VictorJuiz/thesis huggingface dataset:
Equilibrium computation in games and strategic aspects of bitcoin mining

The focus of this thesis is twofold: on one hand we study the query complexity of equilibrium computation in games, and on the other hand, we use equilibrium concepts from game theory as a tool to understand miner incentives in Bitcoin. In terms of query complexity, we mostly focus on algorithms that have access to utility queries in large games and best response queries in bimatrix games. For the former, we demonstrate query-efficient completely uncoupled dynamics that achieve non-trivial approximate equilibria. For the latter, we reduce the problem of query-efficient approximate equilibrium computation to a natural geometric learning problem: approximately learning partitions of an 𝑛-dimensional simplex into disjoint convex polytopes via membership queries. Given this reduction we show query-efficient algorithms for the geometric problem, and ultimately provide an algorithm for computing ε-well-supported Nash equilibria in 𝑚×𝑛 bimatrix games with a query cost that is polynomial in log(1/ε)and max(𝑚,𝑛) provided that min(𝑚,𝑛) is constant.This leads to a polynomial query complexity algorithm for 2-player games,provided that one of the players has a constant number of strategies. As for incentives in Bitcoin, we shed some light into how robust honest mining protocols are to the presence of strategic agents. Our focus is on the strategic aspects of both solo mining and pool mining in Bitcoin. For the former, we take a multiplayer approach and exhibit specific strategy profiles of multiple strategic miners that outperform honest mining, even if said miners would not be incentivised to be dishonest individually. This effectively renders the Bitcoin protocol less secure than previously thought. As for the latter, we propose a new mining pool protocol that is a randomised variant of the already-ubiquitous pay-per-last-N-shares (PPLNS) mining pool scheme in Bitcoin. Our pool protocol, randomised pay-per-last-N-shares (RPPLNS),enjoys the same desirable properties of PPLNS, but with the added benefit of an exponentially reduced state space required to maintain the protocol. More importantly, this reduced state space also allows us to prove robust guarantees against a richer class of strategic pool mining than before.

Keywords: Bitcoin
Query Protocol
Equilibrium Computation
Decentralised Consensus
Revealed Preferences
Incentive Compatibility
Advisor: Goldberg, P
The molecular determinants of Polycomb-mediated gene repression

Precise spatio-temporal regulation of gene expression is required for development of multicellular organisms. Combinatorial activity of DNA-binding transcription factors has been proposed to drive lineage-specific transcriptional programmes. However, in addition to this, the chromatin template, on which transcription occurs, has emerged as another central player in the control of gene expression. The Polycomb repressive system represents one of the most extensively studied paradigms for chromatin-based gene regulation. It is comprised of two multi-subunit complexes, which catalyse post-translational modifications of histone tails - Polycomb repressive complex 1 (PRC1) mono-ubiquitinates histone H2A at lysine 119 (H2AK119ub1) and PRC2 methylates histone H3 at lysine 27 (H3K27me3). Elucidating the molecular mechanisms of Polycomb-mediated transcriptional silencing has proven challenging, as both PRC1 and PRC2 exist as an array of protein assemblies with distinct targeting modules and regulatory activities. Therefore, the primary determinants that underlie target site selection, Polycomb chromatin domain formation and gene repression by the Polycomb system have until now remained elusive.
Here, I have exploited combinatorial genetic perturbations coupled with quantitative genomic approaches to overcome the multiplicity of Polycomb complexes and uncover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. In contrast to the prevailing dogma in the field, I demonstrated that canonical PRC1, which binds Polycomb target sites in a PRC2-dependent manner and mediates higher-order chromatin structures, contributes little to gene repression. Instead, through systematic interrogation of how H2AK119ub1 is placed and kept in check in the genome, I discovered a remarkable degree of synergy between variant PRC1 complexes, which is central to deposition of H2AK119ub1, Polycomb chromatin domain formation and gene repression. Importantly, my observations suggested that the repressive activity of variant PRC1 complexes may rely on their capacity to catalyse H2AK119ub1. Using a conditional genetic strategy to inactivate PRC1, I directly tested this possibility and discovered that PRC1 catalytic activity is the central molecular determinant of Polycomb-mediated gene repression. In conclusion, through systematic dissection of the Polycomb system, I have provided compelling evidence for a variant PRC1-dependent logic for formation of Polycomb chromatin domains and repression of Polycomb target genes. Together, my findings place PRC1 and its catalytic activity at the forefront of Polycomb-mediated transcriptional silencing, paving the way for a mechanistic understanding of Polycomb system function.

Keywords: chromatin
histone modifications
genome engineering
gene regulation
Polycomb
genomics
epigenetics
Advisor: Klose, R
Investigating myoendothelial signalling mechanisms in resistance arteries

The regulation of resistance artery tone is a key determinant of blood pressure and tissue perfusion. It is well-established that endothelial cells (ECs) cause vasodilation by producing nitric oxide (NO) and endothelium-dependent hyperpolarization (EDH) in response to circulating vasoactive factors and flow. However, recent evidence has elucidated an intrinsic signalling mechanism, termed myoendothelial feedback, whereby ECs are activated during contraction independently of direct stimulation. The investigations presented in this thesis aimed to characterise myoendothelial feedback in isolated resistance arteries under isobaric and isometric conditions using pressure and wire myography, respectively. Most significantly, the profile of myoendothelial feedback differed between the two experimental approaches. In arteries studied isometrically, inhibition of NO and EDH production increased sensitivity to contractile agonists. On the other hand, blockade of endothelium-dependent vasodilation in pressurised arteries had no effect on submaximal contraction during sympathetic perivascular nerve stimulation and only augmented the maximum contractile response to agonists. Furthermore, arteries in the pressure myograph were less sensitive to NO, which may reflect pressure-induced smooth muscle Ca2+ sensitization and an abrogated influence of EC-dependent signalling. Additionally, a role for transient receptor potential cation channel subfamily V member 4 (TRPV4) in myoendothelial feedback was probed. However, while promising, this line of investigation was complicated by the observation that TRPV4 inhibition attenuated depolarization- dependent and -independent contraction, as well as endothelium-dependent vasodilation. The findings reported here have significant implications for the study of isolated resistance artery physiology and identify novel avenues of future research.

Keywords: Myoendothelial signalling
Vascular myography
Vascular smooth muscle
Endothelium
Resistance arteries
Advisor: Dora, K
Garland, C
Conformal scattering and analysis of asymptotic properties of gauge theories in general relativity

The study of scattering is a fundamental aspect of mathematical physics. In the second half of the 20th century, mathematical tools were developed by Penrose, Friedlander, Lax, Phillips, and others that have revealed an intriguing underlying geometry of scattering theories.
In the first part of this thesis we study the conformal scattering of Maxwell potentials on a class of asymptotically flat asymptotically simple spacetimes. We construct scattering operators as isomorphisms between Hilbert spaces on past and future null infinity, and (in the flat case) explore the structure of these Hilbert spaces with respect to the symmetries of the spacetime.
In the second part we study the Maxwell-scalar field system on de Sitter space. We prove small data peeling estimates at all orders, and construct bounded and invertible, but nonlinear, scattering operators. We discover that sufficiently regular solutions decay exponentially in time and disperse as linear waves, and find a curious asymptotic decoupling of the scalar field.
In the third part of this thesis we study the Yang–Mills–Higgs equations on the Einstein cylinder. By localizing Eardley & Moncrief's famous L∞ estimates, we extend them to the Einstein cylinder, and remove a small data restriction in a classical theorem of Choquet-Bruhat and Christodoulou from 1981. By using conformal transformations, we deduce large data decay rates for Yang–Mills– Higgs fields on Minkowski and de Sitter spacetimes.

Advisor: Juhasz, A
Mason, L
Design and implementation of feedback control systems for synthetic biology

Synthetic biology is a growing field at the interface of the engineering and biological sciences which aims to apply rational engineering design principles in biological contexts. It has many applications ranging from healthcare and the environment to industrial chemical synthesis and computation. When researchers attempt to apply synthetic biological tools to tackle these problems, they often follow a similar design-build-test cycle to that employed in traditional engineering disciplines. However, there are major challenges at each step in this cycle due to the variability inherent in biological systems, and our limited ability to understand and measure their behaviour. This thesis addresses select problems in each step of the design-build-test cycle as applied to synthetic biology, from a control-theoretic perspective.
To aid the design process of synthetic biological circuits I begin by using traditional control-theoretic analysis to derive structural requirements that biological systems must satisfy if they are to achieve behaviours such as disturbance rejection. I demonstrate how these requirements can be used to inform the biological design process, and highlight the challenges that must be overcome for effective noise attenuation in such circuits.
To refine the build/creation process for synthetic biological systems, I describe the experimental implementation and subsequent analysis of new synthetic biological feedback controllers built from two classes of components; short RNA and Recombinase proteins. Our results demonstrate how these circuits can be used to tune (or create) feedback loops, and reduce the influence of cellular noise on the performance of our synthetic circuits. This work thus has the double benefit of demonstrating new approaches to the engineering of biological systems, as well as creating well-characterised biological circuits that can be applied directly to a range of applications.
Finally, to improve the testing/characterisation process for synthetic biological systems I develop a novel biological approach to measuring cell-to-cell variability, as well as a new automated experimental platform: The Turbidostat. This device provides many of the important measurement and actuation capabilities required for synthetic biological research in a cheap and easy-to-use robotic platform. It can thus be used to automate a diverse range of characterisation experiments that would otherwise be highly laborious and prone to variability/noise. I perform several validation experiments, demonstrating this device’s broad range of capabilities.

Advisor: Papachristodoulou, A
Applications of optimal control for emissions management in road vehicles

Improvements in the availability of sensed and actuated vehicular systems have increased the opportunity for applying automatic control. Classic methods for designing control architectures are no longer sufficient due to the highly non-linear behaviour and heavy coupling between sub-systems. As a result, there is scope to employ computationally powerful optimisation techniques to investigate design trade-offs in these increasingly complex systems.
This thesis intends to take a multi-faceted look into the use of powerful optimal control techniques to solve some of the control problems arising in the automotive sector. In particular, a number of different control problems focused on emissions management are considered.
The first scenario relates to the fuel optimal control of a road vehicle, with a specific focus generating fuel-optimal drive cycle trajectories incorporating emissions constraints. A simplified model will be used initially to examine the solution structure and highlight any important features which occur in the solving of such eco-driving problems. Additionally, there are comparisons to be made between using a continuously variable transmission and a more traditional discrete gearbox. The second scenario considers an optimal driving problem for a vehicle equipped hybrid electric powertrain with a thermal aftertreatment model. A large percentage of tailpipe emissions are produced when the three-way catalytic converter is cold. Increased flexibility of power delivery enables the engine to be powered greater than the tractive demand, which prompts quicker heating and thus producing less total emissions. The drawback to this method is an increase in the tailpipe flowrates during this heating period. The possibility and scope for the reduction of emissions is considered.
The final scenario considered in this thesis will cover the optimal control of gasoline engines with combustion mode switching events. In particular, a turbocharged gasoline engine equipped dual-independent variable valve timing is considered. For engines operating in a stoichiometric regime, three-way catalytic converters are effective at reducing emissions. If the combustion mode is switched to lean, there is an increase in the tailpipe nitrous oxides (NOx). In order to avoid this, a lean-NOx trap is installed in the tailpipe, which requires periodic regeneration to ensure its effectiveness. Dynamic compensation of all actuators vastly improves the performance of the switching control. This thesis presents a number of suitable modelling techniques to investigate these scenarios, the results of which can be used to aid in the design of realtime control algorithms.

Keywords: Optimal Control
Emissions Control
Fuel-optimal Driving
Advisor: Limebeer, D
'What man art thou' imitation, masculinity, and homosociality in the poetry of Edward Herbert

This thesis explores the way that practices of imitation informed early modern ideas about manhood and friendship in the poetry of Edward, Lord Herbert of Cherbury (1582?-1648). Through a series of case studies which situate Herbert’s verse in the homosocial networks in which it was composed, circulated, and read, it uses Herbert’s poetry as a lens to demonstrate the ways that imitation can be collaborative and dialogic, affirming social and familial relationships. Herbert’s poetry also demonstrates how ideas about multiplicity and an anxiety around malleability informed early modern thinking about gender and manhood.
Chapter 1 focuses on Herbert’s exchanges with John Donne, and argues that poetry, imitatio, and friendship were inextricably bound together, as being a good man and a good friend, contemporary theory suggested, meant imitating your friends in verse, sustaining these friendships through poetry, and asserting your own place as a poet in a social and literary lineage. Chapter 2 examines Herbert’s satire addressed to Ben Jonson, exploring ideas of self-satire and anxieties about travelling and imitating and absorbing new fashions and qualities without becoming irreparably changed. Travel and imitation are also themes which dominate Chapter 3, which discusses Herbert and Thomas Carew’s imitations of Giambattista Marino’s poetry and explores how political theories of diplomacy and literary theory intersect, specifically in the rhetorical trope of metonymy, prompting questions about truthful and accurate representation in embassy and poetry. Chapter 4 situates Herbert within the wider household of the Sidney-Herberts, and discusses the ramifications of ‘echo’ as a female-gendered equivalent to ‘male’ imitatio, using various aetiologies of the Echo myth to explore texts circulated within the Sidney-Herbert household. Chapter 5 addresses the publication history of Herbert’s poems and his autobiographical Life of Himself and demonstrates how Herbert’s Life imitated chivalric prose romances in an attempt to fashion himself as a model for imitation. As a whole this thesis shows the importance of understanding practices of imitation within homosocial networks and verse, and particularly argues that imitation was a crucial practice in becoming both a poet and a man.

Advisor: West, P
Questions of value: an evaluative study of self-defense theory and practice in Germany, England, and the United States

Self-defense is a topic about which scholars, legislators, judges, and laymen alike have strongly held—and often strongly divergent—opinions. While some favor ‘tough-on-crime’ approaches according broader leeway to defenders, others advocate for a more empathetic, ‘humanitarian’ construction of the law.
By way of illustration of such polarities of perspective, consider the 20th century German case allowing a farmer to shoot a youthful fruit thief in the back because the ‘right need never yield to the wrong.’ Many contemporary commentators, in contrast, reject deadly force to defend property, considering it justified only when death is threatened. Despite what will be argued is the inherently value-laden nature of such choices, debates surrounding self-defense have in the main more narrowly focused on the ‘technical’ legal aspects of the exercise of self-preferential force.
This thesis tests the hypothesis that values, including protection of the attacker and defender, general and specific deterrence, maintenance of equal standing, and ensuring the primacy of the legal process, provide the rationale for self-defense and should, therefore, be treated as decision-grounds for determining when self-preferential force should be authorized. The hypothesis relatedly posits that such a value-centric approach to self-defense law will improve the transparency and quality of decision-making.
To test this hypothesis, the thesis develops the ‘value-based model’ of self-defense that seeks to offer a plausible (though not the only) value-centric approach. Following a thematic literature review, the thesis uses the value-centric perspective to address certain central theoretical questions underlying self-defense doctrine. Finally, the thesis deploys the value-based model as a template against which to compare the self-defense laws of Germany, the U.S., and England.
The thesis ultimately confirms the hypothesis that a broader consideration of the values implicated in self-defense will improve the transparency and quality of decision-making, and, correspondingly, reduces the impact of hidden normativity.

Keywords: notwehr
provocation
retreat
battery
self-defence
culpability
autonomy
passive
mistake
Dadson
forfeiture
justification
deterrence
conflict
necessity
waiver
proportionality
excuse
Self-defense
imminence
Advisor: Herring, J
Horder, J
Strongly-correlated lattice systems on a finite cylinder

In this thesis, I present my research on the numerical simulation of finite-size strongly-correlated lattice systems using the density matrix renormalisation group (DMRG). Ultracold gases in optical lattices have become the experimental setup of choice to simulate models from condensed-matter physics, because of their high degree of tunability and control. Their inherently finite size and alternative implementation call for a more in-detail study of how to define and characterise the phases of the models that they simulate.
I use DMRG to implement lattice Hamiltonians of highly-correlated systems with long-range interactions and identify their ground states on a finite system geometry. I describe in detail the process of constructing long-range Hamiltonians for their use in DMRG. I then apply these numerical methods to two fundamental models. I study the ground state of a fractional quantum Hall system and identify it as the well-known Laughlin state in a still unexplored parameter regime, by calculating its topological entanglement entropy and by using a set of physical observables that are available in a finite cylindrical geometry. I then study a dipolar Bose-Hubbard model and perform a systematic study of the order parameters that can best be used to characterise its phases in an ultracold gas setting by comparing how different types of observables are sensitive to finite-size and boundary effects. My results are meant to provide guidance for future experimental realisations of bosonic lattice models of small sizes.

Advisor: Jaksch, D
Neural mechanisms of reward-guided behavioural flexibility

Pursuing goals requires us to be flexible. When engaged in goal-directed behaviour, such flexibility is guided by the prospect of reward. The first part of this thesis examines how reward prospect influences flexible updating of task rules, needed to switch between tasks. Chapter 2 investigates how sequential changes in reward prospect influence rule updating across three behavioural experiments. This chapter shows inconclusive evidence for the hypothesis that sequential increases in reward prospect promote flexible rule updating. Chapter 3 examines the neural representation of task rules using multivariate pattern analyses of electroencephalographic data. This shows that high reward prospect boosts the neural encoding of task rules on trials where rules must be flexibly updated but not on trials where rules are repeated. The second part of this thesis examines how reward prospect is used to guide decisions about when to switch from option to another. Chapter 4 examines the theoretical implications of using reward properties of specific alternatives to guide switch decisions. Simulations show that decisions to switch based on specific alternatives tend to produce earlier switch decisions and higher reward overall than switch decisions based on average reward rates. Chapter 5 uses multivariate pattern analyses of electroencephalographic data to investigate how people decide when to switch to a specific option, in the absence of direct sensory cues to indicate its changing value. This reveals preliminary evidence that people track the hidden reward prospect for switching and use this information to regulate switch behaviour. Chapter 6 discusses implications of these results and bridges across cognitive control and decision making studies.

Advisor: Myers, N
Stokes, M