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At least 901 records · Page 50

Isolation and characterization of the betalain biosynthesis gene involved in hypocotyl pigmentation of the allotetraploid Chenopodium quinoa

Highlights: • We developed a green hypocotyl mutant (ghy) by EMS mutagenesis in quinoa. • The ghy mutant is caused by the CqCYP76AD1-1 mutation. • CqCYP76AD1-1 expression in quinoa hypocotyl was revealed to be light-dependent. • Quinoa betalain biosynthesis genes produced betanin in N. benthamiana leaves. In quinoa seedlings, the pigment betalain accumulates in the hypocotyl. To isolate the genes involved in betalain biosynthesis in the hypocotyl, we performed ethyl methanesulfonate (EMS) mutagenesis on the CQ127 variety of quinoa seedlings. While putative amaranthin and celosianin II primarily accumulate in the hypocotyls, this process produced a green hypocotyl mutant (ghy). This MutMap+ method using the quinoa draft genome revealed that the causative gene of the mutant is CqCYP76AD1-1. Our results indicated that the expression of CqCYP76AD1-1 was light-dependent. In addition, the transient expression of CqCYP76AD1-1 in Nicotiana benthamiana leaves resulted in the accumulation of betanin but not isobetanin, and the presence of a polymorphism in CqCYP76A1-2 in the CQ127 variety was shown to have resulted in its loss of function. These findings suggested that CqCYP76AD1-1 is involved in betalain biosynthesis during the hypocotyl pigmentation process in quinoa. To our knowledge, CqCYP76AD1-1 is the first quinoa gene identified by EMS mutagenesis using a draft gene sequence.

60 APPLIED LIFE SCIENCES↗

Chlorinated indium tin oxide electrode by InCl{sub 3} aqueous solution for high-performance organic light-emitting diodes

The authors develop a facile and effective method to produce the chlorinated indium tin oxide (Cl-ITO) treated by InCl{sub 3} aqueous solution and UV/ozone. The work function of the Cl-ITO achieved by this treatment is as high as 5.69 eV, which is increased by 1.09 eV compared with that of the regular ITO without any treatment. Further investigation proved that the enhancement of the work function is attributed to the formation of In-Cl bonds on the Cl-ITO surface. Green phosphorescent organic light-emitting devices based on the Cl-ITO electrodes exhibit excellent electroluminescence performance, elongating lifetime due to the improvement in hole injection.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Upgraded viscous flow analysis of multi-element airfoils

A description of an improved version of the NASA/Lockheed multi-element airfoil analysis computer program is presented. The improvements include several major modifications of the aerodynamic model as well as substantial changes of the computer code. The modifications of the aerodynamic model comprise the representation of the boundary layer and wake displacement effects with an equivalent source distribution, the prediction of wake parameters with Green's lag-entrainment method, the calculation of turbulent boundary layer separation with the method of Nash and Hicks, the estimation of the onset of confluent boundary layer separation with a modified form of Goradia's method, and the prediction of profile drag with the formula of Squire and Young. The modifications of the computer program for which the structured approach to computer software development was employed are also described. Important aspects of the structured program development such as the functional decomposition of the aerodynamic theory and its numerical implementation, the analysis of the data flow within the code, and the application of a pseudo code are discussed.

Brune, G. W.↗

Moderate temperature sintering of BaZr 0.8 Y 0.2 O 3-δ protonic ceramics by A novel cold sintering pretreatment

The state-of-the-art protonic ceramic conductor BaZr 0.8 Y 0.2 O 3-δ (BZY20) requires an extremely high sintering temperature (≥1700 °C) to achieve the desired relative density and microstructure necessary to function as a proton conducting electrolyte. In this work, we developed a cold sintering pretreatment assisted moderate-temperature sintering method for the fabrication of high-quality pure BZY20 pellets. BZY20 pellets with high relative density of ~94% were fabricated with a final sintering temperature of 1500 °C (200 °C lower than the traditional sintering temperature). A comparison with BZY20 control samples indicated that the proper amount of BaCO 3 introduced on the BZY20 particle surface and the high green density achieved by cold sintering pretreatment were the main drivers for lowering the sintering temperature. The electrical conductivity measurement by electrochemical impedance spectroscopy showed that the as-prepared BZY20 pellets have a proton conductivity comparable to the state-of-the-art values. The cold sintering pretreatment outlined in this work has the potential to lower the sintering temperatures for similar types of protonic ceramic materials under consideration for a wide range of energy conversion and storage applications.

36 MATERIALS SCIENCE↗

Upgraded viscous flow analysis of multielement airfoils

A description of an improved version of the NASA/Lockheed multielement airfoil analysis computer program is presented. The improvements include several major modifications of the aerodynamic model as well as substantial changes of the computer code. The modifications of the aerodynamic model comprise the representation of the boundary layer and wake displacement effects with an equivalent source distribution, the prediction of wake parameters with Green's lag-entrainment method, the calculation of turbulent boundary layer separation with the method of Nash and Hicks, the estimation of the onset of confluent boundary layer separation with a modified form of Goradia's method, and the prediction of profile drag with the formula of Squire and Young. The paper further describes the modifications of the computer program for which the structured approach to computer software development was employed. Important aspects of the structured program development such as the functional decomposition of the aerodynamic theory and its numerical implementation, the analysis of the data flow within the code, and the application of a pseudo code are discussed.

Brune, G. W.↗

Entropy Stable h/p-Nonconforming Discretization with the Summation-by-Parts Property for the Compressible Euler and Navier–Stokes Equations

In this paper, we extend the entropy conservative/stable algorithms presented by Del Rey Fernandez and coauthors for the compressible Euler and Navier-Stokes equations on nonconforming p-refined/coarsened curvilinear grids to h/p refinement/coarsening. The main difficulty in developing nonconforming algorithms is the construction of appropriate coupling procedures across nonconforming interfaces. Here, we utilize a computationally simple and efficient approach based upon using decoupled interpolation operators. The resulting scheme is entropy conservative/stable and elementwise conservative. Numerical simulations of the isentropic vortex and viscous shock propagation con firm the entropy conservation/stability and accuracy properties of the method (achieving ~ p + 1 convergence), which are comparable to those of the original conforming scheme. Simulations of the Taylor{Green vortex at R(e) = 1,600 and turbulent flow past a sphere at R(e(infinity)) = 2,000 show the robustness and stability properties of the overall spatial discretization for unstructured grids. Finally, to demonstrate the entropy conservation property of a fully-discrete explicit entropy stable algorithm with h=p refinement/coarsening, we present the time evolution of the entropy function obtained by simulating the propagation of the isentropic vortex using a relaxation Runge-Kutta scheme.

Nonconforming interfaces↗

A fast algorithm for sparse matrix computations related to inversion

We have developed a fast algorithm for computing certain entries of the inverse of a sparse matrix. Such computations are critical to many applications, such as the calculation of non-equilibrium Green’s functions G{sup r} and G{sup <} for nano-devices. The FIND (Fast Inverse using Nested Dissection) algorithm is optimal in the big-O sense. However, in practice, FIND suffers from two problems due to the width-2 separators used by its partitioning scheme. One problem is the presence of a large constant factor in the computational cost of FIND. The other problem is that the partitioning scheme used by FIND is incompatible with most existing partitioning methods and libraries for nested dissection, which all use width-1 separators. Our new algorithm resolves these problems by thoroughly decomposing the computation process such that width-1 separators can be used, resulting in a significant speedup over FIND for realistic devices — up to twelve-fold in simulation. The new algorithm also has the added advantage that desired off-diagonal entries can be computed for free. Consequently, our algorithm is faster than the current state-of-the-art recursive methods for meshes of any size. Furthermore, the framework used in the analysis of our algorithm is the first attempt to explicitly apply the widely-used relationship between mesh nodes and matrix computations to the problem of multiple eliminations with reuse of intermediate results. This framework makes our algorithm easier to generalize, and also easier to compare against other methods related to elimination trees. Finally, our accuracy analysis shows that the algorithms that require back-substitution are subject to significant extra round-off errors, which become extremely large even for some well-conditioned matrices or matrices with only moderately large condition numbers. When compared to these back-substitution algorithms, our algorithm is generally a few orders of magnitude more accurate, and our produced round-off errors stay at a reasonable level.

97 MATHEMATICS AND COMPUTING↗

Bandgap analysis and carrier localization in cation-disordered ZnGeN 2

The bandgap of ZnGeN 2 changes with the degree of cation site disorder and is sought in light emitting diodes for emission at green to amber wavelengths. By combining the perspectives of carrier localization and defect states, we analyze the impact of different degrees of disorder on electronic properties in ZnGeN 2 , addressing a gap in current studies, which largely focus on dilute or fully disordered systems. The present study demonstrates changes in the density of states and localization of carriers in ZnGeN 2 calculated using bandgap-corrected density functional theory and hybrid calculations on partially disordered supercells generated using the Monte Carlo method. We use localization and density of states to discuss the ill-defined nature of a bandgap in a disordered material and identify site disorder and its impact on the structure as a mechanism controlling electronic properties and potential device performance. Decreasing the order parameter results in a large reduction of the bandgap. The reduction in bandgap is due, in part, to isolated, localized states that form above the valence band continuum associated with nitrogen coordinated by more zinc than germanium. The prevalence of defect states in all but the perfectly ordered structure creates challenges for incorporating disordered ZnGeN 2 into optical devices, but the localization associated with these defects provides insight into the mechanisms of electron/hole recombination in the material.

36 MATERIALS SCIENCE↗

Accelerating full waveform inversion via source stacking and cross-correlations

SUMMARY Accurate synthetic seismic wavefields can now be computed in 3-D earth models using the spectral element method (SEM), which helps improve resolution in full waveform global tomography. However, computational costs are still a challenge. These costs can be reduced by implementing a source stacking method, in which multiple earthquake sources are simultaneously triggered in only one teleseismic SEM simulation. One drawback of this approach is the perceived loss of resolution at depth, in particular because high-amplitude fundamental mode surface waves dominate the summed waveforms, without the possibility of windowing and weighting as in conventional waveform tomography. This can be addressed by redefining the cost-function and computing the cross-correlation wavefield between pairs of stations before each inversion iteration. While the Green’s function between the two stations is not reconstructed as well as in the case of ambient noise tomography, where sources are distributed more uniformly around the globe, this is not a drawback, since the same processing is applied to the 3-D synthetics and to the data, and the source parameters are known to a good approximation. By doing so, we can separate time windows with large energy arrivals corresponding to fundamental mode surface waves. This opens the possibility of designing a weighting scheme to bring out the contribution of overtones and body waves. It also makes it possible to balance the contributions of frequently sampled paths versus rarely sampled ones, as in more conventional tomography. Here we present the results of proof of concept testing of such an approach for a synthetic 3-component long period waveform data set (periods longer than 60 s), computed for 273 globally distributed events in a simple toy 3-D radially anisotropic upper mantle model which contains shear wave anomalies at different scales. We compare the results of inversion of 10 000 s long stacked time-series, starting from a 1-D model, using source stacked waveforms and station-pair cross-correlations of these stacked waveforms in the definition of the cost function. We compute the gradient and the Hessian using normal mode perturbation theory, which avoids the problem of cross-talk encountered when forming the gradient using an adjoint approach. We perform inversions with and without realistic noise added and show that the model can be recovered equally well using one or the other cost function. The proposed approach is computationally very efficient. While application to more realistic synthetic data sets is beyond the scope of this paper, as well as to real data, since that requires additional steps to account for such issues as missing data, we illustrate how this methodology can help inform first order questions such as model resolution in the presence of noise, and trade-offs between different physical parameters (anisotropy, attenuation, crustal structure, etc.) that would be computationally very costly to address adequately, when using conventional full waveform tomography based on single-event wavefield computations.

Romanowicz, Barbara↗

CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli

Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a PemrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD600) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

Nucleon electromagnetic form factors from lattice QCD using a nearly physical pion mass

We propose lattice QCD calculations of nucleon electromagnetic form factors using pion masses m π = 149, 202, and 254 MeV and an action with clover-improved Wilson quarks coupled to smeared gauge fields, as used by the Budapest-Marseille-Wuppertal Collaboration. Particular attention is paid to the removal of the effects of excited-state contamination by calculations at three source-sink separations and the use of the summation and generalized pencil-of-function methods. The combination of a calculation at the nearly physical mass m π = 149 MeV in a large spatial volume (m π L s = 4.2) and the removal of excited-state effects yields agreement with experiment for the electric and magnetic form factors G E (Q 2 ) and G M (Q 2 ) up to Q 2 = 0.5 GeV 2 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Artificial intelligence for materials research at extremes

Abstract Materials development is slow and expensive, taking decades from inception to fielding. For materials research at extremes, the situation is even more demanding, as the desired property combinations such as strength and oxidation resistance can have complex interactions. Here, we explore the role of AI and autonomous experimentation (AE) in the process of understanding and developing materials for extreme and coupled environments. AI is important in understanding materials under extremes due to the highly demanding and unique cases these environments represent. Materials are pushed to their limits in ways that, for example, equilibrium phase diagrams cannot describe. Often, multiple physical phenomena compete to determine the material response. Further, validation is often difficult or impossible. AI can help bridge these gaps, providing heuristic but valuable links between materials properties and performance under extreme conditions. We explore the potential advantages of AE along with decision strategies. In particular, we consider the problem of deciding between low-fidelity, inexpensive experiments and high-fidelity, expensive experiments. The cost of experiments is described in terms of the speed and throughput of automated experiments, contrasted with the human resources needed to execute manual experiments. We also consider the cost and benefits of modeling and simulation to further materials understanding, along with characterization of materials under extreme environments in the AE loop. Graphical abstract AI sequential decision-making methods for materials research: Active learning, which focuses on exploration by sampling uncertain regions, Bayesian and bandit optimization as well as reinforcement learning (RL), which trades off exploration of uncertain regions with exploitation of optimum function value. Bayesian and bandit optimization focus on finding the optimal value of the function at each step or cumulatively over the entire steps, respectively, whereas RL considers cumulative value of the labeling function, where the latter can change depending on the state of the system (blue, orange, or green).

36 MATERIALS SCIENCE↗

Approximation of periodic Green's operator in real space using numerical integration and its use in fast Fourier transform-based micromechanical models

In this work, we propose an expression for the periodic first derivative of Green's function in real space. The proposed expression allows an alternative way of computing the periodic Green's operator based on periodically summing the free-space Green's operator in terms of an appropriate quadrature rule. We provide computational examples, which show the accuracy of the proposed approach, together with reduced spurious oscillations in the solution fields.

42 ENGINEERING↗

Science and Measurement Requirements for a Plant Physiology and Functional Types Mission: Measuring the Composition, Function and Health of Global Land and Coastal Ocean Ecosystems

This slide presentation reviews the proposed Plant Physiology and Functional Types (PPFT) Mission. The National Academy of Sciences Decadal Survey, placed a critical priority on a Mission to observe distribution and changes in ecosystem functions. The PPFT satellite mission provides the essential measurements needed to assess drivers of change in biodiversity and ecosystem services that affect human welfare. The presentation reviews the science questions that the mission will be designed to answer, the science rationale, the science measurements, the mission concept, the planned instrumentation, the calibration method, and key signal to noise ratios and uniformity requirements.

science measurements↗

Quantum Monte Carlo solution of the dynamical mean field equations in real time

In this paper we present real-time inchworm quantum Monte Carlo results for single-site dynamical mean field theory on an infinite coordination number Bethe lattice. Our numerically exact results are obtained on the L-shaped Keldysh contour and, being evaluated in real time, avoid the analytic continuation issues typically encountered in Monte Carlo calculations. Our results show that inchworm Monte Carlo methods have now reached a state where they can be used as dynamical mean field impurity solvers and the dynamical sign problem can be overcome. As nonequilibrium problems can be simulated at the same cost, we envisage the main use of these methods as dynamical mean field solvers for time-dependent problems far from equilibrium.

36 MATERIALS SCIENCE↗

Mechanical, electronic, and transport properties of functionalized graphene monolayers from ab initio studies

We present exemplary results of extensive studies of mechanical, electronic and transport properties of covalent functionalization of graphene monolayers (GML). We report new results of ab initio studies for covalent functionalization of GML with −NH{sub 2} groups up to 12.5 % concentration. Our studies are performed in the framework of the density functional theory (DFT) and non-equilibrium Green’s function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and current – voltage I(V) characteristics for these systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic and spin transport properties of graphene nanoribbon mediated by metal adatoms: a study by the QUAMBO-NEGF approach

Structural and electronic properties, including deformation, magnetic moment, Mulliken population, bond order, as well as electronic transport properties, of zigzag graphene nanoribbon (ZGNR) with Co adatoms on hollow sites are investigated by quasi-atomic minimal basis orbits (QUAMBOs), a first-principles tight binding (TB) scheme based on density functional theory (DFT), combined with a non-equilibrium Green&#x27;s function. For electronic transport, below the Fermi level the transmission is strongly suppressed and spin dependent as a result of magnetism by Co adatom adsorption, while above the Fermi level the transmission is slightly distorted and spin independent. Due to the local environment dependence of QUAMBOs–TB parameters, we construct QUAMBOs–TB parameters of ZGNR leads and ZGNR with Co adatoms on hollow center sites by a divide-and-conquer approach, and accurately reproduce the electronic transmission behavior. Our QUAMBO–NEGF method is a new and promising way of examining electronic transport in large-scale systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Advanced electromagnetic methods for aerospace vehicles

High- and low-frequency methods to analyze various radiation elements located on aerospace vehicles with combinations of conducting, nonconducting, and energy absorbing surfaces and interfaces. The focus was on developing fundamental concepts, techniques, and algorithms which would remove some of the present limitations in predicting radiation characteristics of antennas on complex aerospace vehicles. In order to accomplish this, the following subjects were examined: (1) the development of techniques for rigorous analysis of surface discontinuities of metallic and nonmetallic surfaces using the equivalent surface impedance concept and Green's function; (2) the effects of anisotropic material on antenna radiation patterns through the use of an equivalent surface impedance concept which is incorporated into the existing numerical electromagnetics computer codes; and (3) the fundamental concepts of precipitation static (P-Static), such as formulations and analytical models. A computer code was used to model the P-Static process on a simple structure. Measurement techniques were also developed to characterized the electrical properties at microwave frequencies. Samples of typical materials used in airframes were tested and the results are included.

Balanis, Constantine A.↗