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At least 271 records · Page 15

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗

KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states

Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty in obtaining flux and/or concentration data but also due to the computational difficulties of the underlying parameter identification problem. Both the computational demands for parameterization, degeneracy of obtained parameter solutions and interpretability of results has so far limited widespread adoption of large-scale kinetic models despite their potential. Herein, we introduce the Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the (non)steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP is benchmarked against previously parameterized large-scale kinetic models demonstrating an at least an order of magnitude faster convergence than the tool K-FIT while at the same time attaining better data fits. Finally, this versatile toolbox accepts different kinetic descriptions, metabolic fluxes, enzyme levels and metabolite concentrations, under either steady-state or instationary conditions to enable robust kinetic model construction and parameterization. KETCHUP supports the SBML format and can be accessed at https://github.com/maranasgroup/KETCHUP.

59 BASIC BIOLOGICAL SCIENCES↗

Containerless high temperature property measurements by atomic fluorescence

Containerless high temperature processing and material property measurements are discussed. Researchers developed methods for non-contact suspension, heating, and property measurement for materials at temperatures up to 3,680K, the melting point of tungsten. New, scientifically interesting results were obtained in Earth-based research. These results and the demonstration of new methods and techniques form a basis for further advances under the low gravity environment of space where containerless conditions are more easily achieved. Containerless high temperature material property investigations that have been completed in this and our earlier projects include measurements of fluorine LaB sub 6 reaction kinetics at 1,000 to 1,500K; optical property measurements on sapphire (Al2O3) at temperatures up to the melting point (2,327K); and vapor pressure measurements for LaB sub 6 at 2,000 to 2,500K, for molybdenum up to 2,890K and for tungsten up to 3,680K. Gas jet levitation which is applicable to any solid material, and electromagnetic levitation of electrical conductors were used to suspend the materials of interest. Non-contact heating and property measurements were achieved by optical techniques, i.e., laser heating, laser induced fluorescence measurements of vapor concentrations, and optical pyrometry for specimen temperatures.

Nordine, Paul C.↗

Thermoelectric Temperature Measurement of Deforming Solids

Sold phase processing (SPP) utilizes large deformations and elevated but sub-melting temperatures to process materials in an energy-efficient manner to achieve high-performance properties. Studying the fundamental material science and kinetics requires an accurate temperature history of the process, but accurately measuring temperature at the point of deformation is very difficult. This study uses the thermoelectric principle to allow for the direct measurement of a deforming surface by turning the workpieces themselves into the measurement device. By so doing, results measured temperatures are closer to the actual deforming interface, more accurate, more responsive, and more reliable than corresponding measurements taken with standard thermocouples.

36 MATERIALS SCIENCE↗

Energetics of the midlatitude thermosphere

Thermospheric energetics is examined from the point of view of atomic and molecular processes which convert solar EUV radiative energy into kinetic energy of the ambient electron, ion, and neutral gases. The energy flow from photon to photoelectron-ion pair through energy loss and ion-molecule transfer to eventual electron-ion recombination is traced in detail. Upper and lower bounds are placed on the efficiency of conversion of radiative to thermal energy. Implications for the question of consistency of measured solar EUV fluxes and ionospheric models are discussed.

Stolarski, R. S.↗

Stellar fibril magnetic systems. I - Reduced energy state

The remarkable fibril structure of the magnetic fields at the surface of the sun (with fibrils compressed to 1,000-2,000 gauss) lies outside existing statistical theories of magnetohydrodynamic turbulence. The total energy of the fibril field is enhanced by a factor of more than 100 above the energy for the mean field in a continuum state. The magnetic energy density within a fibril is of the order of 100 times the local kinetic energy density, so that no simple application of equipartition principles is possible. It is pointed out that the total energy of the atmosphere (thermal + gravitational + magnetic) is reduced by the fibril state of the field by avoiding the magnetic inhibition of the convective overturning, suggesting that the formation of the observed intense fibril state may be in response to the associated energy reduction. Calculation of the minimum total energy of a polytropic atmosphere permeated by magnetic fibrils yields theoretical fibril fields of the order of 1-5 kilogauss when characteristics appropriate to the solar convective zone are introduced, in rough agreement with the actual fields of 1-2 kilogauss. The polytrope model, although crude, establishes that a large reduction in total energy is made possible by the fibril state.

Parker, E. N.↗

Flux estimation of the FIFE planetary boundary layer (PBL) with 10.6 micron Doppler lidar

A method is devised for calculating wind, momentum, and other flux parameters that characterize the planetary boundary layer (PBL) and thereby facilitate the calibration of spaceborne vs. in situ flux estimates. Single Doppler lidar data are used to estimate the variance of the mean wind and the covariance related to the vertically pointing fluxes of horizontal momentum. The skewness of the vertical velocity and the range of kinetic energy dissipation are also estimated, and the surface heat flux is determined by means of a statistical Navier-Stokes equation. The conclusion shows that the PBL structure combines both 'bottom-up' and 'top-down' processes suggesting that the relevant parameters for the atmospheric boundary layer be revised. The conclusions are of significant interest to the modeling techniques used in General Circulation Models as well as to flux estimation.

Gal-Chen, Tzvi↗

Internal-flow systems for aircraft

An investigation has been made to determine efficient arrangements for an internal-flow system of an aircraft when such a system operates by itself or in combination with other flow systems. The investigation included a theoretical treatment of a problem and tests in the NACA 5-foot vertical wind tunnel of inlet and outlet openings in a flat plate and in a wing. When an internal-flow system tends to decrease the final velocity of it's wake, the results showed that it should be arranged in series with the propulsive system; the inlet opening should be located at a forward stagnation point; and the outlet opening should be so shaped and located as to recover the kinetic energy of the jet without increasing the drag of other portions of the aircraft. When an internal-flow system tends to increase the final velocity new b's wake, as does a propeller, location of the inlet opening in the boundary layer or in the wake of the wing or in the fuselage may be desirable.

Rogallo, F M↗

Growth and Morphology of Phase Separating Supercritical Fluids

The scientific objective is to study the relation between the morphology and the growth kinetics of domains during phase separation. We know from previous experiments performed near the critical point of pure fluids and binary liquids that there are two simple growth laws at late times. The 'fast' growth appears when the volumes of the phases are nearly equal and the droplet pattern is interconnected. In this case the size of the droplets grows linearly in time. The 'slow' growth appears when the pattern of droplets embedded in the majority phase is disconnected. In this case the size of the droplets increases in proportion to time to the power 1/3. The volume fraction of the minority phase is a good candidate to determine this change of behavior. All previous attempts to vary the volume fraction in a single experimental cell have failed because of the extreme experimental difficulties.

Hegseth, John↗

A calcium-dependent protein kinase can inhibit a calmodulin-stimulated Ca2+ pump (ACA2) located in the endoplasmic reticulum of Arabidopsis

The magnitude and duration of a cytosolic Ca(2+) release can potentially be altered by changing the rate of Ca(2+) efflux. In plant cells, Ca(2+) efflux from the cytoplasm is mediated by H(+)/Ca(2+)-antiporters and two types of Ca(2+)-ATPases. ACA2 was recently identified as a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum. Here, we show that phosphorylation of its N-terminal regulatory domain by a Ca(2+)-dependent protein kinase (CDPK isoform CPK1), inhibits both basal activity ( approximately 10%) and calmodulin stimulation ( approximately 75%), as shown by Ca(2+)-transport assays with recombinant enzyme expressed in yeast. A CDPK phosphorylation site was mapped to Ser(45) near a calmodulin binding site, using a fusion protein containing the N-terminal domain as an in vitro substrate for a recombinant CPK1. In a full-length enzyme, an Ala substitution for Ser(45) (S45/A) completely blocked the observed CDPK inhibition of both basal and calmodulin-stimulated activities. An Asp substitution (S45/D) mimicked phosphoinhibition, indicating that a negative charge at this position is sufficient to account for phosphoinhibition. Interestingly, prior binding of calmodulin blocked phosphorylation. This suggests that, once ACA2 binds calmodulin, its activation state becomes resistant to phosphoinhibition. These results support the hypothesis that ACA2 activity is regulated as the balance between the initial kinetics of calmodulin stimulation and CDPK inhibition, providing an example in plants for a potential point of crosstalk between two different Ca(2+)-signaling pathways.

NASA Discipline Plant Biology↗

SN 2010ay is a Luminous and Broad-lined Type Ic Supernova within a Low-metallicity Host Galaxy

We report on our serendipitous pre-discovery detection and detailed follow-up of the broad-lined Type Ic supernova SN2010ay at z approx 0.067 imaged by the Pan-STARRS1 3pi survey just approx 4 days after explosion. Combining our photometric observations with those available in the literature, we estimate the explosion date and the peak luminosity of the SN, M(sub R) approximately equals 20.2 mag, significantly brighter than known GRB-SNe and one of the most luminous SNe Ibc ever discovered. We measure the photospheric expansion velocity of the explosion from our spectroscopic follow-up observations, v(sub ph) approximately equals 19.2 X 10 (exp 3) km/s at approx 40 days after explosion. In comparison with other broad-lined SNe, the characteristic velocity of SN2010ay is 2 - 5 X higher and similar to the measurements for GRB-SNe at comparable epochs. Moreover the velocity declines two times slower than other SNe Ic-BL and GRB-SNe. Assuming that the optical emission is powered by radioactive decay, the peak magnitude implies the synthesis of an unusually large mass of Ni-56, M(sub Ni) = 0.9(+0.1/-0.1) solar mass. Our modeling of the light-curve points to a total ejecta mass, M(sub ej) approx 4.7 Solar Mass, and total kinetic energy, E(sub K,51) approximately equals 11. Thus the ratio of M(sub Ni) to M(sub ej) is at least twice as large for SN2010ay than in GRB-SNe and may indicate an additional energy reservoir. We also measure the metallicity (log(O/H) + 12 = 8.19) of the explosion site within the host galaxy using a high S/N optical spectrum. Our abundance measurement places this SN in the low-metallicity regime populated by GRB-SNe, and approx 0.2(0.5) dex lower than that typically measured for the host environments of normal (broad-lined) Ic supernovae. Despite striking similarities to the recent GRB-SN100316D/2010bh, we show that gamma-ray observations rule out an associated GRB with E(sub gamma) approx < 6 X 10(exp 48) erg (25-150 keV). Similarly, our deep radio follow-up observations with the Expanded Very Large Array rule out relativistic ejecta with energy, E approx > 10(exp 48) erg. These observations challenge the importance of progenitor metallicity for the production of a GRB, and suggest that other parameters also play a key role.

Sanders, N. E.↗

Hydroxyl radical‐driven transformations of bisphenol A and 2,4‐dinitroanisole: Experimental and computational analysis

Abstract This study used experimental and computational analysis to investigate the advanced oxidation of bisphenol A (BPA) and 2,4‐dinitroanisole (DNAN). The pseudo first‐order reaction rate constants depended on the molar peroxide ratio and were between 0.13 and 0.28 min −1 for BPA and between 0.018 and 0.032 min −1 for DNAN. The kinetic differences appear to be due in part to the energy requirements for oxidation, which depended on the reaction mechanism but were typically lower for BPA than they were for DNAN. Density functional theory (DFT) was used to develop transformation pathways that included experimentally‐detected byproducts. The most energetically favored pathway for BPA oxidation begins with the formation of hydroxylated derivatives, while for DNAN, the most energetically favorable degradation pathway begins with the substitution of the methoxy group. Overall, these findings demonstrate the power of combining experimental and computational tools to reveal transformation mechanisms during water treatment. Practitioner Points Advanced oxidation transformations for two emerging water pollutants, bisphenol A and dinitroanisole, was investigated. The observed reaction kinetics depended on molar peroxide ratio in a manner that is in keeping with previous findings. Density functional theory‐based analysis revealed reaction energy requirements and degradation pathways.

Engineering↗

X-ray spectra of supernova remnants

The X-ray spectra of supernova remnants are discussed, and their implications for the emission mechanism are considered. A model-fitting procedure for analyzing spectral information is presented, and alternative data presentations are indicated. Model spectra expected from diffuse X-ray sources, in which X-ray transfer effects are minimized, are calculated for the cases of Compton interactions, synchrotron radiation and bremsstrahlung. The emission mechanisms of supernova remnants are then considered, and it is pointed out that whereas it is certain that the X radiation from the Crab pulsar arises from synchrotron emission, the kinetic mechanisms giving rise to X-ray emission in the nonpulsar SNRs are not understood. Results of Einstein Observatory solid state spectrometer measurements of the Cas A, Tycho and Puppis A are then presented which are fit by two-temperature thermal spectra, and the Crab SNR, fit by a power-law model. Spectral trends in the older and younger SNRs are pointed out, and the role of Einstein imaging data in future detailed modeling necessary to convert apparent abundances into true abundances is indicated.

Holt, S. S.↗

Predicting EBC Temperature Limits for Industrial Gas Turbines

Higher turbine inlet temperatures may require the use of ceramic matrix composites (CMC) such as SiC/SIC, which require environmental barrier coatings (EBCs) to protect them against the detrimental effect of water vapor. Here, the goal of this project is to determine the maximum bond coating temperature for EBCs for land-based turbines, where the minimum coating lifetime is 25,000 h. If the temperature exceeds the 1414°C melting point of the Si bond coating, then coatings without a bond coating also need to be evaluated. Thus, current Yb 2 Si 2 O 7 EBCs with a Si bond coating and next-generation EBCs without a Si bond coating are being evaluated in laboratory testing using 1-h cycles in air+90%H 2 O. For this initial work, coatings were deposited on CVD SiC coupons. Reaction kinetics at 1250°, 1300° and 1350°C have been evaluated by measuring the thickness of the thermally grown silica scale after 100–500 h exposures. For comparison, scale growth rates for uncoated SiC and Si specimens in dry and wet environments were included as minimum and maximum values, respectively. Based on a critical scale thickness failure criteria, estimated maximum temperatures were calculated for both EBC systems using this initial data.

42 ENGINEERING↗

Verification of the kinetic electron role in the microinstabilities in a negative triangularity model equilibrium

Effect of kinetic electrons on negative triangularity plasmas has been investigated and compared against the corresponding positive triangularity plasmas, using the global gyrokinetic code X-point Gyrokinetic Code with scale-separated delta-f option without Coulomb collisions. Our model magnetic equilibria have strong positive and negative triangularities and weak magnetic shear. However, unusually large ρ i > a and low density plasmas are chosen to maximize the nonlocal effect to investigate the finite ρ i effect and to be clearly away from kinetic ballooning modes. Similar conclusions to previous flux tube and global simulations have been obtained in this highly nonlocal model plasma: it is essential to include kinetic electrons in the micro-instability study of negative triangularity plasmas. Most physics findings agree with existing reports, with some disagreement. We offer a new “effective trapping fraction” concept that can add to the explanation of the growth rate difference between NT and PT plasmas, pointing to the significant variation in trapped particle fractions that have turning points in the mode growth regions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Metastability and Ostwald step rule in the crystallisation of diamond and graphite from molten carbon

Abstract Experimental challenges in determining the phase diagram of carbon at temperatures and pressures near the graphite-diamond-liquid triple point are often related to the persistence of metastable crystalline or glassy phases, superheated crystals, or supercooled liquids. A deeper understanding of the crystallisation kinetics of diamond and graphite is crucial for effectively interpreting the outcomes of these experiments. Here, we reveal the microscopic mechanisms of diamond and graphite nucleation from liquid carbon through molecular simulations with first-principles machine learning potentials. Our simulations accurately reproduce the experimental phase diagram of carbon near the triple point and show that liquid carbon crystallises spontaneously upon cooling. Metastable graphite crystallises in the domain of diamond thermodynamic stability at pressures above the triple point. Furthermore, whereas diamond crystallises through a classical nucleation pathway, graphite follows a two-step process in which low-density fluctuations forego ordering. Calculations of the nucleation rates of the two competing phases confirm this result and reveal a manifestation of Ostwald’s step rule, where the strong metastability of graphite hinders the transformation to the stable diamond phase. Our results provide a key to interpreting melting and recrystallisation experiments and shed light on nucleation kinetics in polymorphic materials with deep metastable states.

Science & Technology - Other Topics↗

Discrete breakup arcs and kinetic Alfven waves

Attention is confined to the extremely narrow auroral structures whose characteristic dimensions perpendicular to the magnetic fields are of the order of several hundred meters or even less. The starting point of the model used here is the assumption that discrete breakup arcs are caused by a change in the magnetosphere convection pattern that is localized in space. Particular attention is given to the shear Alfven mode. It is proposed that discrete breakup arcs are a direct manifestation of kinetic interaction between charged particles and an 'mhd' perturbation. It is stressed that the model applies only to narrow structures (thickness of the order of the plasma skin depth) and to short-lived phenomena (time scales shorter than a dispersion time). It is shown that a change of convection pattern in a spatially limited region leads to the emission of a shear-Alfven wave packet which propagates along the magnetic field line with a characteristic velocity.

Goertz, C. K.↗

Preliminary Kinetic Analysis of Non-Equilibrium Plasma- Assisted Methanol Pyrolysis and Oxidation Experiments

Efforts to enhance power generation efficiency and reduce emissions have driven interest in novel combustion techniques, including non-equilibrium plasma (NEP) ignitors. NEP ignitors show promise in improving energy conversion efficiency, fuel reforming, emission control, and lean-flammability limits. However, their adoption is hindered by a limited understanding of the interplay between plasma-enhanced combustion and thermal chemistry, particularly for complex fuels under engine-relevant conditions. Developing experimentally validated kinetic mechanisms is therefore critical. Additionally, the increasing interest in renewable biofuels like ethanol and methanol, coupled with the desirable qualities of NEP ignitors, presents a compelling opportunity for study. Therefore, this work acts as an extension of a previous work (Bopaiah et al., 2023) pertaining to the experimental results of NEP-assisted methanol pyrolysis and oxidation. Experiments were performed with a custom-built plasma flow reactor at 0.5 atm and temperatures from 523-1203 K. All reactive mixtures are extremely diluted to minimize exothermicity due to reactivity, allowing isothermal assumptions and the isolation of plasma chemistry from thermal chemistry. A dielectric barrier discharge plasma, at 14 kV and 15 ns full-width half maximum, was applied to the reactive mixture at varying frequencies to maintain the number of pulses with increasing temperature. Steady-state product speciation was performed downstream of the reactor with ex-situ GC/MS diagnostics. The attained experimental results were examined through in-depth analysis performed by means of an in-development plasma-coupled kinetic mechanism. As discussed in the previous work, the plasma significantly accelerates methanol pyrolysis, increasing stable intermediate production, including oxygenated and nitrile species. Plasma-assisted oxidation shows even faster fuel consumption compared to pyrolysis and a 200 K ignition shift compared to thermal oxidation. For plasma-assisted pyrolysis, the model demonstrates that accelerated fuel consumption stems from dissociative quenching of excited N2 states with fuel and H2, generating H radicals that react to rapidly form CH3 and CH2OH radicals. At low temperatures, these radicals recombine to produce oxygenates, while CH3 drives nitrile and hydrocarbon formation at higher temperatures. While the model captures pyrolysis trends well, discrepancies in methane, ethylene, and ethanol predictions are present. Similarly, the model faces challenges in accurately representing plasma-assisted oxidation, predicting a much steeper fuel gradient and ignition 100 K earlier than the experiment. While a similar scheme to pyrolysis is nested in the reaction pathway, the enhancement of the O and H radical fluxes and their initiation of the OH and HO2 radical pools dominate fuel and intermediate oxidation. The overestimation of these processes is shown to be responsible for the divergence of model from experiment. While the modelling predictions of this preliminary mechanism are not perfect, they serve as a valuable starting point. Primarily, they elicited new reaction pathways that are not otherwise possible in thermal chemistry induced reaction kinetics. The results also provide a basis for the future work that should be performed. For example, theoretical and experimental studies on excited nitrogen species and fuel/fuel radical interactions, quantification of the NOx production, and the kinetics behind the slow ignition observed in oxidation should be emphasized.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗