VictorJuiz/thesis huggingface dataset:
Mathematical modelling of mitotic controls
Keywords: Cdk1
Greatwall
PP2A-B55
Separase

The mitotic cell cycle is fundamental to eukaryotic life. In mitosis, replicated chromosomes are segregated to form two new nuclei. This is essential to ensure the maintenance of chromosome number between parent and daughter cells. In higher eukaryotes, numerous cytological changes occur to facilitate the separation of the genetic material: the nuclear envelope breaks down, the mitotic spindle assembles, and the cell rounds-up. There is a well-conserved control network that regulates these processes to bring about the entry into mitosis, the separation of the genetic material, and the reversal of these processes during mitotic exit. To build a coherent model of these regulatory networks requires us to write the biochemical reactions in mathematical form.
The work in this Thesis pertains to three fundamental switches: entry into mitosis, the metaphase-to-anaphase transition, and exit from mitosis. I present three studies from a systems-level perspective. The first investigates a novel bistable mechanism controlling mitotic entry/exit in vitro using purified proteins. Dephosphorylation of Greatwall kinase by the phosphatase PP2A-B55 creates a double negative feedback loop that gives a bistable system response with respect to cyclin-dependent kinase 1 (Cdk1) activity. The second looks at hysteresis between mitotic entry and mitotic exit in HeLa cells. Hysteresis persists when either of the regulatory loops of Cdk1 or its counter-acting phosphatase PP2A-B55 is removed, but is diminished when they are both removed. Finally, the regulation of separase in the metaphase-to-anaphase transition is analysed. Separase that is liberated from securin inhibition is isomerised by Pin1 into a conformation that can bind to cyclin B1. This binding peaks after separase has cleaved cohesin and initiated anaphase.
Molecular regulation and function of Gata2 in the programming of haemogenic endothelium
Keywords: ATAC-seq
Embryonic development
Haematopoietic stem cells
Haematopoiesis
Zebrafish
CRISPR/Cas9

Haematopoietic stem cells (HSCs) maintain the vertebrate blood system throughout life. Exploiting their clinical potential requires a thorough understanding of the natural origins of the HSCs. They first arise from the haemogenic endothelium (HE), located in the main embryonic artery, the dorsal aorta. Our understanding of the genetic mechanisms underlying HE specification remains incomplete, but one of the crucial transcription factors is Gata2.
We found that a conserved enhancer of zebrafish gata2a gene (i4 enhancer) is active in vivo specifically in endothelial cells, including the HE. To unravel the function of gata2a in specifying the HSCs, we have targeted the i4 enhancer with CRISPR/Cas9, generating the first reported genomic deletion of an endogenous cis-regulatory region in zebrafish. Deletion of the i4 enhancer leads to a decrease in endothelial gata2a expression and a concomitant transient decrease in the number of HSCs. This is marked by an early decrease in the expression of gata2b, a gata2a paralogue previously shown to be required for the initiation of the haematopoietic programme. Our results suggest non-redundant roles of both zebrafish gata2 paralogues in programming of HSCs, providing insights into different roles of GATA2 throughout the programming of HSCs.
We also confirmed the previously reported loss of HSCs upon MO-mediated knockdown of lmo4a, associated with increased gata2a expression in HE. We validated the increase in gata2a levels in TALEN-generated lmo4a mutants. To identify the links between lmo4a, gata2a and the HE programming, we have profiled the transcriptome of lmo4a-deficient endothelial cells, including the HE. Our results suggest that Lmo4a may be a global regulator of the transcriptional programming of the HE. Moreover, Wnt signalling pathway may regulate gata2a downstream of lmo4a. This provides novel insights into the gene regulatory network orchestrating the generation of HSCs in the embryo.
Theory of optical transitions in pi-conjugated polymers
Keywords: Frenkel-Holstein Model
Spectroscopy
Conjugated Polymers

Conjugated Polymers have attracted a great deal of research interest in recent years due to their optoelectronic properties which makes them suitable for applications in organic light-emitting devices (OLEDs) and organic photovoltaics. Their properties are strongly dependent on the electron-electron and electron-nuclear interactions as well as the disorder which is present in almost all systems at finite temperatures.
In this thesis the optical properties of electronically neutral conjugated polymers will be investigated. The results obtained are general and applicable to a wide range of parameters. In order to compare these to experiment the optical properties of poly( paraphenylene), poly(para-phenylene vinylene), and derivatives have been calculated. In these polymers the primary photoexcitations are Frenkel excitons which can be described by the Frenkel-Holstein Hamiltonian, which explicitly takes into account the exciton-nuclear coupling. Disorder can be introduced into this model both as diagonal and off-diagonal disorder within the Hamiltonian.
First the optical transitions in ordered, linear conjugated polymers are investigated. It is found that the length of the polymer has a direct spectroscopic signature in the emission spectrum. When off-diagonal disorder is introduced the excitons localise on portions of the chain and the length of these portions, the conjugation length, then shows a clear emission signature. As such, a disordered polymer can be described theoretically as a chain of shorter segments, which define chromophores in a polymer context.
Following from these calculations the role of conformation was investigated and effects were observed that greatly determine the optical properties of non-linear polymers. Most notable the Herzberg-Teller effect, which renders symmetrically forbidden transitions weakly allowed and greatly affects the absorption and emission spectra. The signatures observed in these spectra allow the determination of the (coarse grained) conformation of the polymer, something that has been difficult to measure directly.
Aspects of work in quantum thermodynamics
Keywords: Landauer
Fluctuation Relations
Single Shot
Jarzynski

Landauer’s principle states that it costs at least kBT ln 2 of work to reset one bit in the presence of a heat bath at temperature T. The bound of kBT ln 2 is achieved in the unphysical infinite-time limit. Here we consider two different finite-time protocols - one with discretised time and the second in the continuous limit. We prove analytically that the discrete time protocol enables one to reset a bit with a work cost close to kBT ln 2 in a finite time. We construct an explicit protocol that achieves this, which involves thermalising and changing the system’s Hamiltonian so as to avoid quantum coherences. Using concepts and techniques pertaining to single-shot statistical mechanics, we furthermore prove that the heat dissipated is exponentially close to the minimal amount possible not just on average, but guaranteed with high confidence in every run. Moreover we exploit the protocol to design a quantum heat engine that works near the Carnot efficiency in finite time. We further contrast this to a continuous time version of the protocol which is substantially less energy sufficient. We also consider the fluctuations in the work cost, and calculate how their magnitude is suppressed by a factor depending on the length of the protocol.
We demonstrate with an experiment how molecules are a natural test-bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. By considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states, we demonstrate that the quantum Jarzynski equality is satisfied in this set-up. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.
Complex phase space representation of plasma waves: theory and applications
Keywords: Waves
Plasma
Wavepackets

This thesis presents results on the description of plasma waves in terms of wavepackets. The wave field is decomposed into a distribution of wavepackets in a space of position, wavevector, time, and frequency. A complex structure joining each pair of Fourier conjugate variables into a single complex coordinate allows the efficient derivation of equations of motion for the phase space distribution by exploiting its analytic properties. The Wick symbol calculus, a mathematical tool generalizing many convenient properties of the Fourier transform to a local setting, is used to derive new exact phase space equations which maintain full information on the phase of the waves and include effects nonlocal in phase space such as harmonic generation. A general purpose asymptotic expansion of the Wick symbol product formula is used to treat dispersion, refraction, photon acceleration, and ponderomotive forces. Examples studied include the nonlinear Schrödinger equation, mode conversion, and the Vlasov equation. The structure of partially coherent wave fields is understood in terms of zeros in the phase space distribution caused by dislocations in its complex phase which are shown to be correlated with the field entropy. Simulations of plasma heating by crossing electron beams are understood by representing the resulting plasma waves in phase space. The local coherence properties of the beam driven Langmuir waves are studied numerically.
Hippo tumour suppressor and Hedgehog pathway crosstalk at the primary cilia
Keywords: Primary Cilia
Hippo pathway
Hedgehog signalling pathway

Inappropriate activation of the Hedgehog signalling pathway is implicated in broad range of cancers, particularly basal cell carcinoma and medulloblastoma. Recent attempts to target Hedgehog signalling clinically have yielded mixed patient responses, highlighting the need for further study into Hedgehog pathway regulation. Vertebrate Hedgehog signalling occurs within, and is dependent on, the primary cilia. The function of a critical negative regulator of Hedgehog signalling, Suppressor of Fused (Sufu), is regulated by post-translational modification within its intrinsically disordered region, spanning amino acids 279-360. Sufu has previously been shown to be stabilised by phosphorylation at Ser342/Ser346 and Ser352, where S342 phosphorylated Sufu appears to localise to the cilium tip. Here, S342 of Sufu was identified as a potential substrate of the Large Tumour Suppressor (LATS) kinases, LATS1 and LATS2, of the Hippo pathway. This project aimed to determine whether Sufu is regulated by LATS1/2 phosphorylation. LATS1/2 were found to interact with and phosphorylate Sufu at S342. This phosphorylation did not appear to affect the levels of Sufu or of its S352 phosphorylated form, indicating that LATS1/2 does not regulate Sufu stability. Immunofluorescent staining of endogenous Sufu confirmed that Sufu localises to the primary cilium and accumulates at the cilium tip. Reduction of LATS1/2 lead to removal of Sufu from primary cilia, suggesting that S342 phosphorylation of Sufu promotes the ciliary localisation of Sufu. Additionally, S352 phosphorylated Sufu localises to the basal body of primary cilia, confirming that Nek2A phosphorylation of Sufu inhibits its entry into the cilium. Comparison of the mRNA expression of two well-known Hedgehog target genes, GLI1 and PTCH1, between wild type and LATS1/2-/- MEFs revealed that loss of LATS1/2 phosphorylation diminishes the repressive activity of Sufu on Hedgehog target gene transcription in response to Hedgehog pathway activation. Thus, LATS1/2 phosphorylation of Sufu at S342 appears to maintain its ability to repress Hedgehog target gene transcription. This adds to the growing body of literature showing that the Hippo and Hedgehog signalling pathways interact and coordinate to regulate cell proliferation. The data presented here unveils a novel role for LATS1/2 in restricting Hedgehog signalling via Sufu, and highlights the importance of LATS1/2 as tumour suppressors. This may identify LATS1/2 as potential targets in the treatment of Hedgehog signalling-dependent tumorigenesis.
On the use of transport and optimal control methods for Monte Carlo simulation
Keywords: Monte Carlo
Markov chain Monte Carlo
Normalizing constants
Sequential Monte Carlo
Optimal control
Annealed importance sampling
Mass transport
Reinforcement learning
Approximate dynamic programming

This thesis explores ideas from transport theory and optimal control to develop novel Monte Carlo methods to perform efficient statistical computation.
The first project considers the problem of constructing a transport map between two given probability measures. In the Bayesian formalism, this approach is natural when one introduces a curve of probability measures connecting the prior to posterior by tempering the likelihood function. The main idea is to move samples from the prior using an ordinary differential equation (ODE), constructed by solving the Liouville partial differential equation (PDE) which governs the time evolution of measures along the curve. In this work, we first study the regularity solutions of Liouville equation should satisfy to guarantee validity of this construction. We place an emphasis on understanding these issues as it explains the difficulties associated with solutions that have been previously reported. After ensuring that the flow transport problem is well-defined, we give a constructive solution. However, this result is only formal as the representation is given in terms of integrals which are intractable. For computational tractability, we proposed a novel approximation of the PDE which yields an ODE whose drift depends on the full conditional distributions of the intermediate distributions. Even when the ODE is time-discretized and the full conditional distributions are approximated numerically, the resulting distribution of mapped samples can be evaluated and used as a proposal within Markov chain Monte Carlo and sequential Monte Carlo (SMC) schemes. We then illustrate experimentally that the resulting algorithm can outperform state-of-the-art SMC methods at a fixed computational complexity.
The second project aims to exploit ideas from optimal control to design more efficient SMC methods. The key idea is to control the proposal distribution induced by a time-discretized Langevin dynamics so as to minimize the Kullback-Leibler divergence of the extended target distribution from the proposal. The optimal value functions of the resulting optimal control problem can then be approximated using algorithms developed in the approximate dynamic programming (ADP) literature. We introduce a novel iterative scheme to perform ADP, provide a theoretical analysis of the proposed algorithm and demonstrate that the latter can provide significant gains over state-of-the-art methods at a fixed computational complexity.
Molecular dynamics simulations of lipase-surface interactions
Keywords: Surface Interactions
Molecular Dynamics
Membranes
Enzymes
Lipases

Lipases are enzymes that play fundamental roles in fat digestion and metabolism, and function at the interface formed between hydrophobic molecules and the surrounding aqueous environment. These interfacial interactions are thought to induce conformational changes in a "lid" region of the lipase, leading to a dramatic increase in activity. This thesis aims to provide insight into the interactions that govern lipase association with interfaces of di erent structural characteristics, and the possible conformational changes that arise as a function of these interactions. A multi-scale molecular simulation approach (combining atomistic and coarse-grained methods) was applied to study two different lipases with a range of interfaces, including "soft" biological surfaces and "hard" non-biological surfaces.
Three major insights were gained from these studies. First, interactions of a small bacterial lipase (M37) with lipid interfaces resulted in substantial structural changes in a lid region, uncovering of the underlying active site. A mechanism of interfacial ac- tivation is proposed for this lipase. Second, the interaction of M37 with non-biological interfaces di er from lipid interfaces, leading to altered interfacial orientations with possible functional consequences. Third, the amino acid composition of the lid region of a yeast lipase (TLL) is shown to play crucial roles in lipase activation and structural stability.
Molecular mechanisms of hedgehog signal transduction by the G-protein coupled receptor smoothened
Keywords: x-ray crystallography
GPCR

The Hedgehog signalling pathway is an essential developmental pathway present in all bilaterians that is involved in embryogenesis, body patterning and stem cell homeostasis. Dysregulation of the Hh pathway leads to various kinds of cancer, such as basal cell carcinoma and medulloblastoma. Smoothened (SMO), a Frizzled-type G-protein coupled receptor (GPCR), is the essential transmembrane signal transducer within the Hh pathway, conveying the signal from the upstream transmembrane protein, Patched1 (Ptc1), to the downstream intracellular proteins. The mechanisms by which SMO transmits the Hh signal from the extracellular environment, through the plasma membrane and to the intracellular proteins are not known. In this thesis, I present my work into the structural and functional characterisation of the extracellular and transmembrane domains (TMD) of human SMO in order to better understand the molecular mechanisms of its signal transduction. The extracellular region of SMO contains a highly conserved cysteine-rich domain (CRD) and a linker domain (LD). I present the first crystal structure of the CRD, LD and TMD of SMO, which is also the first crystal structure of a GPCR with a large functional extracellular domain. This structure revealed a domain architecture for SMO that enables regulation of its transmembrane domain by its extracellular domains. It also revealed a cholesterol molecule bound to the CRD, which we subsequently determined to be a new endogenous small-molecule agonist for SMO. I present five further structures of SMO bound to different small molecule agonists and antagonists. Together, these structures demonstrate that the position of the CRD relative to the TMD reflects the activation state of SMO. We also generated nanobodies against the extracellular region of SMO in order to stabilise its conformation. These studies not only improve our understanding of the workings of a key transmembrane protein within a fundamental signalling pathway but will also aid efforts to develop better therapeutics for an important cancer target.
Residual stress evaluation and modelling at the micron scale
Keywords: FEM
microscopy
synchrotron
fracture mechanics
structural integrity
residual stress
polycrystalline materials
modeling
FIB-DIC

The presence of residual stresses in engineering components may significantly affect damage evolution and progression towards failure. Correct evaluation of residual stress is of crucial importance for assessing mechanical components, predicting response and ensuring reliability. For example, when failure occurs due to cyclic loading, the underlying damage begins at the nano-, and then micro-scale. It is clear that improving engineering reliability at the micro-scale requires the ability to evaluate residual stress and mechanical properties at the appropriate scale.
The key objective of the thesis is to advance the understanding and practice of residual stress evaluation at the micro-scale, and to examine the implications and applications that follow. Significant effort was devoted to the evaluation of two aspects of the relatively novel FIB-DIC micro-ring-core experimental technique: assessing the effects of Ga-ion damage and the quantification of uncertainty in stress evaluation due to unknown crystal orientation.
FIB-DIC micro-ring-core milling was then used alongside with synchrotron XRD to study residual stress effects on fatigue crack growth propagation rate following the occurrence of overload or underload. The effects of the two principal mechanisms of crack retardation following an overload, residual stress and crack closure, were separated by testing samples at different loading ratios. Whilst, the acceleration after an underload was studied using validated non-linear FEM analyses.
Conceptual focus was placed on the macro-micro-nano residual stress decomposition into Type I, II & III according to scale and, detailed examination was conducted experimentally and numerically. In the context of shot-peening surface treatment, residual stresses were modelled using a novel eigenstrain-based modelling procedure for arbitrarily shaped components. Furthermore, a fine scale characterisation was performed of the recast layer produced by EDM, with particular attention paid to the residual stress.
The investigations presented in this thesis open new perspectives for the assessment of material reliability. Improved failure prediction models will be elaborated based on the insights obtained in the present study.
Dynamical circulation regimes in planetary (and exo-planetary) atmospheres
Keywords: super-rotation
macroturbulence
diurnal forcing
planetary atmospheres
seasonal forcing

In this thesis, we study the effect of diurnally- and seasonally-varying forcing on the global circulation of planetary atmospheres explored within a large parameter space. This work focusses on studying the spacial and spectral energy budgets across a large range of planetary parameters as well as the momentum transfer as a response to diurnal and seasonal effects.
We simulate planetary atmospheres using PUMA-GT, a simple GCM co-developed for this work, that is forced by a semi-grey two-band radiative-convective scheme, dissipated by Rayleigh friction and allows for temporally varying insolation. Our parameter regime includes the variation of the planetary rotation rate, frictional timescale in the boundary layer, the thermal inertia of the surface and the atmosphere, as well as the short-wave optical thickness.
We calculate the energy transfer in Martian atmosphere to have a reference case of an atmosphere that is subject to very strong seasonal and diurnal variation. For this we present the first Lorenz energy budget calculated from reanalysis data of a non-Earth planet. A comparison between Martian and Earth atmosphere reveals a fundamentally different behaviour of the barotropic conversion term in the global mean. A significant impact of the thermal tide can be discerned in the generation of eddy kinetic energy, especially during global dust storms.
Our study of seasonal variation reaffirms previous work that the equatorial super-rotating jet in the slow-rotating regime is arrested for strong seasonal variation. We find a novel explanation as to why the Titan atmosphere is able to maintain super-rotation despite strong surface seasonality; for non-zero short-wave absorption in the atmosphere the mechanism that hinders equatorial super-rotation is weakened.
Diurnally-varying forcing can significantly enhance the equatorial super-rotation in cases with non-zero short-wave absorption. In our simulations this enhancement is maintained by a convergence of vertical momentum flux at the equator. Efforts to identify the atmospheric waves involved in this enhancement point towards thermally-excited gravity waves.