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At least 613 records · Page 34

Modeling the Economic and Environmental Impacts of Land Scarcity Under Deep Uncertainty

Abstract Land scarcity is increasing over time, driven by complex multisector dynamics. The impacts of land scarcity on the economy and environment are multi‐faceted and regional, so any action to convert land will contain inherent tradeoffs. These impacts are complicated by the deeply uncertain evolution of the various sectors influencing land scarcity. A need therefore exists to provide multi‐metric and multi‐sector assessments that are robust to myriad uncertainties. Land conservation effectively limits the supply of productive land, while biofuel consumption increases the demand and competition for that land, and how these dynamics individually and jointly propagate to economic and environmental impacts is an important open question. To address this, we adopt the Global Change Analysis Model (GCAM) that has representations of various important systems including the climate, macroeconomic, energy, agriculture and land, and water resources systems. Various scenarios of increased land demand (from biofuels) and decreased land supply (from conservation) under various socioeconomic scenarios drawn from the SSPs were simulated using GCAM. We find that while biofuel consumption and land conservation reduce carbon emissions, this comes at the cost of higher food prices, reduced crop production, and increased water withdrawals. Additionally, some regions experience these tradeoffs more severely than others and are more heavily impacted from the same biofuel mandate or by an additional percent of protected land. These and other findings highlight the importance of multisector modeling frameworks that capture many cross‐sector linkages, and acknowledge the important uncertainties confronting the human‐Earth system when making any analysis of land scarcity impacts.

54 ENVIRONMENTAL SCIENCES↗

Virtual Time III, Part 3: Throttling and Message Cancellation

This is Part 3 of a trio of papers that unify in a natural way the two historically distinct parallel discrete event synchronization paradigms, optimistic and conservative, combining the best properties of both into a single framework called Unified Virtual Time (UVT). In this part, we survey the synchronization effects that can be achieved by restricting to corner cases the relationships permitted among the control variables, GVT, CVT, TVT, and LVT, which were defined in Part 1. Here we also survey various throttling policies from the literature and describe how they can be implemented in UVT by controlling the value of TVT, including policies that can take advantage of rollback in addition to LP blocking. A significant result is a new category of efficient and higher precision throttling algorithms for optimistic execution that are based on optimistic lookahead, defined in a way that is symmetric to what we now call the conservative lookahead information that is traditionally used for conservative synchronization. Finally, we present a novel algorithm allowing the choice between lazy and aggressive cancellation to be made on a message-by-message basis using either external logic expressed in the model code, or policy code internal to the simulator, or a mixture of both.

throttling↗

Systems and methods for data analytics for virtual energy audits and value capture assessment of buildings

A system may provide virtual energy audits of one or more target buildings. The system may retrieve weather data and energy usage data specific to a given target building from a weather server and a utility server, respectively. The system may store predefined building characteristics corresponding to the given target building in local memory. Based on the weather data, energy usage data, and/or predefined building characteristics, the system may generate one or more building markers that characterize the energy usage and efficiency of the given target building. Building efficiency diagnostics and energy conservation prognostics may be generated based on the building markers and may be sent by the system to be displayed via a user interface of a client device. The energy conservation prognostics may include one or more energy conservation measure recommendations and corresponding predicted cost/energy savings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Utilizing digitized occurrence records of Midwestern feral Cannabis sativa to develop ecological niche models

Hemp (Cannabis sativa L.) has historically played a vital role in agriculture across the globe. Feral and wild populations have served as genetic resources for breeding, conservation, and adaptation to changing environmental conditions. However, feral populations of Cannabis, specifically in the Midwestern United States, remain poorly understood. This study aims to characterize the abiotic tolerances of these populations, estimate suitable areas, identify regions at risk of abiotic suitability change, and highlight the utility of ecological niche models (ENMs) in germplasm conservation. The Maxent algorithm was used to construct a series of ENMs. Validation metrics and MOP (Mobility-oriented Parity) analysis were used to assess extrapolation risk and model performance. We also projected the final projected under current and future climate scenarios (2021–2040 and 2061–2080) to assess how abiotic suitability changes with time. Climate change scenarios indicated an expansion of suitable habitat, with priority areas for germplasm collection in Indiana, Illinois, Kansas, Missouri, and Nebraska. This study demonstrates the application of ENMs for characterizing feral Cannabis populations and highlights their value in germplasm conservation and breeding efforts. Populations of feral C. sativa in the Midwest are of high interest, and future research should focus on utilizing tools to aid the collection of materials for the characterization of genetic diversity and adaptation to a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗

Overwintering Distribution and Postspawn Survival of Steelhead in the Upper Columbia River Basin

Abstract Adult summer-run steelhead Oncorhynchus mykiss overwinter in freshwater for several months prior to spawning. In systems supporting mixed populations of fisheries and conservation importance, understanding the distribution and survival of pre- and postspawn fish is necessary for informed management. The upper Columbia River supports hatchery-origin components valued by anglers, natural-origin components of conservation concern, and temporary strays from downstream populations. We used radiotelemetry and PIT telemetry to monitor the behavior, distribution, and survival of adult steelhead during fall, overwintering, spawning, and postspawn periods, with a focus on use of the main stem versus four major tributaries. Adult steelhead (N = 807) were tagged at Priest Rapids Dam in 2015 and 2016. One-fifth of steelhead fell back below Priest Rapids Dam and did not reascend. A slight majority of tagged steelhead that overwintered upstream of Priest Rapids Dam did so in main-stem reservoirs (54%; N = 548). Overwintering in the main-stem Columbia River was more likely for later-arriving steelhead and was concentrated in the upstream-most reservoir. Winter tributary use was highest in the Wenatchee (26%; 2016) and Methow (18%; 2015) rivers, whereas no steelhead overwintered in the Entiat River. Harvest of hatchery-origin steelhead was 18% in 2015 and was near zero in 2016, when the fishery was suspended due to low adult returns. After accounting for reported harvest, annual overwinter survival did not differ between main-stem and tributary habitats, and relatively low adjusted survival of hatchery-origin steelhead in 2015 suggested unreported harvest. In contrast to low iteroparity rates (<3%), the majority of postspawn steelhead (56.5%) exited tributaries as kelts; kelt survival to Bonneville Dam was 65% in 2016 and 23% in 2017. Collectively, the results highlight the importance of understanding patterns of habitat use and mortality in steelhead populations when managers are faced with balancing harvest and conservation goals.

Fuchs, Nathaniel T.↗

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗

Putting the soil health principles to the test in Iowa

One of the most popular soil conservation campaigns is based on the USDA Natural Resource Conservation Service's Soil Health Principles (NRCS-SHPs). The NRCS-SHP program identifies four principles—maximize presence of living roots, minimize disturbance, maximize soil cover, and maximize biodiversity—with the underlying assumption that the more principles one follows, the greater improvements in soil health. Despite the popularity of the NRCS-SHPs, this underlying assumption has not been rigorously tested. To do so, we used nine long-term experiments all located in central Iowa, but with varying degree of NRCS-SHP adoption, to determine if greater adoption increases three slow-changing (maximum water holding capacity, bulk density [BD], and soil organic carbon) and three dynamic (microbial biomass carbon [MBC], potentially mineralizable carbon [PMC], and permanganate oxidizable carbon [POXC]) soil health indicators. We regressed these indicators with a soil health principle score that can scale soil management based on adoption of the NRCS-SHPs. Of the slow-changing soil properties, increased adoption of NRCS-SHPs only decreased soil BD (R2 = 0.22, p = 0.024). On the other hand, increased adoption of NRCS-SHPs strongly predicted increases in both MBC and PMC and across two sampling dates (R2 > 0.23, p < 0.015); POXC, however, did not increase with greater adoption. The consistent increases in MBC and PMC with greater adoption of NRCS-SHPs supports their usefulness as sensitive indicators of positive soil health change. Our study provides scientific evidence to support the NRCS-SHPs concept, improving its usefulness as an extension campaign, and stands as a step toward evidence-based soil conservation.

60 APPLIED LIFE SCIENCES↗

Physics-preserving enriched Galerkin method for a fully-coupled thermo-poroelasticity model

This paper proposes a new numerical method for a fully-coupled, quasi-static thermo-poroelasticity model in a unified enriched Galerkin (EG) method framework. In our method, the mechanics sub-problem is solved using a locking-free EG method, and the flow and heat sub-problems are solved using a locally-conservative EG method. The proposed method offers mass and energy conservation properties with much lower costs than other methods with the same properties, including discontinuous Galerkin methods and mixed finite element methods. The well-posedness and optimal a priori error estimates are carefully derived. Here, several numerical tests confirm the theoretical optimal convergence rates and the mass and energy conservation properties of the new method.

15 GEOTHERMAL ENERGY↗

Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections

The interior Southeastern United States could contain novel germplasm for the bioenergy crop switchgrass due to its diverse habitats and geographic location between genetic subpopulations (Atlantic, Midwest, and Gulf). Collections from this region could accelerate breeding progress, contribute to conservation efforts, and improve understanding of isolated grasslands in the region. This study located 22 sites in the Midsouth region and obtained 1,521,210 single nucleotide polymorphism markers of 202 individuals through genotype-by-sequencing. Here, individuals were evaluated for flowering time, winter survival and tiller number. Comparison to a national diversity panel revealed that branches of two major subpopulations occur in the region with two levels of polyploidy: Atlantic tetraploids and Midwest octoploids. Two locations contained admixed octoploid individuals with Midwest and Gulf genetics. Field performance of the Midwest octoploids conformed with prior reported performance of the Midwest subpopulation, although three sites contained promising late flowering traits. The Atlantic tetraploids had moderate winter survival, short stature, and anomalously early flowering. Atlantic populations mostly occurred in marginal sites and their morphological and flowering time adaptations may be a resource conservation strategy. Demographic inference of historical effective population size variation in a subset of tetraploid locations indicated a widespread recent decline in effective population size. This pattern is consistent with isolation of these switchgrass communities from larger populations and is further supported by evidence of inbreeding within the populations (F I = 0.18). The populations documented in this study contain novel genetic diversity and adaptations to a range of marginal habitats. Therefore, this study provides a new source of germplasm for future breeding and conservation programs.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

59 BASIC BIOLOGICAL SCIENCES↗

Quasilinear theory: the lost ponderomotive effects and why they matter

Quasilinear theory (QLT) has been used for modeling wave–plasma interactions for decades but remains largely heuristic. Plasma inhomogeneity, ponderomotive effects, microscopic fluctuations, and collisions are not easily accommodated from first principles in QLT, and typically are ignored entirely, due to the limitations of the standard Fourier–Laplace global-mode approach. This results in inconsistencies, for example, violation of the action conservation for nonresonant waves. However, these issues can be avoided, and the theory can be substantially generalized and corrected, if QLT is formulated using more suitable analytical tools, particularly, the Weyl symbol calculus. Here, an attempt is made to deliver an accessible review of this modern formulation, provide intuitive calculations for special cases, and elaborate on the connection with the ‘oscillation-center QLT’ originally proposed by Dewar (Phys Fluids 16:1102, 1973). A Fokker–Planck equation for a ‘dressed’ distribution is derived from the Klimontovich equation and captures quasilinear diffusion, ponderomotive forces, and interactions with background fields for a generic Hamiltonian, so many known formulations of QLT for specific plasma models become corollaries of a single unifying theory. Also, waves are allowed to be off-shell (not constrained by a dispersion relation), which allows them to accommodate microscopic fluctuations. This leads to a collision integral of the Balescu–Lenard type that has all the usual properties but is not restricted to any specific plasma model. For on-shell waves, a generalized version of the classic oscillation-center QLT is obtained. Finally, combined with the wave-kinetic equation, this formulation not only conserves particles, momentum, and energy, like the classic QLT but also reinstates the action conservation for nonresonant waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sparse invariant domain preserving discontinuous Galerkin methods with subcell convex limiting

In this paper, we develop high-order nodal discontinuous Galerkin (DG) methods for hyperbolic conservation laws that satisfy invariant domain preserving properties using subcell flux corrections and convex limiting. These methods are based on a subcell flux corrected transport (FCT) methodology that involves blending a high-order target scheme with a robust, low-order invariant domain preserving method that is obtained using a graph viscosity technique. Furthermore, the new low-order discretizations are based on sparse stencils which do not increase with the polynomial degree of the high-order DG method. As a result, the accuracy of the low-order method does not degrade when used with high-order target methods. The method is applied to both scalar conservation laws, for which the discrete maximum principle is naturally enforced, and to systems of conservation laws such as the Euler equations, for which positivity of density and a minimum principle for specific entropy are enforced. Numerical results are presented on a number of benchmark test cases.

97 MATHEMATICS AND COMPUTING↗

The distribution-based remapping of the nodal mass and momentum between arbitrary meshes for staggered arbitrary Lagrangian-Eulerian hydrodynamics

We present a new distribution-based remapping of the nodal mass and momentum between arbitrary source (Lagrangian) and arbitrary target (rezoned) meshes for indirect staggered arbitrary Lagrangian-Eulerian hydrodynamics. Here, the method is based on the following ideas: define cell-centered momentum and mass on the source mesh; conservatively remap those cell-centered quantities from source to target meshes; and use local constrained optimization for each cell of the target mesh to conservatively distribute cell mass and momentum to the nodes of the cell. This new method is efficient, conservative, accurate and bounds preserving.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Towards smarter green infrastructure: Fusing bark ecology and stemflow hydrodynamics on tree stems

A wide array of bark surfaces sheath wooded plants in rural and urban areas alike. Much work has examined the function and role of bark in different contexts and different environs, including urban areas, finding that it is rich in life and can play a role in the transfer of water and matter to the ground surface. Accordingly, this paper presents a first step to weld and fuse bark ecology and stemflow hydrodynamics. It is an effort to develop a physically-based understanding of the transport of water and matter (e.g., solutes, particulates, microorganisms) along tree stems using relevant equations to allow a more informed consideration of bark in green infrastructure initiatives. In particular, the hydrodynamical equations are based on the conservation of water mass, conservation of momentum, and conservation of scalar mass. These equations, coupled with contemplation of corticular life, underpin and substantiate bark’s unifying role as a modulator and cultivator. By elucidating the ‘black box’ of the tree stem and utilizing the formulations set forth in this paper, urban foresters and planners can develop green infrastructure to help advance ecosystem services and sustainability development goals (SDG), especially SDG 11 and SDG 15.

60 APPLIED LIFE SCIENCES↗

Development of a CPU/GPU portable software library for Lagrangian–Eulerian simulations of liquid sprays

The Lagrangian–Eulerian method is widely used for simulations of fuel sprays in turbulent combustion because of the advantage of treating the spray droplets as discrete points. One challenge of the Lagrangian–Eulerian method is the intense computational requirement when tracking the large number of Lagrangian particles needed for high fidelity. We have developed a performance-portable library, Grit, to track the Lagrangian particles in parallel on central processing unit (CPU) and graphics processing unit (GPU) accelerated high performance computing (HPC) architectures. Grit is a C++ library which employs Message Passing Interface (MPI) for distributed memory parallelism and Kokkos programming model for on-node shared memory parallelism with performance portability across different architectures of GPUs and multi-core/manycore CPUs. The parallel algorithms, key parallel kernels, and their performances on the pre-exascale supercomputer, Summit, are presented. Grit is coupled with a direct numerical simulation (DNS) solver, S3D, for multiphase simulations. A conservative formulation has been developed and implemented in Grit for phase coupling with thermodynamic consistency. The formulation separates the conservation of mass, momentum and energy from the physical models to prevent accidental violation of conservation laws due to inconsistent models. The formulation also enforces consistent definitions of enthalpies of the fuel for both phases and the latent heat of evaporation. Finally, simulations of turbulent particle-laden flow and the evaporation of dilute turbulent spray jet are performed to verify the software implementation, and to demonstrate the scalability of Grit for large-scale multiphase simulations.

97 MATHEMATICS AND COMPUTING↗

Quantum Fokker-Planck modeling of degenerate electrons

In this work, an implicit and conservative numerical scheme is proposed for the isotropic quantum Fokker-Planck equation describing the evolution of degenerate electrons subject to elastic collisions with other electrons and ions. The electron-ion and electron-electron collision operators are discretized using a discontinuous Galerkin method, and the electron energy distribution is updated by an implicit time integration method. The numerical scheme is designed to satisfy all conservation laws exactly. Numerical tests and comparisons with other modeling approaches are shown to demonstrate the accuracy and conservation properties of the proposed method.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Implicit shock tracking for unsteady flows by the method of lines

Here, a recently developed high-order implicit shock tracking (HOIST) framework for resolving discontinuous solutions of inviscid, steady conservation laws is extended to the unsteady case. Central to the framework is an optimization problem which simultaneously computes a discontinuity-aligned mesh and the corresponding high-order approximation to the flow, which provides nonlinear stabilization and a high-order approximation to the solution. This work extends the implicit shock tracking framework to the case of unsteady conservation laws using a method of lines discretization via a diagonally implicit Runge-Kutta method by “solving a steady problem at each timestep”. We formulate and solve an optimization problem that produces a feature-aligned mesh and solution at each Runge-Kutta stage of each timestep, and advance this solution in time by standard Runge-Kutta update formulas. A Rankine-Hugoniot based prediction of the shock location together with a high-order, untangling mesh smoothing procedure provides a high-quality initial guess for the optimization problem at each time, which results in rapid convergence of the sequential quadratic programing (SQP) optimization solver. This method is shown to deliver highly accurate solutions on coarse, high-order discretizations without nonlinear stabilization and recover the design accuracy of the Runge-Kutta scheme. We demonstrate this framework on a series of inviscid, unsteady conservation laws in both one- and two- dimensions. We also verify that our method is able to recover the design order of accuracy of our time integrator in the presence of a strong discontinuity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗