Extracting the Structure and Conformations of Biological Entities from Large Datasets

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging diffract & destroy X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of unsorted snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive. It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms able to extract structural and conformational information from large datasets. These computationally efficient algorithms offer a new approach to determining the structure and conformations of viruses and macromolecules. After an introduction, we demonstrate a distributed, exact k-Nearest Neighbor Graph (k-NNG) construction method, in order to establish a firm algorithmic basis for manifold-based analysis. The proposed algorithm uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism in distributed computational environment and it is scalable for different cluster sizes, with each compute node in the cluster containing multiple GPUs. Next, we present applications of manifold-based analysis in determining structure and conformational variability. Using the Diffusion Map algorithm, a new approach is presented, which is capable of determining structure of symmetric objects, such as viruses, to 1/100th of the object diameter, using low-signal diffraction snapshots. This is demonstrated by means of a successful 3D reconstruction of the Satellite Tobacco Necrosis Virus (STNV) to atomic resolution from simulated diffraction snapshots with and without noise. We next present a new approach for determining discrete conformational changes of the enzyme Adenylate kinase (ADK) from very large datasets of up to 20 million snapshots, each with ~104 pixels. This exceeds by an order of magnitude the largest dataset previously analyzed. Finally, we present a theoretical framework and an algorithmic pipeline for capturing continuous conformational changes of the ribosome from ultralow-signal (-12dB) experimental cryo-EM. Our analysis shows a smooth, concerted change in molecular structure in two-dimensional projection, which might be indicative of the way the ribosome functions as a molecular machine. The thesis ends with a summary and future prospects

Simulated Annealing

The book contains 15 chapters presenting recent contributions of top researchers working with Simulated Annealing (SA). Although it represents a small sample of the research activity on SA, the book will certainly serve as a valuable tool for researchers interested in getting involved in this multidisciplinary field. In fact, one of the salient features is that the book is highly multidisciplinary in terms of application areas since it assembles experts from the fields of Biology, Telecommunications, Geology, Electronics and Medicine

Advancements and Breakthroughs in Ultrasound Imaging

Ultrasonic imaging is a powerful diagnostic tool available to medical practitioners, engineers and researchers today. Due to the relative safety, and the non-invasive nature, ultrasonic imaging has become one of the most rapidly advancing technologies. These rapid advances are directly related to the parallel advancements in electronics, computing, and transducer technology together with sophisticated signal processing techniques. This book focuses on state of the art developments in ultrasonic imaging applications and underlying technologies presented by leading practitioners and researchers from many parts of the world

Hydrogen adsorption and dynamics in clay minerals

A new class of hydrogen storage material (HSM), the swelling clay minerals, is introduced by the investigation of laponite, a representative smectite. Simple ion exchange allows for a diverse range of charged species to be studied as possible adsorption sites for H2 within the laponite interlayer, while a sub-monolayer of water pillars the interlayers apart by 2.85 Å, close to the kinetic diameter of H2. Neutron diffraction shows that the 001 peak, representing the clay d-spacing, is directly affected by the introduction of H2 or D2, confirming intercalation into the interlayers. Volumetric adsorption isotherms and neutron scattering show that laponites with 3 wt% H2O rapidly physisorb 0.5-1 wt% H2 at 77 K and 80 bar, with low binding enthalpies (3.40-8.74 kJ mol-1) and consequently low room temperature uptake (0.1 wt% at 100 bar). The higher structural density of clays results in lower H2 densities than MOFs and activated carbons, however some cation-exchanged forms, such as Mg and Cs, show promise for improvement having capacities of 22.8 g H2 per litre at 77K, 80 bar, intermediate between AX-21 and IRMOF-20. At low coverage, INS spectra reveal up to five adsorption sites with low rotational energy barriers (0.7-4.8 kJ mol-1), persisting up to at least 50 K. Analysis of quasielastic neutron scattering (QENS) spectra for Ca-laponite expanded with 3 wt% H2O reveals two populations of interlayer H2: one immobile up to 100 K and localised to the Ca2+ cations, while the other diffuses by jump diffusion at a rate of 1.93 0.23 Å2 ps-1 at 80 K, 60% slower than in the bulk (Dbulk = 4.90 0.84 Å2 ps-1). Arrhenius analysis gives activation energies of 188 28 K for the calcium and 120 32 K for the sodium form, comparable to the range for activated carbons. The adsorbate phase density of H2 in laponite interlayers at 40 K is 67.08 kg m-3, close to the bulk liquid density of 70.6 kg m-3. Jump lengths of 3.2 0.4 Å for Ca-laponite measured by QENS at 40 K are similar to the H2-H2 nearest neighbour distance in condensed H2 (3.79 Å). Thus data from a variety of techniques provides a coherent model for the structure and behaviour of H2 in laponite. The experimental achievement of a two-dimensional film of liquidlike H2 confined within the interlayers up to 40 K is of great interest for the field of superfluidics, since it may be possible to supercool liquid hydrogen confined in laponite interlayers below the predicted Bose-Einstein condensation temperature at 1 K

Sensor Signal and Information Processing II

In the current age of information explosion, newly invented technological sensors and software are now tightly integrated with our everyday lives. Many sensor processing algorithms have incorporated some forms of computational intelligence as part of their core framework in problem solving. These algorithms have the capacity to generalize and discover knowledge for themselves and learn new information whenever unseen data are captured. The primary aim of sensor processing is to develop techniques to interpret, understand, and act on information contained in the data. The interest of this book is in developing intelligent signal processing in order to pave the way for smart sensors. This involves mathematical advancement of nonlinear signal processing theory and its applications that extend far beyond traditional techniques. It bridges the boundary between theory and application, developing novel theoretically inspired methodologies targeting both longstanding and emergent signal processing applications. The topic ranges from phishing detection to integration of terrestrial laser scanning, and from fault diagnosis to bio-inspiring filtering. The book will appeal to established practitioners, along with researchers and students in the emerging field of smart sensors processing

Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u

The Extragalactic Sky at Low Radio Frequencies: A Study of Peaked-Spectrum Sources

We have entered a new era of radio astronomy where the low radio frequency sky is accessible to astronomers at a level of detail never before attainable. In particular, radio surveys are now being completed with incredibly wide fractional bandwidths, which can be exploited to study the unique radio spectra of gigahertz-peaked spectrum sources (GPS) and compact-steep spectrum (CSS) sources. GPS and CSS sources have been hypothesised to be an early stage of radio galaxy evolution due to their small scale morphologies. However, such an interpretation is contentious as there is evidence that these sources are not young but are confined to small spatial scales due to a high density circum-nuclear medium. One of the reasons that there has not been a resolution between these two competing hypotheses is because the absorption mechanism responsible for the turnover in their radio spectra remains ambiguous. In this thesis we produce high quality, low frequency spectra of GPS and CSS sources to test the dominant absorption mechanism in the population. We first study PKS B0008-421, which has the steepest known spectral slope below the turnover and the smallest known spectral width of any GPS source. We find that free-free absorption is responsible for the turnover in the spectrum. This thesis then describes the empirical modelling of the primary beam of the Murchison Widefield Array (MWA) and the production of the GaLactic and Extragalactic All-sky MWA (GLEAM) catalogue. The GLEAM survey represents the widest fractional bandwidth radio survey to date, with the derived extragalactic catalogue constituting an unprecedented database of high quality low frequency spectra. We then use the GLEAM catalogue to double the number of GPS and CSS sources known. We discuss the inconsistency of the standard radio galaxy evolutionary model with the presence of sources with high power and low intrinsic peak frequencies, suggesting that current evolutionary models are deficient

Intelligent Sensors for Human Motion Analysis

The book, "Intelligent Sensors for Human Motion Analysis," contains 17 articles published in the Special Issue of the Sensors journal. These articles deal with many aspects related to the analysis of human movement. New techniques and methods for pose estimation, gait recognition, and fall detection have been proposed and verified. Some of them will trigger further research, and some may become the backbone of commercial systems

Social work with airports passengers

Social work at the airport is in to offer to passengers social services. The main methodological position is that people are under stress, which characterized by a particular set of characteristics in appearance and behavior. In such circumstances passenger attracts in his actions some attention. Only person whom he trusts can help him with the documents or psychologically