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At least 811 records · Page 45

Dynamic Mesh Adaptation for Front Evolution Using Discontinuous Galerkin Based Weighted Condition Number Mesh Relaxation

A new mesh smoothing method designed to cluster mesh cells near a dynamically evolving interface is presented. The method is based on weighted condition number mesh relaxation with the weight function being computed from a level set representation of the interface. The weight function is expressed as a Taylor series based discontinuous Galerkin projection, which makes the computation of the derivatives of the weight function needed during the condition number optimization process a trivial matter. For cases when a level set is not available, a fast method for generating a low-order level set from discrete cell-centered elds, such as a volume fraction or index function, is provided. Results show that the low-order level set works equally well for the weight function as the actual level set. Meshes generated for a number of interface geometries are presented, including cases with multiple level sets. Dynamic cases for moving interfaces are presented to demonstrate the method's potential usefulness to arbitrary Lagrangian Eulerian (ALE) methods.

97 MATHEMATICS AND COMPUTING↗

The role of carbonic anhydrase in C 4 photosynthesis

Current pressures on the global food supply have accelerated the urgency for a second green revolution using novel and sustainable approaches to increase crop yield and efficiency. This proposal outlines experiments to address fundamental questions regarding the biology of C 4 photosynthesis, the method of carbon fixation utilized by the most productive food, feed and bioenergy crops. Carbonic anhydrase (CA) has been implicated in multiple cellular functions including nitrogen metabolism, water use efficiency, and photosynthesis. CA catalyzes the first dedicated step in C 4 photosynthesis, the hydration of CO 2 into bicarbonate, and is potentially rate limiting in C 4 grasses. Using insertional mutagenesis, we have generated CA mutants in maize, and propose the characterization of these mutants using phenotypic, physiological, and transcriptomic profiling to assay the plant’s response to altered CA activity. In addition, florescent protein tagging experiments will be employed to study the subcellular localization of CA paralogs, providing critical data for modeling carbon fixation in C 4 plants. Finally, I propose parallel experiments in Setaria viridis to explore its relevance as model C 4 grass. Using a multifaceted approach, this proposal addresses important questions in basic biology, as well as the need for translation research in response to looming global food challenges.

59 BASIC BIOLOGICAL SCIENCES↗

Scattering by a groove in an impedance plane

An analysis of two-dimensional scattering from a narrow groove in an impedance plane is presented. The groove is represented by a impedance surface and the problem reduces to that of scattering from an impedance strip in an otherwise uniform impedance plane. On the basis of this model, appropriate integral equations are constructed using a form of the impedance plane Green's functions involving rapidly convergent integrals. The integral equations are solved by introducing a single basis representation of the equivalent current on the narrow impedance insert. Both transverse electric (TE) and transverse magnetic (TM) polarizations are treated. The resulting solution is validated by comparison with results from the standard boundary integral method (BIM) and a high frequency solution. It is found that the presented solution for narrow impedance inserts can be used in conjunction with the high frequency solution for the characterization of impedance inserts of any given width.

Bindiganavale, Sunil↗

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity

Nutrient availability is critical for growth of algae and other microbes used for generating valuable biochemical products. Determining the optimal levels of nutrient supplies to cultures can eliminate feeding of excess nutrients, lowering production costs and reducing nutrient pollution into the environment. With the advent of omics and bioinformatics methods, it is now possible to construct genome-scale models that accurately describe the metabolism of microorganisms. In this study, a genome-scale model of the green alga Chlorella vulgaris (iCZ946) was applied to predict feeding of multiple nutrients, including nitrate and glucose, under both autotrophic and heterotrophic conditions. The objective function was changed from optimizing growth to instead minimizing nitrate and glucose uptake rates, enabling predictions of feed rates for these nutrients. The metabolic model control (MMC) algorithm was validated for autotrophic growth, saving 18% nitrate while sustaining algal growth. Additionally, we obtained similar growth profiles by simultaneously controlling glucose and nitrate supplies under heterotrophic conditions for both high and low levels of glucose and nitrate. Finally, the nitrate supply was controlled in order to retain protein and chlorophyll synthesis, albeit at a lower rate, under nitrogen-limiting conditions. This model-driven cultivation strategy doubled the total volumetric yield of biomass, increased fatty acid methyl ester (FAME) yield by 61%, and enhanced lutein yield nearly 3 fold compared to nitrogen starvation. This study introduces a control methodology that integrates omics data and genome-scale models in order to optimize nutrient supplies based on the metabolic state of algal cells in different nutrient environments. This approach could transform bioprocessing control into a systems biology-based paradigm suitable for a wide range of species in order to limit nutrient inputs, reduce processing costs, and optimize biomanufacturing for the next generation of desirable biotechnology products.

59 BASIC BIOLOGICAL SCIENCES↗

An Overview of Gemma FY2021 Verification Activities

Though the method-of-moments implementation of the electric-field integral equation plays an important role in computational electromagnetics, it provides many code-verification challenges due to the different sources of numerical error and their possible interactions. Matters are further complicated by singular integrals, which arise from the presence of a Green's function. In this report, we document our research to address these issues, as well as its implementation and testing in Gemma.

97 MATHEMATICS AND COMPUTING↗

Feasibility study for a numerical aerodynamic simulation facility. Volume 2: Hardware specifications/descriptions

An FMP (Flow Model Processor) was designed for use in the Numerical Aerodynamic Simulation Facility (NASF). The NASF was developed to simulate fluid flow over three-dimensional bodies in wind tunnel environments and in free space. The facility is applicable to studying aerodynamic and aircraft body designs. The following general topics are discussed in this volume: (1) FMP functional computer specifications; (2) FMP instruction specification; (3) standard product system components; (4) loosely coupled network (LCN) specifications/description; and (5) three appendices: performance of trunk allocation contention elimination (trace) method, LCN channel protocol and proposed LCN unified second level protocol.

Green, F. M.↗

A Model with Ellipsoidal Scatterers for Polarimetric Remote Sensing of Anisotropic Layered Media

This paper presents a model with ellipsoidal scatterers for applications to polarimetric remote sensing of anisotropic layered media at microwave frequencies. The physical configuration includes an isotropic layer covering an anisotropic layer above a homogeneous half space. The isotropic layer consists of randomly oriented spheroids. The anisotropic layer contains ellipsoidal scatterers with a preferential vertical alignment and random azimuthal orientations. Effective permittivities of the scattering media are calculated with the strong fluctuation theory extended to account for the nonspherical shapes and the scatterer orientation distributions. On the basis of the analytic wave theory, dyadic Green's functions for layered media are used to derive polarimetric backscattering coefficients under the distorted Born approximation. The ellipsoidal shape of the scatterers gives rise to nonzero cross-polarized returns from the untilted anisotropic medium in the first-order approximation. Effects of rough interfaces are estimated by an incoherent addition method. Theoretical results and experimental data are matched at 9 GHz for thick first-year sea ice with a bare surface and with a snow cover at Point Barrow, Alaska. The model is then used to study the sensitivity of polarimetric backscattering coefficients with respect to correlation lengths representing the geometry of brine inclusions. Polarimetric signatures of bare and snow-covered sea ice are also simulated based on the model to investigate effects of different scattering mechanisms.

Nghiem, S. V.↗

CCKT Calculation of e-H Total Cross Sections

We are in the process of carrying out calculations of e-H total cross sections using the 'complex-correlation Kohn-T' (CCKT) method. In a later paper, we described the methodology more completely, but confined calculations to the elastic scattering region, with definitive, precision results for S-wave phase shifts. Here we extend the calculations to the (low) continuum (1 much less than k(exp 2) much less than 3) using a Green's function formulation. This avoids having to solve integro-differential equations; rather we evaluate indefinite integrals involving appropriate Green's functions and the (complex) optical potential to find the scattering function u(r). From the asymptotic form of u(r) we extract a T(sub L) which is a complex number. From T(sub L), elastic sigma(sub L)(elastic) = 4pi(2L+1)((absolute value of T(sub L))(exp 2)), and total sigma (sub L)(total) = 4pi/k(2L+1)Im(T(sub L)) cross sections follow.

Bhatia, Aaron K.↗

MMIC devices for active phased array antennas

The study of printed circuit discontinuities is necessary in order to design, for example, transitions between rectangular waveguides and printed circuits. New developments with respect to the analytical approaches to this problem are discussed. A summary of the progress in the experimental approach is presented. The accurate solution for the modes in various millimeter-wave waveguides is essential in the analysis of many integrated circuit components, such as filters and impedance transformers. Problems associated with the numerical computation of these modes in two frequently used waveguide forms, namely, the finline and microstrip, are presented. The spectral domain method of formulation, with a moment method solution, is considered. This approach can be readily extended to analyze an arbitrary configuration of dielectric and metallized regions in a shielded enclosure. Galerkin's method is used, where the testing and basic functions are the same. It is shown that the mode functions, or eigenfunctions, are more sensitive to errors than the phase constants, or eigenvalues. The approximate mode functions do not satisfy the orthogonality relationship well, resulting in difficulties when these modal solutions are used to form an approximate Green's function or are used in a mode matching analysis.

Mittra, R.↗

Covalent integration of polymers and porous organic frameworks

Covalent integration of polymers and porous organic frameworks (POFs), including metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and hydrogen-bonded organic frameworks (HOFs), represent a promising strategy for overcoming the existing limitations of traditional porous materials. This integration allows for the combination of the advantages of polymers, i.e., flexibility, processability and chemical versatility etc., and the superiority of POFs, like the structural integrity, tunable porosity and the high surface area, creating a type of hybrid materials. These resulting polymer-POF hybrid materials exhibit enhanced mechanical strength, chemical stability and functional diversity, thus opening up new opportunities for applications across a large variety of fields, such as gas separation, catalysis, biomedical applications, environmental remediation and energy storage. In this review, an overview of synthetic routes and strategies on how to covalently integrate different polymers with various POFs is discussed, especially with a particular focus on methods like polymerization within, on and among POF structures. To investigate the unique properties and functions of these resultant hybrid materials, the characterization techniques, including nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), transmission electron microscopy (TEM) and scanning electron microscopy (SEM), gas adsorption analysis (BET) and computational modeling and machine learning, are also presented. The ability of polymer-POFs to manipulate the pore environments at the molecular level affords these materials a wide range of applications, providing a versatile platform for future advancements in material science. Looking forward, to fully realize the potential of these hybrid materials, the authors highlight the scalability, green synthesis methods, and potential for stimuli-responsive polymer-POF materials as critical areas for future research.

Hossain, Md Amjad↗

Large-scale GW calculations on pre-exascale HPC systems

The ab initio GW approach is a rigorous Green’s-function-based framework that can be employed to compute electronic excitation properties of a wide variety of materials such as extended systems, molecules, as well as confined and nanostructured materials with a very satisfactory accuracy. However, GW calculations on complex systems are often hindered by the high computational cost associated with the method. Here, in this study, we demonstrate how to significantly speedup GW calculations with a novel algorithm for the computationally intense kernel based on a non-blocking chunked cyclic communication scheme that minimizes latency in MPI messages, allows for overlapping of communication and computation, and improves cache usage in matrix multiplication operations. The optimized version of the code, implemented in the BerkeleyGW software package, is capable of scaling well to the full Cori computer at NERSC (Cray XC40) and achieves over 11 Peta FLOP/s of sustained performance. We showcase our work by performing large-scale GW calculations of defect structures on silicon, which require simulation cells containing over 1700 atoms, and which can now be efficiently executed in just a few minutes on large pre-exascale high-performance computing systems.

97 MATHEMATICS AND COMPUTING↗

Stochastic resolution of identity second-order Matsubara Green’s function theory

We create a stochastic resolution of identity representation to the second-order Matsubara Green’s function (sRI-GF2) theory. Using a stochastic resolution of the Coulomb integrals, the second order Born self-energy in GF2 is decoupled and reduced to matrix products/ contractions, which reduces the computational cost from O(N 5 ) to O(N 3 ) (with N being the number of atomic orbitals). Currently, the method can be viewed as an extension to our previous work on stochastic resolution of identity second order Møller-Plesset perturbation theory [T. Y. Takeshita et al., J. Chem. Theory Comput. 13, 4605 (2017)] and offers an alternative to previous stochastic GF2 formulations [D. Neuhauser et al., J. Chem. Theory Comput. 13, 5396 (2017)]. We show that sRI-GF2 recovers the deterministic GF2 results for small systems, is computationally faster than deterministic GF2 for N > 80, and is a practical approach to describe weak correlations in systems with 10 3 electrons and more.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laparoscopic Isolated Total Caudate Lobectomy for Hepatocellular Carcinoma Located in the Paracaval Portion of the Cirrhotic Liver

Background: Despite the widespread use of laparoscopic hepatectomies in past decades, laparoscopic isolated total caudate lobectomy for hepatocellular carcinoma (HCC) remains challenging,{sup 1,2} especially for patients with cirrhosis. Moreover, a laparoscopic isolated total caudate lobectomy for HCC originating in the paracaval portion of the caudate lobe is very rare. We herein present a video showing laparoscopic total caudate lobectomy for a cirrhotic patient with HCC located in the paracaval portion of the caudate lobe. Methods: A 58-year-old woman who suffered from hepatitis C virus-related cirrhosis was admitted to our institution. The preoperative computed tomography showed a 2.5 × 2.0 cm liver mass located in segment I that was very close to the right hepatic pedicle. Although her liver function was Child–Pugh A, the indocyanine green (ICG)-15 test was high at 10.9%. Right hepatectomy plus caudate lobectomy was not adopted because of the severe cirrhosis and the elevated ICG-15. Thus, laparoscopic isolated total caudate lobectomy was contemplated. Results: The patient was placed in the supine position. After full mobilization, the caudate lobe was exposed. The third porta of the liver was then dissected and the short hepatic veins were controlled with clips and LigaSure. The dissection was finished when the whole third porta of the liver was freed. Subsequently, the portal branches to the caudate lobe were ligated and cut. The combination between the left- and right-sided laparoscopic approaches was used to transect liver parenchyma. The superficial parenchyma was divided using an harmonic scalpel, while the deeper tissue was divided using a Cavitron ultrasonic aspirator (CUSA). The Pringle maneuver was used intermittently during the parenchymal transection as necessary. In the left-sided approach, the caudate lobe was resected along the left and middle hepatic vein toward the right side, to expose the dorsal semicircle of the right hepatic vein. In the right-sided approach, the resection started from the right border of the process portion to the root of the right hepatic vein in the cranial direction. Finally, the whole caudate lobe was resected and the three main hepatic veins were exposed on the cutting plane. The specimen was removed from suprapubic incision. The operative time was 300 min and the total Pringle time was 50 min. The postoperative course was uneventful. Conclusions: A laparoscopic isolated total caudate lobectomy for HCC located in the paracaval portion of the cirrhotic liver seems to be feasible and safe in selected patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Derivation and Testing of Consumptive Water Use Fraction for Specialty Crops

The Crop Consumptive Use Fraction (CCUF) expresses beneficial water use in the form of seasonal evapotranspiration of applied water (ETAW), relative to total irrigation volume. The metric is an indicator of the efficiency of agricultural water use and is a recommended component for preparation of agricultural water management plans in California. An FAO-56 based web application has been developed to facilitate retrospective evaluation of ETAW, and hence CCUF, at field level. The current application is optimized for prevailing climate in four of the state’s main growing regions: San Joaquin Valley, Sacramento Valley, Central Coast, and North Coast. User inputs include crop type, soil texture, irrigation method, daily irrigation volume, daily rainfall, and seasonal start/stop dates to define the analysis period. Time series of fractional green canopy cover (Fc), based on Landsat and Sentinel-2 Earth-resource satellite observations, are imported from NASA’s Satellite Irrigation Management Support (SIMS) system. Grass reference evapotranspiration (ETo) time series are accessed from Spatial CIMIS (California Irrigation Management Information System). Daily crop height (h) is estimated as a simple function of typical maximum height for the given crop type (from FAO-56) and Fc. A vegetation density coefficient (Kd) is derived from Fc and h. Stomatal control factors during mid-and late-season are applied to tree and vine crops. Typical values for minimum daily relative humidity and mean daily windspeed, derived from historical CIMIS weather data, are used to correct for regional deviations from standard climate (defined as RHmin=45%, windspeed =2m/s). The resulting daily basal crop coefficient (Kcb) represents the ET of a well-watered crop with minimal soil evaporation, relative to ETo. A soil water balance sub-model for the top 0.1 m is used to calculate daily evaporation coefficients (Ke). A second sub-model applies to the root zone to calculate crop water stress coefficients (Ks) and effective precipitation (Pe), which is the fraction of rainfall that is available for crop use. Those coefficients are combined with Kcb and ETo to calculate daily ETc. ETAW is then derived as cumulative ETc less cumulative Pe. For verification purposes, sensor installations were used to measure seasonal ETc in commercial fields for several annual and perennial specialty crops by soil water balance and energy balance methods. Model estimates of seasonal ETc show mean absolute error of <10% compared to the ground measurements.

Derivation↗

Shape- and Orientation-Dependent Scattering of Isolated Gold Nanostructures Using Polarized Dark-Field Microscopy

In this work, we demonstrate a simple and robust method for measuring the shape- and orientation-dependent optical scattering of various plasmonic nanostructures adsorbed onto a solid surface using polarized dark-field microscopy. By analyzing the dark-field scattering images of gold nanostructures using grazing incidence polarized light with a bench-top microscope, we are able to correlate optical scattering from the individual nanostructures with their shape and orientation. Depending on the size, shape, and orientation of the plasmonic nanostructures, they exhibit characteristic angle- and polarization-dependent scattering signals. Extracting the red, green, and blue channels of the scattering signals from a color-imaging detector as a function of azimuthal angle provides a polar plot of color intensity values that is characteristic of the underlying nanostructure. Examples are presented for various nanostructures, including spherical nanoparticles, nanotriangles, and nanorods. Experimental results are complemented by numerical calculations of the scattering spectra of representative model nanostructures. We demonstrate that the polarization- and orientation-dependent scattering behavior is a consequence of various localized surface plasmon modes existing in the nanostructures and can be used to verify the shape of individual objects as well as quickly identify the orientation of numerous objects on a densely populated substrate. We anticipate that this method will provide a rapid and efficient complement to the typical structural analysis of nanoparticles that is achieved by electron microscopy as well as providing a simple method for generating detailed information of the optical scattering of various types of individual plasmonic nanostructures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the surface brightness and geometric albedo of some Martian areas

High-quality photographs of Mars (red, yellow, green, and blue) are used to analyze the surface, limb, and south-polar-cap brightness of Mars. The surface brightness can be fitted with the Lommel-Seeliger reflection law. For the limb and polar-cap brightness, the method suggested by Lumme (1974) has been used to correct for smearing effects. It is found that the brightness increases noticeably when approaching the limb, that the upper limit to optical thickness of the atmosphere in the blue is 0.16, and that the corresponding single-scattering albedo is 0.55, both with uncertainties of about 15%. Values for the geometric albedo and the phase function (at 37-deg phase angle) are also obtained for both the atmosphere and the ground for a central meridian of 0 deg. The south polar cap in September 1973 was nearly circular, with a radius of about 8 deg (heliocentric longitude of 0 deg) and geometric albedos of 0.68 (red), 0.68 (yellow), 0.60 (green), and 0.53 (blue).

Lumme, K.↗

New correction procedures for the fast field program which extend its range

A fast field program (FFP) algorithm was developed based on the method of Lee et al., for the prediction of sound pressure level from low frequency, high intensity sources. In order to permit accurate predictions at distances greater than 2 km, new correction procedures have had to be included in the algorithm. Certain functions, whose Hankel transforms can be determined analytically, are subtracted from the depth dependent Green's function. The distance response is then obtained as the sum of these transforms and the Fast Fourier Transformation (FFT) of the residual k dependent function. One procedure, which permits the elimination of most complex exponentials, has allowed significant changes in the structure of the FFP algorithm, which has resulted in a substantial reduction in computation time.

West, M.↗

Damping in coupled bending and torsion - An experiment

Traditional experimental modal testing methods are used to determine the damping properties of a Euler-Bernoulli beam with offset inertial tip mass. Both viscous and strain rate damping models are considered in bending and in torsion. A partial differential equation model of the coupled system is used. Eigenfunctions are derived for the coupled system by using a Green's function approach to derive the approximate uncoupled eigenfunctions. These eigenfunctions are used in a decoupled fashion with experimental modal data to estimate the damping parameters of the coupled system. The experimental modal data were obtained from both free and impulse responses using a combined translational and rotational accelerometer.

Umland, Jeffrey W.↗