understand the long term evolution of natural, in situ fractures. Here we develop a novel fracture exposure dating technique, grounded in modern advances in luminescence geochronology. We apply our new dating method to a granitic boulder from a glacial outwash terrace in California, US. We conclude that the longest, clast-splitting E-W fracture appeared shortly after the boulder's deposit, whereas the secondary N-S fracture appeared 5 ka after the deposition, approximately correlating with the Last Glacial Maximum and Younger Dryas periods of the region, respectively. However, dating of the third fracture (<< 50 µm width) which does not fully split the rock, is ambiguous due to negligible daylight penetration and poor determination of fracture width. The fracture dating method presented herein brings with it the potential to decipher relationships that are crucial for the interpretation and modeling of, for example, long-term landscape and atmospheric evolution relating rock weathering to climate change and erosion.

58 GEOSCIENCES↗

CompF2: Theoretical Calculations and Simulation Topical Group Report

This report summarizes the work of the Computational Frontier topical group on theoretical calculations and simulation for Snowmass 2021. We discuss the challenges, potential solutions, and needs facing six diverse but related topical areas that span the subject of theoretical calculations and simulation in high energy physics (HEP): cosmic calculations, particle accelerator modeling, detector simulation, event generators, perturbative calculations, and lattice QCD (quantum chromodynamics). The challenges arise from the next generations of HEP experiments, which will include more complex instruments, provide larger data volumes, and perform more precise measurements. Calculations and simulations will need to keep up with these increased requirements. The other aspect of the challenge is the evolution of computing landscape away from general-purpose computing on CPUs and toward special-purpose accelerators and coprocessors such as GPUs and FPGAs. These newer devices can provide substantial improvements for certain categories of algorithms, at the expense of more specialized programming and memory and data access patterns.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Increased Arctic NO3− Availability as a Hydrogeomorphic Consequence of Permafrost Degradation and Landscape Drying

Climate-driven permafrost thaw alters the strongly coupled carbon and nitrogen cycles within the Arctic tundra, influencing the availability of limiting nutrients including nitrate (NO3−). Researchers have identified two primary mechanisms that increase nitrogen and NO3− availability within permafrost soils: (1) the ‘frozen feast’, where previously frozen organic material becomes available as it thaws, and (2) ‘shrubification’, where expansion of nitrogen-fixing shrubs promotes increased soil nitrogen. Through the synthesis of original and previously published observational data, and the application of multiple geospatial approaches, this study investigates and highlights a third mechanism that increases NO3− availability: the hydrogeomorphic evolution of polygonal permafrost landscapes. Permafrost thaw drives changes in microtopography, increasing the drainage of topographic highs, thus increasing oxic conditions that promote NO3− production and accumulation. We extrapolate relationships between NO3− and soil moisture in elevated topographic features within our study area and the broader Alaskan Coastal Plain and investigate potential changes in NO3− availability in response to possible hydrogeomorphic evolution scenarios of permafrost landscapes. These approximations indicate that such changes could increase Arctic tundra NO3− availability by ~250–1000%. Thus, hydrogeomorphic changes that accompany continued permafrost degradation in polygonal permafrost landscapes will substantially increase soil pore water NO3− availability and boost future fertilization and productivity in the Arctic.

54 ENVIRONMENTAL SCIENCES↗

Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra: Modeling Archive

This dataset is a model archive of the paper Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra (in prep) to support a modeling study investigating how projected increases in Arctic temperature and precipitation will jointly influence hydrologic conditions in ice-rich tundra landscapes. With this dataset, this study is to address the research question: Will Arctic tundra landscapes become wetter or drier with increasing precipitation and temperature in the future when thaw-induced ground subsidence and associated microtopographic evolution are represented? The simulations focus on ice-wedge polygon tundra, a widespread form of ice-rich permafrost terrain that is highly sensitive to thaw-driven landscape change. This dataset contains model input and output data for four study watersheds in Alaska: Anaktuvuk, Utqiagvik (formerly Barrow), Brooks Foothills, and Prudhoe Bay. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.5), a physics-rich integrated surface–subsurface hydrologic model. For each watershed, ten modeling cases were performed representing two landscape evolution conditions (with subsidence and without subsidence) combined with five climate forcing scenarios derived from Shared Socioeconomic Pathways (SSP5, SSP5 with precipitation trend, SSP2, SSP2 with precipitation trend, and SSP2 with double precipitation trend). Particularly, for each watershed under the forcing SSP2 with precipitation trend, there are two additional simulations considering spatially heterogeneous subsidence distributions: one assumes randomly distributed scaling and the other includes elevation dependent distribution scaling. These simulations span 1980–2099 and include spin-up runs (1980–2009) followed by transient projections (2010–2099). To facilitate reproducibility of simulations, all datasets are organized by watershed. For each study watershed, the dataset contains: (1) Pre-partitioned mesh files for 32-core modeling (.par.32.XX), located in EACH_WATERSHED/mesh/basin; and also a non-partitioned mesh file (.exo) located in EACH_WATERSHED/mesh; (2) Climate forcings corresponding to the five SSP scenarios (.h5), located in EACH_WATERSHED/data; (3) Final states (.h5) from column spin-up modeling used to initialize historical watershed-scale spin-up runs from 1980 to 2009, located in EACH_WATERSHED/PreSpinupHistorical; (4) Final states (.h5) of historical watershed-scale spin-up runs from 1980 to 2009 used to initialize projection runs, located in EACH_WATERSHED/Spinup_daymetERA5; (5) ATS modeling input files (.xml), located in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/inputfiles; (6) ATS modeling output files (.dat), located in in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/combined_obs; (7) For the Brooks Foothills watershed, additional spatial model outputs are provided (.h5) for selected years (2033 and 2093) used to generate spatial figures in this study, located in Brooksfoothills/EACH_SIMULATION_SCENARIO/results-WITH/WITHOUT_SUBSIDENCE-year2033/2093. All data files with suffix .h5 can be accessible through Python h5py, and all data files with suffix of .dat can be imported by Python pandas. Mesh file with .exo can be visualized through Paraview or read by Python netCDF. The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research. Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

EARTH SCIENCE > ATMOSPHERE > PRECIPITATION↗

Long‐term growth and persistence of granitic inselbergs in a semi‐arid cratonic landscape

Granitic inselbergs are enduring landforms that punctuate planation surfaces in tectonically stable settings, yet the mechanisms and timescales of their persistence remain debated. Here, in this study, we present a multinuclide cosmogenic dataset ( 10 Be, 26 Al and 21 Ne) from bedrock, fluvial sediments and planation surfaces in the semi-arid Central Ceará Domain, north-eastern Brazil, to quantify denudation rates and reconstruct the long-term dynamics of residual relief formation. This triple-nuclide approach enables independent validation of denudation contrasts and long-term exposure histories, providing quantitative constraints on inselberg evolution that a single-nuclide approach could not resolve. Bedrock denudation rates (1–4 m Myr −1 ) are systematically lower than basin-wide rates (8–14 m Myr −1 ), revealing a regional pattern of vertical differential denudation. When combined with summit elevations and surface exposure ages of up to 5 Myr, these contrasts suggest that cumulative relief growth has been operating over timescales of tens of millions of years (1–57 Myr). Morphological and structural observations further indicate localized mass wasting and heterogeneous erosion styles, modulated by rock fabric and joint density. Cosmogenic nuclide inventories in detrital sediments reveal partial reworking from older sediment stocks, including surface pebbles with exposure ages up to 5 Myr, which record multistage of burial and re-exposure histories and reflect episodic remobilization in low-connectivity, semi-arid catchments. Rather than static relicts of ancient surfaces, inselbergs in this cratonic setting emerge as dynamic landforms actively sustained by slow but persistent differential denudation. These results provide new constraints on long-term cratonic landscape evolution and underscore the interplay between lithological resistance, structural inheritance and sediment transfer processes in sustaining topographic relief. They also call for a critical reassessment of classical inselberg models, suggesting that hybrid mechanisms, rather than single-process paradigms, more accurately capture the complexity of residual landform development in cratonic interiors.

Cosmogenic nuclides↗

Data Repository for Power system Open models With Evolving Resources (DR POWER) (Final Scientific/Technical Report)

Pacific Northwest National Laboratory (PNNL) and the National Rural Electric Cooperative Association (NRECA) created a Data Repository for Power system Open models With Evolving Resources (DR POWER) to establish, curate, and evolve open-access power grid models and scenarios, and measurements and observations, collectively referred to as datasets. Existing open-access datasets are inadequate (too small and not representative of the complexity of the modern grid, and scattered all over the world wide web) for the investigation and benchmarking of the advanced optimization methods needed for next-generation grids. Open-access datasets are static and inadequate in other aspects: they do not provide format transformation tools; there is missing information needed for advanced applications; hard to cite; no model evolution history; difficult to update current collections; and little to no community involvement and feedback. Overall, the current landscape is hindering model evolution and benchmarking standards needed for transformational approaches to be developed, tested, and accepted by the power modeling community.

24 POWER TRANSMISSION AND DISTRIBUTION↗

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Models of dislocation glide and strengthening mechanisms in bcc complex concentrated alloys

Abstract The mechanical response of complex concentrated alloys (CCAs) deviates from that of their pure and dilute counterparts due to the introduction of a combinatorially sized chemical concentration dimension. Compositional fluctuations constantly alter the energy landscape over which dislocations move, leading to line roughness and the appearance of defects such as kinks and jogs under stress and temperature conditions where they would ordinarily not exist in pure metals and dilute alloys. The presence of such chemical defects gives rise to atomic-level mechanisms that fundamentally change how CCAs deform plastically at meso- and macroscales. In this article, we provide a review of recent advances in modeling dislocation glide processes in CCAs, including atomistic simulations of dislocation glide using molecular dynamics, kinetic Monte Carlo simulations of edge and screw dislocation motion in refractory CCAs, and phase-field models of dislocation evolution over complex energy landscapes. We also discuss pathways to develop comprehensive simulation methodologies that connect an atomic-level description of the compositional complexity of CCAs with their mesoscopic dislocation-mediated plastic response with an eye toward improved design of CCA with superior mechanical response. Graphical abstract

36 MATERIALS SCIENCE↗

Femtosecond control of phonon dynamics near a magnetic order critical point

The spin-phonon interaction in spin density wave (SDW) systems often determines the free energy landscape that drives the evolution of the system. When a passing energy flux, such as photoexcitation, drives a crystalline system far from equilibrium, the resulting lattice displacement generates transient vibrational states. Manipulating intermediate vibrational states in the vicinity of the critical point, where the SDW order parameter changes dramatically, would then allow dynamical control over functional properties. Here we combine double photoexcitation with an X-ray free-electron laser (XFEL) probe to control and detect the lifetime and magnitude of the intermediate vibrational state near the critical point of the SDW in chromium. We apply Landau theory to identify the mechanism of control as a repeated partial quench and sub picosecond recovery of the SDW. Our results showcase the capabilities to influence and monitor quantum states by combining multiple optical photoexcitations with an XFEL probe. They open new avenues for manipulating and researching the behaviour of photoexcited states in charge and spin order systems near the critical point.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗