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DOE OSTI2026

Conjugation-based genome engineering enables rapid prototyping and bioproduction in non-model bacteria

Abstract Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a broad-host-range platform that enables predictable, iterative genomic integration in transformation-resistant bacteria. cSAGE combines conjugative DNA delivery, standardized low-copy vectors, orthogonal recombinases, and modular genetic parts to support rapid pathway assembly and cross-host benchmarking. Using purple nonsulfur bacteria as a testbed, we integrate promoter engineering, multi-payload genome modification, and genome-scale metabolic modeling to empirically evaluate host-dependent pathway performance. Applying this workflow, we identify strain-specific differences in photosynthetic conversion of lignin-derived p -coumarate to the thermoplastic precursor p -vinylphenol. By enabling genome engineering and functional comparison across diverse bacteria using a single plasmid system, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.

Guzman, Michael S. [Department of Chemical Enginee↗

DOE OSTI2024

ORBIT: Oak Ridge Base Foundation Model for Earth System Predictability

Earth system predictability is challenged by the complexity of environmental dynamics and the multitude of variables involved. Current AI foundation models, although advanced by leveraging large and heterogeneous data, are often constrained by their size and data integration, limiting their effectiveness in addressing the full range of Earth system prediction challenges. To overcome these limitations, we introduce the Oak Ridge Base Foundation Model for Earth System Predictability (ORBIT), an advanced vision transformer model that scales up to 113 billion parameters using a novel hybrid tensor-data orthogonal parallelism technique. As the largest model of its kind, ORBIT surpasses the current climate AI foundation model size by a thousandfold. Performance scaling tests conducted on the Frontier supercomputer have demonstrated that ORBIT achieves 684 petaFLOPS to 1.6 exaFLOPS sustained throughput, with scaling efficiency maintained at 41% to 85% across 49,152 AMD GPUs. These breakthroughs establish new advances in AI-driven climate modeling and demonstrate promise to significantly improve the Earth system predictability.

Wang, Xiao↗

DOE OSTI2020

Near-axis expansion of stellarator equilibrium at arbitrary order in the distance to the axis

A direct construction of equilibrium magnetic fields with toroidal topology at arbitrary order in the distance from the magnetic axis is carried out, yielding an analytical framework able to explore the landscape of possible magnetic flux surfaces in the vicinity of the axis. This framework can provide meaningful analytical insight into the character of high-aspect-ratio stellarator shapes, such as the dependence of the rotational transform and the plasma beta limit on geometrical properties of the resulting flux surfaces. The approach developed here is based on an asymptotic expansion on the inverse aspect ratio of the ideal magnetohydrodynamics equation. The analysis is simplified by using an orthogonal coordinate system relative to the Frenet–Serret frame at the magnetic axis. The magnetic field vector, the toroidal magnetic flux, the current density, the field line label and the rotational transform are derived at arbitrary order in the expansion parameter. Moreover, a comparison with a near-axis expansion formalism employing an inverse coordinate method based on Boozer coordinates (the so-called Garren–Boozer construction) is made, where both methods are shown to agree at lowest order. Finally, as a practical example, a numerical solution using a W7-X equilibrium is presented, and a comparison between the lowest-order solution and the W7-X magnetic field is performed.

Physics↗

DOE OSTI2025

Architectures and random properties of symplectic quantum circuits

Parametrized and random unitary (or orthogonal) n-qubit circuits play a central role in quantum information. As such, one could naturally assume that circuits implementing symplectic transformations would attract similar attention. However, this is not the case, as $\mathbb{SP}(d/2)$—the group of d × d unitary symplectic matrices—has thus far been overlooked. In this work, we aim at starting to fill this gap. We begin by presenting a universal set of generators $\mathcal{G}$ for the symplectic algebra $\mathfrak{sp}(d/2)$, consisting of one- and two-qubit Pauli operators acting on neighboring sites in a one-dimensional lattice. Here, we uncover two critical differences between such set, and equivalent ones for unitary and orthogonal circuits. Namely, we find that the operators in $\mathcal{G}$ cannot generate arbitrary local symplectic unitaries and that they are not translationally invariant. We then review the Schur–Weyl duality between the symplectic group and the Brauer algebra, and use tools from Weingarten calculus to prove that Pauli measurements at the output of Haar random symplectic circuits can converge to Gaussian processes. As a by-product, such analysis provides us with concentration bounds for Pauli measurements in circuits that form t-designs over $\mathbb{SP}(d/2)$. To finish, we present tensor-network tools to analyze shallow random symplectic circuits, and we use these to numerically show that computational-basis measurements anti-concentrate at logarithmic depth.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

The overlapping fragment approach for non-orthogonal configuration interaction with fragments

The non-orthogonal configuration interaction with fragments (NOCI-F) approach is extended opening the possibility to study intramolecular processes and materials with covalent or ionic lattices. So far, NOCI-F has been applied to study intermolecular energy and electron transfer employing ensembles of fragments that do not have atoms or bonds in common. The here presented approach divides the target system into two overlapping fragments that share one or more atoms and/or one or more bonds. After the construction of a collection of (multiconfigurational) fragment wave functions in a state specific optimization procedure, the fragment wave functions are combined to form many-electron basis functions for the non-orthogonal configuration interaction of the whole system. The orbitals in the overlapping fragment are defined by a corresponding orbital transformation of the fragment orbitals through a singular value decomposition. The overlapping fragments approach is first illustrated for a model system and then used to highlight some possible applications of NOCI with overlapping fragments. In conclusion, the results of excited state diffusion in transition metal oxide, intramolecular singlet fission and magnetic interactions in organic biradicals and ionic compounds are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A split ribozyme system for in vivo plant RNA imaging and genetic engineering

RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops with improved resilience, quality and productivity. In general, traditional methods for analysis of RNA abundance in plants require destructive, labour-intensive and time-consuming assays. To overcome these limitations, we developed a transformative innovation for in vivo RNA imaging in plants. Specifically, we established a synthetic split ribozyme system that converts various RNA signals to orthogonal protein outputs, enabling in vivo visualisation of various RNA signals in plants. We demonstrated the utility of this system in transient expression experiments (i.e., leaf infiltration in Nicotiana benthamiana ) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Also, we successfully engineered a split ribozyme-based biosensor in Arabidopsis thaliana for in vivo visualisation of endogenous gene expression at the cellular level, demonstrating the feasibility of multi-scale (e.g., cellular and tissue level) RNA imaging in plants. Furthermore, we developed a platform for easy incorporation of different protein outputs, allowing for flexible choice of reporters to optimise the detection of target RNAs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Optical Characterization of the Keck Array and BICEP3 CMB Polarimeters from 2016 to 2019

The BICEP/Keck experiment (BK) is a series of small-aperture refracting telescopes observing degree-scale cosmic microwave background (CMB) polarization from the South Pole in search of a primordial B-mode signature. This B-mode signal arises from primordial gravitational waves interacting with the CMB and has amplitude parametrized by the tensor-to-scalar ratio r. Since 2016, BICEP3 and the Keck Array have been observing with 4800 total antenna-coupled transition-edge sensor detectors, with frequency bands spanning 95, 150, 220, and 270 GHz. Here we present the optical performance of these receivers from 2016 to 2019, including far-field beams measured in situ with an improved chopped thermal source and instrument spectral response measured with a field-deployable Fourier transform spectrometer. As a pair differencing experiment, an important systematic that must be controlled is the differential beam response between the co-located, orthogonally polarized detectors. We generate per-detector far-field beam maps and the corresponding differential beam mismatch that is used to estimate the temperature-to-polarization leakage in our CMB maps and to give feedback on detector and optics fabrication. The differential beam parameters presented here were estimated using improved low-level beam map analysis techniques, including efficient removal of non-Gaussian noise as well as improved spatial masking. These techniques help minimize systematic uncertainty in the beam analysis, with the goal of constraining the bias on r induced by temperature-to-polarization leakage to be subdominant to the statistical uncertainty. This is essential as we progress to higher detector counts in the next generation of CMB experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Hydrodynamic and frictional modulation of deformations in switchable colloidal crystallites

Displacive transformations in colloidal crystals may offer a pathway for increasing the diversity of accessible configurations without the need to engineer particle shape or interaction complexity. To date, binary crystals composed of spherically symmetric particles at specific size ratios have been formed that exhibit floppiness and facile routes for transformation into more rigid structures that are otherwise not accessible by direct nucleation and growth. There is evidence that such transformations, at least at the micrometer scale, are kinetically influenced by concomitant solvent motion that effectively induces hydrodynamic correlations between particles. Here, we study quantitatively the impact of such interactions on the transformation of binary bcc-CsCl analog crystals into close-packed configurations. We first employ principal-component analysis to stratify the explorations of a bcc-CsCl crystallite into orthogonal directions according to displacement. We then compute diffusion coefficients along the different directions using several dynamical models and find that hydrodynamic correlations, depending on their range, can either enhance or dampen collective particle motions. These two distinct effects work synergistically to bias crystallite deformations toward a subset of the available outcomes.

42 ENGINEERING↗

DOE OSTI2025

Real classical shadows

Efficiently learning expectation values of a quantum state using classical shadow tomography has become a fundamental task in quantum information theory. In a classical shadows protocol, one measures a state in a chosen basis $\mathcal{W}$ after it has evolved under a unitary transformation randomly sampled from a chosen distribution $\mathcal{U}$. In this work we study the case where $\mathcal{U}$ corresponds to either local or global orthogonal Clifford gates, and $\mathcal{W}$ consists of real-valued vectors. Our results show that for various situations of interest, this ‘real’ classical shadow protocol improves the sample complexity over the standard scheme based on general Clifford unitaries. For example, when one is interested in estimating the expectation values of arbitrary real-valued observables, global orthogonal Cliffords typically decrease the required number of samples by a factor of two. More dramatically, for k-local observables composed only of real-valued Pauli operators, sampling local orthogonal Cliffords leads to a reduction by an exponential-in-k factor in the sample complexity over local unitary Cliffords. Finally, we show that by measuring in a basis containing complex-valued vectors, orthogonal shadows can, in the limit of large system size, exactly reproduce the original unitary shadows protocol.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Modeling the role of local crystallographic correlations in microstructures of Ti-6Al-4V using a correlated structure visco-plastic self-consistent polycrystal plasticity formulation

This paper presents a multi-level crystal plasticity-based simulation framework for modeling mechanical response and microstructure evolution of Ti-6Al-4V with α-lath/lamellar microstructures. Here, the model is a correlated structure visco-plastic self-consistent (CS-VPSC) formulation linking three scales: a single crystals micro-scale, a lath/lamellar colony meso-scale, and a lath/lamellar aggregate macro-scale. A selected hardening law for the evolution of critical resolved shear stress per slip system used in CS-VPSC is phenomenological. However, it adjusts the resistances of basal and prismatic slip systems based on the geometry of slip transfer between adjacent lamellae. Consistent with experimental evidences, the resolved shear stress on the pyramidal slip planes is dependent not only on the stress in the direction of slip but also on the two orthogonal shear stress components and the three normal stress components (non-Schmid effects). Electron backscatter diffraction (EBSD) data in conjunction with a procedure relying on α→β phase transformation is used to construct paired variants of α-laths/lamellae satisfying their local crystallographic correlations. The procedure fits volume fractions of individual laths/lamellae with the experimental EBSD data and selects a distribution of habit planes between adjacent variants with respect to the loading direction. The simulation framework is applied to interpret the deformation behavior in tension and compression along two sample directions of Ti-6Al-4V fabricated via laser powder bed fusion. Moreover, the model is used to simulate texture evolution during rolling of the material to large strains. It is demonstrated that the model is capable of predicting plastic anisotropy/asymmetry and the concomitant texture evolution. While the model reveals a significant effect of habit plane inclination with respect to the loading direction on yield stress, the comparison of the data and model predictions shows that a random distribution of habit planes fits the flow response. It is further inferred that the tension-compression asymmetry arises from the non-Schmid effects.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Surface Properties of Double-Fin Generated Shock-Wave/Boundary-Layer Interactions

Shock-Wave/Boundary-Layer Interaction (SBLI) is ubiquitous in high-speed air vehicles. SBLI surface flowfield properties of crossing shocks induced by symmetric Double-Fins (DFs) at fin angles of 8° and 10° at Mach 2 are experimentally investigated; a 10° Single-Fin (SF) is also explored as a comparison. Surface visualization is used to capture distinct flowfield structures such as separation and upstream influence. Steady and unsteady Pressure-Sensitive Paints (PSPs) are used to obtain global surface pressure fields. Characteristics of DF-SBLI surface topology are discussed by comparing the corresponding SF-SBLI. Here, the effect of fin angle on DF-SBLI is characterized, and unsteady dynamics of the pressure field are examined. Spectral Proper Orthogonal Decomposition (SPOD) is performed on unsteady PSP, and traveling surface pressure waves and their frequency-dependent behavior are discussed. Dispersion relation of surface pressure waves is revealed by performing two-dimensional space–time Fourier transform on unsteady PSP, and the results are compared with the phase velocity distributions obtained from SPOD. Accompanying group velocity behavior is examined for distinct SBLI regions wherein wave propagation is found dependent on its frequency. Steady surface pressures along the centerline are compared with previous experimental data. Fin-tip spacing is found to be an essential parameter for scaling of upstream influence length.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2022

Photobiocatalysis for Abiological Transformations

Harnessing biocatalysts for novel abiological transformations is a longstanding goal of synthetic chemistry. Combining the merits of biocatalysis and photocatalysis allows for selective transformations fueled by visible light and offers many advantages including new reactivity, high enantioselectivity, greener syntheses, and high yields. Photoinduced electron or energy transfer enables synthetic methodologies that complement conventional two electron processes or offer orthogonal pathways for developing new reactions. Enzymes are well suited and can be tuned by directed evolution to exert control over radical intermediates thereby suppressing undesirable reactions and delivering high chemo- and stereoselectivities. Within the past decade, the combination of biocatalysis and photocatalysis was mainly focused on exploiting light-regenerated cofactors to increase native enzymatic activity. However, recent developments have demonstrated that the combination can unlock new-to-nature chemistry. Particularly, the discovery and application of new strategies are well poised to expand the applications of photobiocatalysis. In the past three years, our lab has been studying the combinations of photocatalysis and biocatalysis which can be applied to create new synthetic methodologies and solve challenges in synthetic organic chemistry. Our efforts have expanded the strategies for combining external photocatalysts with enzymes through the construction of a synergistic cooperative stereoconvergent reduction system consisting of photosensitized energy transfer and ene-reductase catalyzed alkene reduction. Additionally, our efforts have also extended the capability of cofactor-dependent photoenzymatic systems to include enantioselective bimolecular radical hydroalkylations of alkenes by irradiating electron donor-acceptor complexes comprised of enzymatic redox active cofactors and unnatural substrates. In this Account, we highlight strategies developed by our group and others for combining biocatalysis and photocatalysis with the aim of introducing nonnatural reactivity to enzymes. Presently, strategies applied to achieve this goal include the repurposing of newly discovered photoactive enzymes, the elucidation of new photoreactivity within cofactor-dependent enzymes, the combination of external photocatalysts with enzymes, and the construction of artificial photoenzymes. By demonstrating the successful application of these strategies for achieving selective new-to-nature transformations, we hope to spur interest in the expanding the scope of photobiocatalytic systems through the use and extension of these strategies and creation of new strategies. In addition, we hope to elucidate the intuition in synergizing the unique capabilities of biocatalysis and photocatalysis so that photobiocatalysis can be recognized as a potential solution to difficult challenges in synthetic organic chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Flow structures of the cross-flow over a five-layer helically coiled steam generator geometry

The helically-coiled heat exchanger (HCSG) offers advantages over straight tubes such as compactness in geometry, increased heat transfer coefficients, and capability to absorb thermal expansion. In this study, the time-resolved velocity field data of shell-side crossflow over a five-layer helically coiled steam generator geometry was obtained using Particle Image Velocimetry (PIV) between adjacent rods in four regions with up to 5000 frames per second (5 kHz) at approximately Re u = 3600. The slant rod bundle created different flow patterns in different regions. Proper Orthogonal Decomposition (POD) revealed high-energy-mode flow structures. Due to the confined flow channel geometry, the large flow structures were not advected resulting in no strong POD mode paring. Continuous Wavelet Transform (CWT) visualized the characteristics of flow fluctuation in time and frequency domain simultaneously, which ranged in Strouhal number, S u , between 0.03 and 1.17. In the wake regions of the rods, flows changed in both pattern and magnitude over time. Once a pattern formed, it continued for relatively shorter than straight tube arrays, before changing the pattern again. The histograms of the POD time coefficients presented this multimodal flow characteristics. The current study focuses more on whole flow field analyses in the selected regions rather than local point-wise analyses. Finally, this study revealed that various Strouhal numbers can exist in the helically coiled heat exchanger geometry, which was not observed in straight tube arrays. In particular, Strouhal numbers smaller than 0.1 do not seem to be caused by vortex shedding but seem to be the result of the combination of complex geometry and possible multimodal trends. Based on the current observation, further works would involve intensive instantaneous point-wise analyses on the interactions between important locations such as separation points, stagnation points, shear layers, etc.

42 ENGINEERING↗

DOE OSTI2022

MENUS—Materials engineering by neutron scattering

Materials engineering by neutron scattering (MENUS) at the second target station will be a transformational high-flux, versatile, multiscale materials engineering diffraction beamline with unprecedented new capabilities for the study of complex materials and structures. It will support both fundamental and applied materials research in a broad range of fields. MENUS will combine unprecedented long-wavelength neutron flux and unique detector coverage to enable real-time studies of complex structural and functional materials under external stimuli. The incorporated small angle neutron scattering and transmission/imaging capabilities will extend its sensitivity to larger length scales and higher spatial resolution. Multimodal MENUS will provide crystallographic and microstructure data to the materials science and engineering community to understand lattice strain/phase transition/microstructure/texture evolution in three orthogonal directions in complex material systems under combined extreme applied conditions. Finally, the capabilities of MENUS will open new scientific opportunities and meet the research needs for science challenges to enable studies of a range of phenomena and answer the key questions in material design/exploration, advanced material processing, transformative manufacturing, and material operations of national impacts in our daily life.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Electrochemically Initiated Depolymerization of Poly(Methyl Methacrylate)

Efficient depolymerization of polymers with all-carbon backbones under mild conditions would be valuable in chemically recycling commodity plastics. Poly(methyl methacrylate) (PMMA) is a commodity thermoplastic that is currently depolymerized under temperatures in excess of 400 °C. Herein, we lower the temperatures needed to achieve depolymerization of PMMA by performing radical generation and depropagation with orthogonal stimuli. This first demonstration of electrochemically initiated PMMA depolymerization relies on reduction of phthalimide esters that, upon subsequent decarboxylation, generate polymer-centered radicals. These radicals then spontaneously unzip the polymer back to its monomeric constituents at temperatures as low as 105 °C. We studied the mechanism and efficiency of this transformation as a function of phthalimide ester placement, incorporation density, and polymer molecular weight. We found that chain-end activation is effective for modest molecular weights but suffers diminished efficiency at higher degrees of polymerization. In contrast, pendent-group activation is more effective for depolymerizing higher molecular weight species. Integrating higher molar amounts of phthalimide ester pendants leads to more effective depolymerization, with >95% depolymerization in copolymers with 5 mol% phthalimide ester incorporation. We leveraged this understanding to create a custom electro-distillation apparatus that allowed us to simultaneously electrochemically depolymerize PMMA and directly distill methyl methacrylate in >22% yield, which could ultimately be repolymerized. These findings establish electrochemistry as a versatile and orthogonal stimulus for vinyl polymer depolymerization and provide a foundation for closed-loop electrochemical recycling of widely used plastics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A high-order WENO-limited finite-volume algorithm for atmospheric flow using the ADER-differential transform time discretization

A high-order-accurate weighted essentially non-oscillatory (WENO) limited upwind finite-volume scheme is detailed for the compressible, nonhydrostatic, inviscid Euler equations using an arbitrary derivatives (ADER) time-stepping scheme based on differential transforms (DTs). A second-order-accurate alternating Strang dimensional splitting is compared against multidimensional simulation with 2D transport using solid body rotation of various data. The two were found to give nearly identical accuracy in orthogonal, Cartesian coordinates. Orders of convergence are demonstrated at up to ninth-order accuracy with 2D transport. 1D transport is used to confirm that error decreases monotonically with increasing order of accuracy with WENO limiting even for discontinuous data. Further, WENO limiting always decreased the error compared with simulation without limiting in the L 1 norm. A series of standard 2D compressible nonhydrostatic Euler equation test cases were validated against previous results from literature. Finally, it was demonstrated that increasing the order of accuracy led to better resolved features and increased power for kinetic energy at small wavelengths.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Fermionic mean-field dynamics for spin systems beyond free fermions

We introduce the fermionized time-dependent Hartree–Fock (fTDHF), a real-time quantum dynamics method for spin-1/2 Hamiltonians following their mapping to fermions via the Jordan-Wigner transformation. fTDHF is formally equivalent to exact dynamics in the case of free fermions, and can efficiently handle non-local string operators arising from long-range interactions via transition matrix elements between non-orthogonal Slater determinants. We show that the fTDHF method can be implemented on a classical computer with a cost that scales polynomially with system size, and linearly with the time steps. We benchmark fTDHF against exact dynamics on three separate spin-1/2 models, representing adiabatic preparation of states with long-range correlations, disorder-driven observation of many-body localization, and particle production in the Schwinger model. For each of these systems, fTDHF is shown to reproduce the qualitative dynamics generated by the exact evolutions, while maintaining a simple physical picture due to its mean-field nature.

Dutta, Rishab↗

DOE OSTI2025

RNAi and genome editing of sugarcane: Progress and prospects

SUMMARY Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan‐genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or Agrobacterium ‐mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture‐free technologies, such as spray‐induced gene silencing, virus‐induced gene silencing, or virus‐induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.

Brant, Eleanor [Agronomy Department, Plant Molecul↗