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At least 19 records

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Microbiology↗

Native Two-Qubit Gates in Fixed-Coupling, Fixed-Frequency Transmons Beyond Cross-Resonance Interaction

Fixed-frequency superconducting qubits demonstrate remarkable success as platforms for stable and scalable quantum computing. Cross-resonance gates have been the workhorse of fixed-coupling, fixed-frequency superconducting processors, leveraging the entanglement generated by driving one qubit resonantly with a neighbor’s frequency to achieve high-fidelity, universal controlled- () gates. Here, we use on-resonant and off-resonant microwave drives to go beyond cross-resonance, realizing natively interesting two-qubit gates that are not equivalent to gates. In particular, we implement and benchmark native i , , i SWAP , and b gates; in fact, any SU ( 4 ) unitary can be achieved using these techniques. Furthermore, we apply these techniques for an efficient construction of the B gate: a perfect entangler from which any two-qubit gate can be reached in only two applications. We show that these native two-qubit gates are better than their counterparts compiled from cross-resonance gates. We elucidate the resonance conditions required to drive each two-qubit gate and provide a novel frame tracking technique to implement them in Qiskit. Published by the American Physical Society 2024

Physics↗

Minimizing Optimal Transport for Functions with Fixed-Size Nodal Sets

Consider the class of zero-mean functions with fixed L ∞ and L 1 norms and exactly N ϵ N nodal points. Which functions f minimize W p (f + ,f – ), the Wasserstein distance between the measures whose densities are the positive and negative parts? We provide a complete solution to this minimization problem on the line and the circle, which provides sharp constants for previously proven “uncertainty principle”-type inequalities, i.e., lower bounds on N • W p (f + ,f – ). We further show that, while such inequalities hold in many metric measure spaces, they are no longer sharp when the non-branching assumption is violated; indeed, for metric star-graphs, the optimal lower bound on W p (f + ,f – ) is not inversely proportional to the size of the nodal set, N. Here, based on similar reductions, we make connections between the analogous problem of minimizing W p (f + ,f – ) for f defined on Ω C R d with an equivalent optimal domain partition problem.

97 MATHEMATICS AND COMPUTING↗

Investigating the effect of aluminum oxide fixed charge on Schottky barrier height in molybdenum oxide-based selective contacts

A tunneling atomic layer deposited (ALD) AlO x layer was inserted in a Si|SiO x |AlO x |MoO x |metal tunnel diode structure to investigate the impact of fixed interface charge on Schottky barrier height. ALD AlO x provides a synthesis-tunable fixed charge and can provide excellent field effect passivation at the SiO x |AlO x interface. A large (>1 × 10 12 q.cm –2 ) negative fixed charge density was expected to decrease Schottky barrier height on p-type silicon and increase Schottky barrier height on n-type silicon by up to 0.4 eV based on an electrostatic model. Fixed charge density and interface trap state density were measured using a thick layer of AlO x in metal oxide semiconductor capacitor structures (MOSCAPs); Schottky barrier height and specific contact resistivity were measured using a tunneling-active layer of AlO x in contacted structures with MoO x . In some samples, HfO x interface layers were inserted between AlO x and silicon to quench the fixed negative charge. The Schottky barrier height was found to vary with processing conditions but did not have a strong correlation with expected fixed charge density. Here, while fixed charge may play a role in determining the Schottky barrier height, other parameters also have significant affect. Further work is needed to minimize contact resistivity and elucidate other factors impacting the Schottky barrier height.

14 SOLAR ENERGY↗

Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase

ABSTRACT All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N 2 ) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif , vnf , and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif , vnf , and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N 2 but not with NH 4 Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N 2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.

Biotechnology & Applied Microbiology↗

Fixed-Site KAZR b1 Data Processing: Corrections, Calibrations, and Processing Report

The U.S. Department of Energy’s (DOE) Atmospheric Radiation Measurement (ARM) User Facility operates three fixed-site observatories: Eastern North Atlantic (ENA), North Slope of Alaska (NSA), and Southern Great Plains (SGP). Each fixed site has a wide variety of atmospheric instrumentation that has been collecting data for at least 10 years (NSA and SGP over 25 years). Each site is unique because it represents a different climate state. The environment at ENA is characterized by marine stratocumulus clouds and one of the key scientific areas of focus is the interaction of these clouds with aerosols. At NSA the focus is on arctic climate and cloud and radiative processes in a high-latitude environment. SGP represents a mid-latitude, mid-continent climate that experiences environmental cycles on diurnal and seasonal time scales. The ARM observatories are all meant to improve understanding of atmospheric processes that can then be better incorporated into weather and climate models. Another common thread between the fixed sites is the focus on cloud processes. Each site is equipped with at least one radar that provides continuous remote-sensing observations of clouds and precipitation. This report details the analysis of a1-level radar data at the fixed sites and the process for generating b1-level data. While b1-level data have been produced for ARM campaigns at the mobile facilities, this is the first analysis led by ARM radar mentors to correct data at the fixed sites. In particular, we focus on calibrations and corrections of the Ka-band ARM Zenith Radars (KAZRs) at ENA, NSA, and SGP. Ongoing and future work will involve corrections applied to other fixed-site radars.

54 ENVIRONMENTAL SCIENCES↗

All polymer microfluidic chips—A fixed target sample delivery workhorse for serial crystallography

The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around “workhorse” for serial crystallography measurements. In conclusion, this Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.

59 BASIC BIOLOGICAL SCIENCES↗

Fully gauge-fixed SU(2) Hamiltonian for quantum simulations

Here, we demonstrate how to construct a fully gauge-fixed lattice Hamiltonian for a pure SU(2) gauge theory. Our work extends upon previous work, where a formulation of an SU(2) lattice gauge theory was developed that is efficient to simulate at all values of the gauge coupling. That formulation utilized maximal-tree gauge, where all local gauge symmetries are fixed and a residual global gauge symmetry remains. By using the geometric picture of an SU(2) lattice gauge theory as a system of rotating rods, we demonstrate how to fix the remaining global gauge symmetry. In particular, the quantum numbers associated with total charge can be isolated by rotating between the lab and body frames using the three Euler angles. The Hilbert space in this new “sequestered” basis partitions cleanly into sectors with differing total angular momentum, which makes gauge-fixing to a particular total charge sector trivial, particularly for the charge-zero sector. In addition to this sequestered basis inheriting the property of being efficient at all values of the coupling, we show that, despite the global nature of the final gauge-fixing procedure, this Hamiltonian can be simulated using quantum resources scaling only polynomially with the lattice volume.

Lattice gauge theory↗

A Quantum Approach for Implementing Fixed-Point Arithmetic in Solving Ordinary Differential Equations

Differential equations (DEs) serve as fundamental tools in mathematical modeling across scientific disciplines, yet classical numerical solvers face limitations with large-scale or computationally intensive problems. This study explores a quantum-inspired approach to solving DEs, combining quantum-inspired techniques with classical methods. It focuses on fixed-point arithmetic on quantum circuits, utilizing basic quantum gates to manipulate DE solutions. We expand upon the techniques introduced by Zanger et al. [Quantum, 5, 502 (2021)] by offering a precise computation for a fixed-point signed multiplication scheme, while also presenting a quantum circuit capable of executing the fixed-point division algorithm. We demonstrate the feasibility of our approach through the simulation of a linear Ordinary Differential Equation (ODE), where initial conditions and parameters are encoded into quantum circuits using fixed-point representation. By executing sequences of quantum gates mimicking numerical integration steps, we obtain approximate solutions to the ODE with specified fixed-point precision.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Investigation of the Cyanothece nitrogenase cluster in Synechocystis : a blueprint for engineering nitrogen-fixing photoautotrophs

ABSTRACT The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria, such asCyanothece, is frequently selected by nature for nitrogen-fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain underexplored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of aSynechocystis6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, thenifgenes fromCyanothece51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genesnifHDK,nifBSUENPVZTXW, as well ashesAB, are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar-powered conversion of atmospheric nitrogen into nitrogen-rich compounds, a stride toward a greener world. IMPORTANCE Integrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen-rich products in a green and energy-efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen-fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen-fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen-fixing ability.

Microbiology↗

Exploiting Fixed Charge at Selective Contacts for Silicon Photovoltaics

The goal of this work was to examine and exploit fixed interface charges in ultra-thin (0-3 nm thickness) tunnel dielectric layers sandwiched between silicon and selective contact metal oxides (molybdenum oxide, MoO x , titanium oxide, TiO 2 ). Specifically, the interface fixed charge was varied by changing processing conditions and materials over a wide range and the effect on the current-voltage behavior and the Schottky barrier height was quantified. In budget period 1 (year 1), the objective was to grow aluminum oxide tunnel layers with quantified fixed charge over a range of ~1E12 to ~-2E12 cm -2 and combine these with MoO x and TiO 2 layers on Czochralsi (CZ) mono p- and n-Si, respectively. We sought conditions that maximize fixed charge and minimize Schottky barrier height to MoO x contacts to p-Si. This objective, along with investigating the effects of silicon surface terminations, occupied the majority of the project timeline (Q1-Q8) due to complications with high specific contact resistivity values. In the last two quarters of the project period, the objective was to insert HfO2 layers between Si and aluminum oxide layers to quench the fixed charge for layers with otherwise identical thermal history. Another objective was to lower the barrier height at TiO 2 -based contacts on n-type Si, but that was never investigated completely.

14 SOLAR ENERGY↗

A Quantum Approach for Implementing Fixed-Point Arithmetic in Solving Ordinary Differential Equations

Differential equations (DEs) serve as fundamental tools in mathematical modeling across scientific disciplines, yet classical numerical solvers face limitations with large-scale or computationally intensive problems. This study explores a quantum-inspired approach to solving DEs, combining quantum- inspired techniques with classical methods. It focuses on fixed- point arithmetic on quantum circuits, utilizing basic quantum gates to manipulate DE solutions. We expand upon the techniques introduced by Zanger et al. [Quantum, 5, 502 (2021)] by offering a precise computation for a fixed-point signed multiplication scheme, while also presenting a quantum circuit capable of executing the fixed-point division algorithm. We demonstrate the feasibility of our approach through the simulation of a linear Ordinary Differential Equation (ODE), where initial conditions and parameters are encoded into quantum circuits using fixed- point representation. By executing sequences of quantum gates mimicking numerical integration steps, we obtain approximate solutions to the ODE with specified fixed-point precision.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Pressure-stabilized fixed-stress iterative solutions of compositional poromechanics

We consider the numerical behavior of the fixed-stress splitting method for coupled poromechanics as undrained regimes are approached. We explain that pressure stability is related to the splitting error of the scheme, not the fact that the discrete saddle point matrix never appears in the fixed-stress approach. This observation reconciles previous results regarding the pressure stability of the splitting method. Using examples of compositional poromechanics with application to geological CO sequestration, we see that solutions obtained using the fixed-stress scheme with a low order finite element-finite volume discretization which is not inherently inf-sup stable can exhibit the same pressure oscillations obtained with the corresponding fully implicit scheme. Moreover, pressure jump stabilization can effectively remove these spurious oscillations in the fixed-stress setting, while also improving the efficiency of the scheme in terms of the number of iterations required at every time step to reach convergence.

42 ENGINEERING↗

A Decision-Relevant Factor-Fixing Framework: Application to Uncertainty Analysis of a High-Dimensional Water Quality Model

Factor Fixing (FF) is a common method for reducing the number of model parameters to lower computational cost. FF typically starts with distinguishing the insensitive parameters from the sensitive and pursues uncertainty quantification (UQ) on the resulting reduced-order model, fixing each insensitive parameter at a fixed value. There is a need, however, to expand such a common approach to consider the effects of decision choices in the FF-UQ procedure on metrics of interest. Therefore, to guide the use of FF and increase confidence in the resulting dimension-reduced model, we propose a new adaptive framework consisting of four principles: (a) re-parameterize the model first to reduce obvious non-identifiable parameter combinations, (b) focus on decision relevance especially with respect to errors in quantities of interest (QoI), (c) conduct adaptive evaluation and robustness assessment of errors in the QoI across FF choices as sample size increases, and (d) reconsider whether fixing is warranted. The framework is demonstrated on a spatially-distributed water quality model. The error in estimates of QoI caused by FF can be estimated using a Polynomial Chaos Expansion (PCE) surrogate model. Built with 70 model runs, the surrogate is computationally inexpensive to evaluate and can provide global sensitivity indices for free. For the selected catchment, just two factors may provide an acceptably accurate estimate of model uncertainty in the average annual load of Total Suspended Solids (TSS), suggesting that reducing the uncertainty in these two parameters is a priority for future work before undertaking further formal uncertainty quantification.

54 ENVIRONMENTAL SCIENCES↗

Integration of fixed-frequency and FM-CW (frequency-modulated continuous-wave) reflectometers for coincident turbulence measurements on LTX- β (Lithium Tokamak eXperiment- β )

The fixed-frequency and frequency-modulated continuous-wave (FM-CW) reflectometers on LTX-β (Lithium Tokamak eXperiment-β) have been configured to use the same transmission lines and antenna arrays for coincident views of the core and edge plasma. The fixed-frequency channels (13.1–20.5 and 20–40 GHz, tunable between discharges) provide time-resolved measurements of density fluctuations, while the FM-CW channels (13.1–20.2 and 19.5–33.5 GHz) measure the density profile and fluctuations, with high spatial resolution and a sampling rate determined by the frequency sweep interval (5 μs). Data from both reflectometers are synchronously acquired to simultaneously leverage the wide bandwidth and high spatial resolution of the respective systems. Experiments showed that mutual crosstalk interference is momentary and does not diminish the capability of either system. Spectral analysis indicated broad power spectra (several hundreds of kHz) and suggests that the signals from the FM-CW system are consistent with under-sampled fixed-frequency signals. Radial correlations were explored using data from the two reflectometers, as well as from the FM-CW system alone. The core channels showed high levels of agreement between these two comparisons, suggesting that the data from the reflectometers are interchangeable for statistical estimates. For the edge channels, comparisons using data from the FM-CW reflectometer alone showed significant decorrelation due to time lag caused by the finite frequency up-sweep duration. Alternatively, this effect is eliminated when cross-correlating data from the different reflectometers. Finally, these results highlight the advantages of operating the fixed-frequency and FM-CW reflectometers in this manner, where the combined system can overcome the limitations of each separate system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Viruses of Nitrogen-Fixing Mesorhizobium Bacteria in Globally Distributed Chickpea Root Nodules

Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on the population size and, therefore, the function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants ( Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (viral operational taxonomic units [vOTUs]) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of the Mesorhizobium isolates. Per metagenome, 1 to 16 putative Mesorhizobium vOTUs were detected, with more than half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.

Microbiology↗

In situ counter-diffusion crystallization and long-term crystal preservation in microfluidic fixed targets for serial crystallography

Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X-ray beamline. Despite the advantages of counter-diffusion protein crystallization, there are few fixed-target devices that utilize counter diffusion for crystallization. In this article, different designs of user-friendly counter-diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed-target chip. Methods for rapid chip fabrication using commercially available thin-film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X-ray beam time. Importantly, the fixed-target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed-target utilization by crystallographers.

Liu, Zhongrui↗

Exploring gauge-fixing conditions with gradient-based optimization

Lattice gauge fixing is required to compute gauge-variant quantities, for example those used in RI-MOM renormalization schemes or as objects of comparison for model calculations. Recently, gauge-variant quantities have also been found to be more amenable to signal-to-noise optimization using contour deformations. These applications motivate systematic parameterization and exploration of gauge-fixing schemes. This work introduces a differentiable parameterization of gauge fixing which is broad enough to cover Landau gauge, Coulomb gauge, and maximal tree gauges. The adjoint state method allows gradient-based optimization to select gauge-fixing schemes that minimize an arbitrary target loss function.

Detmold, William↗