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At least 1,765 records · Page 98

Patient-Specific Mathematical Model of the Clear Cell Renal Cell Carcinoma Microenvironment

The interactions between cells and molecules in the tumor microenvironment can give insight into the initiation and progression of tumors and their optimal treatment options. In this paper, we developed an ordinary differential equation (ODE) mathematical model of the interaction network of key players in the clear cell renal cell carcinoma (ccRCC) microenvironment. We then performed a global gradient-based sensitivity analysis to investigate the effects of the most sensitive parameters of the model on the number of cancer cells. The results indicate that parameters related to IL-6 have high a impact on cancer cell growth, such that decreasing the level of IL-6 can remarkably slow the tumor’s growth.

60 APPLIED LIFE SCIENCES↗

A multigrid solver for semi-implicit global shallow-water models

A multigrid solver is developed for the discretized two-dimensional elliptic equation on the sphere that arises from a semiimplicit time discretization of the global shallow-water equations. Different formulations of the semiimplicit scheme result in variable-coefficient Helmholtz-type equations for which no fast direct solvers are available. The efficiency of the multigrid solver is optimal, in the sense that the total operation count is proportional to the number of unknowns. Numerical experiments using initial data derived from actual 300-mb height and wind velocity fields indicate that the present model has very good accuracy and stability properties.

Barros, Saulo R. M.↗

Evolution of Galaxies and the Star Formation Rate in the Infrared

A central goal of extragalactic observational astronomy is to understand how normal galaxies evolve with redshift, and particularly when galaxies formed their stars. While optical and rest-frame UV (ultraviolet) observations have begun to address these issues, the interpretation of such data is particularly challenging because of the sensitivity to dust obscureness (at optical and UV wavelengths). The absorbed light is re-radiated at IR (infrared) wavelengths, hence the optimal indicators of the star formation rate (SFR) is at a rest-frame of (lambda) (is approximately equal to) 60 microns. The SIRTF (space infrared telescope facility) mission will revolutionize the study of the global evolution of the SFR by providing mass-selected, complete samples of galaxies and fares estimators of the SFR. This research program is to study the SFR using statistical samples of galaxies in the local universe, at intermediate redshifts, and set the stage for continuing studies up to z = 5.

Pahre, Michael, A.↗

Exploring the Production of NOx by Lightning and Its Impact on Tropospheric Ozone

Our quantitative understanding of free tropospheric (FT) chemistry is quite poor. State-of-the-art regional air quality models (e.g., US EPA's CMAQ) perform very poorly in simulating FT chemistry, with Uniform ozone around 70 ppb throughout the FT in summer, while ozonesonde data show much higher levels of ozone and much spatial-temporal structure. Such models completely neglect lightning-NOx (LNOx) emissions (the most significant source of NOx in the FT), and also contain large uncertainties in the specifications of intercontinental transport, stratosphere-troposphere exchange (STE) and PBLFT exchange (PFTE). Global air chemistry models include LNOx, but in very crude fashion, with the frequency and distribution of lightning being based on modeled cloud parameters (hence large uncertainty), lightning energetics being assumed to be constant for all flashes (literature value, while in reality there is at least a two-orders of magnitude variability from flash-to-flash), and the production of NOx in the surrounding heated air, per Joule of heating, being assumed to be constant also (literature value, while in fact it is a non-linear function of the dissipated heat and local air density, p). This situation is commonly blamed on paucity of pertinent observational data, but for the USA, there is now a wealth of surface- and satellite-based data of lightning available to permit much improved observation-based estimation of LNOx emissions. In the FT, such NOx has a long residence time, and also the ozone production efficiency from NOx there is considerably higher than in the PBL. It is, therefore, of critical importance in FT chemistry. This paper will describe the approach and data products of an ongoing NSSTC project aimed at a much-improved quantification of not only LNOx production on the scale of continental USA based on local and regional lightning observations, but also of intercontinental transport, STE and PFTE, all in upgraded simulations of tropospheric transport and chemistry. In our approach for LNOx, (a) we utilize continuous observed lightning information from the NLDN ground network and from satellite imagers (OTD and LIS) to quantify lightning frequency and distribution at the spatial-temporal scales of models such as CMAQ; (b) we develop new methodologies to quantify flash-specific lightning energy dissipation as heat (epsilon) using data from the research-grade lightning measurement facility at NASA-KSC, and to parameterize epsilon based on regional lightning monitoring data (ground- and satellite-based); and, (c) we develop a new parameterization of NOx production as a function of epsilon and rho. Based on such observation-based information, we are working to develop a gridded, episodic LNOx emissions inventory for the USA for use in models like CMAQ. We are also developing approaches for global(MOZART)- regional(CMAQ) chemistry coupling to improve intercontinental transport and STE. Finally, we are developing new methodologies for assimilation of satellite-observed (GOES) clouds into meteorological modeling (MM5), to improve PFTE and to optimize co-location of cloud convection and observed lightning. We will incorporate these improvements in CMAQ simulations over the USA to better understand FT processes and chemistry, and its impact on ground-level ozone.

Gillani, Noor↗

Impact of Measurement System Characteristics on Advanced Sounder Information Content

Advanced satellite sensors are tasked with improving global observations of the Earth's atmosphere, clouds, and surface to enable enhancements in weather prediction, climate monitoring capability, and environmental change detection. Achieving such an improvement in geophysical information inferred from these observations requires optimal usage of data from current systems as well as instrument system enhancements for future sensors. This presentation addresses results of tradeoff studies evaluating the impact of spectral resolution, spectral coverage, instrument noise, and a priori knowledge on remote sensing system information content, with a specific emphasis on thermodynamic state and trace species information obtainable from advanced atmospheric sounders. Particular attention will be devoted toward information achievable from the Atmospheric InfraRed Sounder (AIRS) on the NASA EOS Aqua satellite in orbit since 2002, the Infrared Atmospheric Sounding Interferometer (IASI) aboard MetOp-A since 2006, and the Cross-track Infrared Sounder (CrIS) instrument to fly aboard the NPP and JPSS series of satellites expected to begin in late 2011. While all of these systems cover nearly the same infrared spectral extent, they have very different number of channels, instrument line shapes, coverage continuity, and instrument noise. AIRS is a grating spectrometer having 2378 discrete spectral channels ranging from about 0.4 to 2.2/cm resolution; IASI is a Michelson interferometer with 8461 uniformly-spaced spectral channels of 0.5/cm (apodized) resolution; and CrIS is a Michelson interferometer having 1305 spectral channels of 0.625, 1.250, and 2.50/cm (unapodized) spectral resolution, respectively, over its three continuous but non-overlapping bands. Results of tradeoff studies showing information content sensitivity to assumed measurement system characteristics will be presented.

Larar, Allen M.↗

Adaptive Implicit Non-Equilibrium Radiation Diffusion

We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

Philip, Bobby↗

Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards an Optimal Estimation Retrieval of Cirrus Cloud Optical and Microphysical Properties Using Hyperspectral Shortwave Instruments and A Fast Radiative Transfer Algorithm

Cirrus cloud retrieval products (here, cloud optical depth, effective particle size, and cloud top height) are important inputs into numerical weather and climate models. Uncertainties in such retrieval products, as a matter of course, propagate downstream, impacting model calculations. Improvements in high-quality global cirrus cloud optical and microphysical data products from satellite observations are needed to understand and reduce retrieval uncertainties. Hyperspectral shortwave instruments produce high-resolution and information-dense spectra, thus offering the opportunity to reduce uncertainties in retrieval products. We are in the process of developing a retrieval that uses the very fast Principal Component Radiative Transfer Model in the solar spectral region (PCRTM-Solar) in the forward model calculations. This retrieval will use measured reflectances from the NASA Earth Surface Mineral Dust Source Investigation (EMIT) and the forthcoming Climate Absolute Radiance and Refractivity Observatory Pathfinder (CLARREO-Pathfinder) instruments. In this manuscript we present progress towards a reference retrieval employing a widely used, verified, accurate, yet computationally slower radiative transfer modeling technique. The reference retrieval, while too slow for using the complete hyperspectral measurement, will allow us to study the behavior of retrieval products and help us verify results from our in-development fast retrieval. Both retrievals will use the optimal estimation retrieval framework. In this manuscript we present results from an uncertainty analysis considering three uncertainty sources for a cirrus cloud retrieval in the form of error covariance matrices: reflectance uncertainty due to water vapor, the reflectance uncertainty due to ice crystal scattering assumptions, and the instrument measurement uncertainty. Results show that the uncertainty due to habit selection is the largest, while that due to water vapor is at most 0.6% relative to channel reflectance. As a first step, the retrieval is being designed for single layer ice clouds over open ocean water.

Cirrus cloud↗

Optimality of Gradient-MUSIC for Spectral Estimation

We introduce the Gradient-MUSIC algorithm for estimating the unknown frequencies and amplitudes of a nonharmonic signal from noisy time samples. While the classical MUSIC algorithm performs a computationally expensive search over a fine grid, Gradient-MUSIC is significantly more efficient and eliminates the need for discretization over a fine grid by using optimization techniques. It coarsely scans the 1D landscape to find initialization simultaneously for all frequencies followed by parallelizable local refinement via gradient descent. We also analyze its performance when the noise level is sufficiently small and the signal frequencies are separated by at least 8π/m, where π/m is the standard resolution of this problem. Even though the 1D landscape is nonconvex, we prove a global convergence result for Gradient-MUSIC: coarse scanning provably finds suitable initialization and gradient descent converges at a linear rate. In addition to convergence results, we also upper bound the error between the true signal frequencies and amplitudes with those found by Gradient-MUSIC. For example, if the noise has $\ell^\infty$ norm at most ϵ, then the frequencies and amplitudes are recovered up to error at most Cϵ/m and Cϵ respectively, which are minimax optimal in m and ϵ. Our theory can also handle stochastic noise with performance guarantees under nonstationary independent Gaussian noise. Our main approach is a comprehensive geometric analysis of the landscape, a perspective that has not been explored before.

97 MATHEMATICS AND COMPUTING↗

Insensitivity of the Cloud Response to Surface Warming Under Radical Changes to Boundary Layer Turbulence and Cloud Microphysics: Results From the Ultraparameterized CAM

We study the cloud response to a +4K surface warming in a new multi- scale climate model that uses enough interior resolution to begin explicitly resolving boundary layer turbulence (i.e. Ultra-Parameterization or UP), and the associated low clouds. UP's predictions are compared against those from standard Super-Parameterization (SP). The mean global cloud feedback turns out to be remarkably neutral across all of our simulations, despite some radical changes in both cloud microphysical parameter settings and cloud resolving model grid resolution. The overall cloud response to warming is the positive low-cloud feedbacks over land, negative feedbacks at high latitudes, and weak feedbacks over the low-latitude oceans. The most distinct effects of UP appear to be the result of tuning decisions impacting high latitude cloud feedback. UP's microphysics are tuned to optimize the model present-day, top-of-atmosphere radiation fluxes against CERES observations, by lowering the cloud ice-liquid phase-shift temperature ramp, adjusting the ice/liquid autoconversion rate, and increasing the ice fall speed. This reduces baseline high-latitude low cloud amounts, damping the phase change cloud feedback at high latitudes, leading to a slightly more positive global cloud feedback compared to SP. A sensitivity test that isolates these microphysical impacts from UP's grid resolution conrms that the microphysical settings are mostly responsible for the dierences between SP and UP cloud feedback.

54 ENVIRONMENTAL SCIENCES↗

Formulation of an explicit-multiple-time-step time integration method for use in a global primitive equation grid model

With appropriate modifications, a recently proposed explicit-multiple-time-step scheme (EMTSS) is incorporated into the UCLA model. In this scheme, the linearized terms in the governing equations that generate the gravity waves are split into different vertical modes. Each mode is integrated with an optimal time step, and at periodic intervals these modes are recombined. The other terms are integrated with a time step dictated by the CFL condition for low-frequency waves. This large time step requires a special modification of the advective terms in the polar region to maintain stability. Test runs for 72 h show that EMTSS is a stable, efficient and accurate scheme.

Chao, W. C.↗

Educating local radial basis functions using the highest gradient of interest in three dimensional geometries: EDUCATING LOCALIZED RBF-SCHEMES

We present a novel methodology to effectively localize radial basis function approximation methods in three dimensions. The local scheme requires shape parameter-dependent functions that can be used to approximate gradients of scattered data and to solve partial differential operators. The optimum shape parameter is obtained from the highest gradient of interest, where a known analytical function, when boundary conditions are not present, or a shape parameter-free global approximation are used to educate the localized scheme. The later option is applicable to problems where the operator needs to be solved multiple times, like in time evolution or stochastic integration. Past shape parameter's optimizations, for two-dimensional domains, based on the condition number of the interpolant matrix, were unable to provide satisfactory approximations. The applicability of our method is illustrated in the context of an analytical expression interpolation and during a Ginzburg-Landau relaxation of a free energy functional. In general, the optimum shape parameter depends on geometry, node distribution, and density, whereas the approximation errors decrease as the node density and the local stencil size increase. The effective localization of radial basis functions motivates its use in moving boundary problems and accelerates solutions through sparse matrix solvers.

free energy functional↗

Effect of Preheated Microstructure Vis-à-vis Process Parameters and Characterization of Orange Peel in Incremental Forming of AA1050 Sheets

The present investigation systematically analyzes and compares the influence of microstructure and crystallographic texture of AA1050 sheet to that of the most critical process parameters, namely tool dimension, and incremental step depth, in single-point incremental forming (SPIF) process. The sheet samples were preheated at different temperatures to reform the original, i.e., distorted and misoriented grain distribution. The results from experimental and statistical analyses report higher sensitivity of global spring back, surface topography and forming limits strains to variations in microstructure and texture than tool diameter and incremental step depth. The preheating of the sheets resulted in the formation of preferential texture by grain reformation, which leads to the increase in the fraction of homogeneous orientated grains. Such grains increase the maximum forming limit strains and reduce the global spring back in SPIF. Fractography analysis of the failed components revealed that improvement in formability due to grain homogenization (developed texture) may be attributed to larger average void diameter. Empirical models were also developed, and optimized levels of parameters were identified to maximize the efficiency of the SPIF process. Further, qualitative and quantitative characterization of orange peel roughness was carried out by segregating the external formed surface into surfaces subjected to orange peel roughness and tool-induced texture.

36 MATERIALS SCIENCE↗

Production of biofuels and chemicals from xylose using native and engineered yeast strains

Numerous metabolic engineering strategies have allowed yeasts to efficiently assimilate xylose, the second most abundant sugar component of lignocellulosic biomass. During the investigation of xylose utilization by yeasts, a global rewiring of metabolic networks upon xylose cultivation has been captured, as opposed to a pattern of glucose repression. A clear understanding of the xylose-induced metabolic reprogramming in yeast would shed light on the optimization of yeast-based bioprocesses to produce biofuels and chemicals using xylose. In this review, we delved into characteristics of yeast xylose metabolism, and potential benefits of using xylose as a carbon source to produce various biochemicals with examples. Transcriptomic and metabolomic patterns of xylose-grown yeast cells were distinct from those on glucose—a conventional sugar of industrial biotechnology—and the gap might lead to opportunities to produce biochemicals efficiently. Indeed, limited glycolytic metabolic fluxes during xylose utilization could result in enhanced production of metabolites whose biosynthetic pathways compete for precursors with ethanol fermentation. Also, alleviation of glucose repression on cytosolic acetyl coenzyme A (acetyl-CoA) synthesis, and respiratory energy metabolism during xylose utilization enhanced production of acetyl-CoA derivatives. Consideration of singular properties of xylose metabolism, such as redox cofactor imbalance between xylose reductase and xylitol dehydrogenase, is necessary to maximize these positive xylose effects. As a result, this review argues the importance and benefits of xylose utilization as not only a way of expanding a substrate range, but also an effective environmental perturbation for the efficient production of advanced biofuels and chemicals in yeasts.

09 BIOMASS FUELS↗

Automated identification of dominant physical processes

The identification of processes that locally and approximately dominate dynamical system behavior has enabled significant advances in understanding and modeling nonlinear differential dynamical systems. Conventional methods of dominant process identification involve piecemeal and ad hoc (non-rigorous, informal) scaling analyses to identify dominant balances of governing equation terms and to delineate the spatiotemporal boundaries (boundaries in space and/or time) of each dominant balance. For the first time, we present an objective global measure of the fit of dominant balances to observations, which is desirable for automation, and was previously undefined. Furthermore, we propose a formal definition of the dominant balance identification problem in the form of an optimization problem. Here, we show that the optimization can be performed by various machine learning algorithms, enabling the automatic identification of dominant balances. Our method is algorithm agnostic and it eliminates reliance upon expert knowledge to identify dominant balances which are not known beforehand.

42 ENGINEERING↗

A review of computational methods for studying oscillating water columns – the Navier-Stokes based equation approach

This review evaluates the state-of-the-practice numerical tools used to predict the performance of Oscillating Water Column (OWC). The OWC is a widely studied Wave Energy Converter that provides a reliable form of renewable form of electricity that can potentially meet global energy needs. However, the fluid-flow phenomena affecting its hydrodynamic performance are not fully understood. While there has been the successful full-scale deployment of OWCs, various computational methods are being explored to optimize this technology. Potential flow theory is commonly used to evaluate the efficiency of OWCs; however, this assumption tends to over-predict the hydrodynamic performance. Recently, numerical studies using a diverse set of commercial, open-source, or in-house Computational Fluid Dynamics (CFD) using Reynolds Averaged Navier Stokes (RANS) and Large-Eddy Simulation codes show a better comparison to available experimental results but are computationally expensive. ANSYS Fluent was found to be the most widely used CFD code applied to the study of the OWCs, with a high degree of accuracy in terms of experimental validation of numerical results.

16 TIDAL AND WAVE POWER↗

Fixed-angle conjectures for the quantum approximate optimization algorithm on regular MaxCut graphs

The quantum approximate optimization algorithm (QAOA) is a near-term combinatorial optimization algorithm suitable for noisy quantum devices. However, little is known about performance guarantees for p > 2. A recent work computing MaxCut performance guarantees for 3-regular graphs conjectures that any d-regular graph evaluated at particular fixed angles has an approximation ratio greater than some worst-case guarantee. In this work, we provide numerical evidence for this fixed angle conjecture for p < 12. We compute and provide these angles via numerical optimization and tensor networks. These fixed angles serve for an optimization-free version of QAOA and have universally good performance on any 3-regular graph. Heuristic evidence is presented for the fixed angle conjecture on graph ensembles, which suggests that these fixed angles are "close" to global optimum. Under the fixed angle conjecture, QAOA has a larger performance guarantee than the Goemans Williamson algorithm on 3-regular graphs for p >= 11.

Wurtz, Jonathan↗