Composable code generation for high order, compatible finite element methods

It has been widely recognised in the HPC communities across the world, that exploiting modern computer architectures, including exascale machines, to a full extent requires software commu- nities to adapt their algorithms. Computational methods with a high ratio of floating point op- erations to bandwidth are favorable. For solving partial differential equations, which can model many physical problems, high order finite element methods can calculate approximations with a high efficiency when a good solver is employed. Matrix-free algorithms solve the corresponding equations with a high arithmetic intensity. Vectorisation speeds up the operations by calculating one instruction on multiple data elements. Another recent development for solving partial differential are compatible (mimetic) finite ele- ment methods. In particular with application to geophysical flows, compatible discretisations ex- hibit desired numerical properties required for accurate approximations. Among others, this has been recognised by the UK Met office and their new dynamical core for weather and climate fore- casting is built on a compatible discretisation. Hybridisation has been proven to be an efficient solver for the corresponding equation systems, because it removes some inter-elemental coupling and localises expensive operations. This thesis combines the recent advances on vectorised, matrix-free, high order finite element methods in the HPC community on the one hand and hybridised, compatible discretisations in the geophysical community on the other. In previous work, a code generation framework has been developed to support the localised linear algebra required for hybridisation. First, the framework is adapted to support vectorisation and further, extended so that the equations can be solved fully matrix-free. Promising performance results are completing the thesis.Open Acces

A learning approach to the detection of gravitational wave transients

We investigate the class of quadratic detectors (i.e., the statistic is a bilinear function of the data) for the detection of poorly modeled gravitational transients of short duration. We point out that all such detection methods are equivalent to passing the signal through a filter bank and linearly combine the output energy. Existing methods for the choice of the filter bank and of the weight parameters rely essentially on the two following ideas: (i) the use of the likelihood function based on a (possibly non-informative) statistical model of the signal and the noise, (ii) the use of Monte-Carlo simulations for the tuning of parametric filters to get the best detection probability keeping fixed the false alarm rate. We propose a third approach according to which the filter bank is "learned" from a set of training data. By-products of this viewpoint are that, contrarily to previous methods, (i) there is no requirement of an explicit description of the probability density function of the data when the signal is present and (ii) the filters we use are non-parametric. The learning procedure may be described as a two step process: first, estimate the mean and covariance of the signal with the training data; second, find the filters which maximize a contrast criterion referred to as deflection between the "noise only" and "signal+noise" hypothesis. The deflection is homogeneous to the signal-to-noise ratio and it uses the quantities estimated at the first step. We apply this original method to the problem of the detection of supernovae core collapses. We use the catalog of waveforms provided recently by Dimmelmeier et al. to train our algorithm. We expect such detector to have better performances on this particular problem provided that the reference signals are reliable.Comment: 22 pages, 4 figure

Aeronautical Engineering: A continuing bibliography, supplement 120

This bibliography contains abstracts for 297 reports, articles, and other documents introduced into the NASA scientific and technical information system in February 1980

Elastic-Plastic Finite Element Analysis of Fatigue Crack Growth in Mode 1 and Mode 2 Conditions

Presented is an alternate cost-efficient and accurate elastic-plastic finite element procedure to analyze fatigue crack closure and its effects under general spectrum loading. Both Modes 1 and 2 type cycling loadings are considered. Also presented are the results of an investigation, using the newly developed procedure, of various factors that cause crack growth acceleration or retardation and delay effects under high-to-low, low-to-high, single overload, and constant amplitude type cyclic loading in a Mode 1 situation. Further, the results of an investigation of a centercracked panel under external pure shear (Mode 2) cyclic loading, of constant amplitude, are reported

A numerical investigation of the finite element method in compressible primitive variable Navier-Stokes flow

The results of a comprehensive numerical investigation of the basic capabilities of the finite element method (FEM) for numerical solution of compressible flow problems governed by the two-dimensional and axis-symmetric Navier-Stokes equations in primitive variables are presented. The strong and weak points of the method as a tool for computational fluid dynamics are considered. The relation of the linear element finite element method to finite difference methods (FDM) is explored. The calculation of free shear layer and separated flows over aircraft boattail afterbodies with plume simulators indicate the strongest assets of the method are its capabilities for reliable and accurate calculation employing variable grids which readily approximate complex geometry and capably adapt to the presence of diverse regions of large solution gradients without the necessity of domain transformation

34th Midwest Symposium on Circuits and Systems-Final Program

Organized by the Naval Postgraduate School Monterey California. Cosponsored by the IEEE Circuits and Systems Society. Symposium Organizing Committee: General Chairman-Sherif Michael, Technical Program-Roberto Cristi, Publications-Michael Soderstrand, Special Sessions- Charles W. Therrien, Publicity: Jeffrey Burl, Finance: Ralph Hippenstiel, and Local Arrangements: Barbara Cristi

Transient absorption imaging of hemeprotein in fresh muscle fibers

2022 Summer.Includes bibliographical references.Mitochondrial diseases affect 1 in 4000 individuals in the U.S. among adults and children of all races and genders. Nevertheless, these diseases are hard to diagnose because they affect each person differently. Meanwhile the gold standard diagnosis methods are usually invasive and time- consuming. Therefore, a non-invasive and in-vivo diagnosis method is highly demanded in this area. Our goal is to develop a non-invasive diagnosis method based on the endogenous nonlinear optical effect of the live tissues. Mitochondrial disease is frequently the result of a defective electron transport chain (ETC). Our goal is to develop a non-invasive way to measure redox within the ETC, specifically, of cytochromes. Cytochromes are iron porphyrins that are essential to the ETC. Their redox states can indicate cellular oxygen consumption and mitochondrial ATP production. So being able to differentiate the redox states of cytochromes will offer us a method to characterize mitochondrial function. Meanwhile, Chergui's group found out that the two redox states of cytochrome c have different pump-probe spectroscopic responses, meaning that the transient absorption (TA) decay lifetime can be a potential molecular contrast for cytochrome redox state discrimination. Their research leads us to utilize the pump-probe spectroscopic idea to develop a time-resolved optical microscopic method to differentiate not only cytochromes from other chemical compounds but also reduced cytochromes from oxidized ones. This dissertation describes groundbreaking experiments where transient absorption is used to reveal excited-state lifetime differences between healthy controls and an animal model of mitochondrial disease, in addition to differences between reduced and oxidized ETC in isolated mitochondria and fresh preparations of muscle fibers. For our initial experiments, we built a pump-probe microscopic system with a fiber laser source, producing 530nm pump and 490nm probe using a 3.5kHz laser scanning rate. The pulse durations of pump and probe are both 800fs. For the preliminary results, we have successfully achieved TA decay contrast between reduced and oxidized cytochromes in solution form. Then we have achieved SNR enhanced pump-probe image of BGO crystal particles with the help of the software- based adaptive filter noise canceling method. We also have installed a FPGA-based adaptive filter to enhance the pump-probe signals of the electrophoresis gels that contain different mitochondrial respiratory chain supercomplexes. However, because the noise floor was still 30 dB higher than shot noise limit, cytochrome imaging in live tissues was still problematic. We then built another pump-probe microscope with a solid- state ultrafast laser source. In that way, we do not need to worry about laser relative intensity noise (RIN) anymore, since the noise floor of the solid-state laser source can reach the shot noise limit at MHz region. One other advantage of the new laser source is that it can provide one tunable laser output that can be directly converted to the probe pulse with tunable center wavelength. Its tunability can cover the entire visible spectrum. We realized a pump-probe microscopy with a 520nm pump pulse and a tunable probe pulse. The tunability on the probe arm allows us to explore better pump-probe contrast between two redox states. What's more, I will introduce my preliminary results of utilizing supercontinuum generation in a photonic crystal fiber (PCF) to realize tunability on pump wavelength. In that way, more possibilities will be unlocked. And the hyperspectral pump-probe microscope will be able to distinguish more molecules