VictorJuiz/thesis huggingface dataset:
Computational and biophysical models of the brain

Widely distributed brain networks display highly coherent activity at rest. In this work, we combined bottom-up and top-down approaches to investigate the dynamics and underlying mechanisms of this spontaneous activity. We developed a realistic network model to simulate resting-state data, which incorporates biophysical regional dynamics, empirical brain connectivity, time delays, and background noise. At moderately weak coupling strengths, the model produces spontaneous metastable oscillatory states and a novel form of frequency depression, resulting in transient synchronizations between brain regions at reduced collective frequencies.
We used fixed and sliding window correlation approaches on the power of band-limited MEG data, and show that brain regions exhibit significant functional connectivity (FC) in the alpha and beta frequency bands on slow (&GT;1sec) time scales. We also show that temporal non-stationarity and bistability in FC occur in the same pairs of brain areas, and in the same frequency bands, as stationary measures of FC. We find that the network model reproduces the same frequency-dependency, time-scales, and non-stationary nature of FC as we found in real MEG data. Furthermore, seed-based correlations and independent component analysis also reveal a similar spatial profile of FC in empirical and simulated data, with the existence of widely distributed transient resting state networks in the same frequency bands. Finally, we used the network model simulations to evaluate a range of network estimation methods, and find that often the simplest linear measures perform best and some of the common non-linear measures can often give erroneous estimates.
Overall, our results suggest that structured interactions between brain regions in the presence of delays and noise result in spontaneous synchronizations leading to the organized power fluctuations across brain regions, and some of the simplest statistical measures provide excellent estimates of this connectivity. Our work also highlights the potential of computational models in exploring neural mechanisms.

Advisor: Woolrich, M
Smith, S
Democracy and the disengaged: a multi-dimensional study of voter mobilization in Alabama

This thesis investigates if and how poor, mostly minority citizens can be mobilized by a campaign whose principal policy objective would materially enhance their lives by including them in a major public program. The question is put to the test through a multi-dimensional study of voter mobilization in Alabama during the 2014 election for Governor. At stake in the election was whether Alabama would expand Medicaid through the Affordable Care Act in Alabama, an issue emblematic of "submergedness" (Mettler, 2011). In order to understand the extent to which the policy was submerged—measured by knowledge and awareness of the policy, along with its key provisions—I distributed a survey to 868 Alabamians weeks before the election. The survey used the experimental design of conjoint analysis to test which aspects of the policy were most persuasive among the target population. Additionally, I performed a randomized field experiment across the four major metropolitan areas of Alabama, micro-targeting 6,021 registered voters living in the "Coverage Gap," citizens who could gain health insurance if Medicaid were expanded. The campaign yielded negligible effects on voter turnout among subjects in the Coverage Gap, even though the interventions shifted voter knowledge, “surfacing” the policy. In addition to the survey and field experiments, this research benefits from qualitative insights gathered in 22 semi-structured interviews conducted among poor Alabamians, many of whom were uninsured. From these interviews, it became clear that the political disengagement of the poor is deeply entrenched, prohibitive of policy-based mobilization. Disengagement is driven by a complex mix of barriers to registration and perceptions of political inefficacy based on interpretations of extant policy designs. These results have important implications for our understanding of the limitations of policy-based mobilization, suggesting that more attention must be paid to how current policies shape predispositions for mobilization.

Keywords: Health politics
Voter turnout
Political participation
Policy design
Advisor: Bowles, N
Eggers, A
Community structure in temporal multilayer networks, and its application to financial correlation networks

Many real-world applications in the social, biological, and physical sciences involve large systems of entities that interact together in some way. The number of components in these systems can be extremely large, so some simplification is typically needed for tractable analysis. A common representation of interacting entities is a network. In its simplest form, a network consists of a set of nodes that represent entities and a set of edges between pairs of nodes that represent interactions between those entities. In this thesis, we investigate clustering techniques for time-dependent networks.
An important mesoscale feature in networks is communities. Most community-detection methods are designed for time-independent networks. A recent framework for representing temporal networks is multilayer networks. In this thesis, we focus primarily on community detection in temporal networks represented as multilayer networks. We investigate three main topics: a community-detection method known as multilayer modularity maximization, the development of a benchmark for community detection in temporal networks, and the application of multilayer modularity maximization to temporal financial asset-correlation networks. We first investigate theoretical and computational issues in multilayer modularity maximization. We introduce a diagnostic to measure persistence of community structure in a multilayer network partition and we show how communities one obtains with multilayer modularity maximization reflect a trade-off between time-independent community structure within layers and temporal persistence between layers. We discuss computational issues that can arise when solving this method in practice and we suggest ways to mitigate them. We then propose a benchmark for community detection in temporal networks and carry out various numerical experiments to compare the performance of different methods and computational heuristics on our benchmark. We end with an application of multilayer modularity maximization to temporal financial correlation networks.

Keywords: Multilayer Networks
Clustering
Temporal Networks
Network Science
Advisor: Porter, M
Howison, S
Verifying information flow and metaprogramming in dynamically typed languages

The ubiquity of JavaScript in Web applications means that its analysis has become an important security problem. This thesis develops techniques for analysing information flow in JavaScript programs and verifying the absence of undesirable flows (for example, of sensitive data to untrusted third parties).
JavaScript presents a unique combination of challenges not usually addressed by information flow analyses: its semantics are quaint and poorly specified, making formal reasoning largely infeasible; it is dynamically typed, which precludes the use of the most advanced existing analyses; and its eval construct, which executes a string as program code, allows arbitrary behaviour to result from data manipulated within the program.
The thesis focuses on the last of these problems. It considers an idealised subset of JavaScript and augments it with staged metaprogramming, a formalism that captures the construction, execution and manipulation of code templates. The resulting language is called SLamJS. An information flow analysis for SLamJS is developed and its correctness is proved. This builds on the existing analysis 0CFA, but adds support for metaprogramming (paying particular attention to the difficult behaviour of variable capture) and information flow.
In order to demonstrate the applicability of this analysis to JavaScript, where eval-using programs operate on code strings formed through concatenation, rather than splicing of templates, an algorithm to transform an eval-using program into one that uses staged metaprogramming is also developed. The transformation repurposes an existing lexer/parser (for example, one produced by the popular tools lex and yacc) to parse fragments of program code out-of-order.
The transformed program is then a suitable target for the analysis. This multi-step approach is vital to allow subdivision of the complex overall problem into smaller, more manageable parts.

Keywords: metaprogramming
dynamically typed languages
static analysis
information flow
Advisor: Ong, L
The creative process in performance: a study of clarinettists

This thesis examines creativity in performance through the study of the performance practices of professional clarinettists. Creativity research has tended to emphasise the innovative, revelatory qualities of the creative process, rather than the more pragmatic activities related to notated performance. This corresponds to a tension between the perceived creative opportunities of improvisation and notated music, and has resulted in a discourse that associates improvisation with spontaneity and novelty, and notated performance with repetition and reproduction. How might this discourse be challenged?
Through a series of case studies documenting clarinettists working in a variety of collaborative settings, I examine how performers’ constructions of creativity might complement or challenge the perceived creative affordances of notated music, and how the presence of, and/or collaboration with a living composer affects the creative process. A broadly ethnographic methodology is employed, drawing on thematic analysis of qualitative data obtained through semi-structured interviews with musicians, and audio-visual footage of workshops, rehearsals and performances. Conceptually, the thesis adopts an ecological perspective (Ingold 2011; Clarke, Doffman, and Lim 2013), proposing that creativity is a distributed phenomenon, entangled within a complex interweaving of social, material, and historical influences. It draws on work by Richard Sennett (2008) and Tim Ingold (2013) on craft and material engagement, suggesting that the interaction between a practitioner and a tradition entails a synthesis of action, perception and prior experience.
I argue that this orientation is useful for developing an analytical framework that accounts for the dimensions of performance that might otherwise be taken for granted. The research offers insights into the performance practices of contemporary concert musics – a line of inquiry that remains largely unaddressed. More broadly, it makes room for a more forward-looking model of creativity based on processes rather than outcomes, and one that better appreciates the fluid pathways between performers and scores.

Advisor: Clarke, E
Effect of shear patterns and EPS on fouling in microfiltration

Concentration polarisation and fouling reduce performance as well as increase costs. In order to mitigate these effects, understanding the cause and effects of these phenomena is crucial. It has been hypothesized, and to a certain extent shown, that amelioration of fouling can be achieved through the use of time varying shear for example use of air-sparging or sharp changes in crossflow velocity. Nevertheless the effect of shear on membrane fouling, in particular its effect on the foulant deposition and the transmission of small molecules in microfiltration, is not well understood.
The goal of this project was to achieve an understanding of various foulant behaviour. The work was divided into two parts. Firstly, the observations of fouling by freshwater algae, Chlorella Sorokiniana, were carried out at Nanyang Technological University, Singapore. Observations using macroscopic parameters were examined with an optical non-invasive observation technique called Direct Observation Through Membrane (DOTM). The result yielded a novel relationship between operating flux, crossflow velocity and transmission of extracellular polysaccharide. Interestingly shear was shown to have positive as well as negative effects on fouling of microfiltration membrane. The analysis of permeate has clearly shown that a maximisation of shear rate was not ideal.
The second part was concerned with observations of the effect of shear patterns on membrane fouling using newly fabricated special membrane filtration cell, Direct Shear Stress Test Cell (DSSTC), designed to fit an Anton Paar rheometer and operate at constant flux. Unlike the constant-shear-filtration cells, one could impose a very wide variety of shear regimes including intermittent sharp changes of direction and sinusoidal oscillations in the DSSTC. The effect of shear patterns on transmission and fouling of a model polysaccharide (Dextran Blue) through microfiltration membranes was carried out at various conditions. Again, the results showed that the maximisation of shear rate was not ideal. The effect of shear patterns and EPS on fouling by yeast suspension was also studied using the DSSTC. The benefit of oscillatory shear is foulant dependent. For example, square wave oscillatory shear led to lower relative fouling for yeast EPS, but it resulted in higher relative fouling for unwashed yeast.

Keywords: membrane
extracellular polysaccharides
fouling
transmission
microfiltration
shear
Advisor: Field, R
Cui, Z
Organomediated approaches to 18F-radiochemistry for PET

This thesis has focussed on 18F-fluorination reactions activated by an organomediator, with the aim of broadening the scope of metal-free reactions in 18F-radiosynthesis.
Chapter 1 provides an introduction to positron emission tomography (PET) and 18Fradiochemistry, including radioisotope production and modes of activation in 18Fradiosynthesis.
In Chapter 2, the concept of chirality and its relevance in the context of radiotracer design is introduced. The previously disconnected fields of organomediated asymmetric fluorination and 18F-radiosynthesis are merged for the first time via investigation of three distinct activation modes: chiral non-racemic secondary amine-mediated asymmetric α-18F-fluorination of aldehydes employing [18F]N-fluorobenzenesulfonimide; use of a phase transfer reagent for asymmetric 18F-fluorocyclisation and application of a chiral nonracemic 18F-fluorinating agent, chiral [18F]Selectfluor bis-triflate. Application of the first of these approaches to the radiosynthesis of the PET tracer (2S,4S)-4-[18F]fluoroglutamic acid with high d.r. is described.
Chapter 3 explores the use of hypervalent iodine reagents to mediate the oxidative fluorination of N-arylsulfonamides with nucleophilic fluoride via an umpolung approach. Preliminary studies on translation to radiosynthesis with [18F]fluoride are also disclosed.
In Chapter 4, experimental data is provided for all compounds, as well as analytical and chiral HPLC traces for 18F-reactions.

Keywords: radiochemistry
organomediated
fluorination
18F
asymmetric
Advisor: Gouverneur, V
Mechanical microscopy of the interface between yttria-partially-stabilised zirconia and porcelain in dental prostheses

In recent decades, the high strength, high toughness and appealing aesthetics of Yttria-Partially-Stabilised Zirconia (YPSZ) has made this ceramic the material of choice for dental prostheses. During manufacture YPSZ copings are veneered with porcelain to match the appearance of natural teeth and to reduce wear. However, near-interface chipping of the veneer is observed as a persistent primary failure mode. Recent studies suggest that failure is associated with the mechanical and microstructural state within a few microns of the interface. This insight has provided the motivating driver for this study: to develop and implement new characterisation techniques to improve the understanding of the YPSZ-porcelain interface and thereby reduce failure rates.
Microscale characterisation of the interface was performed using energy dispersive X-ray spectroscopy, Raman spectroscopy, X-ray Diffraction (XRD) and transmission electron microscopy. These studies indicated that YPSZ phase variation, elemental composition gradients and distinct microstructural features are present within 10 μm of the interface. Porcelain nanoscale voiding was found at the interface, and small angle neutron scattering confirmed that this is induced by tensile creep.
High resolution (microscale) residual stress analysis was performed in YPSZ using XRD and Raman spectroscopy, and in porcelain using a new pair distribution function analysis technique. Cross-validation of these results was performed using improved implementations of the ring-core focused ion beam milling and digital image correlation technique. The variation of Young's modulus, yield strength and fracture toughness were determined using spatially resolved micropillar compression and splitting. Improved evaluation of the single-crystal stiffness of YPSZ was also performed using a new neutron diffraction based technique.
The results of this analysis indicate a complex interaction within the first 50 μm of the YPSZ-porcelain interface which leads to a significant reduction in porcelain toughness and an increased propensity to fail at this location.

Keywords: Yttria partially stabilised zirconia
Dental materials
Stress modelling
Micropillar splitting
Raman spectroscopy
Phase analysis
Dental porcelain
Single crystal stiffness
Micropillar compression
Focused ion beam milling
High temperature creep
Microscale characterisation
Microscopy
Transmission electron microscopy
Neutron diffraction
Ring-core FIB milling and DIC
Energy dispersive X-ray spectroscopy
Nanovoiding
X-ray diffraction
Engineering
Residual stresses
Molecular dynamics
Advisor: Korsunsky, A
Gyrokinetic simulations of fusion plasmas using a spectral velocity space representation

Magnetic confinement fusion reactors suffer severely from heat and particle losses through turbulent transport, which has inspired the construction of ever larger and more expensive reactors. Numerical simulations are vital to their design and operation, but particle collisions are too infrequent for fluid descriptions to be valid. Instead, strongly magnetised fusion plasmas are described by the gyrokinetic equations, a nonlinear integro-differential system for evolving the particle distribution functions in a five-dimensional position and velocity space, and the consequent electromagnetic field. Due to the high dimensionality, simulations of small reactor sections require hundreds of thousands of CPU hours on cutting-edge High Performance Computing platforms.
We develop a Hankel–Hermite spectral representation for velocity space that exploits structural features of the particle streaming, gyroaveraging, and collision terms in the gyrokinetic system. This representation exactly conserves a discrete free energy in the absence of explicit dissipation, while our Hermite hypercollision operator captures Landau damping with as few as ten variables. Calculation of the electromagnetic fields also becomes purely local. This eliminates all inter-processor communication in, and hence vastly accelerates, searches for linear instabilities. We implement these ideas in SpectroGK, an efficient parallel code.
Turbulent fusion plasmas may dissipate free energy through linear phase mixing to fine scales in velocity space, as in Landau damping, or through a nonlinear cascade to fine scales in physical space, as in hydrodynamic turbulence. Using SpectroGK to study saturated electrostatic drift-kinetic turbulence in Cartesian geometry, we find that the nonlinear cascade completely suppresses linear phase mixing at energetically-dominant scales, so the turbulence is fluid-like. We use these observations to derive Fourier–Hermite spectra for the electrostatic potential and distribution function, and confirm these spectra with SpectroGK simulations.

Advisor: Dellar, P
Multidisciplinary concurrent optimization of gas turbine blades

This thesis presents the study and development of optimization methods that can perform concurrent aerodynamic-aeroelastic blade optimization in a multi-bladerow environment, and for realistic turbomachinery blade geometries.
The Nonlinear Harmonic Phase Solution Method has been chosen as the flow solution method of this work because of its capability to calculate the aeroelasticity features of interest (blade flutter) and the main flow aerodynamic performance in steady flow timescales.
The first optimization method that is shown is a more generic non-gradient method with an improved version of a quadratic Response Surface Model. The new Re-Scaled Response Surface Model has shown marked convergence and performance improvements against traditional surrogate models. However, the computational cost of this method for cases with a large number of design variables limits its real applications.
A gradient-based adjoint method is presented next as a cost-independent alternative that can accomplish efficient multi-bladerow optimization for a large number of variables within the current levels of computational power. The continuous adjoint system has been developed based on the same methodology as the flow solution method and it shows a more consistent relation between the flow field and its corresponding adjoint field, in agreement with the "anti-physics" information path. An adjoint interface treatment has been developed as an extension of the flow harmonic interface treatment. This unique treatment allows capture of the damping sensitivities of the vibrating blade to shape changes in adjacent rows. The application of this method to the design optimization of compressor and turbine stages has shown its capability to perform efficient multicomponent and multi-disciplinary design optimization of turbomachinery blades.

Keywords: Adjoint
Turbomachinery
Aeroelastics
Turbine
Optimization
Advisor: He, L