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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics

The Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme–substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steady state for the enzyme–substrate complex and that the product genesis from enzyme–substrate complex is much slower than the equilibration between enzyme–substrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis–Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis–Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis–Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln k 2 + of the reaction velocity v with respect to the maximum product genesis rate k 2 + , persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln k 1 + of v with respect to the intrinsic substrate affinity k 1 + , persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln [ E ] T of v with respect the total enzyme concentration [ E ] T , and persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln [ S ] T of v with respect to the total substrate concentration [ S ] T . Meanwhile, the reverse Michaelis–Menten kinetics persistently underpredicts ∂ ln v / ∂ ln k 2 + and ∂ ln v / ∂ ln [ E ] T , and persistently overpredicts ∂ ln v / ∂ ln k 1 + and ∂ ln v / ∂ ln [ S ] T . In contrast, the equilibrium chemistry approximation kinetics always gives consistent predictions of ∂ ln v / ∂ ln k 2 + , ∂ ln v / ∂ ln k 1 + , ∂ ln v / ∂ ln [ E ] T , and ∂ ln v / ∂ ln [ S ] T , indicating that ECA-based models will be more calibratable if the modeled processes do obey the law of mass action. Since the equilibrium chemistry approximation kinetics includes advantages from both the Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics and it is applicable for almost the whole range of substrate and enzyme abundances, land biogeochemical modelers therefore no longer need to choose when to use the Michaelis–Menten kinetics or the reverse Michaelis–Menten kinetics. I expect that removing this choice ambiguity will make it easier to formulate more robust and consistent land biogeochemical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Fully Kinetic versus Reduced-kinetic Modeling of Collisionless Plasma Turbulence

We report the results of a direct comparison between different kinetic models of collisionless plasma turbulence in two spatial dimensions. The models considered include a first-principles fully kinetic (FK) description, two widely used reduced models (gyrokinetic (GK) and hybrid-kinetic (HK) with fluid electrons), and a novel reduced gyrokinetic approach (KREHM). Two different ion beta (β{sub i}) regimes are considered: 0.1 and 0.5. For β{sub i}=0.5, good agreement between the GK and FK models is found at scales ranging from the ion to the electron gyroradius, thus providing firm evidence for a kinetic Alfvén cascade scenario. In the same range, the HK model produces shallower spectral slopes, presumably due to the lack of electron Landau damping. For β{sub i}=0.1, a detailed analysis of spectral ratios reveals a slight disagreement between the GK and FK descriptions at kinetic scales, even though kinetic Alfvén fluctuations likely still play a significant role. The discrepancy can be traced back to scales above the ion gyroradius, where the FK and HK results seem to suggest the presence of fast magnetosonic and ion Bernstein modes in both plasma beta regimes, but with a more notable deviation from GK in the low-beta case. The identified practical limits and strengths of reduced-kinetic approximations, compared here against the FK model on a case-by-case basis, may provide valuable insight into the main kinetic effects at play in turbulent collisionless plasmas, such as the solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Kinetic-j : A computational kernel for solving the linearized Vlasov equation applied to calculations of the kinetic, configuration space plasma current for time harmonic wave electric fields

We present the Kinetic-j code, a computational kernel for evaluating the linearized Vlasov equation withapplication to calculating the kinetic plasma response (current) to an applied time harmonic wave electricfield. This code addresses the need for a configuration space evaluation of the plasma current to enablekinetic full-wave solvers for waves in hot plasmas to move beyond the limitations of the traditional Fourierspectral methods. We benchmark the kernel via comparison with the standard k-space forms of the hotplasma conductivity tensor.

Green, David L.↗
DOE OSTI2014

Investigation of ion kinetic effects in direct-drive exploding-pusher implosions at the NIF

Measurements of yield, ion temperature, areal density (ρR), shell convergence, and bang time have been obtained in shock-driven, D 2 and D 3 He gas-filled “exploding-pusher” inertial confinement fusion (ICF) implosions at the National Ignition Facility to assess the impact of ion kinetic effects. These measurements probed the shock convergence phase of ICF implosions, a critical stage in hot-spot ignition experiments. The data complement previous studies of kinetic effects in shock-driven implosions. Ion temperature and fuel ρR inferred from fusion-product spectroscopy are used to estimate the ion-ion mean free path in the gas. A trend of decreasing yields relative to the predictions of 2D draco hydrodynamics simulations with increasing Knudsen number (the ratio of ion-ion mean free path to minimum shell radius) suggests that ion kinetic effects are increasingly impacting the hot fuel region, in general agreement with previous results. Lastly, the long mean free path conditions giving rise to ion kinetic effects in the gas are often prevalent during the shock phase of both exploding pushers and ablatively driven implosions, including ignition-relevant implosions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Kinetic Activation-Relaxation Technique and Self-Evolving Atomistic Kinetic Monte Carlo: Comparison of on-the-fly kinetic Monte Carlo algorithms

Here, we present a comparison of the Kinetic Activation–Relaxation Technique (k-ART) and the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC), two off-lattice, on-the-fly Kinetic Monte Carlo (KMC) techniques that were recently used to solve several materials science problems. We show that if the initial displacements are localized the dimer method and the Activation–Relaxation Technique nouveau provide similar performance. We also show that k-ART and SEAKMC, although based on different approximations, are in agreement with each other, as demonstrated by the examples of 50 vacancies in a 1950-atom Fe box and of interstitial loops in 16,000-atom boxes. Generally speaking, k-ART’s treatment of geometry and flickers is more flexible, e.g. it can handle amorphous systems, and rigorous than SEAKMC’s, while the later’s concept of active volumes permits a significant speedup of simulations for the systems under consideration and therefore allows investigations of processes requiring large systems that are not accessible if not localizing calculations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH{sub 2} group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C{sub 2v} symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice–Ramsperger–Kassel–Marcus/multi-well master equation simulations, the results of which reveal the formation of (NO{sub 2} + H{sub 2}O) to be the major decomposition path. Furthermore, we provide fundamental interpretations for the experimental results of Klapötke et al. [Combust. Flame 139, 358–366 (2004)] regarding the thermal stability of MNB and DNB, and their decomposition products. Notably, a fundamental understanding of fuel stability, decomposition mechanism, and key reactions leading to ignition is essential in the design and manipulation of molecular systems for the development of new energetic materials for advanced propulsion applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Formic Acid Decomposition on Au catalysts: DFT, Microkinetic Modeling, and Reaction Kinetics Experiments

A combined theoretical and experimental approach is presented that uses a comprehensive mean-field microkinetic model, reaction kinetics experiments, and scanning transmission electron microscopy imaging to unravel the reaction mechanism and provide insights into the nature of active sites for formic acid (HCOOH) decomposition on Au/SiC catalysts. All input parameters for the microkinetic model are derived from periodic, self-consistent, generalized gradient approximation (GGA-PW91) density functional theory calculations on the Au(111), Au(100), and Au(211) surfaces and are subsequently adjusted to describe the experimental HCOOH decomposition rate and selectivity data. It is shown that the HCOOH decomposition follows the formate (HCOO) mediated path, with 100% selectivity toward the dehydrogenation products (CO21H2) under all reaction conditions. An analysis of the kinetic parameters suggests that an Au surface in which the coordination number of surface Au atoms is 4 may provide a better model for the active site of HCOOH decomposition on these specific supported Au catalysts.

active sites↗
DOE OSTI2014

Reconciling disparate views of template-directed nucleation through measurement of calcite nucleation kinetics and binding energies

The physical basis for how macromolecules regulate the onset of mineral formation in calcifying tissues is not well established. A popular conceptual model assumes the organic matrix provides a stereochemical match during cooperative organization of solute ions. In contrast, another uses simple binding assays to identify good promoters of nucleation. Here, we reconcile these two views and provide a mechanistic explanation for template-directed nucleation by correlating heterogeneous nucleation barriers with crystal–substrate-binding free energies. We first measure the kinetics of calcite nucleation onto model substrates that present different functional group chemistries (carboxyl, thiol, phosphate, and hydroxyl) and conformations (C11 and C16 chain lengths). We find rates are substrate-specific and obey predictions of classical nucleation theory at supersaturations that extend above the solubility of amorphous calcium carbonate. Analysis of the kinetic data shows the thermodynamic barrier to nucleation is reduced by minimizing the interfacial free energy of the system, ?. We then use dynamic force spectroscopy to independently measure calcite–substrate-binding free energies, ?Gb. Moreover, we show that within the classical theory of nucleation, ? and ?Gb should be linearly related. The results bear out this prediction and demonstrate that low-energy barriers to nucleation correlate with strong crystal–substrate binding. This relationship is general to all functional group chemistries and conformations. These findings provide a physical model that reconciles the long-standing concept of templated nucleation through stereochemical matching with the conventional wisdom that good binders are good nucleators. The alternative perspectives become internally consistent when viewed through the lens of crystal–substrate binding.

Hamm, Laura M.↗
DOE OSTI2015

Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

Simulations of decaying magnetohydrodynamic (MHD) turbulence are performed with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k{sub ⊥}{sup −1.3}. The kinetic code shows a spectral slope of k{sub ⊥}{sup −1.5} for smaller simulation domain, and k{sub ⊥}{sup −1.3} for larger domain. We estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. This work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Asymmetric “melting” and “freezing” kinetics of the magnetostructural phase transition in B2-ordered FeRh epilayers

Synchrotron X-ray diffraction was used to study the phase transformation processes during the magnetostructural transition in a B2-ordered FeRh (001)-oriented epilayer grown on MgO by sputtering. Out-of-plane lattice constant measurements within the hysteretic regime of the transition reveal a microstructure consistent with the coexistence of lattice-expanded and contracted phases in spatially distinct regions. It was found that the phase separation is more pronounced during cooling than heating. Furthermore, whilst lattice-expanded domains that span the height of the film can be undercooled by several kelvins, there is no equivalent superheating. This asymmetry between the cooling and heating processes in FeRh is consistent with the difference in the kinetics of generic freezing and melting transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗