Topology and Polarisation of Subbeams Associated With Pulsar 0943+10's ``Drifting''-Subpulse Emission: I. Analysis of Arecibo 430- and 111-MHz Observations

The ``drifting'' subpulses exhibited by some radio pulsars have fascinated both observers and theorists for 30 years, and have been widely regarded as one of the most critical and potentially insightful aspects of their emission. Here, we report on detailed studies of pulsar B0943+10, whose nearly coherent sequences of ``drifting'' subpulses have permitted us to identify their origin as a system of subbeams that appear to circulate around the star's magnetic axis. We introduce several new techniques of analysis, and we find that both the primary and secondary features in the star's fluctuation spectra are aliases of their actual values. We have also developed a method of tracing the underlying pattern responsible for the observed sequences, using a ``cartographic'' transform and its inverse, permitting us to study the characteristics of the polar-cap emission ``map'' and to confirm that such a ``map'' in turn represents the observed sequence. We apply these techniques to the study of three different Arecibo observations. The ``B''-mode sequences are consistent in revealing that the emission pattern consists of 20 subbeams, which rotate around the magnetic axis in about 37 periods or 41 seconds. Even in the ``Q'' mode sequence, we find evidence of a compatible circulation time. The similarity of the subbeam patterns at different radio frequencies strongly suggests that the radiation is produced within a set of columns, which extend from close to the stellar surface up though the emission region and reflect some manner of a ``seeding''phenomenon at their base. The subbeam emission is then tied neither to the stellar surface nor to the field.Comment: 25 pages with 26 figures; in press in MNRA

Where are the X-ray QPOs in active galaxies?

In this paper we address the question of whether existing X-ray observations of Seyfert galaxies are sufficiently sensitive to detect quasi-periodic oscillations (QPOs) similar to those observed in the X-ray variations of Galactic Black Holes (GBHs). We use data from XMM-Newton and simulated data based on the best RXTE long-term monitoring light curves, to show that if X-ray QPOs are present in Seyfert X-ray light curves - with similar shapes and strengths to those observed in GBHs, but at lower frequencies commensurate with their larger black hole masses - they would be exceedingly difficult to detect. Our results offer a simple explanation for the present lack of QPO detections in Seyferts. We discuss the improvements in telescope size and monitoring patterns needed to make QPO detections feasible. The most efficient type of future observatory for searching for X-ray QPOs in AGN is an X-ray All-Sky Monitor (ASM). A sufficiently sensitive ASM would be ideally suited to detecting low frequency QPOs in nearby AGN. The detection of AGN QPOs would strengthen the AGN-GBH connection and could serve as powerful diagnostics of the black hole mass, and the structure of the X-ray emitting region in AGN.Comment: 10 pages. 9 figures. Accepted for publication in MNRA

Design of a Transceive Coil Array for Parallel Imaging at 9.4T

The main goal of this thesis is to design and develop a transmit/receive (transceive) coil array for small animal imaging at 9.4T. The goal is achieved by following basic RF design principles with a methodical construction approach and demonstrating viable applications. As operational frequencies increase linearly with higher static fields, the wavelength approaches the size of the sample being imaged. The resulting standing wave mode deteriorates image homogeneity. Fortunately, with multi-channel coil arrays, the produced Bi field can be tailored to produce a homogeneous excitation in the region of interest, thus overcoming the so called dielectric resonance effect. We examined a solution to achieve a higher level of Bx homogeneity and we compared the improvement of RF wavelength effects reduction against the results obtained with a similar-sized conventional birdcage coil. An additional benefit of this design lies in the fact that the use of multiple receiving coil elements is necessary for the implementation of fast imaging acquisition techniques such as parallel imaging. This is possible because the distinct element sensitivities are used to reconstruct conventional images from undersampled (or accelerated) data. The greatest advantage of parallel imaging is thus the reduction of total acquisition time. In functional MRI (fMRI), single-shot EPI is one of the standard imaging technique. Unfortunately, EPI suffers from significant limitations, precisely because all of the data is acquired following a single RF excitation. As a result EPI images can manifest artifacts and blurring due to susceptibility mismatch, off-resonance effects and reduced signal at the edges of k-space. Fortunately, parallel imaging can be used to decrease such unwanted effects by reducing the total k-space data acquired. Presented in this thesis is the logical progression of the construction of a transceive coil from surface coil fundamentals to high field applications such as field focusing and parallel imaging techniques

COMPUTER SIMULATIONS OF PROTEIN FOLDING

Understanding how proteins fold and interact with each other is key to understanding virtually all biological processes. Recent advances in computer power and modeling techniques make it possible to study proteins and other microscopic systems on biologically relevant time and length scales, closing the gap between simulations and experiments. At the same time, the emergence of more accurate models, derived from more rigorous physical principles, allows us to address a number of fundamental questions. The present work relies on molecular dynamics (MD) simulations to investigate several important aspects of protein behavior. First, we introduce the associative memory, water mediated, structure and energy model (AWSEM) and demonstrate its structure prediction capabilities. AWSEM is a coarse-grained protein force field that consists of many physically motivated potentials and a bioinformatically based term, which accounts for many-body local effects by matching its short sequential fragments to the sequences of experimentally resolved structures. We show that the AWSEM force field can be used for de novo structure prediction, as well as for kinetics and dynamics studies. Next, we use AWSEM to study protein-protein association. Our results indicate that the model not only can successfully predict the native dimeric interfaces but can also correctly reproduce the two and three state behavior of obligatory and nonobligatory dimers. We also find that both monomer geometry and specific non-bonded interactions play an important role in protein-protein association. Subsequently, we investigate protein folding under environmental fluctuations with a simple Go-like model. More specifically, we study the effect of an oscillating cellular environment on protein folding dynamics through modulating the strength of inter-residue interactions. The results show that, when occurring at some specific timescales, both deterministic and random fluctuations significantly accelerate the folding

Structured low-rank methods for robust 3D multi-shot EPI

Magnetic resonance imaging (MRI) has inherently slow acquisition speed, and Echo-Planar Imaging (EPI), as an efficient acquisition scheme, has been widely used in functional magnetic resonance imaging (fMRI) where an image series with high temporal resolution is needed to measure neuronal activity. Recently, 3D multi-shot EPI which samples data from an entire 3D volume with repeated shots has been drawing growing interest for fMRI with its high isotropic spatial resolution, particularly at ultra-high fields. However, compared to single-shot EPI, multi-shot EPI is sensitive to any inter-shot instabilities, e.g., subject movement and even physiologically induced field fluctuations. These inter-shot inconsistencies can greatly negate the theoretical benefits of 3D multi-shot EPI over conventional 2D multi-slice acquisitions. Structured low-rank image reconstruction which regularises under-sampled image reconstruction by exploiting the linear dependencies in MRI data has been successfully demonstrated in a variety of applications. In this thesis, a structured low-rank reconstruction method is optimised for 3D multi-shot EPI imaging together with a dedicated sampling pattern termed seg-CAIPI, in order to enhance the robustness to physiological fluctuations and improve the temporal stability of 3D multi-shot EPI for fMRI at 7T. Moreover, a motion compensated structured low-rank reconstruction framework is also presented for robust 3D multi-shot EPI which further takes into account inter-shot instabilities due to bulk motion. Lastly, this thesis also investigates into the improvement of structured low-rank reconstruction from an algorithmic perspective and presents the locally structured low-rank reconstruction scheme

STAND-ALONE IMAGE RECONSTRUCTION FOR MULTI-SLICE ECHO-PLANAR IMAGING, WITH APPLICATIONS TO STUDY HUMAN BRAIN FUNCTIONS

Optimizing the speed of image acquisition in magnetic resonance imaging (MRI) is a significant consideration to reduce patient examination time and/or to increase temporal resolution in dynamic studies. The advancement of simultaneous, multi-slice imaging increased the acquisition efficiency of MRI data. This technique for reducing scan time has opened a new door for functional MRI studies and diffusion-based fiber tractography to visualize the structural networks in the human brain [1]. The problem with the existing multi-slice image reconstruction algorithm using the MATLAB [2] program is that it is completely dependent on the MATLAB environment. In addition, the algorithm can be performed only on offline, preventing monitoring of subject motion and brain activation during scanning in order to adjust task presentation and for utilizing the brain signal to control other equipment and neurofeedback. To date, there is no stand-alone method for image reconstruction for multi-slice EPI data. To meet this need, I propose C/C++ programming language-based image reconstruction using the Slice-GRAPPA [3] algorithm for multi-slice acquisition and GRAPPA [4] algorithm for accelerating the image acquisition in the phase encoding direction. The main advantage of this reconstruction based on C/C++ is that it is stand-alone. In addition, optimizing the reconstruction program speed will enable it to be embedded into software to be applied in real time fMRI studies. This process was validated through matching the images from C/C++ language-based reconstruction with MATLAB environment-based reconstruction results. This thesis documents the process used to determine the efficacy of the proposed methodology