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At least 1,135 records · Page 63

Evidence linking calcium to increased organo-mineral association in soils

Geochemical indicators are emerging as important predictors of soil organic carbon (SOC) dynamics, but evidence concerning the role of calcium (Ca) is scarce. This study investigates the role of Ca prevalence in SOC accumulation by comparing otherwise similar sites with (CaCO 3 -bearing) or without carbonates (CaCO 3 -free). We measured the SOC content and indicators of organic matter quality (C stable isotope composition, expressed as δ 13 C values, and thermal stability) in bulk soil samples. We then used sequential sonication and density fractionation (DF) to separate two occluded pools from free and mineral-associated SOC. The SOC content, mass, and δ 13 C values were determined in all the fractions. X-ray photoelectron spectroscopy was used to investigate the surface chemistry of selected fractions. Our hypothesis was that occlusion would be more prevalent at the CaCO 3 -bearing site due to the influence of Ca on aggregation, inhibiting oxidative transformation, and preserving lower δ 13 C values. Bulk SOC content was twice as high in the CaCO 3 -bearing profiles, which also had lower bulk δ 13 C values, and more occluded SOC. Yet, contrary to our hypothesis, occlusion only accounted for a small proportion of total SOC (< 10%). Instead, it was the heavy fraction (HF), containing mineral-associated organic C, which accounted for the majority of total SOC and for the lower bulk δ 13 C values. Overall, an increased Ca prevalence was associated with a near-doubling of mineral-associated SOC content. Future investigations should now aim to isolate Ca-mediated complexation processes that increase organo-mineral association and preserve organic matter with lower δ 13 C values.

58 GEOSCIENCES↗

Microscale mechanical modeling of deformable geomaterials with dynamic contacts based on the numerical manifold method

Abstract Micromechanical modeling of geomaterials is challenging because of the complex geometry of discontinuities and potentially large number of deformable material bodies that contact each other dynamically. In this study, we have developed a numerical approach for micromechanical analysis of deformable geomaterials with dynamic contacts. In our approach, we detect contacts among multiple blocks with arbitrary shapes, enforce different contact constraints for three different contact states of separated, bonded, and sliding, and iterate within each time step to ensure convergence of contact states. With these features, we are able to simulate the dynamic contact evolution at the microscale for realistic geomaterials having arbitrary shapes of grains and interfaces. We demonstrate the capability with several examples, including a rough fracture with different geometric surface asperity characteristics, settling of clay aggregates, compaction of a loosely packed sand, and failure of an intact marble sample. With our model, we are able to accurately analyze (1) large displacements and/or deformation, (2) the process of high stress accumulated at contact areas, (3) the failure of a mineral cemented rock samples under high stress, and (4) post-failure fragmentation. The analysis highlights the importance of accurately capturing (1) the sequential evolution of geomaterials responding to stress as motion, deformation, and high stress; (2) large geometric features outside the norms (such as large asperities and sharp corners) as such features can dominate the micromechanical behavior; and (3) different mechanical behavior between loosely packed and tightly packed granular systems.

58 GEOSCIENCES↗

Growth and survival rates of dispersing free embryos and settled larvae of pallid sturgeon ( Scaphirhynchus albus ) in the Missouri River, Montana and North Dakota

We released nearly 1.0 million 1-day post-hatch (dph) and 5-dph pallid sturgeon (Scaphirhynchus albus) free embryos in the Missouri River on 1 July 2019 and sequentially captured survivors at multiple sites through a 240-km river reach to quantify daily growth and survival rates during the early life stages. Genetic analysis was used to assign captured fish to released family lots and known ages. Growth rate was similar (0.74–0.75 mm day –1 ) between the 1- and 5-dph age groups during the 3–4-day dispersal period when water temperature averaged 16.8 °C. Daily survival rate was 0.64 during 1–4 dph for the original 1-dph age group and 0.80 during 5–7 dph for the original 5-dph age group. Total survival during free embryo dispersal (hatch to 9 dph) was estimated as 0.0437. The transition from dispersing as free embryos to settling as benthic larvae was verified for fish originally released as 5 dph. Growth of settled larvae was quantified with a Gompertz model through 75 dph (9 September; 112 mm) when water temperature was 18.8–21.0 °C in the rearing areas. Settled larvae had an estimated daily survival rate of 0.96, and estimated total survival during 9–75 dph was 0.0714. This study provides the first empirical survival estimates for pallid sturgeon early life stages in natural settings and is one of few studies reporting similar information for other sturgeon species. Applications of this work extend to pallid sturgeon restoration programs where population models are being developed to predict recruitment potential and population responses to river management alternatives.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient Multigrid Reduction-in-Time for Method-of-Lines Discretizations of Linear Advection

Parallel-in-time methods for partial differential equations (PDEs) have been the subject of intense development over recent decades, particularly for diffusion-dominated problems. It has been widely reported in the literature, however, that many of these methods perform quite poorly for advection-dominated problems. In this report we analyze the particular iterative parallel-in-time algorithm of multigrid reduction-in-time (MGRIT) for discretizations of constant-wave-speed linear advection problems. We focus on common method-of-lines discretizations that employ upwind finite differences in space and Runge-Kutta methods in time. Using a convergence framework we developed in previous work, we prove for a subclass of these discretizations that, if using the standard approach of rediscretizing the fine-grid problem on the coarse grid, robust MGRIT convergence with respect to CFL number and coarsening factor is not possible. This poor convergence and non-robustness is caused, at least in part, by an inadequate coarse-grid correction for smooth Fourier modes in space-time known as characteristic components. We propose an alternative coarse-grid operator that provides a better correction of these modes. This coarse-grid operator is related to previous work and uses a semi-Lagrangian discretization combined with an implicitly treated truncation error correction. Theory and numerical experiments show the proposed coarse-grid operator yields fast MGRIT convergence for many of the method-of-lines discretizations considered, including for both implicit and explicit discretizations of high order. Parallel results demonstrate speed-up over sequential time-stepping.

97 MATHEMATICS AND COMPUTING↗

Using Filter Methods to Guide Convergence for ADMM, with Applications to Nonnegative Matrix Factorization Problems

Nonconvex, nonlinear optimization problems arise naturally in parameter fitting and machine learning. While augmented Lagrangian methods have demonstrated robust convergence for classes of these problems, their convergence for block updates has been relatively unexplored outside of the context of the alternating direction method of multipliers (ADMM). ADMM has seen extensive use in these applications, but may exhibit uncertain convergence behavior in many practical nonconvex settings, and struggles with general nonlinear constraints. In contrast, filter methods have proved effective in enforcing convergence for sequential quadratic programming methods and interior point methods with feasibility criteria. We develop an ADMM-filter method for highly nonlinear and nonconvex problems. Here, we show convergence under mild assumptions for several types of coordinate descent schemes, and demonstrate our algorithm on nonnegative matrix factorization and completion problems in imaging and chemical spectrum analysis.

Nonconvex optimization↗

Powering DNA strand-displacement reactions with a continuous flow reactor

Living systems require a sustained supply of energy and nutrients to survive. These nutrients are ingested, transformed into low-energy waste products, and excreted. In contrast, synthetic DNA strand-displacement reactions typically run within closed systems provided with a finite initial supply of reactants. Once the reactants are consumed, all net reactions halt and the system ceases to function. In the study, we ran DNA strand-displacement reactions in a continuous flow reactor, infusing fresh reactants and withdrawing waste, enabling the system to dynamically update its outputs in response to changing inputs. Running DNA strand-displacement reactions inside of continuous flow reactors allows the system to be re-used for multiple rounds of computation, which could enable the execution of more elaborate information processing tasks, including single-rail negation and sequential logic circuits.

59 BASIC BIOLOGICAL SCIENCES↗

Exploratory Investigation of Coal in Nonequilibrium Plasma

Coal is an abundant natural resource and there is motivation to find new uses for it that do not intrinsically involve combustion. One approach is to explore new ways of processing coal, and in this work, we focus on the transformation of coal in a nonequilibrium plasma generated from an equimolar mixture of nitrogen and hydrogen. The outcome of the nonequilibrium plasma reaction is fundamentally different than a thermal control reaction carried out using the same gas composition, pressure, and temperature range. The nonequilibrium plasma produces a gas mixture that is enriched in acetylene and its derivatives. Furthermore, when compared to the thermal control experiment, the solid char byproduct of the nonequilibrium plasma has a very reactive surface and is spontaneously combustible at ambient temperature. Experiments performed to characterize the reaction kinetics of coal in the plasma suggest that the mechanism proceeds through a sequential process by which the coal particle temperature rises to a point where devolatilization can occur, the devolatilization reaction happens, followed by parallel reactions of released organic vapors in the plasma phase and surface activation. In conclusion, the reaction rate appears to be limited by the time it takes for the coal particle temperature to rise, consistent with previous results reported for reactions of coal in thermal plasma.

Acetylene↗

Low soil phosphorus availability triggers maize growth stage specific rhizosphere processes leading to mineralization of organic P

Phosphorus (P) is one of the essential nutrients for all living organisms. High-quality mineral P fertilizer is a finite resource with only an estimated 80-100 years of reserves remaining globally. Both plants and microbes have developed several mechanisms such as secretion of organic acids, acidification of the rhizosphere, and production of extracellular enzymes to enhance the acquisition of P from soils. Increased activity of phosphatase occurs in response to P deficiency as part of P starvation responses which catalyze the hydrolysis of P o from soil organic matter (SOM) and release inorganic P (P i ). However, the specific interactions between plants and microbial communities in the rhizosphere soil triggered by P deficiency are largely unknown. In a greenhouse study we grew maize plants in low and high P containing soils and examined the role of rhizosphere processes on mineralization of organic P (P o ) in soils with low and high P availability and different P speciation 23 (Po dominated versus P i dominated) and determine its effect on plant growth. Plant biomass was determined and rhizosphere soils, and soil samples from pots with and without plants were collected at key vegetative growth stages (VGS). A variety of biogeochemical parameters (e.g. microbial biomass C and P, potential phosphatase activities, plant biomass P, soil P species etc.) were determined using both conventional (sequential chemical extraction) and advanced (e.g. high resolution mass spectrometry (FTICR-MS) and 3129 P solution NMR) techniques. Here, we used phospholipid fatty acid (PLFA) and DNA based microbial community analysis to track changes in microbial community structure and diversity. Low P availability induced changes in biogeochemical processes and microbial community composition in the rhizosphere soils of plants grown in low P containing soil. At early VGS, the plants in low P soil were visually struggling which correlated with greater rhizosphere potential acid phosphatase activity and a reduction in P o fractions. At late VGS, the plants appeared to recover which correlated with a decrease in Meh (III) extractable P, an increase in microbial biomass C and P and greater total P in the plant biomass (roots, shoots and leaves). In high P containing soil, on the other hand, greater P availability masked these rhizosphere processes. Our results confirmed the degradation of SOM and Po mineralization in rhizosphere soils driven by microbe and plant need for P. P deficiency may have favored the abundance of fungi which utilized easily degradable root exudates for the production of extracellular enzymes responsible for the mineralize of SOM P o . This study highlights the intertwined mechanisms involved, and emphasizes the importance of, P o sources for plant nutrition and survival in marginal soils.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Bayesian projection pursuit regression

In projection pursuit regression (PPR), a univariate response variable is approximated by the sum of $M$ “ridge functions,” which are flexible functions of one-dimensional projections of a multivariate input variable. Traditionally, optimization routines are used to choose the projection directions and ridge functions via a sequential algorithm, and $M$ is typically chosen via cross-validation. Here, we introduce a novel Bayesian version of PPR, which has the benefit of accurate uncertainty quantification. To infer appropriate projection directions and ridge functions, we apply novel adaptations of methods used for the single ridge function case ($M$=1), called the Bayesian Single Index Model; and use a Reversible Jump Markov chain Monte Carlo algorithm to infer the number of ridge functions $M$. We evaluate the predictive ability of our model in 20 simulated scenarios and for 23 real datasets, in a bake-off against an array of state-of-the-art regression methods. Finally, we generalize this methodology and demonstrate the ability to accurately model multivariate response variables. Its effective performance indicates that Bayesian Projection Pursuit Regression is a valuable addition to the existing regression toolbox.

97 MATHEMATICS AND COMPUTING↗

$\mathrm{PPT}$-Multicore: performance prediction of Open$\mathrm{MP}$ applications using reuse profiles and analytical modeling

In this report we present PPT-Multicore, an analytical model embedded in the Performance Prediction Toolkit (PPT) to predict parallel applications’ performance running on a multicore processor. PPT-Multicore builds upon our previous work towards a multicore cache model. We extract LLVM basic block labeled memory trace using an architecture-independent LLVM-based instrumentation tool only once in an application’s lifetime. The model uses the memory trace and other parameters from an instrumented sequentially executed binary. We use probabilistic and computationally efficient reuse profiles to predict the cache hit rates and runtimes of OpenMP programs’ parallel sections. We model Intel’s Broadwell, Haswell, and AMD’s Zen2 architectures and validate our framework using different applications from PolyBench and PARSEC benchmark suites. The results show that PPT-Multicore can predict cache hit rates with an overall average error rate of 1.23% while predicting the runtime with an error rate of 9.08%.

97 MATHEMATICS AND COMPUTING↗

Reactive Transport Modeling with Physics-Informed Machine Learning for Critical Minerals Applications

This study presents a physics-informed neural network (PINN) framework for reactive transport modeling for simulating fast bimolecular reactions in porous media. Accurate characterization of cAhemical interactions and product formation in surface and subsurface environments is essential for advancing critical mineral extraction and related geoscience applications. The proposed methodology sequentially addresses the flow and diffusion–reaction subproblems. The flow field is computed using a mixed formulation, while the diffusion–reaction system is modeled via two uncoupled tensorial diffusion equations reformulated in terms of chemical invariants. PINNs are employed to solve the governing equations, enabling data-efficient, mesh-free prediction of chemical concentration fields. The framework is validated through a series of benchmark problems involving flow in heterogeneous porous media. Initial verification is conducted using patch tests for the flow field, followed by validation of the transport problem with emphasis on preserving non-negativity of concentrations. The complete fast bimolecular reaction scenario is then solved, yielding spatial distributions of reactants and product species. Results demonstrate that the PINNs-based approach effectively captures sharp, mixing-limited reaction fronts and dispersive mixing behavior, offering reliable predictions of reactive plume evolution. These capabilities are crucial for evaluating long-term subsurface behavior in applications such as fluid storage, energy extraction, and efficient extraction of critical minerals.

42 ENGINEERING↗

Formal verification and validation of run-to-completion style state charts using Event-B

State chart notations with ‘run to completion’ semantics are popular with engineers for designing controllers that react to environment events with a sequence of state transitions but lack formal refinement and rigorous verification methods. State chart models are typically used to design complex control systems that respond to environmental triggers with a sequential process. The model is usually constructed at a concrete level and verified and validated using animation techniques relying on human judgement. Event-B, on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. Abstraction and formal verification provide greater assurance that critical (e.g. safety or security) properties are not violated by the control system. In this paper, we introduce a notion of refinement into a ‘run to completion’ state chart modelling notation and leverage Event-B’s tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Event-B refinements and suggest a solution. We illustrate our approach and show how models can be validated at different refinement levels using our scenario checker animation tools. We show how critical invariant properties can be verified by proof despite the reactive nature of the system and how behavioural aspects of the system can be verified by testing the expected reactions using a temporal logic, model checking approach. To verify liveness, we outline a proof that the run to completion is deadlock-free and converges to complete the run.

97 MATHEMATICS AND COMPUTING↗

Residual Stress Modeling with Phase Transformation for Wire Arc Additive Manufacturing of B91 Steel

Wire arc additive manufacturing (WAAM) is an energy-efficient manufacturing technique used for near-net-shape production of functional industrial components. However, heat accumulation during deposition and the associated mechanical and metallurgical changes result in complex residual stress profiles across the cross section of the fabricated components. These residual stresses are detrimental to the service life of the components. In this study, sequentially coupled thermomechanical analysis of WAAM B91 steel is conducted to quantify the residual stress variation across the component. The thermomechanical analysis includes a transient heat transfer model and a static stress model that incorporates the transformation-induced plasticity due to martensitic phase transformation. Here, the experimentally calibrated heat transfer model mirrors the temperature variation of the system during the deposition. The results from the stress model are validated via x-ray diffraction measurements, and the numerical results are in good agreement with the experimental data.

20 FOSSIL-FUELED POWER PLANTS↗

Adoption of image-driven machine learning for microstructure characterization and materials design: A Perspective

Microstructure characterization enables the development of structure-processing-property relationships critical to several research areas within the broad field of materials science, from alloy design to the assessment of corrosion resistance, and failure analysis. Conventional approaches to material characterization have relied on either qualitative inference by the human ex-pert or software applications that can extract high-level features from images, such as boundary segmentation, average grain diameter, etc. Such approaches rely heavily on subject matter expert user intervention and knowledge of what phases or more generally, what microstructural features, are of interest. The recent surge in the adoption of machine learning techniques to address problems in materials engineering has brought with it an increased interest and application of Image Driven Machine Learning (IDML) approaches. In this work, we review the applications of IDML to the field of materials characterization. A canonical hierarchy of stages is defined, which when put sequentially together completes an IDML study: problem definition, dataset building, model selection and training, model evaluation, and integration with existing instrumentation or simulation workflow. The studies reviewed in this work are analyzed from the perspective of each of these stages. Such a review permits agranular assessment of the field, for example the impact of IDML on materials characterization at the nanoscale, the size of a typical dataset required to train a semantic segmentation model on electron microscopy images, ubiquitousness of transfer learning in the domain, etc. Finally, we discuss the importance of interpretability and explainability in the field of IDML for materials characterization, and provide an overview of two emerging techniques in the field: semantic segmentation and generative adversarial networks.

Baskaran, Arun↗

Enhancing Surface Finish of Additively Manufactured 316L Stainless Steel with Pulse/Pulse Reverse Electropolishing

To improve the reliable integration of additively manufactured (AM) metal components, there is an urgent need for surface finishing methods capable of processing rough, “as-printed” surfaces. Here, we present a new and scalable electropolishing (EP) technique for use on AM 316L stainless steel (SS) that is capable of achieving a surface roughness equivalent to a machined finish, with arithmetic mean heights (S a ) as low as 1.0 µm. This technique utilizes the sequential application of a new, NaCl/H 2 O pulse/pulse reverse (P/PR) EP step along with a conventional DC (direct current) EP step, where P/PR expands the capability of EP by removing roughness features > 1 µm, which has been previously unattainable with DC EP alone without substantial material removal. This is achieved by independently varying pulse parameters, such as pulse width and height, allowing more control over electrodynamic processes at the part-electrolyte interface. Additionally, P/PR EP resulted in higher smoothing efficiency, where a higher degree of smoothing was achieved with less material removal when compared with conventional DC EP alone. This minimizes unwanted change in geometry from excessive metal dissolution.

36 MATERIALS SCIENCE↗

Process model for multilayer slide coating of polymer electrolyte membrane fuel cells

Slide coating is a precision method suitable for depositing multiple liquid-film layers simultaneously. Originally developed in the photographic film industry, it has been deployed for manufacturing of other products that benefit from multilayer coatings. One emerging application is the manufacture of polymer electrolyte membrane fuel cells (PEMFCs), which are used to produce electricity through electrochemical reactions of hydrogen and oxygen gas. The membrane-electrode assembly (MEA), in which key electrochemical reactions occur, consists of three layers that are typically deposited separately in serial fashion and then laminated together to form the three-layer MEA, i.e., three sequential steps of coat and dry. Adapting the process to simultaneous, multilayer slide coating of all three layers will save equipment cost and space while minimizing possible exposure to contaminants during transition between the steps. We are developing a three-layer slide coating model to aid the manufacturing process design of PEMFC. The model accounts for rheology of each layer, which typically exhibit shear thinning behavior. Model predictions are used to investigate simultaneous coatability of catalyst inks and to determine the best layer-by-layer ink selection.

25 ENERGY STORAGE↗

Multi-site Milling Strategy Reveals Significant Variation in Biomass Composition of Switchgrass ( Panicum virgatum ) Grown at Ten Locations

Cell wall composition influences biomass use as a forage and as a feedstock for biofuel and chemical conversion. To examine the influence of environment on composition of switchgrass (Panicum virgatum L.), we utilized a multi-environment experiment consisting of clones of switchgrass genotypes grown at up to ten locations in the continental US. We tested the influence of different milling treatments on biomass composition trait predictions via near-infrared reflectance spectroscopy (NIRS). We found that most compositional trait predictions (29/34) were significantly different (P < 0.05) when a single lot of biomass was subjected to disparate milling treatments, i.e., knife milling vs. knife milling with an additional cyclone milling. Further, depending on the plant material tested, three to eight compositional trait predictions vary (P < 0.05) when identical biomass was knife milled at different sites followed by cyclone milling at a single site, including for traits such as Klason lignin, nitrogen, and carbon. In some cases, variation due to milling site exceeded environmentally induced compositional variation of a single switchgrass genotype grown at different sites. From these observations, we recommend a protocol with two sequential millings that decouples growth environment from a particular mill. Utilizing this approach, we found that 46/46 biomass composition traits from the warm season herbaceous forage and switchgrass bioethanol NIRS equations vary significantly (P < 0.001) in clones of a switchgrass genotype (WBC) grown at ten sites, with the growth site representing the largest average source of variation (41%). This multi-site milling approach can be used to examine environmental and gene-by-environment influences on composition with the goal of optimizing cell wall composition in different environments for biomass utilization.

09 BIOMASS FUELS↗