A probabilistic approach for the estimation of earthquake source parameters from spectral inversion

The characterization of the mechanisms of earthquake generation and propagation is a major challenge in understanding the Earth engine. Although the seismic rupture non-linearly combines several space and time scales, some macroscopic parameters can provide insights in its evolution, such as the earthquake size and the stress drop released during a seismic event. However, the estimation of these parameters is very uncertain (Cotton et al., 2013), owing to uncertainties in data and models and to the strong coupling between source effects and wave propagation up to the observation sites. The objective of this thesis is the characterization of the seismic source parameters using the amplitude spectrum of the displacement records and assuming that the earthquake behaves as a circular crack (Keilis-Borok, 1959). Several methods for the characterization of the source using a spectral analysis have been proposed in literature. Systematic comparison between different methodologies highlighted the dependence of the results on the fitting model, due to the high correlation between the parameters, especially comparing EGF and TGF based techniques (Ide et al. 2003; Oye et al., 2005). A probabilistic approach can allow to investigate such a correlation, defining a probability density function (PDF) in the parameter space and allowing for a consistent estimate of the uncertainties. Using the probabilistic framework developed by Tarantola (2005), and specifically the notion of conjunction of states of information, I developed a probabilistic approach to retrieve the source parameters seismic moment (through the low-frequency spectral level), the corner frequency (that is a proxy of the rupture length) and the high-frequency decay parameter. Information on the source of an earthquake requires the modeling of the wave propagation too; I choose to use in this work a theoretical Green’s function, adding one parameter to invert related to the propagation (a frequency-independent Q-factor) beyond the three source parameter that I want to retrieve. I model the observations with an operator, defined on these four parameters, which is non-linear; thus, a global exploration of the model space is required in order to find the best solution to describe the data. Additionally, the joint a-posteriori probability density function (PDF) is computed around the best model, to extract the correlation matrix of the parameters. This allows to obtain estimates and uncertainties from the PDF, that are taking into account the correlations. The global exploration relies on the building of a Markov chain in the parameter space and on the combination of a deterministic minimization with a random exploration of the space (Basin-Hopping method, Wales and Doye, 1997; Wales, 2003). The main advantages of this new methodology are the following : • A fully probabilistic approach associated with a global exploration method can provide a robust information about the “best-fit” model, with correct estimation of uncertainties and parameter correlation. • The shape of the estimated PDF can assess the quality of the solutions, allowing to rule out noisy data and thus enabling the use of the method for automatic processing of large datasets. I performed three applications of the method. In Chapter 4, I analyzed the Central Italy 2016-2017 sequence, characterizing the source of all the earthquakes with Ml > 4 (56 events); in Chapter 5 I characterized the source of more than 10000 LFEs occurred in the Nankai region (Japan) during the period 2012-2016; in Chapter 6 I analyzed the micro-seismicity (Ml between 0 and 4.5, 1061 events) occurred from 2016 to 2017 in the Northern Ibaraki region (Japan)

Computational Approaches to Drug Profiling and Drug-Protein Interactions

Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

Digital watermark technology in security applications

With the rising emphasis on security and the number of fraud related crimes around the world, authorities are looking for new technologies to tighten security of identity. Among many modern electronic technologies, digital watermarking has unique advantages to enhance the document authenticity. At the current status of the development, digital watermarking technologies are not as matured as other competing technologies to support identity authentication systems. This work presents improvements in performance of two classes of digital watermarking techniques and investigates the issue of watermark synchronisation. Optimal performance can be obtained if the spreading sequences are designed to be orthogonal to the cover vector. In this thesis, two classes of orthogonalisation methods that generate binary sequences quasi-orthogonal to the cover vector are presented. One method, namely "Sorting and Cancelling" generates sequences that have a high level of orthogonality to the cover vector. The Hadamard Matrix based orthogonalisation method, namely "Hadamard Matrix Search" is able to realise overlapped embedding, thus the watermarking capacity and image fidelity can be improved compared to using short watermark sequences. The results are compared with traditional pseudo-randomly generated binary sequences. The advantages of both classes of orthogonalisation inethods are significant. Another watermarking method that is introduced in the thesis is based on writing-on-dirty-paper theory. The method is presented with biorthogonal codes that have the best robustness. The advantage and trade-offs of using biorthogonal codes with this watermark coding methods are analysed comprehensively. The comparisons between orthogonal and non-orthogonal codes that are used in this watermarking method are also made. It is found that fidelity and robustness are contradictory and it is not possible to optimise them simultaneously. Comparisons are also made between all proposed methods. The comparisons are focused on three major performance criteria, fidelity, capacity and robustness. aom two different viewpoints, conclusions are not the same. For fidelity-centric viewpoint, the dirty-paper coding methods using biorthogonal codes has very strong advantage to preserve image fidelity and the advantage of capacity performance is also significant. However, from the power ratio point of view, the orthogonalisation methods demonstrate significant advantage on capacity and robustness. The conclusions are contradictory but together, they summarise the performance generated by different design considerations. The synchronisation of watermark is firstly provided by high contrast frames around the watermarked image. The edge detection filters are used to detect the high contrast borders of the captured image. By scanning the pixels from the border to the centre, the locations of detected edges are stored. The optimal linear regression algorithm is used to estimate the watermarked image frames. Estimation of the regression function provides rotation angle as the slope of the rotated frames. The scaling is corrected by re-sampling the upright image to the original size. A theoretically studied method that is able to synchronise captured image to sub-pixel level accuracy is also presented. By using invariant transforms and the "symmetric phase only matched filter" the captured image can be corrected accurately to original geometric size. The method uses repeating watermarks to form an array in the spatial domain of the watermarked image and the the array that the locations of its elements can reveal information of rotation, translation and scaling with two filtering processes

Molecular Dynamics Simulation

Condensed matter systems, ranging from simple fluids and solids to complex multicomponent materials and even biological matter, are governed by well understood laws of physics, within the formal theoretical framework of quantum theory and statistical mechanics. On the relevant scales of length and time, the appropriate ‘first-principles’ description needs only the Schroedinger equation together with Gibbs averaging over the relevant statistical ensemble. However, this program cannot be carried out straightforwardly—dealing with electron correlations is still a challenge for the methods of quantum chemistry. Similarly, standard statistical mechanics makes precise explicit statements only on the properties of systems for which the many-body problem can be effectively reduced to one of independent particles or quasi-particles. [...

Methods for the Efficient Comparison of Protein Binding Sites and for the Assessment of Protein-Ligand Complexes

In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. These programs are utilized to screen entire libraries of molecules for a possible ligand of a binding site and to furthermore estimate in which conformation the ligand will most likely bind. By employing this information, molecule libraries can be filtered for subsequent affinity assays and molecular structures can be refined with regard to affinity and selectivity

Proceedings of the NASA Conference on Space Telerobotics, volume 5

Papers presented at the NASA Conference on Space Telerobotics are compiled. The theme of the conference was man-machine collaboration in space. The conference provided a forum for researchers and engineers to exchange ideas on the research and development required for the application of telerobotics technology to the space systems planned for the 1990's and beyond. Volume 5 contains papers related to the following subject areas: robot arm modeling and control, special topics in telerobotics, telerobotic space operations, manipulator control, flight experiment concepts, manipulator coordination, issues in artificial intelligence systems, and research activities at the Johnson Space Center

Cognitive Radio Systems

Cognitive radio is a hot research area for future wireless communications in the recent years. In order to increase the spectrum utilization, cognitive radio makes it possible for unlicensed users to access the spectrum unoccupied by licensed users. Cognitive radio let the equipments more intelligent to communicate with each other in a spectrum-aware manner and provide a new approach for the co-existence of multiple wireless systems. The goal of this book is to provide highlights of the current research topics in the field of cognitive radio systems. The book consists of 17 chapters, addressing various problems in cognitive radio systems

Advanced Mobile Robotics: Volume 3

Mobile robotics is a challenging field with great potential. It covers disciplines including electrical engineering, mechanical engineering, computer science, cognitive science, and social science. It is essential to the design of automated robots, in combination with artificial intelligence, vision, and sensor technologies. Mobile robots are widely used for surveillance, guidance, transportation and entertainment tasks, as well as medical applications. This Special Issue intends to concentrate on recent developments concerning mobile robots and the research surrounding them to enhance studies on the fundamental problems observed in the robots. Various multidisciplinary approaches and integrative contributions including navigation, learning and adaptation, networked system, biologically inspired robots and cognitive methods are welcome contributions to this Special Issue, both from a research and an application perspective

Proceedings of the Second International Mobile Satellite Conference (IMSC 1990)

Presented here are the proceedings of the Second International Mobile Satellite Conference (IMSC), held June 17-20, 1990 in Ottawa, Canada. Topics covered include future mobile satellite communications concepts, aeronautical applications, modulation and coding, propagation and experimental systems, mobile terminal equipment, network architecture and control, regulatory and policy considerations, vehicle antennas, and speech compression

Designing topological quantum matter in and out of equilibrium

Recent advances in experimental condensed matter physics suggest a powerful new paradigm for the realization of exotic phases of quantum matter in the laboratory. Rather than conducting an exhaustive search for materials that realize these phases at low temperatures, it may be possible to design quantum systems that exhibit the desired properties. With the numerous advances made recently in the fields of cold atomic gases, superconducting qubits, trapped ions, and nitrogen-vacancy centers in diamond, it appears that we will soon have a host of platforms that can be used to put exotic theoretical predictions to the test. In this dissertation, I will highlight two ways in which theorists can interact productively with this fast-emerging field. First, there is a growing interest in driving quantum systems out of equilibrium in order to induce novel topological phases where they would otherwise never appear. In particular, systems driven by time-periodic perturbations—known as “Floquet systems”—offer fertile ground for theoretical investigation. This approach to designer quantum matter brings its own unique set of challenges. In particular, Floquet systems explicitly violate conservation of energy, providing no notion of a ground state. In the first part of my dissertation, I will present research that addresses this problem in two ways. First, I will present studies of open Floquet systems, where coupling to an external reservoir drives the system into a steady state at long times. Second, I will discuss examples of isolated quantum systems that exhibit signatures of topological properties in their finite-time dynamics. The second part of this dissertation presents another way in which theorists can benefit from the designer approach to quantum matter; in particular, one can design analytically tractable theories of exotic phases. I will present an exemplar of this philosophy in the form of coupled-wire constructions. In this approach, one builds a topological state of matter from the ground up by coupling together an array of one-dimensional quantum wires with local interactions. I will demonstrate the power of this technique by showing how to build both Abelian and non-Abelian topological phases in three dimensions by coupling together an array of quantum wires