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141 records · Page 8

Mechanism-Based Energy Regularization in Computational Modeling of Quasibrittle Fracture

Abstract Quasibrittle materials are featured by a strain-softening constitutive behavior under many loading scenarios, which could eventually lead to localization instability. It has long been known that strain localization would result in spurious mesh sensitivity in finite element (FE) simulations. Previous studies have shown that, for the case of fully localized damage, the mesh sensitivity can be mitigated through energy regularization of the material constitutive law. However, depending on the loading configuration and structural geometry, quasibrittle structures could exhibit a complex damage process, which involves both localized and diffused damage patterns at different stages of loading. This study presents a generalized energy regularization method that considers the spatial and temporal evolution of damage pattern. The method introduces a localization parameter, which describes the local damage pattern. The localization parameter governs the energy regularization of the constitutive model, which captures the transition from diffused to localized damage during the failure process. The method is cast into an isotropic damage model, and is further extended to rate-dependent behavior. The energy regularization scheme is directly incorporated into the kinetics of damage growth. The model is applied to simulate static and dynamic failures of ceramic specimens. It is shown that the present model is able to effectively mitigate the spurious mesh sensitivity in FE simulations of both types of failure. The present analysis demonstrates the essential role of mechanism-based energy regularization of constitutive relation in FE simulations of quasibrittle fracture.

Mechanics↗

Fiber-optic diagnostic system for future accelerator magnets

The next generation high energy physics accelerators will require magnetic fields at ~20 T. HTS coils will be an essential component of future accelerator magnets and several efforts are currently dedicated on designing 20 T HTS- LTS hybrid magnets. Among the existing challenges, there is the lack of a robust quench detection system for hybrid magnet technology. Another big challenge is represented by the high number of training quenches required by Nb3Sn magnets to reach performance level. In this framework it is important to find a tool that allow local real-time monitoring of magnet strain and temperature. In this paper, we propose the use of fiber optics sensors for diagnostic and quench detection in future accelerator superconducting magnets. Discrete and distributed fiber optic sensors have demonstrated to be a promising tool. The goal is to instrument hundreds of accelerator superconducting magnets and to move beyond the proof-of-concept level. Significant developments are still needed. Here, we are going to present the most recent results and discuss the most urgent technical developments in order to make those sensors a robust and reliable diagnostic tool for accelerator superconducting magnets over the next 10 year. We foresee that discrete fiber sensors will be a stable diagnostic probe for superconducting magnets over the next 3 to 5 years. More R&D work will be necessary for distributed fibers. The most urgent needs are the increase of sample rate and sensitivity. Close collaboration with vendors will be necessary to improve mechanical properties and fabrication processes in order to produce hundreds of meters of fiber and instrument a large number of accelerator superconducting magnets. Those R&D efforts will last up to 10 years with a founding level that spans between 5-10 M$.

43 PARTICLE ACCELERATORS↗

An Eulerian crystal plasticity framework for modeling large anisotropic deformations in energetic materials under shocks

Here, this paper demonstrates a novel Eulerian computational framework for modeling anisotropic elastoplastic deformations of organic crystalline energetic materials (EM) under shocks. While Eulerian formulations are advantageous for handling large deformations, constitutive laws in such formulations have been limited to isotropic elastoplastic models, which may not fully capture the shock response of crystalline EM. The present Eulerian framework for high-strain rates, large deformation material dynamics of EM incorporates anisotropic isochoric elasticity via a hypo-elastic constitutive law and visco-plastic single-crystal models. The calculations are validated against atomistic calculations and experimental data and benchmarked against Lagrangian (finite element) crystal plasticity computations for shock-propagation in a monoclinic organic crystal, octahydro-1,3,5,7-tetranitro-1,3,5,7 tetrazocine (β-HMX). The Cauchy stress components and the resolved shear stresses calculated using the present Eulerian approach are shown to be in good agreement with the Lagrangian computations for different crystal orientations. The Eulerian framework is then used for computations of shock-induced inert void collapse in β-HMX to study the effects of crystal orientations on hotspot formation under different loading intensities. The computations show that the hotspot temperature distributions and the collapse profiles are sensitive to the crystal orientations at lower impact velocities (viz., 500 m/s); when the impact velocity is increased to 1000 m/s, the collapse is predominantly hydrodynamic and the role of anisotropy is modest. The present methodology will be useful to simulate energy localization in shocked porous energetic material microstructures and other situations where large deformations of single and polycrystals govern the thermomechanical response.

42 ENGINEERING↗

Experimental verification of a crystal plasticity-based simulation framework for predicting microstructure and geometric shape changes: Application to bending and Taylor impact testing of Zr

This paper is concerned with experimental verification of a recently developed multi-scale simulation framework for plastic deformation of metallic materials from quasi-static to impact deformation conditions. The framework is a visco-plastic self-consistent (VPSC) polycrystalline model embedded in an implicit finite element method (FE-VPSC) to provide a microstructure-sensitive constitutive response at each material point. Each material point of the FEM model is a polycrystalline aggregate with crystallographic deformation mechanisms operating at the single crystal scale with their evolving activity based on a dislocation density-based hardening law and texture. Four beams and three cylinders machined in different orientations from a textured plate of high-purity zirconium are tested quasi-statically in 4-point bending and at speeds of 100 m/s, 170 m/s and 243 m/s during Taylor impact tests, respectively. The variation in dimensional changes resulting from different sample orientations in the plate with respect to loading directions is measured for each sample. Moreover, texture and twinning characterization is performed using electron backscattered diffraction (EBSD). The deformation processes and underlying evolution of microstructure are successfully simulated using the FE-VPSC framework. In doing so, the model parameters are optimized and validated across a broad range of strain rates and temperatures. Simulation results in terms of geometrical changes and microstructural evolution are compared with the experimental measurements. The model predicts anisotropic material flow resulting from the hard-to-deform crystallographic directions, the development of gradients in texture and twinning through the geometries, tension–compression asymmetry, as well as the extent of plasticity under impact.

42 ENGINEERING↗

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%–94% of the variance in aneuploid strains’ growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.

genic load↗

Microstructure-sensitive modeling of high temperature creep in grade-91 alloy

Predicting the effects of microstructure on high-temperature creep responses of steel components is critical to minimize the risks of failure and maximize economic viability in the energy sector. In this research, a recently developed advanced mechanistic constitutive model is employed to study the effect of microstructure on the creep responses and to rationalize experimentally reported variability in the performances of grade-91 alloy. Hundreds of experimental creep tests from the literature are used to assess the predictability of the model. The model proposed is shown to accurately predict the steady-state creep rates and also the less commonly considered, yet important, primary-to-secondary transients for a wide range of creep conditions. Further, the model is capable of extrapolating the creep response of grade 91 alloy even outside of the calibration regime. Using this model, the roles of initial microstructure described in terms of grain size, dislocation density, and precipitate content, on the creep responses are investigated. The effect of initial microstructure on the steady-state creep rates and creep-strain is found to vary with stress and temperature. Grain size plays a significant role in the low-stress creep, where the diffusional creep is dominant. On the other hand, the effects of dislocation densities and precipitate content are significant in the dislocation-plasticity-dominated high-stress and temperature regimes. Furthermore, by comparing model predictions against a large experimental creep database, it is found that variability in the creep responses can be rationalized on the basis of differences in the initial microstructure. Overall, this work provides a robust pathway for microstructure-aware engineering design, verification, and validation of metallic components for energy applications.

36 MATERIALS SCIENCE↗

Binder-jetted AISI M2 tool steel during hot isostatic pressing: Densification and carbide transformation

Binder jetting (BJ) enables fabrication of complex components from high-alloy steels such as AISI M2; however, residual porosity after sintering limits mechanical performance. This study investigates the coupled effects of binder chemistry, sintering conditions, cooling rate, and subsequent hot isostatic pressing (HIP) on densification, microstructure, and mechanical response in binder-jetted M2 tool steel. HIP increased relative density from ∼93 to 95% to >99% and improved compressive strength by ∼40-70%. Densification was governed by initial pore morphology, where closed porosity was effectively eliminated, while interconnected porosity limited full consolidation. Microstructural analysis (XRD, EBSD, SEM) shows that HIP promotes dissolution of metastable carbides and redistribution of alloying elements (W, Mo, V), transforming heterogeneous carbide networks into finer and more uniformly distributed M 2 C, MC, and M 6 C phases through diffusion-assisted homogenization. Among the investigated conditions, the FluidFuse binder combined with sintering at 1270 °C for 60 min and furnace cooling produced the most balanced response, achieving ∼99.7% density, ∼855 HV hardness, ∼4130 MPa compressive strength, and ∼24% strain. In contrast, higher sintering temperatures promoted carbide coarsening, reducing ductility despite high density. HIP reduces microstructural heterogeneity and drives the system toward a near-equilibrium state with reduced sensitivity to prior processing history. A comparative assessment with conventional and additive manufacturing routes (LPBF, DED, EBM, FFF) shows that the BJ-HIP approach achieves competitive densification and mechanical performance. These findings provide a mechanistic basis for controlling densification and microstructure in high-alloy steels processed via BJAM.

AISI M2 tool steel↗

A non-isothermal breakage-damage model for plastic-bonded granular materials incorporating temperature, pressure, and rate dependencies

Plastic-bonded granular materials (PBM) are widely used in industrial sectors, including building construction, abrasive applications, and defense applications such as plastic-bonded explosives. The mechanical behavior of PBM is highly nonlinear, irreversible, rate dependent, and temperature sensitive governed by various micromechanical attributions such as grain crushing and binder damage. This paper presents a thermodynamically consistent, microstructure-informed constitutive model to capture these characteristic behaviors of PBM. Key features of the model include a breakage internal variable to upscale the grain-scale information to the continuum level and to predict grain size evolution under mechanical loading. In addition, a damage internal state variable is introduced to account for the damage, deterioration, and debonding of the binder matrix upon loading. Temperature is taken as a fundamental external state variable to handle non-isothermal loading paths. The proposed model is able to capture with good accuracy several important aspects of the mechanical properties of PBM, such as pressure-dependent elasticity, pressure-dependent yield strength, brittle-to-ductile transition, temperature dependency, and rate dependency in the post-yielding regime. Furthermore, the model is validated against multiple published datasets obtained from confined and unconfined compression tests, covering various PBM compositions, confining pressures, temperatures, and strain rates.

Breakage↗

Interpreting strain tensor data to characterize and monitor reservoirs for CO2 storage and other applications

Recent advances in instrumentation have made it feasible to measure the transient strain tensor caused by small changes in fluid volume or pressure in the subsurface and this has opened the door to new opportunities for characterization and monitoring. We have deployed strainmeters and then conducted injection well tests in an underlying reservoir at 530m depth. The resulting data indicated that the horizontal strain at shallow strainmeters (30 to 40m depth) was tensile and the vertical strain was compressive. The radial strain was less than the horizontal strain, and the strain rates decreased from 100 nanostrain/day to roughly 10 n/d over a few days. The signal at two strainmeters at shallow depth were consistent, although the magnitude of the horizontal strains were different reflecting the different radial directions from the well. The signal at a deep strainmeter deployed at reservoir depth was much different, with tensile vertical strains and compressive horizontal strains. These data can be interpreted by inverting poroelastic forward models developed using numerical and analytical methods. The average horizontal strain in the caprock resembles the transient pressure in the underlying reservoir and classic type-curve methods from transient well testing can be used for preliminary interpretations of strain data. We have developed closed-form analytical solutions to a pressurized poroelastic inclusion and inhomogeneity in a half-space. This model is fast and can be inverted to estimate reservoir stiffness and geometry. Numerical models developed using finite element methods allow more details of the subsurface to be included in the inversion, but they require much longer run times and this makes inversion cumbersome using standard methods. We have developed an inversion approach that uses a proxy model created using machine learning to do most of the forward calculations. The proxy model is periodically updated and refined using the finite element model to ensure accuracy. This approach significantly reduces the computational requirements and makes it feasible to use Bayesian inversion with large numerical models. We have shown that the strain tensor in the caprock is sensitive to pressure in the reservoir, boundaries in the reservoir, and pressure in the caprock caused by leaks. These results indicate that coupling strain tensor data with inversion has the potential to help evaluate reservoirs during initial characterization, and to monitor them during the CO2 injection and storage process.

Murdoch, Larry↗

Temperature effect on turbulent burning velocity of lean premixed hydrogen/air flames

Hydrogen has drawn great attention in recent years as a carbon-free fuel. The turbulent burning velocity (S T ) is an important parameter for the design and modeling of hydrogen-fueled engines given the high propagation speed of hydrogen flames. It has been well documented that S T of hydrogen flames can be dramatically increased by thermo-diffusive effects which are sensitive to thermodynamic conditions. Previous studies have mainly focused on the pressure effect on S T of lean hydrogen flames, while the temperature effect has been largely ignored. Here, in the present study, the turbulent burning velocity for a lean hydrogen/air mixture over a wide range of temperatures (300–641 K) and pressures (1–15 atm) is investigated through direct numerical simulations of statistically planar turbulent premixed flames. Results show that the variation of normalized turbulent burning velocity (S T /S L , where S L is the laminar flame speed) with temperature and pressure is mainly controlled by the variation of the stretching factor I 0 . While S T /S L is only marginally dependent on temperature at the atmospheric pressure, it exhibits a decreasing trend with temperature at an elevated pressure (10 atm). This is associated with different temperature dependencies of flame surface area enlargement at the two different pressures, despite the monotonically decreasing trends of I 0 with temperature at both pressures. In addition, under engine-relevant conditions where the temperature and pressure increase simultaneously, the promotion effect of pressure is found to be largely canceled out by the suppression effect of temperature, leading to only a slight increase in I 0 and S T /S L . The observed trends are further explained through detailed flame dynamic analysis. Furthermore, I 0 at different temperatures and pressures is found to correlate very well with the enhancement of fuel consumption rate in the critically strained laminar flames. The present study elucidates the strong impact of temperature on S T of lean premixed hydrogen/air flames at elevated pressures and provides new insights into the modeling of S T , especially for engine-relevant conditions.

Wang, Yiqing [Argonne National Laboratory (ANL), A↗

Mechanistic assessment of tolerance to iron deficiency mediated by Trichoderma harzianum in soybean roots

Abstract Aims Iron (Fe) deficiency in soil is a continuing problem for soybean (Glycine max L.) production, partly as a result of continuing climate change. This study elucidates how Trichoderma harzianum strain T22 (TH) mitigates growth retardation associated with Fe-deficiency in a highly sensitive soybean cultivar. Methods and Results Soil TH supplementation led to mycelial colonization and the presence of UAOX1 gene in roots that caused substantial improvement in chlorophyll score, photosynthetic efficiency and morphological parameters, indicating a positive influence on soybean health. Although rhizosphere acidification was found to be a common feature of Fe-deficient soybean, the upregulation of Fe-reductase activity (GmFRO2) and total phenol secretion were two of the mechanisms that substantially increased the Fe availability by TH. Heat-killed TH applied to soil caused no improvement in photosynthetic attributes and Fe-reductase activity, confirming the active role of TH in mitigating Fe-deficiency. Consistent increases in tissue Fe content and increased Fe-transporter (GmIRT1, GmNRAMP2a, GmNRAMP2b and GmNRAMP7) mRNA levels in roots following TH supplementation were observed only under Fe-deprivation. Root cell death, electrolyte leakage, superoxide (O2•–) and hydrogen peroxide (H2O2) substantially declined due to TH in Fe-deprived plants. Further, the elevation of citrate and malate concentration along with the expression of citrate synthase (GmCs) and malate synthase (GmMs) caused by TH suggest improved chelation of Fe in Fe-deficient plants. Results also suggest that TH has a role in triggering antioxidant defence by increasing the activity of glutathione reductase (GR) along with elevated S-metabolites (glutathione and methionine) to stabilize redox status under Fe-deficiency. Conclusions TH increases the availability and mobilization of Fe by inducing Fe-uptake pathways, which appears to help provide resistance to oxidative stress associated with Fe-shortage in soybean. Significance and Impact of the Study These findings indicate that while Fe deficiency does not affect the rate or degree of TH hyphal association in soybean roots, the beneficial effects of TH alone may be Fe deficiency-dependent.

59 BASIC BIOLOGICAL SCIENCES↗

A crystal plasticity model with an atomistically informed description of grain boundary sliding for improved predictions of deformation fields

Crystal plasticity (CP) is a powerful meso-scale technique for deformation modeling in polycrystalline materials. Crystal plasticity models typically do not include an explicit description of grain boundary (GB) sliding, which could lead to inaccurate predictions of strain distributions, especially in the vicinity of GBs. In the present study, a CP model is developed that includes GB sliding as an additional deformation mechanism and models the interaction between slip and GB sliding. Atomistic simulations are used to formulate the constitutive model for GB sliding and its interaction with incident slip. The deformation fields and structure of the GBs are obtained directly from experimental characterization and are faithfully reproduced as bicrystal systems for molecular dynamics simulations. The GBs are modeled as random-type (non-coincidence, asymmetrical) boundaries as observed from experimental data. The underlying atomistic-scale mechanism for pure sliding of random GBs was found to be analogous to fluid-flow. The interaction between incident slip and a sliding GB caused local increases in stress concentration, which further led to a momentary increase in the local sliding rate. The displacement profiles at the sliding GBs computed from the CP model with sliding accommodation are 38% more accurate than the baseline CP model as quantified by the mean squared error between the simulations and experiment. Here these results help improve the sophistication and accuracy of deformation modeling by including physics-based descriptions for GB sliding and its interaction with slip, eventually leading to more reliable predictions of micromechanical quantities.

36 MATERIALS SCIENCE↗

Demonstrate new plasticity models for doped UO 2 that capture dislocation mechanisms

In light water reactors, fuel vendors are investigating the use of dopants to modify the properties of UO 2 pellets, with the goal of improving pellet-cladding mechanical interactions during operation. Dopants are expected to ‘soften’ the pellets; that is, the doped pellets have higher plastic deformation than conventional UO 2 . This leads to a reduction in the severity of mechanical pellet-cladding interactions, helping to reduce the hoop strain on the cladding. By minimizing the strain exerted by the pellet on the cladding, it is anticipated that cladding performance under accident conditions can be enhanced (i.e., lowering the risk of burst during a LOCA). Dopants such as chromium (Cr) promote grain growth during pellet fabrication, leading to larger grains; therefore, understanding the link between chemistry, microstructure and mechanical deformation (enhanced creep rates) behavior of UO 2 is critical to helping operators further substantiate the benefits of doping UO 2 . Historically, the nuclear energy industry has relied on empirical models to make assessments of performance. Compared to empirical models, mechanistic physics-based models provide benefits, such as, fewer data points for validation and better extrapolation where experimental data is scarce or non-existent. In this report, Bayesian inference techniques have been applied to a previously developed lower length-scale-informed diffusional creep model. The objective is to i) infer lower-length-scale parameter distributions from available experiment and then ii) determine the uncertainties in the measurable quantity (in this case creep rates) after propagating the inferred lower length scale parameter uncertainties. The approach requires many evaluations of the model, which becomes computationally insurmountable; therefore, a neural-network model is trained to data obtained by sampling the full model over the most important parameters. This neural-network is then used in the Bayesian inference approach to determine probability distributions in the parameter values that represent the uncertainty in the model given what is known from the experiments (posterior). A significant reduction compared to conservative initial (prior) uncertainties is achieved through inference against the experimental data, demonstrating the efficacy of this approach. Furthermore, by accounting for uncertainties in the experimental conditions and sample non-stoichiometry, it is possible to resolve apparent discrepancies in experimental measurements within a self-consistent grain boundary (Coble) creep model that is sensitive to chemistry. This work has been written up and submitted to Nuclear Technology for a special issue on accelerated fuel qualification (AFQ). This uncertainty quantification (UQ) work not only improves the diffusional model, while accounting for uncertainty, but also establishes a framework which can readily be applied to the mechanistic models of dislocation deformation developed in this study. The most likely values from the Bayesian analysis are incorporated into our UO 2 diffusional creep model and a lower length scale-informed irradiation UO 2 creep mechanistic model to generate a dataset. This dataset has been provided to our INL collaborators for training an artificial neural network surrogate model, which will be implemented in the BISON fuel performance code to assess how the results differ from those currently obtained using a fully empirical model and that of using the nominal (uncalibrated) atomic scale parameters in our mechanistic model. Plastic deformation (creep and glide) in UO 2 is a complex phenomenon, governed by multiple underlying processes such as local defect concentrations, applied stresses, and microstructural characteristics. Consequently, there is a need for a meso-scale model with polycrystalline resolution capable of extrapolating to large grain sizes applicable to doped UO 2 , where data is limited and the model can help bridge the knowledge gap. By integrating atomistic data into the polycrystal LApx code, it becomes possible to predict dislocation climb and glide plasticity that simple analytical models cannot accurately represent. The application of atomic-scale data within LApx demonstrated the importance of climb and glide mechanisms in reproducing high-stress UO 2 behavior. Behaviors such as this are crucial to capture and implement in BISON, as parts of the fuel pellet can reach temperatures where glide can occur before pellet cracking. This model which captures dislocation based mechanisms for UO 2 is then used to stand up the doped model accounting for larger grain sizes. It was found that larger grain sizes can lead to enhanced deformation rates in the glide regime, and therefore can help with the pellet cladding mechanical interaction. Therefore if the fuel pellet reaches conditions (stress/temperature) where glide is active, the enhanced creep rates for larger grains in the glide regime (doped UO 2 ) can help with pellet cladding mechanical interactions. Plastic deformation in UO 2 involves multiple mechanisms, including diffusional creep, dislocation climb, and glide. This milestone contains two parts: (1) UQ of a pre-existing lower length scale informed mechanistic diffusional creep model, and (2) development of a new LApx based model for dislocation-mediated creep mechanisms in UO 2 , with application to large-grain doped UO 2 .

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Unbalancing Symbiotic Nitrogen Fixation: Can We Make Effectiveness More Effective?

One of the most critical uses of carbon fuels is in generating nitrogen fertilizer. Atmospheric dinitrogen is too stable to be used directly by plants, so plants need other chemical forms of nitrogen. Nitrogen fertilizer production uses ~4% of the world’s natural gas. Making N fertilizers leverages methane’s energy content by enabling additional energy to be captured into food and fiber through increased photosynthesis. Manufacturing fertilizer is essential—without it there would only be enough combined nitrogen to feed ~3 billion of the world’s ~7 billion people. How to alter this addiction is not obvious, but the best chance to secure substantial and sustainable amounts of future N might be through symbiotic nitrogen fixation (SNF). SNF describes mutualistic interactions where nitrogen-fixing bacteria provide fixed nitrogen to their plant hosts, freeing them from the need for nitrogen fertilizers. SNF already occurs on a large scale; "biological nitrogen” contributes about 5 Tg N/yr to American agriculture, a quarter of the nitrogen needed. Improving SNF and replacing inorganic fertilizers are both important goals in establishing sustainable and more energy-efficient farming. SNF has been used in agriculture for millennia, largely by using legumes like beans or alfalfa in mixed cropping systems. Legume SNF occurs in root nodules, organs that develop after a growing root is infected by bacteria called rhizobia. In the plant cells of a legume nodule, specialized forms of rhizobia fix nitrogen and can produce enough ammonia to supply the growing plant. The exchange of photosynthetically derived plant carbon compounds for nitrogen reduced by the bacteria is the engine that drives the symbiosis. Important details about the organization of development and metabolism in SNF remain to be determined, such as how plant and bacterial metabolism are coordinated as nitrogen is being fixed and what governs the overall level of nitrogen fixation. Most bacterial mutations that affect SNF completely block fixation (e.g. are Fix – ), providing a limited window into the feedback interactions that must be part of the process. We have investigated an unusual mutant of Sinorhizobium meliloti, a symbiotic partner of alfalfa, that fixes dinitrogen at a normal rate (i.e., it is Fix + ) but is not effective in supporting plant growth (i.e., it is ineffective or Eff – ). We have shown that the mutant has a specific mutation in the glnD gene, which codes for a protein that regulates the bacterial response to nitrogen stress, among other key pathways. A Fix + Eff – phenotype contains an unavoidable puzzle—how is it possible for the bacteria to fix nitrogen at a normal rate and without benefiting the nitrogen starved plant host? After eliminating other possibilities, we proposed that the bacteria synthesize a nitrogen-containing compound that the plant can’t use so that acquiring this compound does not relieve plant nitrogen stress. Extracts of nodules made by glnD mutant strains have high concentrations of pyruvate canaline oxime (PCO), a derivative of the plant defensive compound canaline, a toxic analog of ornithine, an amino acid. Many legumes produce canaline and the related arginine mimic canavanine. For reasons we do not yet understand, the mutation in glnD appears to trigger significant overproduction of canaline in a defense response that leads to substantial synthesis of PCO. We expected the bacteria to be able to use PCO, but we have not been able to grow S. meliloti on PCO under several conditions. PCO thus appears to be a metabolic dead end for both the plant and bacteria. We also examined bacterial catabolic pathways that degrade arginine and canavanine and showed that mutation of these did not alter the symbiosis in an obvious way. In related experiments to examine the metabolic development of root nodules, we carried out an ambitious experiment to simultaneously measure metabolites and protein changes during nodule maturation. For these experiments we used a related symbiotic interaction between S. medicae and Medicago truncatula. M. truncatula has a simpler genome than alfalfa so we could identify plant proteins based on predictions from the DNA sequence. Nodules formed on Medicago grow linearly, with the least mature tissues at the tip. Because development of nitrogen fixation is accompanied by the production of the pigmented plant oxygen carrier protein leghemoglobin, we were able to locate and manually separate the tip, transitional, and mature nitrogen-fixing regions from each other. Advances in proteomic and metabolomic techniques allowed us to analyze these tissues from a pool of as few as 10 nodules. We observed correlated transitions of various enzymes in the plant and bacterial proteomes from those characteristic of free-living metabolism to the microaerobic metabolism of the nitrogen-fixing tissues. The metabolome could not be separated into plant and bacterial domains but was consistent with this overall transition. A subsequent paper examined proteolysis in nodule bacteria. Protein turnover in mature regions of the nodule is significant. We were able to show complexes between various proteins and important proteases, using precipitation capture techniques to isolate the proteases and sensitive proteomic analysis to reveal the associated proteins.

09 BIOMASS FUELS↗