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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis

Family 1 Coenzyme A transferases (CtfAB) from the extremely thermophilic bacterium, Thermosipho melanesiensis, has been used for in vivo acetone production up to 70°C. This enzyme has tentatively been identified as the rate-limiting step, due to its relatively low-binding affinity for acetate. However, existing kinetic and mechanistic studies on this enzyme are insufficient to evaluate this hypothesis. Here, kinetic analysis of purified recombinant T. melanesiensis CtfAB showed that it has a ping-pong bi-bi mechanism typical of Coenzyme A (CoA) transferases with Km values for acetate and acetoacetyl-CoA of 85 mM and 135 μM, respectively. Product inhibition by acetyl-CoA was competitive with respect to acetoacetyl-CoA and non-competitive with respect to acetate. Crystal structures of wild-type and mutant T. melanesiensis CtfAB were solved in the presence of acetate and in the presence or absence of acetyl-CoA. These structures led to a proposed structural basis for the competitive and non-competitive inhibition of acetyl-CoA: acetate binds independently of acetyl-CoA in an apparent low-affinity binding pocket in CtfA that is directly adjacent to a catalytic glutamate in CtfB. Similar to other CoA transferases, acetyl-CoA is bound in an apparent high-affinity binding site in CtfB with most interactions occurring between the phospho-ADP of CoA and CtfB residues far from the acetate binding pocket. This structural-based mechanism also explains the organic acid promiscuity of CtfAB. High-affinity interactions are predominantly between the conserved phospho-ADP of CoA, and the variable organic acid binding site is a low-affinity binding site with few specific interactions.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Kinetic simulations of anomalous resistivity in high-temperature current carrying plasmas

Anomalous resistivity caused by lower hybrid drift instabilities (LHDIs) has been extensively studied in the literature, and has been invoked to explain the rates of magnetic diffusion and plasma profile evolution in the low-density plasma periphery of theta and screw pinch plasmas. In this article, we present a fully kinetic simulation study of LHDIs with a realistic mass ratio using the particle-in-cell code Chicago over a large range of drift speeds, 0.5 < v$^{2}_{di}$/v$^{2}_{ti}$ < 14.5, plasma β, β ≥ 2×10 –5 , and temperature ratios, 0.1 < T e /T i < 10. The resistivity quantified from the simulations is compared with the analytic estimates from the literature and a generalized resistivity expression is presented, which can be applied over the entire range of plasma environments that were simulated in this study. This expression uses the amplitude of the LHDI fluctuations resulting from instability saturation by electron resonance broadening rather than plateau formation, current relaxation, or ion trapping. The generalized resistivity expression is appropriate for full-scale fluid simulations that encounter a large range of plasma conditions, and has better agreement with the resistivity quantified from kinetic simulations than previous expressions in the literature, particularly at low plasma β. Anomalous resistivity has also been considered as an explanation of the rapid magnetic field dissipation during magnetic reconnection events at large plasma β. At a large β, the magnetic field fluctuations of LHDIs can dominate the electrostatic fluctuations and this article investigates enhanced collisionality due to the nonlinear magnetic force, δJ×δB/c.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Deep learning surrogate model for kinetic Landau-fluid closure with collision

In this work, the kinetic Landau-fluid (LF) closure with collision and periodic boundary condition is used in the development of the deep learning (DL) surrogate model. A classical neural network, namely, feedforward neural network or sometimes termed multilayer perceptron, is constructed and trained to learn the kinetic LF closure in the static limit and arbitrary mean free path in configuration space. The preliminary relation between best hyperparameters and critical parameters for data generation is found. Compared with the numerical approach (non-Fourier method) of the LF closure, the deep learning surrogate model shows an order of magnitude of improvement in terms of accuracy. Perhaps most importantly, the surrogate model closure has been integrated for the first time with fluid simulations. Our DL-enabled fluid simulations, for the first time, give the correct Landau damping rate for a wide range of wave vectors, while the Hammett–Perkins closure cannot produce the correct damping rate. We correctly connect the collisionless Hammett–Perkins closure and collisional Braginskii closure to reproduce the intrinsic nonlocal feature of the heat flux with DL techniques. We address the most concerning error accumulation problem and find that simulations with the deep learning surrogate model are as good as, if not better than, simulations with the analytic closure in terms of long-term numerical stability in the linear Landau damping test.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Accelerated kinetic Monte Carlo: A case study; vacancy and dumbbell interstitial diffusion traps in concentrated solid solution alloys

Vacancy and self-interstitial atomic diffusion coefficients in concentrated solid solution alloys can have a non-monotonic concentration dependence. Here, the kinetics of monovacancies and $\langle$100$\rangle$ dumbbell interstitials in Ni–Fe alloys are assessed using lattice kinetic Monte Carlo (kMC). The non-monotonicity is associated with superbasins, which impels using accelerated kMC methods. Detailed implementation prescriptions for first passage time analysis kMC (FPTA-kMC), mean rate method kMC (MRM-kMC), and accelerated superbasin kMC (AS-kMC) are given. The accelerated methods are benchmarked in the context of diffusion coefficient calculations. The benchmarks indicate that MRM-kMC underestimates diffusion coefficients, while AS-kMC overestimates them. In this application, MRM-kMC and AS-kMC are computationally more efficient than the more accurate FPTA-kMC. Our calculations indicate that composition dependence of migration energies is at the origin of the vacancy’s non-monotonic behavior. In contrast, the difference between formation energies of Ni–Ni, Ni–Fe, and Fe–Fe dumbbell interstitials is at the origin of their non-monotonic diffusion behavior. Additionally, the migration barrier crossover composition—based on the situation where Ni or Fe atom jumps have lower energy barrier than the other one—is introduced. KMC simulations indicate that the interplay between composition dependent crossover of migration energy and geometrical site percolation explains the non-monotonic concentration-dependence of atomic diffusion coefficients.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Marcus–Hush–Chidsey kinetics at electrode–electrolyte interfaces

Electrochemical kinetics at electrode–electrolyte interfaces limit the performance of devices including fuel cells and batteries. While the importance of moving beyond Butler–Volmer kinetics and incorporating the effect of electronic density of states of the electrode has been recognized, a unified framework that incorporates these aspects directly into electrochemical performance models is still lacking. In this work, we explicitly account for the density functional theory-calculated density of states numerically in calculating electrochemical reaction rates for a variety of electrode–electrolyte interfaces. We first show the utility of this for two cases related to Li metal electrodeposition and stripping on a Li surface and a Cu surface (anode-free configuration). The deviation in reaction rates is minor for cases with flat densities of states such as Li, but is significant for Cu due to nondispersive d-bands creating large variation. Finally, we consider a semiconducting case of a solid-electrolyte interphase consisting of LiF and Li2CO3 and note the importance of the Fermi level at the interface pinned by the redox reaction occurring there. We identify the asymmetry in reaction rates as a function of discharge/charge naturally within this approach.

Kurchin, Rachel (ORCID:0000000221474809)↗
DOE OSTI2021

Transition characteristics and electron kinetics in microhollow cathode discharges

We demonstrate the transition characteristics and electron kinetics of microdischarges in a microgap with a cathode having microstructures using two-dimensional particle-in-cell/Monte Carlo collision (2d3v) simulations. It is found that the microdischarge is inside the hollow cavity at lower pressures, forming microhollow cathode discharges (MHCDs), while the dominant discharge moves outside the cavity at higher pressures, locating above the cathode rectangular protrusion tip. The spatial distributions of the microdischarge parameters (e.g., electric potential and electron density) are presented by capturing the transition characteristics. The electron kinetics of the microdischarges are examined based on the moment analysis of the electron Boltzmann equation. The collisional and non-collisional components of the electron power absorption are decomposed, which were seldomly investigated for microdischarges previously. The results provide fundamental insights into MHCD formation with a structured electrode at varying pressure conditions, which could be beneficial for the design and fabrication of microplasma devices in practical applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

The scaling of kinetic and transport behaviors in the solution-phase chemistry of a plasma–liquid interface

The reactions at a plasma–liquid interface often involve species such as the solvated electron or the hydroxyl radical, which initiate the reduction or oxidation of solution-phase reactants (so-called scavengers) or are consumed by their own second-order recombination. Here, the mathematical scaling of the reaction–diffusion equations at the interface is used to obtain a characteristic time that can be used to determine the transition from highly efficient scavenger reduction or oxidation to lower efficiencies due to transport limitations. The characteristic time (tc) is validated using numerical solutions of the reaction–diffusion equations. When the scavenger kinetics are faster than second-order recombination, this characteristic transition time scales proportionally with the scavenger diffusivity (Ds) and the square of the scavenger bulk concentration (SB) and inversely proportional to the electron flux (J) squared; that is, t c = D s S B 2 F 2 /J 2 , where F is Faraday’s constant. However, when the scavenger kinetics are comparable or slower than second-order recombination, this scaling does not hold. Extending this analysis to three-dimensional systems shows that the profile of the electron flux on the surface affects the spatial location where reactions are most effective. Finally, the assessment of the implications of these behaviors for the reactor design highlights how effectively controlling the electron flux and solution transport may be necessary to improve the efficiency of scavenger reactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

An E and B gyrokinetic simulation model for kinetic Alfvén waves in tokamak plasmas

The gyrokinetic particle simulation is a powerful tool for studies of transport, nonlinear phenomenon, and energetic particle physics in tokamak plasmas. While most gyrokinetic simulations make use of the scalar and vector potentials, a new model (GK-E&B) has been developed by using the E and B field in a general form and has been implemented in simulating kinetic Alfvén waves in uniform plasma. In our work, the Chen et al. GK-E&B model has been expressed, in general, tokamak geometry using the local orthogonal coordinates and general tokamak coordinates. Its reduction for uniform plasma is verified, and the numerical results show good agreement with the original work. The theoretical dispersion relation and numerical results in the local model in screw pinch geometry are also in excellent agreement. Numerical results show excellent performance in a realistic parameter regime of burning plasmas with high values of β/(M e k$^{2}_{⊥}$ρ$^{2}_{i}$), which is a challenge for traditional methods due to the “cancellation” problem. As one application, the GK-E&B model is implemented with kinetic electrons in the local single flux surface limit. With the matched International Tokamak Physics Activity-Toroidicity-induced Alfvén Eigenmodes parameters adopted, numerical results show the capability of the GK-E&B in treating the parallel electron Landau damping for realistic tokamak plasma parameters. As another application, the global GK-E&B model has been implemented with the dominant electron contribution in the cold electron limit. Its capability in simulating the finite E || due to the finite electron mass is demonstrated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Fuel–shell mix and yield degradation in kinetic shock-driven inertial confinement fusion implosions

Fuel–shell mix in kinetic plasma conditions is probed using nuclear and x-ray self-emission in shock-driven, D 3 He-gas-filled inertial confinement fusion implosions. As initial gas fill density decreases, measured nuclear yields and ion temperatures are lower than expected as compared to radiation-hydrodynamic simulations. Spatially and temporally resolved x-ray emissions indicate significant mixing at the fuel–shell interface in implosions with low initial gas fill density. In conclusion, this observed fuel–shell mix introduces a substantial amount of shell ions into the center of the implosion prior to and during shock flash and is the key mechanism needed in the kinetic-ion simulations to match experimental nuclear yields.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Experimental and computational studies of the kinetics of the reaction of hydrogen peroxide with the amidogen radical

In this work, the pulsed-laser photolysis/laser-induced fluorescence method is used to study the kinetics of the reaction of NH 2 with H 2 O 2 to yield a second-order rate constant of (2.42 ± 0.55) × 10 –14 cm 3 molecule –1 s –1 at 412 K in 10–22 mbar of Ar bath gas. There are no prior measurements for comparison. To check this value and enable reliable extrapolation to other temperatures, we also compute thermal rate constants for this process over the temperature range 298–3000 K via multi-structural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT). The CVT/SCT rate constants are derived using a dual-level direct dynamics approach utilizing single-point CCSD(T)-F12b/cc-pVQZ-F12 energies—corrected for core-valence and scalar relativistic effects—and M06-2X/MG3S geometries, gradients, and Hessians—for all stationary and non-stationary points along the reaction path. The multistructural method with torsional anharmonicity, based on a coupled torsional potential, is then employed to calculate correction factors for the rate constants, accounting for the comprehensive effects of torsional anharmonicity on the kinetics of this reaction system. The final MS-CVT/SCT rate constants are found to be in good agreement with our measurements and can be expressed in modified Arrhenius form as 2.13 × 10 –15 (T/298 K) 4.02 exp(–513 K/T) cm 3 molecule –1 s –1 over the temperature range of 298–3000 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Initial decomposition mechanisms of 2,4,6-triamino-1,3,5-trinitrobenzene (TATB) and their kinetic isotope effect

2,4,6-triamino-1,3,5-trinitrobenzene (TATB) is an insensitive High Explosive (HE) that is widely studied to better understand the physical properties of safety and sensitivity of HE. A dominant initial decomposition mechanism of TATB is believed to be a dehydration reaction that forms mono- and di-furazans, although other mechanisms have been reported. In this work, seven initial decomposition mechanisms were modeled with ab initio simulations to calculate its free energy barriers, decomposition rates, and kinetic isotope effects. The energy barrier for mono-benzofurazan mechanisms was found to be high, >61 kcal/mol in the gas phase; however, the reaction energy can decrease significantly in a disordered condensed state. The predicted kinetic isotope effect ratio of the furazan mechanism was found to be k h /k d ≈ 1.41 at 60K, in agreement with the experiment. The NO 2 scission mechanism was found to be an entropy-driven mechanism because the free energy barrier decreased significantly with temperature, making it the most energetically favorable mechanism at high temperatures in the gas phase. So the results provide a better understanding of the atomistic decomposition mechanisms of TATB and may be useful for improving models of safety and sensitivity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Role of kinetic energy on Nb 3 Sn thin films by low-temperature co-sputtering

Nb 3 Sn is a promising thin film material for superconducting radio frequency (SRF) applications. Although surface resistivity, critical temperature, and critical field are advantageous in comparison to pure Nb, currently the performance of Nb 3 Sn is lacking behind due to its complex defect structure and phase inhomogeneities. In this work, the influence of the kinetic energy of the deposited particles on the defect structure in Nb 3 Sn thin films synthesized at low temperatures is investigated. A combination of extended x-ray absorption fine structure analysis, x-ray absorption spectroscopy mapping, and transmission electron microscopy reveals an improved local order and elemental homogeneity of the Nb 3 Sn films induced by higher kinetic energies of the elemental species during deposition. Even more, these process conditions lead to suppressed local inhomogeneities at grain boundaries, which can be one of the causes of critically reduced superconducting properties of low temperature sputter-coated Nb 3 Sn thin films. Finally, we show that the magnetic field-induced reduction of critical currents across weak-links formed at grain boundaries can be eliminated by the suggested materials’ synthesis.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Inference of strength and phase transition kinetics in dynamically-compressed tin

Dynamic compression experiments in condensed matter are of interest in part because they provide opportunities to examine material response under extreme conditions; however, the inference of material behavior from dynamic experiments is challenging in the presence of phase transitions exhibiting kinetic processes. Demonstrating an approach to quantitative interpretation of such dynamic experiments, here we present a Bayesian model calibration of strength and phase transformation parameters to data drawn from pulsed power and gas gun shot experiments. The posterior predictions of the Bayesian model capture the experimental measurements and account for the various uncertainties in the experimental configurations. This holistic approach to model calibration utilizing multiple types of experimental data identifies important cross correlations among kinetics, strength, and the phase boundary. Improved insight into potential sources of current model form error is provided by comparing the differences between calibrations against different subsets of the experimental data.

42 ENGINEERING↗
DOE OSTI2024

Topanga: A kinetic ion plasma code for large-scale ionospheric simulations on magnetohydrodynamic timescales

Topanga is a kinetic ion code developed for simulating large-scale plasma phenomena in the Earth's ionosphere on magnetohydrodynamic timescales. It is a domain-decomposed parallel code that runs on high-performance computing platforms. Features of Topanga include spherical geometry for simplified boundary conditions and computational efficiency; a hybrid plasma model with inertia-less fluid electrons, kinetic ions, and an electric field specified via an Ohm's law; a Maxwell-FDTD (finite difference time domain) plasma model which retains the displacement current in Maxwell's equations and models electron currents in the ionosphere with a tensor conductivity; sponge-layer boundary conditions for absorption of electromagnetic and plasma waves incident on the domain boundaries; and a novel mixed-implicit algorithm for evolving the EM fields inside the Maxwell-FDTD region that is stable over many orders of magnitude in the electron–ion collision frequency. We verify the numerical methods used in Topanga on a pair of test problems. The first test involves modeling a three-dimensional collisionless shock using the hybrid set of equations. The second test involves modeling a spherical TEM mode in vacuum using the Maxwell-FDTD set of equations. Finally, we demonstrate how using the combined set of hybrid and Maxwell-FDTD equations to model the Starfish Prime high-altitude nuclear test recovers a “missing” EM signal on the ground that is not present when using only the hybrid set of equations. The magnitude of this signal in the simulation containing the Maxwell-FDTD region agrees well with the E3a portion of the magnetohydrodynamic electromagnetic pulse from Starfish Prime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Generalized kinetic equation for tokamak plasma equilibrium distribution function

A generalised kinetic equation for the equilibrium distribution function in a finite beta, arbitrary tokamak plasma is derived. The equation is correct to second order in ρ/L (ρ is the particle Larmor radius and L is the system size). Resolving finite Larmor radius length scales with no restriction on the ratio of poloidal to total equilibrium magnetic field, B $\vartheta$ /B, it generalises the drift kinetic theory of [Hazeltine Phys. Plasmas 15 (1973) 77] to the limit of B $\vartheta$ /B ~ 1 (e.g. to ensure validity for spherical tokamaks). Two cases are considered. The first provides the equilibrium distribution function, consistent with the generalised gyrokinetic formalism of [Dudkovskaia et al. Plasma Phys. Control. Fusion 65 (2023) 045010], derived specifically to capture neoclassical equilibrium currents in gyrokinetic stability analyses in strong gradient regions. The second assumes short length scales in the direction perpendicular to the magnetic field, which can occur as a result of small coherent magnetic structures in the plasma, such as neoclassical tearing mode magnetic islands close to threshold. This then extends the drift island equations of [Dudkovskaia et al. Nucl. Fusion 63 (2023) 016020] for the plasma response to magnetic islands to a spherical tokamak plasma configuration. In conclusion, resolving ρ ~ ρ $\vartheta$ (or B $\vartheta$ ~ B), where ρ $\vartheta$ is the particle poloidal Larmor radius, is also expected to influence calculations of the magnetic island propagation frequency and the associated contributions to the island onset conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Interface-modulated kinetic differentials in electron and hole transfer rates as a key design principle for redox photocatalysis by Sb2VO5/QD heterostructures

The efficient conversion of solar energy to chemical energy represents a critical bottleneck to the energy transition. Photocatalytic splitting of water to generate solar fuels is a promising solution. Semiconductor quantum dots (QDs) are prime candidates for light-harvesting components of photocatalytic heterostructures, given their size-dependent photophysical properties and band-edge energies. A promising series of heterostructured photocatalysts interface QDs with transition-metal oxides which embed midgap electronic states derived from the stereochemically active electron lone pairs of p-block cations. Here, we examine the thermodynamic driving forces and dynamics of charge separation in Sb2VO5/CdSe QD heterostructures, wherein a high density of Sb 5s2-derived midgap states are prospective acceptors for photogenerated holes. Hard-x-ray valence band photoemission spectroscopy measurements of Sb2VO5/CdSe QD heterostructures were used to deduce thermodynamic driving forces for charge separation. Interfacial charge transfer dynamics in the heterostructures were examined as a function of the mode of interfacial connectivity, contrasting heterostructures with direct interfaces assembled by successive ion layer adsorption and reaction (SILAR) and interfaces comprising molecular bridges assembled by linker-assisted assembly (LAA). Transient absorption spectroscopy measurements indicate ultrafast (<2 ps) electron and hole transfer in SILAR-derived heterostructures, whereas LAA-derived heterostructures show orders of magnitude differentials in the kinetics of hole (<100 ps) and electron (∼1 ns) transfer. The interface-modulated kinetic differentials in electron and hole transfer rates underpin the more effective charge separation, reduced charge recombination, and greater photocatalytic efficiency observed for the LAA-derived Sb2VO5/CdSe QD heterostructures.

Chemistry↗
DOE OSTI2024

Onset of kinetic effects on Rayleigh–Taylor instability: Advective–diffusive asymmetry

In nature and engineering applications, the Rayleigh–Taylor instability (RTI) occurs over a wide range of Atwood, Reynolds, Mach, and Knudsen numbers. At low Atwood, Mach, and Knudsen numbers, the classic advective instability causes quasi-symmetric bubble and spike growth on the two sides of the interface. However, recent findings suggest that at high degrees of rarefaction, advective effects are suppressed and molecular diffusion leads to planar growth of the density fronts on either side of the interface. This study aims to investigate the flow physics of the transition from advective to diffusive behavior, focusing on the onset of the kinetic effects. Using the gas kinetic methodology, RTI is simulated over a range of Knudsen and Mach numbers in the transition regime. The simulation results reveal the various stages of transformation from advective instability to diffusive transport. For the first time, the study demonstrates the existence of a Knudsen–Mach parameter regime where the bubble side exhibits advective instability, while the other side shows a planar density front due to molecular diffusion, rather than the canonical advective spike shape. The dominance of different mechanisms on the two sides of the interface leads to the advective–diffusive asymmetry. In conclusion, the findings of this study can lead to a more comprehensive understanding of RTI over a wide range of Mach and Knudsen numbers.

42 ENGINEERING↗
DOE OSTI2025

Formation of distinctive nanostructured metastable polymorphs mediated by kinetic transition pathways in germanium

High-pressure β -Sn germanium may transform into diverse metastable allotropes with distinctive nanostructures and unique physical properties via multiple pathways under decompression. However, the mechanism and transition kinetics remain poorly understood. Here, we investigate the formation of metastable phases and nanostructures in germanium via controllable transition pathways of β -Sn Ge under rapid decompression at different rates. High-resolution transmission electron microscopy reveals three distinct metastable phases with the distinctive nanostructures: an almost perfect st12 Ge crystal, nanosized bc8/r8 structures with amorphous boundaries, and amorphous Ge with nanosized clusters (0.8–2.5 nm). Fast in situ x-ray diffraction and x-ray absorption measurements indicate that these nanostructured products form in certain pressure regions via distinct kinetic pathways and are strongly correlated with nucleation rates and electronic transitions mediated by compression rate, temperature, and stress. This work provides deep insight into the controllable synthesis of metastable materials with unique crystal symmetries and nanostructures for potential applications.

36 MATERIALS SCIENCE↗