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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Engineering Crassulacean Acid Metabolism in C 3 and C 4 Plants

Carbon dioxide (CO 2 ) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO 2 reduction. Additionally, plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C 3 or C 4 photosynthesis. Therefore, there is a great potential for engineering CAM in C 3 or C 4 crops to enhance food/biomass production and carbon sequestration on arid, semiarid, abandoned, or marginal lands. Recent progresses in CAM plant genomics and evolution research, along with new advances in plant biotechnology, have provided a solid foundation for bioengineering to convert C 3 /C 4 plants into CAM plants. Here, we first discuss the potential strategies for CAM engineering based on our current understanding of CAM evolution. Then we describe the technical approaches for engineering CAM in C 3 and C 4 plants, with a focus on an iterative four-step pipeline: (1) designing gene modules, (2) building the gene modules and transforming them into target plants, (3) testing the engineered plants through an integration of molecular biology, biochemistry, metabolism, and physiological approaches, and (4) learning to inform the next round of CAM engineering. Finally, we discuss the challenges and future opportunities for fully realizing the potential of CAM engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reaction dynamics and in-medium nucleon-nucleon cross section with 12 C+ 1 H at 95 MeV/nucleon

Reaction dynamics and effective in-medium nucleon-nucleon (NN) cross section are studied, using the antisymmetrized molecular dynamics (AMD) model with one of the simplest heavy ion collisions, 12 C+ ⁢1 H. The roles of different stochastic processes are studied, which are installed in the original AMD. One is the diffusion process as a part of the quantum fluctuation originated from the Fermi motion during the time evolution of the wave packets in the mean field (AMD/D). The second is a coalescence treatment for light clusters with A ≤ 8 (AMD/D-COALS). The third is the collision process, installed in AMD with different form of the in-medium NN cross sections. These different processes are examined, using the experimental angular distributions and energy spectra of light charged particles and intermediate mass fragments. The effective in-medium NN cross sections are evaluated from the simulated AMD events and compared with the experimentally extracted values. A good agreement is obtained between the AMD values from the 12 C + 1 H reaction at 95 MeV/nucleon and the experimental results for nuclear matter.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Vapor-Phase Aggregation of Cerium Oxide Nanoparticles in a Rapidly Cooling Plasma

Local conditions, such as temperature and oxygen availability, have a pronounced effect on the formation and evolution of fallout following a nuclear explosion. While the behavior of nuclear-relevant materials such as uranium has begun to be explored under a wider range of environments, little is known about the behavior of plutonium. Here, using cerium as a surrogate, we track the vapor-phase aggregation of cerium oxide nanoparticles created in a plasma flow reactor under conditions of controlled temperature at two different oxygen fugacities. In situ optical emission spectroscopy is used to measure the variations in the spectral intensity of atomic and molecular species with temperature and oxygen content. We find that the relative rate of gas-phase oxidation of cerium is highly dependent on both temperature and local redox conditions within the flow reactor, to the extent that doubling the oxygen availability effectively doubles the amount of vapor-phase cerium monoxide at high temperatures (>2000 K). Condensed cerium oxide nanoparticles are also collected and analyzed ex situ via transmission electron microscopy and grazing-incidence small-angle X-ray scattering to determine their elemental composition, crystal structure, and size distribution. The size and morphology of the condensed nanoparticles are independent of local redox conditions, forming the same crystal type with the same size distribution regardless of oxygen availability. Postcondensation particle evolution, however, is found to be predominantly driven by temperature, with the average particle size increasing as particles cool and subsequently aggregate. These results expand our understanding of the chemical and physical behavior of refractory oxides that form during the early stages of fallout formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A chromosome-scale reference genome of trifoliate orange ( Poncirus trifoliata ) provides insights into disease resistance, cold tolerance and genome evolution in Citrus

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosomescale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/ DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/ Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Photocatalytic Semi‐Hydrogenation of Acetylene to Polymer‐Grade Ethylene with Molecular and Metal–Organic Framework Cobaloximes

Abstract The semi‐hydrogenation of acetylene in ethylene‐rich gas streams is a high‐priority industrial chemical reaction for producing polymer‐grade ethylene. Traditional thermocatalytic routes for acetylene reduction to ethylene, despite progress, still require high temperatures and high H 2 consumption, possess relatively low selectivity, and use a noble metal catalyst. Light‐powered strategies are starting to emerge, given that they have the potential to use directly the abundant and sustainable solar irradiation, but are ineffective. Here an efficient, >99.9% selective, visible‐light powered, catalytic conversion of acetylene to ethylene is reported. The catalyst is a homogeneous molecular cobaloxime that operates in tandem with a photosensitizer at room temperature and bypasses the use of non‐environmentally friendly and flammable H 2 gas feed. The reaction proceeds through a cobalt‐hydride intermediate with ≈100% conversion of acetylene under competitive (ethylene co‐feed) conditions after only 50 min, and with no evolution of H 2 or over‐hydrogenation to ethane. The cobaloxime is further incorporated as a linker in a metal–organic framework; the result is a heterogeneous catalyst for the conversion of acetylene under competitive (ethylene co‐feed) conditions that can be recycled up to six times and remains catalytically active for 48 h, before significant loss of performance is observed.

Stone, Aaron E. B. S.↗
DOE OSTI2021

Strengthening of tungsten by coherent rhenium precipitates formed during low fluence irradiation

Experimental data show that the accumulation of rhenium and osmium from transmutation reactions severely affect the microstructural evolution and property degradation of tungsten-based materials under neutron irradiation. Theory and modeling have confirmed that Re atom transport in W is by irradiation-produced migrating self-interstitial atoms. With this diffusion mode in operation, a specific microstructure evolution is realized when at relatively low neutron fluence the Re-rich precipitates are formed, while the void and interstitial loop population development is suppressed, affecting the mechanical properties. Here, this research shows the effect of small coherent Re-rich precipitates on the dislocation glide under stress, investigated using the molecular dynamics approach with empirical interatomic potentials. The results are compared with an earlier simulation of void hardening in W. It is demonstrated that small coherent Re-rich precipitates of less than 6 nm diameter represent relatively weak obstacles for moving edge dislocations. The implication of these results on the interpretation of experimental results is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

X-ray scattering signatures of early-time accelerations in iodine dissociation

Ultrafast time-resolved x-ray scattering (TRXS) from a photoexcited molecular ensemble measures a distribution $S(Q, τ)$ of the x-ray momentum transfer Q and pump-probe delay τ in which all modes of motion induced by the excitation overlap. Frequency-resolved x-ray scattering (FRXS) based on $\tilde {S}\left(Q,\omega \right)$ separates each oscillation and dissociation channel in the TRXS data, enabling measurements of vibrational frequencies and phases, and dissociation velocities and time shifts. In this work, we extend FRXS analysis to study early-time accelerations as well. We show how these appear as diffuse scattering patterns with characteristic phase evolution in FXRS and we develop a set of transformations that isolate individual channels to measure the early-time accelerated motion. This procedure is used to analyze diatomic iodine x-ray scattering data with multiple dissociations, and the ability of this technique to characterize early-time accelerations of one dissociation channel even in the presence of another dissociation is demonstrated.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Revitalizing Iron Redox by Anion-Insertion-Assisted Ferro- and Ferri-Hydroxides Conversion at Low Alkalinity

Iron hydroxides are desirable alkaline battery electrodes for low cost and environmental beneficence. However, hydrogen evolution on charging and Fe 3 O 4 formation on discharging cause low storage capacity and poor cycling life. Here, we report that green rust (GR) (Fe 2+ 4 Fe 3+ 2 (HO – ) 12 SO 4 ), formed via sulfate insertion, promotes Fe(OH) 2 /FeOOH conversion and shows a discharge capacity of ~211 mAh g –1 in half-cells and Coulombic efficiency of 93% after 300 cycles in full-cells. Theoretical calculations show that Fe(OH) 2 /FeOOH conversion is facilitated by intercalated sulfate anions. Classical molecular dynamics simulations reveal that electrolyte alkalinity strongly impacts the energetics of sulfate solvation, and low alkalinity ensures fast transport of sulfate ions. Anion-insertion-assisted Fe(OH) 2 /FeOOH conversion, also achieved with Cl – ion, paves a pathway toward efficient utilization of Fe-based electrodes for sustainable applications.

25 ENERGY STORAGE↗
DOE OSTI2023

Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes

Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η 5 -pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η 4 -pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2′-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)] + , an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)] + . Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.

08 HYDROGEN↗
DOE OSTI2025

Implementing hydrogen oxidation reaction on Pt for controlling counter electrode processes

The search for active, stable, and durable materials for electrochemical energy technologies requires increasing levels of precision to establish true structure-function relationships and guide materials design from atomic and molecular scale. This increases the level of control required over the experimental system for proper materials evaluation. The choice of counter electrode material become crucial, as Pt dissolution at high voltages may cause contamination to the working electrode, especially when studying reductive processes in reactions such as oxygen reduction reaction (ORR), H 2 evolution reaction (HER), and the CO 2 reduction reaction. The learnings from “old school” electrochemistry groups lead us to leverage H 2 reactions over Pt to construct a counter electrode system with controlled potential that eliminates Pt ion contamination concerns. In here we discuss the construction of such Pt|H 2 counter electrode where key experimental aspects such as the H 2 flow rate and effective distribution determines the maximum current this counter electrode can accommodate before switching to high voltage and triggering Pt dissolution. Lastly, we demonstrate the use of the Pt|H 2 counter electrode in aqueous electrolytes during HER occurring on the working electrode at varying currents, showing that the Pt content in the cell remains below parts per trillion (ppt) up to 10 mA, and below 50 ppt at 100 mA up to 1 h of constant current hold. This work provides a guide to the implementation of Pt|H 2 counter electrodes to improve the precision of electrochemical experiments in search of highly active, selective, and durable materials for energy technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Hadronic structure on the light front. VIII. Light scalar and vector mesons

We use the QCD instanton vacuum model to discuss the emergence of the light scalar and vector mesons on the light front. We take into account both the instanton and anti-instanton single and molecular interactions on the light quarks, in the form of nonlocal effective interactions. Although the molecular induced interactions are suppressed by a power of the packing fraction, they are still sufficient to bind the vector mesons, while keeping most of the scalar spectrum relatively unchanged. We explicitly derive the light front distribution amplitudes and partonic functions for the scalar and vector mesons, and compare them after pertinent QCD evolution, to the available empirical and lattice measured counterparts. The Dirac electric form factors for both the pion and ρ meson are derived, and shown to compare well with current data. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2023

Mechanistic Insights on Permeation of Water over Iron Cations in Nanoporous Silicon Oxide Films for Selective H 2 and O 2 Evolution

Electrocatalysts encapsulated by an ultrathin and semipermeable oxide layer offer a promising avenue for efficient, selective, and cost-effective production of hydrogen through photoelectrochemical water splitting. This architecture is especially attractive for Z-scheme water splitting, for which a nanoporous oxide film can be leveraged to mitigate undesired, yet kinetically facile, reactions involving redox shuttles, such as aqueous iron cations, by limiting transport of these species to catalytically active sites. In this work, molecular dynamics simulations were combined with electrochemical measurements to provide a mechanistic understanding of permeation of water and Fe(III)/Fe(II) redox shuttles through nanoporous SiO 2 films. It is shown that even for SiO 2 pores with a width as small as 0.8 nm, water does not experience any energy barrier for permeating into the pores due to a favorable interaction with hydrophilic silanol groups on the oxide surface. In contrast, permeation of Fe(III) and Fe(II) into microporous SiO 2 pores is limited due to high energy barriers, which stem from a combination of distortion and dehydration of the second and third ion solvation shells. Furthermore, our simulations and experimental results show that SiO 2 coatings can effectively mitigate undesired Fe(III)/Fe(II) redox reactions at underlying electrodes by attenuating permeation of iron cations, while allowing water to permeate and thus participate in water splitting reactions. In a broader context, our study demonstrates that selectivity of solvated cations can be manipulated by controlling the pore size and surface chemistry of oxide films.

14 SOLAR ENERGY↗
DOE OSTI2021

High Resolution Infrared Spectroscopy of Highly Reactive Chemical Intermediates: Berkeley Inspiration and a C.B. Moore Retrospective

One of the long-standing paradoxes in chemistry is that the molecular species of greatest interest are often highly reactive chemical intermediates and thus present only at vanishingly small concentrations under typical steady state conditions. Here, this has proven both a key frustration and powerful motivation for physical chemists in probing such species, particularly for high resolution laser spectroscopic methods in the infrared. Over the past 4-5 decades, this fundamental sensitivity challenge has stimulated the development of many novel techniques for efficient generation, cooling, and infrared probing of such transient chemical intermediates, achieving increasingly sophisticated levels of spectroscopic detail, chemical insight, and a testbed for comparison with first principles ab initio quantum calculations. Two of the pioneering contributors to this scientific arena have been George Pimentel and C. Bradley Moore, both responsible for nourishing DJN’s own enduring fascination with spectroscopic IR study of elusive chemical intermediates. This chapter is not intended to provide a comprehensive review of this large and enormously successful field, but it rather more simply attempts to capture a few selective “Moore-centric” snapshots of the Nesbitt group scientific evolution, specifically in i) advances by Pimentel for the original development of rapid scan flash kinetic spectroscopy based on spectrometers with rapidly rotating IR gratings, ii) the modernization/extension of these methods in the Moore group toward the first high resolution IR laser spectroscopy of singlet/triplet methylene 1,3 CH 2 diradical, and finally to iii) the development of slit supersonic discharge expansion methods at JILA for sub-Doppler infrared laser study of multiple radicals, jet cooled molecular ions, and highly reactive chemical intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Quantum Simulation of Molecular Dynamics Processes─A Benchmark Study Using a Classical Simulator and Present-Day Quantum Hardware

Here, we explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this issue, we designed a shallower quantum circuit for preparing a Gaussian-like initial wave packet, which improves the performance of real hardware. Next, quantum circuits are implemented to apply the kinetic and potential energy operators for the evolution of a wave function over time. The results of our modeling on classical emulators of quantum hardware agree perfectly with the results obtained using the traditional (classical) methods. This serves as a benchmark and demonstrates that the quantum algorithms and Qiskit codes we developed are accurate. However, the results obtained on the actual quantum hardware available today, such as IBM’s superconducting qubits and IonQ’s trapped ions, indicate large discrepancies due to hardware limitations. This work highlights both the potential and challenges of using quantum computers to solve fundamental quantum molecular dynamics problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Double Membrane Formation in Heterogeneous Vesicles

Lipids are capable of forming a variety of structures, including multi-lamellar vesicles. Layered lipid membranes are found in cell organelles, such as autophagosomes and mitochondria. Here, we present a mechanism for the formation of a double-walled vesicle (i.e., two lipid bilayers) from a unilamellar vesicle through the partitioning and phase separation of a small molecule. Using molecular dynamics simulations, we show that double membrane formation proceeds via a nucleation and growth process – i.e., after a critical concentration of the small molecules, a patch of double membrane nucleates and grows to cover the entire vesicle. In this paper, we discuss the implications of this mechanism and theoretical approaches for understanding the evolution and formation of double membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure of ice confined in silica nanopores

Observed anomalous thermodynamic properties of confined water such as deviations in the melting point and freezing point motivate the determination of the structure of confined water as a function of pore size and temperature. Here, we investigate the dynamic evolution of the structure of confined ice in SBA-15 porous materials with pore diameters of 4 nm, 6 nm, and 8 nm at temperatures ranging from 183 K to 300 K using in operando Wide-Angle X-Ray Scattering (WAXS) measurements, X-Ray Partial Distribution Function (PDF) measurements, and classical Molecular Dynamics (MD) simulations. Formation of hexagonal ice structures is noted in all the three pore sizes. In silica nanopores with diameters of 4 nm, cubic ice formation is noted in addition to hexagonal ice. Longer lasting hydrogen bonds and longer residence times of the water molecules in the first coordination shell contribute to observed crystalline organization of ice in confinement. Self-diffusion coefficients of confined liquid water, predicted from classical MD simulations, are four orders of magnitude higher compared to ice formed in confinement. These experimental and simulation results provide comprehensive insights underlying the organization of confined water and ice in silica nanopores and the underlying physico-chemical interactions that contribute to the observed structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fundamental limitations on photoisomerization from thermodynamic resource theories

Small, out-of-equilibrium, and quantum systems defy simple thermodynamic expressions. Such systems are exemplified by molecular switches, which exchange heat with a bath. These molecules can photoisomerize, or change conformation, or switch, on absorbing light. The photoisomerization probability depends on kinetic details that couple the molecule’s energetics to its dissipation. Therefore, a simple, general, thermodynamic-style bound on the photoisomerization probability seems out of reach. We derive such a bound using a resource theory. The resource-theory framework is a set of mathematical tools, developed in quantum information theory, used to generalize thermodynamics to small and quantum settings. From this toolkit has been derived a generalization of the second law, the thermomajorization preorder. We use thermomajorization to upper-bound the photoisomerization probability. Then, we compare the bound with an equilibrium prediction and with a Lindbladian model. We identify a realistic parameter regime in which the Lindbladian evolution saturates the thermomajorization bound. We also quantify the energy coherence in the electronic degree of freedom, and we argue that this coherence cannot promote photoisomerization. Overall, this work illustrates how quantum-information-theoretic thermodynamics can elucidate complex quantum processes in nature, experiments, and synthetics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗