Introduction to Microwave Background Polarization

Microwave background polarization, though presently undetected, is a fundamental prediction of any viable cosmological model. These lectures review the theoretical description of polarization, its physical interpretation, and potentially interesting polarization signals.Comment: Lectures given at the International School of Space Sciences, L'Aquila, Italy, September 2-12, 1998. 18 pages with 2 figures; Elsevier tex macro

Determining Alpha-Helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps, Master\u27s Thesis, May 2007

Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed light on how the protein folds in space. The central theme of our approach is to cast the correspondence problem as that of shape matching between the 3D volume and the 1D sequence. We model both the shapes as attributed relational graphs, and formulate a constrained inexact graph matching problem. To compute the matching, we developed an optimal algorithm based on the A*-search with several choices of heuristic functions. As demonstrated in a suite of real protein data, the shape-modeling approach is capable of correctly identifying helix correspondences in noise-abundant volumes with minimal or no user intervention

Data Analysis for the E and B EXperiment and Instrumentation Development for Cosmic Microwave Background Polarimetry

The E and B EXperiment (EBEX) was a balloon-borne instrument designed to measure the polarization of the cosmic microwave background (CMB) while simultaneously characterizing Galactic dust emission. The instrument was based on a two-mirror ambient temperature Gregorian-Dragone telescope coupled with cooled refractive optics to a kilo-pixel array of transition edge sensor (TES) bolometeric detectors. To achieve sensitivity to both the CMB signal and Galactic foregrounds, EBEX observed in three signal bands centered on 150, 250, and 410 GHz. Polarimetry was achieved via a stationary wire-grid polarizer and a continuously rotating achromatic half-wave plate (HWP) based on a superconducting magnetic bearing (SMB). EBEX launched from McMurdo station, Antarctica on December 29, 2012 and collected ~ 1.3 TB of data during 11 days of observation. This thesis is presented in two Parts. Part I reviews the data analysis we performed to transform the raw EBEX data into maps of temperature and polarization sky signals, with a particular focus on post-flight pointing reconstruction; time stream cleaning and map making; the generation of model sky maps of the expected signal for each of the three EBEX signal bands; removal of the HWP-synchronous signal from the detector time streams; and our attempts to identify, characterize, and correct for non-linear detector responsivity. In Part II we present recent developments in instrumentation for the next generation of CMB polarimeters. The developments we describe, including advances in lumped-element kinetic inductance detector (LEKID) technology and the development of a hollow-shaft SMB-based motor for use in HWP polarimetry, were motivated in part by the design for a prospective ground-based CMB polarimeter based in Greenland

On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation

Volumetric crystal structure indexing and orientation mapping are key data processing steps for virtually any quantitative study of spatial correlations between the local chemistry and the microstructure of a material. For electron and X-ray diffraction methods it is possible to develop indexing tools which compare measured and analytically computed patterns to decode the structure and relative orientation within local regions of interest. Consequently, a number of numerically efficient and automated software tools exist to solve the above characterisation tasks. For atom probe tomography (APT) experiments, however, the strategy of making comparisons between measured and analytically computed patterns is less robust because many APT datasets may contain substantial noise. Given that general enough predictive models for such noise remain elusive, crystallography tools for APT face several limitations: Their robustness to noise, and therefore, their capability to identify and distinguish different crystal structures and orientation is limited. In addition, the tools are sequential and demand substantial manual interaction. In combination, this makes robust uncertainty quantifying with automated high-throughput studies of the latent crystallographic information a difficult task with APT data. To improve the situation, we review the existent methods and discuss how they link to those in the diffraction communities. With this we modify some of the APT methods to yield more robust descriptors of the atomic arrangement. We report how this enables the development of an open-source software tool for strong-scaling and automated identifying of crystal structure and mapping crystal orientation in nanocrystalline APT datasets with multiple phases.Comment: 36 pages, 19 figures, preprin

CMBPol Mission Concept Study: Prospects for polarized foreground removal

In this report we discuss the impact of polarized foregrounds on a future CMBPol satellite mission. We review our current knowledge of Galactic polarized emission at microwave frequencies, including synchrotron and thermal dust emission. We use existing data and our understanding of the physical behavior of the sources of foreground emission to generate sky templates, and start to assess how well primordial gravitational wave signals can be separated from foreground contaminants for a CMBPol mission. At the estimated foreground minimum of ~100 GHz, the polarized foregrounds are expected to be lower than a primordial polarization signal with tensor-to-scalar ratio r=0.01, in a small patch (~1%) of the sky known to have low Galactic emission. Over 75% of the sky we expect the foreground amplitude to exceed the primordial signal by about a factor of eight at the foreground minimum and on scales of two degrees. Only on the largest scales does the polarized foreground amplitude exceed the primordial signal by a larger factor of about 20. The prospects for detecting an r=0.01 signal including degree-scale measurements appear promising, with 5 sigma_r ~0.003 forecast from multiple methods. A mission that observes a range of scales offers better prospects from the foregrounds perspective than one targeting only the lowest few multipoles. We begin to explore how optimizing the composition of frequency channels in the focal plane can maximize our ability to perform component separation, with a range of typically 40 < nu < 300 GHz preferred for ten channels. Foreground cleaning methods are already in place to tackle a CMBPol mission data set, and further investigation of the optimization and detectability of the primordial signal will be useful for mission design.Comment: 42 pages, 14 figures, Foreground Removal Working Group contribution to the CMBPol Mission Concept Study, v2, matches AIP versio