VictorJuiz/thesis huggingface dataset:
Modelling and verification for DNA nanotechnology

DNA nanotechnology is a rapidly developing field that creates nanoscale devices from DNA, which enables novel interfaces with biological material. Their therapeutic use is envisioned and applications in other areas of basic science have already been found. These devices function at physiological conditions and, owing to their molecular scale, are subject to thermal fluctuations during both preparation and operation of the device. Troubleshooting a failed device is often difficult and we develop models to characterise two separate devices: DNA walkers and DNA origami. Our framework is that of continuous-time Markov chains, abstracting away much of the underlying physics. The resulting models are coarse but enable analysis of system-level performance, such as ‘the molecular computation eventually returns the correct answer with high probability’. We examine the applicability of probabilistic model checking to provide guarantees on the behaviour of nanoscale devices, and to this end we develop novel model checking methodology.
We model a DNA walker that autonomously navigates a series of junctions, and we derive design principles that increase the probability of correct computational output. We also develop a novel parameter synthesis method for continuous-time Markov chains, for which the synthesised models guarantee a predetermined level of performance. Finally, we develop a novel discrete stochastic assembly model of DNA origami from first principles. DNA origami is a widespread method for creating nanoscale structures from DNA. Our model qualitatively reproduces experimentally observed behaviour and using the model we are able to rationally steer the folding pathway of a novel polymorphic DNA origami tile, controlling the eventual shape.

Keywords: verification
nanotechnology
DNA walkers
DNA Nanotechnology
self-assembly
probabilistic model checking
uniformization
DNA folding
Markov chain
molecular motors
uniformisation
DNA
parameter synthesis
DNA Origami
model checking
DNA self-assembly
Advisor: Kwiatkowska, M
Turberfield, A
Kant's Deduction of the Categories

This thesis defends an interpretation of the argument that Immanuel Kant calls his Transcendental Deduction of the Categories. It is divided into four chapters. The subject of the first chapter is the aim of Kant’s Deduction of the Categories. It is argued that what Kant has set out to find is an answer to the question how it is that the Categories are able to serve as representations of objects. This chapter also includes a detailed account of what Kant thinks is required for a concept to serve as a representation of an object. The subject of the second chapter is the strategy of Kant’s Deduction of the Categories. It is argued that what Kant thinks he needs to do in order to deduce the Categories is to show that an object must conform to the Categories if we are to make a judgment about this object. The third chapter is concerned with the central claim of Kant’s Deduction of the Categories, viz. the Principle of the Original Synthetic Unity of Apperception. It is argued that this principle consists in the claim that if we are to make a judgment about an object then we must be able to achieve a special sort of consciousness – specifically, the consciousness of what Kant calls the necessary unity of synthesis. The fourth and final chapter of the thesis is concerned with Kant’s justification for the Principle of the Original Synthetic Unity of Apperception. It is argued that Kant’s commitment to this principle is based on his recognition of a key fact about an act of judgment, viz. the fact that in making a judgment about an object, part of what we think is that our representations ought to be connected in a particular way.

Advisor: Walker, R
Influences of visuospatial mental processes and cortical excitability on numerical cognition and learning

Numerical cognition has been shown to share many aspects of spatial cognition, both behavioural and neurological. However, it is unclear whether a particular type of spatial cognition, visuospatial mental imagery (VSMI), may play a role in symbolic numerical representation. In this thesis, I first show that mental rotation, a form of VSMI, is related to two measures of basic numerical representation. I then show that number-space synaesthesia (NSS), a rare type of VSMI involving visualised spatial layouts for numbers, does not show an advantage in mental rotation, but shows interference in number line mapping. I next present a study investigating links between NSS and the ability to learn novel numerical symbols. I demonstrate that NSS shows an advantage at learning novel numerals, and that transcranial random noise stimulation, which increases cortical excitability, confers broadly similar advantages that nonetheless differ in subtle ways. I present a study of transcranial alternating current stimulation on the same symbol learning paradigm, which fails to demonstrate effects. Lastly, I present data showing that strength of numerical representation in these newly-learnt symbols is correlated with a measure of mental rotation, and also with visual recognition ability for the symbols after, but not before, training. All together, these findings suggest that VSMI does indeed play a role in numerical cognition, and that it may do so from an early stage of learning symbolic numbers.

Keywords: number-space
number cognition
non-invasive brain stimulation
numerical representation
numerical cognition
synesthesia
synaesthesia
transcranial alternating current stimulation
transcranial random noise stimulation
spatial cognition
transcranial direct current stimulation
cognitive neuroscience
Advisor: Kadosh, R
Analysis of the hindfoot and tibia segment-based axes in the Oxford Foot Model - anatomy and accuracy

The Oxford Foot Model (OFM) is a multi-segment foot model, which consists of three rigid segments (tibia, hindfoot and forefoot). The segments are defined by surface markers placed on bony landmarks on the foot and leg. The accuracy of the OFM angle calculations depends on how the markers and segment axes relate to the underlying anatomy. Several previous studies have reported particularly large variability in the hindfoot-tibia rotation and this finding has made gait data interpretation and, consequently, treatment recommendation more uncertain. The aim of this research project was to investigate the agreement between marker-based and anatomy-based hindfoot and tibia segment axes in the Oxford Foot Model. Twentyone adult females participated in the study (42 feet). The calcaneus and talus first principal axes, as well as 3D coordinates of markers and of the points corresponding to the ideal marker locations, were extracted from CT images. Gait analysis was used to measure lower-limb joint kinematics during level walking trials. The results showed that there is a significant discrepancy between the OFM hindfoot (A P) axis and the calcaneus first principal axis in the transverse plane. This relationship suggested a clinical implication that the A-P axis definition in relation to the underlying anatomy is likely to be less accurate in a deformed foot like clubfoot. Moreover, the insignificant root mean squared difference between the hindfoot-tibia kinematics, estimated by a rigid-body transformation method and that computed from the standard stereophotogrammetric procedure implied that the hindfoot and tibia rigidity assumption was valid in estimating the motion of the underling anatomy from the marker-based segment axes definition. Furthermore, a discrepancy between the OFM hindfoot and tibia axes and the corrected OFM hindfoot and tibia axes in the transverse plane was evident, and this led to differences in the transverse plane joint angles during walking. Therefore it can be inferred that these two reasons instigate the large variability in transverse plane hindfoot-tibia kinematics, as reported by past literatures. This information has potential to optimise the hindfoot and tibia segment definitions in accurately describing the motion of the underlying anatomy and thus improve interpretation of gait data and subsequently treatment recommendations for patients with foot deformity.

Advisor: Zavatsky, A
Stebbins, J
Georges Rouault's modernism and the question of materiality

The central concern of my thesis is to bring into focus the problematic relation between Georges Rouault’s (1871-1958) pictorial vocabulary and his subject matter: on the one hand, abstract mark-making and on the other, a refusal to cede to abstraction or formalism through an insistence that these marks remain yoked to representation. The result is an examination a way of painting that embraces its state of uncertainty, which interrogates its own construction, and strains against the very materiality it simultaneously celebrates. Chapter one traces the critical reaction to Rouault’s painting in the early years of the twentieth century, which was at best mystification, and at worst, disgust. This chapter also analyses the thick painterly terms of these paintings and their resistance to conventional meaning, arguing that there are parallels between Rouault’s project and contemporary experimental forms of art and literature within modernism. Chapter two continues this exploration, attending to the various relationships between surface and depth that are interrogated by Rouault’s canvases. These relationships reveal the deep philosophical and theological questions at stake Rouault’s painting. Chapter three explores a theological reading of Rouault’s work beginning with the aesthetics of his associate, the French Catholic philosopher, Jacques Maritain – a reading that shows how painting can be true to its material conditions and strain towards a higher, albeit obscure, form of knowledge. Against this, the last chapter argues that the paintings also support the possibility of a bleaker world-view, aligned with Dostoyevsky’s kenotic theology, in which matter potentially overwhelms the possibility of transcendental meaning. In conclusion, I argue that Rouault’s painting interrogates the vocabulary of modernism and presents the ‘fallen’ or ‘wounded’ state of a painting that acknowledges its material conditions.

Advisor: Wright, A
Riverine and desert animals in predynastic Upper Egypt: material culture and faunal remains

Animals were given a preponderant position in Egyptian art, symbolism, and cultual practices. This thesis centres on the relationship between humans and animals during the predynastic period in Upper Egypt (Naqada I–IIIB, 4th millennium BCE), focusing on hippopotamus and crocodile as representatives of the Nile environment and antelope species as representatives of the desert environment.
Depictions of these animals are analysed and compared with contemporary faunal remains derived from activities such as cult, funerary, or every day consumption. The material analysed covers several centuries: temporal evolutions and changes have been identified. The animals studied in this thesis were first used by the Naqada I–IIB elites as means to visually and practically express their power, which they envisioned in two contrasting and complementary ways. The responsibilities of the leaders were symbolised by the annihilation of negative wild forces primarily embodied by antelope species. In contrast, they symbolically appropriated positive wild forces, chief among them being the hippopotamus, from which they symbolically derived their power.
Faunal remains from after mid-Naqada II are few, depictions of hippopotamus disappeared and those of crocodile became rare. Antelope species became preponderant, especially on D-ware vessels, which were accessible to non-elite people. However, toward the end of the predynastic period, antelope species came to be depicted almost exclusively on high elite material; they lost their individuality and became generic representatives of chaotic forces that the leaders and early rulers had to annihilate in order to maintain control and order.

Advisor: Baines, P
Friedman, R
The role of anisotropy and fiber dispersion in the mechanics and remodeling of biological tissues

In many soft biological tissues mechanical strength and anisotropy are determined primarily by the presence of fibers, in particular collagen.
When an isotropic material is subject to a uniaxial tension, the principal strain transverse to the direction of applied load is always negative. However, in fiber reinforced materials the transverse principal strain can change its sign as the load increases, passing through the zero-points, known as perversions. We investigate how the number of perversions in a material reinforced by two symmetrically aligned families of distributed fibers depends both on the degree of fiber dispersion and the model used for fiber dispersion. Angular integration and three variants of the generalized structure tensor approach are considered and discussed. The study of perversions clearly demonstrates the qualitative difference between these approaches in the case of high dispersion of fibers. The results suggest that this difference is primarily due to the way compressive fibers are modeled.
Fiber alignment in biological tissues is created and maintained by the cells, which respond to mechanical stimuli arising from properties of the surrounding material. This coupling between mechanical anisotropy and tissue remodeling can be modeled in nonlinear elasticity by a fiber-reinforced hyperelastic material where remodeling is represented as the change in fiber orientation. We study analytically a simple model of fiber reorientation in a rectangular elastic tissue reinforced by two symmetrically arranged families of fibers subject to constant external loads. In this model, the fiber direction tends to align with the maximum principal stretch or strain. We characterize the global behaviour of the system for all material parameters and applied loads, and show that provided the fibers are tensile initially, the system converges to a stable equilibrium, which corresponds to either complete or intermediate fiber alignment.
Finally, we consider a model for the coupled growth and fiber reorientation in an elastic incompressible disk. The dynamics of our model is extremely sensitive to the initial condition and characterized by an infinite number of equilibrium states of fiber arrangement. We observed that the stress-induced fiber reorientation and growth laws used in our model produce specific fiber orientation pattern, which suggest a possible mechanism for self-organisation.

Keywords: finite elasticity
fiber reinforced materials
Nonlinear elasticity
soft biological tissue
growth and remodeling
fiber dispersion
anisotropy
The role of dispersal in life history and population dynamics: an experimental and theoretical approach

Understanding the evolution and maintenance of phenotypic and genetic variation within populations is a key challenge in population biology. Discrete phenotypic variation such as alternative reproductive strategies and dispersal strategies are extreme forms of this. To understand phenotypic variations, such as male dimorphisms and dispersal expression, requires investigating the costs and benefits of these different phenotypes. In this thesis I do so. First, at the individual level, I determine trade-offs between life-history traits and phenotypic expression. The influence of male morph expression is assessed by determining whether male morph survival is frequency dependent. Costs of dispersal expression were assessed by comparing individuals that expressed the dispersal phenotype during their ontogeny with individuals that did not. Second, at the population level, I specifically investigate costs of phenotype expression to the natal population when dispersers fail to disperse. To determine any demographic costs to natal populations, I used structured integral population models to calculate population biology quantities, which I compared between populations that produced dispersers that fail to disperse and populations that produced no dispersers. I show that expressing a dispersal morph is costly to life-history traits and skews the male morph ratio, indicating that these two conditional strategies interact during ontogeny. This questions whether current models explaining single conditional strategies, such as the environmental threshold model, should consider interactions between different conditional strategies. In natal populations where dispersal is expressed, but dispersers fail to disperse, populations suffer reduced fitness and this demographic cost is enhanced in stochastic environments. These results do not include benefits of successful dispersal or other costs such as inbreeding. However, they do provide a cost of dispersal expression which indicates what the benefits of dispersal would need to be for dispersal to evolve. One aspect that the results do not inform on is possible eco-evolutionary dynamics in populations. Future work should look to incorporate eco-evolutionary feedback, within a metapopulation structure, to identify the maintenance and evolution of male dimorphism and dispersal.

Keywords: dispersal
complex life cycle
environmental variation
population dynamics
Integral Projection Model
life-history
Advisor: Coulson, T
Smallegange, IM
Probing molecular gas and its physical conditions in disc galaxies

New observations of multiple molecular gas tracers in nearby early- and late-types galaxies are presented and are used to study the physical conditions of the gas within different morphological structures. The CO Tully-Fisher relation is also constructed for a sample of star-forming galaxies at z = 0:05 - 0:3, probing their mass and size evolution.
First, using single-dish observations of multiple locations within the nearby spiral galaxy NGC 6946, extensive CO ladders are generated. The molecular line ratios reveal a large variety of physical conditions across the molecular gas complexes, depending primarily on the presence of current or recent star formation, itself compared with that in the centre of the galaxy and other galaxies.
Second, interferometric observations of CO and high density molecular tracers in the nearby edge-on early-type galaxies NGC 4710 and NGC 5866 are presented. The gas kinematics reveals that the galaxies are barred, with most of the gas contained within a nuclear disc and a distinct inner ring. Using the molecular line ratios to probe the physical conditions of the gas, the nuclear discs appear to have a more diffuse and hotter molecular medium than the inner rings, with more embedded dense clumps. This suggests that the conditions in the nuclear discs are similar to those in photo-dissociation regions, with intense UV radiation from young stars and few cosmic rays. Indeed, the observed molecular line ratios are also intermediate between those of spiral galaxies and starbursts, with even milder star formation in the inner rings.
Third, homogeneously measuring the line widths in the CO spectra of star-forming disc galaxies at z = 0:05 - 0:3, their Ks-band CO Tully-Fisher relation is constructed. A comparison to local star-forming galaxy TFRs from the literature provides mild evidence that our sample galaxies are ≈ 0:89 mag brighter than local ones at a given rotational velocity, a result entirely consistent with our stellar mass TFR, suggesting that our sample galaxies are more massive than local ones by ≈ 0:35 dex. While they deserve further scrutiny, we suspect that these results are due to our sample galaxies being more heavily star-forming (and thus brighter at a given mass) than the comparison sample galaxies.

Keywords: star formation
molecular gas
galaxies
Advisor: Bureau, M
Diffusion-weighted magnetic resonance imaging with readout-segmented echo-planar imaging

Diffusion-weighted (DW) magnetic resonance imaging is an important neuroimaging technique that has successful applications in diagnosis of ischemic stroke and methods based on diffusion tensor imaging (DTI). Tensor measures have been used for detecting changes in tissue microstructure and for non-invasively tracing white matter connections in vivo. The most common image acquistion strategy is to use a DW single-shot echo-planar imaging (ss-EPI) pulse sequence, which is attractive due to its robustness to motion artefacts and high imaging speed. However, this sequence has limited achievable spatial resolution and suffers from geometric distortion and blurring artefacts.
Readout-segmented echo-planar imaging (rs-EPI) is a DW sequence that is capable of acquiring high-resolution images by segmenting the acquisition of k- space into multiple shots. The fast, short readouts reduce distortion and blurring and the problem of artefacts due to motion-induced phase changes between shots can be overcome with navigator techniques.
The rs-EPI sequence has two main shortcomings. (i) The method is slow to produce image volumes, which is limiting for clinical scans due to patient welfare and prevents us from acquiring very many directions in DTI. (ii) The sequence (like other diffusion techniques) is far from the optimum repetition time (TR) for acquiring data with the highest possible signal-to-noise ratio (SNR) in a given time. The work in this thesis seeks to address both of these important issues using a range of approaches.
In Chapter 4 a partial Fourier extension is presented, which addresses point (i) by reducing the number of readout segments acquired and estimating the missing data. This allows reductions in scan time by approximately 40% and the reliability of the images is demonstrated in comparisons with the original images.
The application of a simultaneous multi-slice scheme to rs-EPI, to address points (i) and (ii), is described in Chapter 5. Using the slice-accelerated rs-EPI sequence, tractography data were compared to ss-EPI data and high-resolution trace-weighted data were acquired in clinically relevant scan times.
Finally, a 3D multi-slab extension that addresses point (i) is presented in Chapter 6. A 3D sequence could also allow higher resolution in the slice direction than 2D multi-slice methods, which are limited by the difficulties in exciting thin, accurate slices. A 3D version of rs-EPI was simulated and implemented and a k-space acquisition synchronised to the cardiac cycle showed substantial improvements in image artefacts compared to a conventional k-space acquisition.

Keywords: 3D multi-slab diffusion MRI
High-resolution diffusion MRI
Simultaneous multi-slice acceleration
Advisor: Jezzard, P
Miller, K