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Results for “Kinetic analyses”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Investigation of evolution-related aspects of bacterial rhodopsins

We have investigated evolution-related aspects of bacterial rhodopsins, the unique retinal-based energy transducing systems of halophilic archae. The approach was to describe both structural and functional aspects: the structure by sequencing genes to explore which regions are conserved, and the function by comparing proton and chloride transport in the closely related systems, bacteriorhodopsin and halorhodopsin, respectively. In the latter, we have made a good start toward the ultimate goal of separating the attributes of the general principles of retinal-based ionic pumps from those of the specific ion specificities, by determining the thermodynamics of the internal steps of the protein-mediated active transport process, as well as some of the intraprotein ion-transfer steps. Our present emphasis is on continuing to acquire the tools for studying what distinguishes proton transport from chloride transport. We consider it important, therefore, that we have been able to provide firm mathematical grounds for the kinetics analyses which underlies these studies. Our molecular biological studies have received a great boost from the expression vector for the bop gene based on a halobacterial plasmid, that we recently developed.

Source record↗
NASA NTRS1993

Ecophysiological Characteristics of Obligate Methanotrophic Bacteria and Methane Oxidation In Situ

Most of the obligate methane-oxidizing bacteria (MOB) described to date are neutrophilic mesophiles that grow optimally in dilute media. Kinetic analyses generally indicate that bacterial methane uptake occurs by transport systems with a K(sub m) greater than l micronM. These and other properties of MOB are inconsistent with characteristics of methane oxidation in situ. The inconsistencies indicate a need for greater attention to the ecophysiological characteristics of isolates and the design of enrichment and isolation schemes which emphasize ecologically relevant parameters (e.g., low temperature, limited and diverse substrate availability, low water potential).

King, Gary M.↗
NASA NTRS1998

Time-Resolved O3 Chemical Chain Reaction Kinetics Via High-Resolution IR Laser Absorption Methods

Excimer laser photolysis in combination with time-resolved IR laser absorption detection of OH radicals has been used to study O3/OH(v = 0)/HO2 chain reaction kinetics at 298 K, (i.e.,(k(sub 1) is OH + 03 yields H02 + 02 and (k(sub 2) is H02 + 03 yields OH + 202). From time-resolved detection of OH radicals with high-resolution near IR laser absorption methods, the chain induction kinetics have been measured at up to an order of magnitude higher ozone concentrations ([03] less than or equal to 10(exp 17) molecules/cu cm) than accessible in previous studies. This greater dynamic range permits the full evolution of the chain induction, propagation, and termination process to be temporally isolated and measured in real time. An exact solution for time-dependent OH evolution under pseudo- first-order chain reaction conditions is presented, which correctly predicts new kinetic signatures not included in previous OH + 03 kinetic analyses. Specifically, the solutions predict an initial exponential loss (chain "induction") of the OH radical to a steady-state level ([OH](sub ss)), with this fast initial decay determined by the sum of both chain rate constants, k(sub ind) = k(sub 1) + k(sub 2). By monitoring the chain induction feature, this sum of the rate constants is determined to be k(sub ind) = 8.4(8) x 10(exp -14) cu cm/molecule/s for room temperature reagents. This is significantly higher than the values currently recommended for use in atmospheric models, but in excellent agreement with previous results from Ravishankara et al.

Kulcke, Axel↗
NASA NTRS1999

Non-unity molecular heritability demonstrated by continuous evolution in vitro

INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

Non-NASA Center↗
NASA NTRS2012

In-situ Measurements of the Radiolytic Destruction of Glycine in Ices: Applications to the Martian Subsurface

Amino acids and other organic molecules are thought to be easily destroyed on the surface of Mars by the high flux of incident ultraviolet rays or by chemical interactions with oxidizing substances in the soil. However, organic molecules may survive in the subsurface, where chemical processes are driven by penetrating galactic cosmic rays such as MeV protons. Models of the radiation dose as a function of depth on Mars have shown that the contribution of galactic cosmic rays dominates from about one centimeter to a few meters [1 J. Theoretical models have also been published to aid in understanding molecular destruction at these depths, but these usually are based on room-temperature laboratory data, studies of single-component samples, and ex-situ methods of chemical analysis. Recent studies of amino-acid survivability include those involving UV photolysis [2, 3J and gamma radiolysis [4], but nearly all chemical and kinetic analyses from such experiments involved room-temperature measurements on samples irradiated and then removed from sealed containers. We report new laboratory studies of the radiation-induced destruction of glycine-containing ices. In-situ infrared spectroscopy was used to study decay rates as a function of temperature and initial glycine concentrations. Our results indicate that glycine's destruction rate depends on temperature, the presence of H20-ice, and the initial relative abundance of glycine. These trends are not obvious in previous work, suggesting that room-temperature measurements on pure glycine's radiation stability are not directly applicable to Mars and other environments.

Gerakines, Perry A.↗
NASA NTRS2021

Evaluating the De Hoffmann-Teller Cross-Shock 2 Potential at Real Collisionless Shocks

Shock waves are common in the heliosphere and beyond. The collisionless nature of most astrophysical plasmas allows for the energy processed by shocks to be partitioned amongst particle sub-populations and electromagnetic fields via physical mechanisms that are not well understood. The electrostatic potential across such shocks is frame dependent. In a frame where the incident bulk velocity is parallel to the magnetic field, the deHoffmann-Teller frame, the potential is linked directly to the ambipolar electric field established by the electron pressure gradient. Thus measuring and understanding this potential solves the electron partition problem, and gives insight into other competing shock processes. Integrating measured electric fields in space is problematic since the measurements can have offsets that change with plasma conditions. The offsets, once integrated, can be as large or larger than the shock potential. Here we exploit the high-quality field and plasma measurements from NASA’s Magnetospheric Multiscale mission to attempt this calculation. We investigate recent adaptations of the deHoffmann-Teller frame transformation to include time variability, and conclude that in practice these face difficulties inherent in the 3D time-dependent nature of real shocks by comparison to 1D simulations. Potential estimates based on electron fluid and kinetic analyses provide the most robust measures of the deHoffmann-Teller potential, but with some care direct integration of the electric fields can be made to agree. These results suggest that it will be difficult to independently assess the role of other processes, such as scattering by shock turbulence, in accounting for the electron heating.

Steven J Schwartz↗
DOE OSTI2016

HCV kinetic and modeling analyses indicate similar time to cure among sofosbuvir combination regimens with daclatasvir, simeprevir or ledipasvir

Recent clinical trials of direct-acting-antiviral agents (DAAs) against hepatitis C virus (HCV) achieved >90% sustained virological response (SVR) rates, suggesting that cure often took place before the end of treatment (EOT). We sought to evaluate retrospectively whether early response kinetics can provide the basis to individualize therapy to achieve optimal results while reducing duration and cost. 58 chronic HCV patients were treated with 12-week sofosbuvir + simeprevir (n = 19), sofosbuvir + daclatasvir (n = 19), or sofosbuvir + ledipasvir in three French referral centers. HCV was measured at baseline, day 2, every other week, EOT and 12 weeks post EOT. Furthermore, mathematical modeling was used to predict the time to cure, i.e., <1 virus copy in the entire extracellular body fluid. All but one patient who relapsed achieved SVR. Mean age was 60 ± 11 years, 53% were male, 86% HCV genotype-1, 9% HIV coinfected, 43% advanced fibrosis (F3), and 57% had cirrhosis. At weeks 2, 4 and 6, 48%, 88% and 100% of patients had HCV <15 IU/ml, with 27%, 74% and 91% of observations having target not detected, respectively. Modeling results predicted that 23 (43%), 16 (30%), 7 (13%), 5 (9%) and 3 (5%) subjects were predicted to reach cure within 6, 8, 10, 12 and 13 weeks of therapy, respectively. The modeling suggested that the patient who relapsed would have benefitted from an additional week of sofosbuvir + ledipasvir. Adjusting duration of treatment according to the modeling predicts reduced medication costs of 43–45% and 17–30% in subjects who had HCV <15 IU/ml at weeks 2 and 4, respectively. Finally, the use of early viral kinetic analysis has the potential to individualize duration of DAA therapy with a projected average cost saving of 16–20% per 100-treated persons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chemical kinetic interactions and sensitivity analyses for 2-ethylhexyl nitrate-doped PRF91 using a reduced mechanism

A numerical and experimental investigation about the chemical kinetic interactions between 2-ethylhexylnitrate (EHN) and PRF91 was performed in this study. Rapid compression machine experiments were conducted to investigate the effect of EHN on the autoignition reactivity of the fuel, and a reduced chemical kinetic mechanism was developed including an EHN sub-model. Experiments showed that the ignition delay decreases as the fuel is doped with EHN, but the effect of the doping level of EHN on the ignition is highly non-linear. Moreover, experiments showed that the EHN effectiveness is lowest during the transition between the low-temperature regime and the negative temperature coefficient (NTC) regime, and it rapidly increases as the temperature increases. Both detailed and (developed) reduced mechanisms were validated against the experimental results, allowing a more in-depth EHN-fuel chemistry study. Additionally, ignition delay sensitivity and EHN effectiveness sensitivity analyses were performed with the reduced mechanism to identify the reactions that control the interaction between EHN and the fuel. As the result, EHN thermal decomposition is only relevant for very low temperatures. The chemistry of EHN-doped fuel is more sensitive to intermediate temperature reactions than that of straight fuel, especially at lower temperatures, due to the effect of EHN on the NTC behavior of the fuel. Finally, the chemistry of EHN-doped fuel is very sensitive to NO 2 -to-NO reactions, especially at high temperatures, because these reactions transform the NO 2 generated by EHN into NO, which is a very effective fuel reactivity enhancer.

2-ethylhexyl nitrate↗
DOE OSTI2020

Extracting meaningful standard enthalpies and entropies of activation for surface reactions from kinetic rates

While analyses based on the Arrhenius kinetic model have been successfully applied since its introduction, the Arrhenius model neglects to describe pre-exponential factor in a scientifically meaningful fashion. Since the 1930s, transition-state theory (TST), has met with success in interpreting the pre-exponential factor’s value, allowing a standard entropy of activation to be estimated. However, analyses based on TST’s assumptions have been applied inconsistently in the literature, particularly in corrosion science, leading to difficulty in comparison of standard entropy of activations from different studies. In this work, the foundational principles of TST and standard states are discussed and a standard method to apply TST in analyzing rates of surface reactions is recommended. When full details are not available, reacting species’ concentrations should be normalized to the concentration of active surface sites. For corrosion reactions, conversion relationships are given to convert from units of corrosion rate to surface reaction rate, consistent with TST. This method is dubbed a surface reactant equi-density approximation. Application of this standard to reported data results in adjustments of the standard entropy of activation between - 65 and +50 J/mol K and brings reported entropies into a narrower range of values.

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

Molecular Statics Analyses of Thermodynamics and Kinetics of Hydrogen Cottrell Atmosphere Formation Around Edge Dislocations in Aluminum

Aluminum alloys are being explored as lightweight structural materials for use in hydrogen-containing environments. In this paper, to understand hydrogen effects on deformation, we perform molecular statics studies of the hydrogen Cottrell atmosphere around edge dislocations in aluminum. First, we calculate the hydrogen binding energies at all interstitial sites in a periodic aluminum crystal containing an edge dislocation dipole. This allows us to use the Boltzmann equation to quantify the hydrogen Cottrell atmosphere. Based on these binding energies, we then construct a continuum model to study the kinetics of the hydrogen Cottrell atmosphere formation. Finally, we compare our results with existing theories and discuss the effects of hydrogen on deformation of aluminum-based alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Analysis and prediction of reaction kinetics using the degree of rate control

“Degree of rate control” (DRC) analysis provides a quantitative approach for analysing the kinetics of multi-step reaction mechanisms that has been widely applied to both heterogeneous and homogeneous catalysis research, as well as electrocatalysis. The DRC of any given transition state or intermediate is defined as a partial derivative such that it approximately equals the fractional increase in net rate to the product of interest per differential decrease in its standard-state free energy for that species (÷RT), holding constant the standard-state free energies of all other transition states and intermediates. Even very complex mechanisms usually have only a few species with non-zero DRCs and are thus the species whose interactions with the catalyst most strongly affect the net rate. These key DRC values thus offer a simple and intuitive route to optimize catalyst materials, especially with the assistance of computational methods like density functional theory (DFT). These high-DRC species are also the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic model for any reaction mechanism. In simple cases with a single “rate-determining step”, the DRC for its transition state (TS) is + 1. Catalyst-bound intermediates, on the other hand, often have negative DRCs equal to a small integer times their fractional occupancy of catalyst sites. The apparent activation energy equals a weighted average of the standard-state enthalpies (relative to reactants) of all the species (intermediates, transition states and products) in the reaction mechanism, each weighted by its DRC (+RT). It has been shown that the apparent transfer coefficient in electrocatalysis, an inverted form of the Tafel slope, is a weighted average of the number of electrons transferred to generate each intermediate or product species in the mechanism, weighted again by the DRC. Quantitative analysis of kinetic isotope effects (KIEs, or the ratio of net rates for different reactant isotopes) in complex mechanisms has shown that the logarithm of the KIE equals the weighted average over all species in the mechanism of the difference between the two isotopes in their standard-state free energies (÷RT), again weighted by the DRC. The reaction orders with respect to fluid-phase concentrations of reactants, products and intermediates have also been proven to be directly related to DRCs. Thus, there are numerous experimental observables which equate to short linear combinations of DRCs, so that combinations of experimental measurements might provide access to DRC values. Since its invention for transition states in 1994 and its generalization to include intermediates in 2009, the DRC has thus far mainly been calculated for microkinetic models based either entirely on DFT or on DFT with the key energies (i.e., those for high-DRC species) being fine-tuned to match experiments. The relationships summarized in this work provide new opportunities for using experiments earlier in the development and optimization of microkinetic models that require input from computational catalysis.

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

Removal of Ni(II), Zn(II) and Pb(II) ions from single metal aqueous solution using rice husk-based activated carbon

An attempt was made to investigate the potential of rice husk-based activated carbon as an alternative low-cost adsorbent for the removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Rice husk-based activated carbon was prepared via treatment of rice husk with NaOH followed by the carbonization process at 400°C for 2 hours. Three samples, i.e. raw rice husk, rice husk treated with NaOH and rice husk-based activated carbon, were analyzed for their morphological characteristics using field-emission scanning electron microscope/energy dispersive X-ray (FESEM/EDX). These samples were also analyzed for their carbon, hydrogen, nitrogen, oxygen and silica contents using CHN elemental analyzer and FESEM/EDX. The porous properties of rice husk-based activated carbon were determined by Brunauer-Emmett-Teller (BET) surface area analyzer, and its surface area and pore volume were 255 m{sup 2}/g and 0.17 cm{sup 2}/g, respectively. The adsorption studies for the removal of Ni(II), Zn(II) and Pb(II) ions from single metal aqueous solution were carried out at a fixed initial concentration of metal ion (150 ppm) with variation amount of adsorbent (rice husk-based activated carbon) as a function of varied contact time at room temperature. The concentration of each metal ion was analyzed using atomic absorption spectrophotometer (AAS). The results obtained from adsorption studies indicate the potential of rice husk as an economically promising precursor for the preparation of activated carbon for removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Isotherm and kinetic model analyses suggested that the experimental data of adsorption studies fitted well with Langmuir, Freundlich and second-order kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Growth kinetics of indium metal atoms on Si(1 1 2) surface

Graphical abstract: Controlled growth of indium atoms on Si(1 1 2) surface has been carried out systematically and the influence of substrate temperature on the kinetics is analysed under various growth conditions. Temperature induced anomalous layer-to-clusters transformation during thermal desorption has also been reported. - Highlights: • Controlled growth of indium atoms on Si(1 1 2) surface & their thermal stability. • Influence of substrate temperature on the kinetics under various growth conditions. • Temperature induced layer-to-clusters transformation during thermal desorption. - Abstract: The growth kinetics and desorption behavior of indium (In) atoms grown on high index Si(1 1 2) surface at different substrate temperatures has been studied. Auger electron spectroscopy analysis revealed that In growth at room temperature (RT) and high substrate temperature (HT) ∼250 °C follows Frank–van der Merve growth mode whereas at temperatures ≥450 °C, In growth evolves through Volmer–Weber growth mode. Thermal desorption studies of RT and 250 °C grown In/Si(1 1 2) systems show temperature induced rearrangement of In atoms over Si(1 1 2) surface leading to clusters to layer transformation. The monolayer and bilayer desorption energies for RT grown In/Si(1 1 2) system are calculated to be 2.5 eV and 1.52 eV, while for HT-250 °C the values are found to be 1.6 eV and 1.3 eV, respectively. This study demonstrates the effect of temperature on growth kinetics as well as on the multilayer/monolayer desorption pathway of In on Si(1 1 2) surface.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Stability and dissociation dynamics of N{sub 2}{sup ++} ions following core ionization studied by an Auger-electron–photoion coincidence method

An Auger-electron–photoion coincidence (AEPICO) method has been applied to study the stability and dissociation dynamics of dicationic states after the N K-shell photoionization of nitrogen molecules. From time-of-flight and kinetic energy analyses of the product ions, we have obtained coincident Auger spectra associated with metastable states of N{sub 2}{sup ++} ions and dissociative states leading to N{sub 2}{sup ++} → N{sup +} + N{sup +} and N{sup ++} + N. To investigate the production of dissociative states, we present two-dimensional AEPICO maps which reveal the correlations between the binding energies of the Auger final states and the ion kinetic energy release. These correlations have been used to determine the dissociation limits of individual Auger final states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

Yeast tRNA ligase (Trl1) is an essential trifunctional enzyme that catalyzes exon-exon ligation during tRNA biogenesis and the non-conventional splicing of HAC1 mRNA during the unfolded protein response (UPR). The UPR regulates the protein folding capacity of the endoplasmic reticulum (ER). ER stress activates Ire1, an ER-resident kinase/RNase, which excises an intron from HAC1 mRNA followed by exon-exon ligation by Trl1. The spliced product encodes for a potent transcription factor that drives the UPR. Here we report the crystal structure of Trl1 RNA ligase domain from Chaetomium thermophilum at 1.9 Å resolution. Structure-based mutational analyses uncovered kinetic competition between RNA ligation and degradation during HAC1 mRNA splicing. Incompletely processed HAC1 mRNA is degraded by Xrn1 and the Ski/exosome complex. We establish cleaved HAC1 mRNA as endogenous substrate for ribosome-associated quality control. We conclude that mRNA decay and surveillance mechanisms collaborate in achieving fidelity of non-conventional mRNA splicing during the UPR.

59 BASIC BIOLOGICAL SCIENCES↗