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  1. Free, publicly-accessible full text available March 1, 2025
  2. Free, publicly-accessible full text available December 31, 2024
  3. Organisms that live in different environments face different evolutionary pressures. As such, organisms that have more successful phenotypes reproduce more frequently, but differing selective pressures acting at the organismal level can influence genes, and thus proteins. Understanding how proteins adapt across environments may therefore be useful in engineering proteins for specific environments as well as to improve our understanding of basic biology. In this work, we explicitly compare homologous (read: paired) proteins from different environments. While previous studies have explored the relevant evolutionary pressures in one of these environments [11], [17] and genomic responses to those pressures [1], [28], no prior computational study of their proteins has been performed. We apply ESM-2 [20] and although there is no signal in our negative control (two divergent yeast strains) as expected, we obtain near perfect prediction accuracy for our selected environmental gradient–the well-established subsurface vs. surface biome. We further show that ESM-2 is able to capture relevant fine-grained biological patterns in its embedding space, even in its smallest model. Significantly, we demonstrate that these embeddings can be interpreted using a novel visualization pipeline built using explainable AI techniques. 
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  4. Abstract

    Superfluid3He is a paradigm for odd-parity Cooper pairing, ranging from neutron stars to uranium-based superconducting compounds. Recently it has been shown that3He, imbibed in anisotropic silica aerogel with either positive or negative strain, preferentially selects either the chiral A-phase or the time-reversal-symmetric B-phase. This control over basic order parameter symmetry provides a useful model for understanding imperfect unconventional superconductors. For both phases, the orbital quantization axis is fixed by the direction of strain. Unexpectedly, at a specific temperatureTx, the orbital axis flops by 90, but in reverse order for A and B-phases. Aided by diffusion limited cluster aggregation simulations of anisotropic aerogel and small angle X-ray measurements, we are able to classify these aerogels as either “planar and “nematic concluding that the orbital-flop is caused by competition between short and long range structures in these aerogels.

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  5. Abstract

    Non-equilibrium inductively coupled plasmas (ICPs) operating in hydrogen are of significant interest for applications including large-area materials processing. Increasing control of spatial gas heating, which drives the formation of neutral species density gradients and the rate of gas-temperature-dependent reactions, is critical. In this study, we use 2D fluid-kinetic simulations with the Hybrid Plasma Equipment Model to investigate the spatially resolved production of atomic hydrogen in a low-pressure planar ICP operating in pure hydrogen (10–20 Pa or 0.075–0.15 Torr, 300 W). The reaction set incorporates self-consistent calculation of the spatially resolved gas temperature and 14 vibrationally excited states. We find that the formation of neutral-gas density gradients, which result from spatially non-uniform electrical power deposition at constant pressure, can drive significant variations in the vibrational distribution function and density of atomic hydrogen when gas heating is spatially resolved. This highlights the significance of spatial gas heating on the production of reactive species in relatively high-power-density plasma processing sources.

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  6. Abstract

    Deciduous tree cover is expected to increase in North American boreal forests with climate warming and wildfire. This shift in composition has the potential to generate biophysical cooling via increased land surface albedo. Here we use Landsat-derived maps of continuous tree canopy cover and deciduous fractional composition to assess albedo change over recent decades. We find, on average, a small net decrease in deciduous fraction from 2000 to 2015 across boreal North America and from 1992 to 2015 across Canada, despite extensive fire disturbance that locally increased deciduous vegetation. We further find near-neutral net biophysical change in radiative forcing associated with albedo when aggregated across the domain. Thus, while there have been widespread changes in forest composition over the past several decades, the net changes in composition and associated post-fire radiative forcing have not induced systematic negative feedbacks to climate warming over the spatial and temporal scope of our study.

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    Free, publicly-accessible full text available October 23, 2024
  7. Free, publicly-accessible full text available September 1, 2024
  8. Abstract

    In streams where water temperatures stress native biota, management of riparian shade or hyporheic exchange are both considered viable management strategies for reducing the peaks of daily and seasonal stream channel temperature cycles. Although shade and hyporheic exchange may have similar effects on stream temperatures, their mechanisms differ. Improved understanding of the heat‐exchange mechanisms influenced by shade and hyporheic exchange will aid in the appropriate application of either stream temperature management strategy. To illustrate a conceptual model highlighting shade as ‘thermal insulation’ and hyporheic exchange imparting ‘thermal capacitance’ to a stream reach, we conducted an in‐silico simulation modelling experiment increasing shade or hyporheic exchange parameters on an idealized, hypothetical stream. We assessed the potential effects of increasing shade or hyporheic exchange on a stream reach using an established process‐based heat‐energy budget model of stream‐atmosphere heat exchange and incorporated an advection‐driven hyporheic heat exchange routine. The model tracked heat transport through the hyporheic zone and exchange with the stream channel, while including the effects of hyporheic water age distribution on upwelling hyporheic temperatures. Results showed that shade and hyporheic exchange similarly damped diurnal temperature cycles and differentially altered seasonal cycles of our theoretical stream. In winter, hyporheic exchange warmed simulated channel temperatures whereas shade had little effect. In summer, both shade and hyporheic exchange cooled channel temperatures, though the effects of shade were more pronounced. Our simple‐to‐grasp analogies of ‘thermal insulation’ for shade effects and ‘thermal capacitance’ for hyporheic exchange effects on stream temperature encourage more accurate conceptualization of complex, dynamic heat exchange processes among the atmosphere, stream channel, and alluvial aquifer.

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    Free, publicly-accessible full text available September 1, 2024
  9. Wildfire activity is increasing in boreal forests as climate warms and dries, increasing risks to rural and urban communities. In black spruce forests of Interior Alaska, fuel reduction treatments are used to create a defensible space for fire suppression and slow fire spread. These treatments introduce novel disturbance characteristics, making longer-term outcomes on ecosystem structure and wildfire risk reduction uncertain. We remeasured a network of sites where fuels were reduced through hand thinning or mechanical shearblading in Interior Alaska to assess how successional trajectories of tree dominance, understory composition, and permafrost change over ∼ 20 years after treatment. We also assessed if these fuel reduction treatments reduce modeled surface rate of fire spread (ROS), flame length, and fireline intensity relative to an untreated black spruce stand, and if surface fire behavior changes over time. In thinned areas, soil organic layer (SOL) disturbance promoted tree seedling recruitment but did not change over time. In shearbladed sites, by contrast, both conifer and broad-leaved deciduous seedling density increased over time and deciduous seedlings were 20 times more abundant than spruce. Thaw depth increased over time in both treatments and was greatest in shearbladed sites with a thin SOL. Understory composition was not altered by thinning but in shearbladed treatments shifted from forbs and horsetail to tall deciduous shrubs and grasses over time. Modeled surface fire behavior was constant in shearbladed sites. This finding is inconsistent with expert opinion, highlighting the need for additional fuels-specific data to capture the changing vegetation structure. Treatment effectiveness at reducing modeled surface ROS, flame length, and fireline intensity depended on the fuel model used for an untreated black spruce stand, pointing to uncertainties about the efficacy of these treatments at mitigating surface fire behavior. Overall, we show that fuel reduction treatments can promote low flammability, deciduous tree dominated successional trajectories, and that shearblading has strong effects on understory composition and permafrost degradation that persist for nearly two decades after disturbance. Such factors need to be considered to enhance the design, management, and predictions of fire behavior in these treatments. 
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    Free, publicly-accessible full text available October 1, 2024