Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible

Wireless realtime motion tracking system using localised orientation estimation

A realtime wireless motion tracking system is developed. The system is capable of tracking the orientations of multiple wireless sensors, using a semi-distributed implementation to reduce network bandwidth and latency, to produce real-time animation of rigid body models, such as the human skeleton. The system has been demonstrated to be capable of full-body posture tracking of a human subject using fifteen devices communicating with a basestation over a single, low bandwidth, radio channel. The thesis covers the theory, design, and implementation of the tracking platform, the evaluation of the platform’s performance, and presents a summary of possible future applications

DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization

The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity

PASSIVE SUPPRESSION OF AEROELASTIC INSTABILITIES OF IN-FLOW WINGS BY TARGETED ENERGY TRANSFERS TO LIGHTWEIGHT ESSENTIALLY NONLINEAR ATTACHMENTS

Theoretical and experimental suppression of aeroelastic instabilities by means of broadband passive targeted energy transfers has been recently studied. A single-degree-offreedom (SDOF) nonlinear energy sink (NES) was coupled to a 2-DOF rigid wing modeled in the low-speed, subsonic regime with quasi-steady aerodynamic theory. The nonlinear attachment was designed and optimized to suppress the critical nonlinear modal energy exchanges between the flow and the (pitch and heave) wing modes, thus suppressing the (transient) triggering mechanism of aeroelastic instability. We performed bifurcation analysis to find regions of robust passive aeroelastic suppression in parameter space. Then, we employed multi-degreeof-freedom nonlinear energy sinks (MDOF NESs) to improve robustness of the aeroelastic instability suppression. Bifurcation analysis by a numerical continuation technique demonstrated that controlling the occurrence of a limit point cycle (LPC or saddle-node) bifurcation point above a Hopf bifurcation point is crucial to enhancing suppression robustness. MDOF NESs not only can enhance robustness of suppression against even strong gust-like disturbances, but they require lower NES mass compared to SDOF NES designs. The validity of the theoretical findings was proven by a series of wind tunnel experiments

Empirical Mode Decomposition in the Reduced-Order Modeling of Aeroelastic Systems

peer reviewedA relationship between IntrinsicMode Functions (IMFs), derived from the Empirical Mode Decomposition (EMD), and the slow-flow model of a nonlinear dynamical system has been exploited in the development of the Slow Flow Model Identification (SFMI) method for strongly nonlinear systems, in which the physical parameters of such systems are identified from experimental data. Both the slow flows and IMFs provide the means to expand a general multicomponent signal in terms of a series of simpler, dominant, monocomponent signals. The slow flows are obtained analytically, for example through application of the method of complexification and averaging (CxA), which transforms the equations of motion into a set of approximate equations in amplitude and phase for each modeled frequency component. In contrast, the EMD characterizes a signal through the envelope and phase of its elemental components, the IMFs. Thus, between nonlinear transitions, the equations derived using the CxA method govern the amplitude and phase of the modeled IMFs. Application of SFMI has, until now, been limited to low-dimensional systems subjected to impulsive excitation. Herein, the method is extended to identification of a planar rigid airfoi

Galaxy Cluster Pressure Profiles as Determined by Sunyaev Zel'dovich Effect Observations with MUSTANG and Bolocam I: Joint Analysis Technique

We present a technique to constrain galaxy cluster pressure profiles by jointly fitting Sunyaev-Zel'dovich effect (SZE) data obtained with MUSTANG and Bolocam for the clusters Abell 1835 and MACS0647. Bolocam and MUSTANG probe different angular scales and are thus highly complementary. We find that the addition of the high resolution MUSTANG data can improve constraints on pressure profile parameters relative to those derived solely from Bolocam. In Abell 1835 and MACS0647, we find gNFW inner slopes of $\gamma = 0.36_{-0.21}^{+0.33}$ and $\gamma = 0.38_{-0.25}^{+0.20}$, respectively when $\alpha$ and $\beta$ are constrained to 0.86 and 4.67 respectively. The fitted SZE pressure profiles are in good agreement with X-ray derived pressure profiles.Comment: 12 pages, 12 figures. Submitted to Ap