In this thesis we are concerned with the existence of infrared fixed points and the conformal window for gauge theories with fermions. We are particularly interested in those theories that are candidates for walking technicolor. We discuss the background of technicolor and the techniques relevant to a theoretical understanding of the conformal window. Following this we extend the ideas of metric confinement and causal analyticity to theories with fermions in non-fundamental representations. We use these techniques to, respectively, provide a lower bound on the lower end of the conformal window and to provide a measure of perturbativity. As well as analytic calculations we use lattice techniques to investigate two particular candidate theories for walking technicolor - SU(2) with two adjoint fermions and with six fundamental fermions. We use Schrodinger Functional techniques to investigate the running of the theory across a wide range of scales. We measure both the running of the coupling and an estimator for the fermion mass anomalous dimension, $gamma$. We find that both theories are consistent with an infrared fixed-point. However, paying particular attention to our error estimates, we are unable to absolutely confirm their existence. This is a not unexpected result for SU(2) with two adjoint fermions but is rather surprising for SU(2) with only six fundamental fermions. In the region where we are consistent with a fixed point we find $0.05<gamma<0.56$ for $SU(2)$ with two adjoint fermions and $0.135<gamma<1.03$ for $SU(2)$ with six fundamental fermions. The measurement of $gamma$ for $SU(2)$ with two adjoint fermions is the first determination of $gamma$ for any candidate theory of walking technicolor.

In this work we analyze various implications of the presence of large field vacum expectation values (VEVs) along supersymmetric flat directions during the early universe. First, we discuss supersymmetric leptogenesis and the gravitino bound. Supersym- metric thermal leptogenesis with a hierarchical right-handed neutrino mass spectrum normally requires the mass of the lightest right-handed neutrino to be heavier than about 109 GeV. This is in conflict with the upper bound on the reheating temperature which is found by imposing that the gravitinos generated during the reheating stage after inflation do not jeopardize successful nucleosynthesis. We show that a solution to this tension is actually already incorporated in the framework, because of the presence of flat directions in the supersymmetric scalar potential. Massive right- handed neutrinos are efficiently produced non-thermally and the observed baryon asymmetry can be explained even for a reheating temperature respecting the gravitino bound if two conditions are satisfied: the initial value of the flat direction must be close to Planckian values and the phase-dependent terms in the flat direction potential are either vanishing or sufficiently small. We then show that flat directions also contribute to the total curvature perturbation. Such perturbation is generated at the first oscillation of the flat direction condensate when the latter relaxes to the minimum of its potential after the end of inflation. If the contribution to the total curvature perturbation from supersymmetric flat direction is the dominant one, then a significant level of non-Gaussianity in the cosmological perturbation is also naturally expected. Finally, we argue that supersymmetric flat direction VEVs can decay non perturbatively via preheating even in the case where they undergo elliptic motion in the complex plane instead of radial motion through the origin. It has been generally argued that in this case adiabaticity is never violated and preheating is inefficient. Considering a toy U(1) gauge theory, we explicitly calculate the scalar potential, in the unitary gauge, for excitations around several flat directions. We show that the mass matrix for the excitations has non-diagonal entries which vary with the phase of the flat direction vacuum expectation value. Furthermore, this mass matrix has zero eigenvalues whose eigenstates change with time. We show that these light degrees of freedom are produced copiously in the non-perturbative decay of the flat direction VEV.

In the first part of this thesis we study baryonic U(1) symmetries dual to Betti multiplets in the AdS_4/CFT_3 correspondence for M2 branes at Calabi-Yau four-fold singularities. Such short multiplets originate from the Kaluza-Klein compactification of eleven-dimensional supergravity on the corresponding Sasaki-Einstein seven-manifolds. Analysis of the boundary conditions for vector fields in AdS_4 allows for a choice where wrapped M5 brane states carrying non-zero charge under such symmetries can be considered. We begin by focusing on isolated toric singularities without vanishing six-cycles, which we classify, and propose for them field theory duals. We then study in detail the cone over the well-known Sasaki-Einstein space Q^111, which is a U(1) fibration over CP^1 x CP^1 x CP^1. The boundary conditions considered are dual to a CFT where the gauge group is U(1)^2 x SU(N)^4. We find agreement between the spectrum of gauge-invariant baryonic-type operators in this theory and M5 branes wrapping five-cycles in the Q^111 space. Moreover, the physics of vacua in which these symmetries are spontaneously broken precisely matches a dual gravity analysis involving resolutions of the singularity, where we are able to match condensates of the baryonic operators, Goldstone bosons and global strings. We then study the implications of turning on a closed three-form with non-zero periods through torsion three cycles in the Sasaki-Einstein manifold. This three-form, otherwise known as torsion G-flux, non-trivially affects the supergravity dual of Higgsing, and we show that the supergravity and field theory analyses precisely match in an example based on the Sasaki-Einstein manifold Y^1,2(CP^2), which is a S^3 bundle over CP^2. We then explain how the choice of M-theory circle in the background can result in exotic renormalization group flows in the dual field theory, and study this in detail for the Sasaki-Einstein manifold Y^1,2(CP^2). We also argue more generally that theories where the resolutions have six-cycles are expected to receive non-perturbative corrections from M5 brane instantons. We give a general formula relating the instanton action to normalizable harmonic two-forms, and compute it explicitly for the Sasaki-Einstein Q^222 example, which is a Z_2 orbifold of Q^111 in which the free Z_2 quotient is along the R-symmetry U(1) fibre. The holographic interpretation of such instantons is currently unclear. In the second part of this thesis we study the breaking of baryonic symmetries in the AdS_5/CFT_4 correspondence for D3 branes at Calabi-Yau three-fold singularities. This leads, for particular vacuum expectation values, to the emergence of non-anomalous baryonic symmetries during the renormalization group flow. We identify these vacuum expectation values with critical values of the NS-NS B-field moduli in the dual supergravity backgrounds. We study in detail the C^3/Z_3 orbifold theory and the dual supergravity backgrounds that correspond to the breaking of the emerging baryonic symmetries, and identify the expected Goldstone bosons and global strings in the infra-red. In doing so we confirm the claim that the emerging symmetries are indeed non-anomalous baryonic symmetries.

We calculate the string tensions, mass spectrum, and deconfining temperatures of <i>SO(N</i>) gauge theories in 2+1 dimensions. After a review of lattice field theory, we describe how we simulate the corresponding lattice gauge theories, construct operators to project on to specific states, and extrapolate values to the continuum limit. We discuss how to avoid possible complications such as finite size corrections and the bulk transition. <i>SO(N</i>) gauge theories have become recently topical since they do not have a fermion sign problem, are orbifold equivalent to <i>SU(N</i>) gauge theories, and share a common large-<i>N</i> limit in their common sector of states with <i>SU(N</i>) gauge theories. This motivates us to compare the physical properties of <i>SO(N</i>) and <i>SU(N</i>) gauge theories between 'group equivalences', which includes Lie algebra equivalences such as <i>SO</i>(6) and <i>SU</i>(4), and particularly a large-<i>N</i> equivalence. We discuss the large-<i>N</i> orbifold equivalence between <i>SO(N</i>) and <i>SU(N</i>) gauge theories, which relates the large-<i>N</i> gauge theories perturbatively. Using large-<i>N</i> extrapolations at fixed 't Hooft coupling, we test to see if <i>SO(N</i>) gauge theories and <i>SU(N</i>) gauge theories share non-perturbative properties at the large-<i>N</i> limit. If these group equivalences lead to similar physics in the gauge theories, then we could imagine doing finite chemical potential calculations that are currently intractable in <i>SU(N</i>) gauge theories by calculating equivalent quantities in the corresponding <i>SO(N</i>) gauge theories. We show that the <i>SO(N</i>) and <i>SU(N</i>) values match between group equivalences and at the large-<i>N</i> limit.

Hadronic collider experiments have played a major role in particle physics phenomenology over the last few decades. Data recorded at the Tevatron at Fermilab is still of interest, and its successor, the Large Hadron Collider (LHC) at CERN, has recently announced the discovery of a particle consistent with the Standard Model Higgs boson. Hadronic colliders look set to guide the field for the next fifteen years or more, with the discovery of more particles anticipated. The discovery and detailed study of new particles relies crucially on the availability of high-precision theoretical predictions for both the signal and background processes. This requires observables to be calculated to next-to-leading order (NLO) in perturbative quantum chromodynamics (QCD). Many hadroproduction processes of interest contain multiple particles in the final state. Until recently, this caused a bottleneck in NLO QCD calculations, due to the difficulty in calculating one-loop corrections to processes involving three or more final state particles. Spectacular developments in on-shell methods over the last six years have made these calculations feasible, allowing highly accurate predictions for final state observables at the Tevatron and LHC. A particular realisation of on-shell methods, generalised unitarity, is used to compute the NLO QCD cross-sections and distributions for two processes: the hadroproduction of W⁺ W^-jj, and the hadroproduction of W⁺ W^-jj. The NLO corrections to both processes serve to reduce the scale dependence of the results significantly, while having a moderate effect on the central scale choice cross-sections, and leaving the shapes of the kinematic distributions mostly unchanged. Additionally, the gluon fusion contribution to the next-to-next-to-leading order (NNLO) QCD corrections to W⁺ W^-j productions are studied. These contributions are found to be highly depen- dent on the kinematic cuts used. For cuts used in Higgs searches, the gluon fusion effect can be as large as the NLO scale uncertainty, and should not be neglected. All of the higher-order QCD corrections increase the accuracy and reliability of the theoretical predictions at hadronic colliders.

String theory is currently the best-known candidate for a theory of quantum gravity, having the necessary ingredients to describe all known elementary particles and interactions. It also includes several novel features, arising, for instance, from the additional six compact dimensions required for its internal consistency, making it the natural arena to construct extensions of the Standard Model. In this thesis, we analyze some of the new phenomenological aspects introduced by string theory within the framework of low energy effective theories, focusing on their applications to cosmology, astrophysics and collider experiments. We first consider a particular realization of the brane-world scenario in branonium bound states, showing that the orbital motion of a probe antibrane about a central brane stack leads to a resonant amplification of its world-volume scalar modes. We analyze the cosmological development of this process and also its potential relevance for either dark or baryonic matter generation in the early universe. We then focus on the spectrum of quark and lepton string excitations in warped compactifications, modeled by an effective 5-dimensional Randall- Sundrum throat. Motivated by the observed fermion mass hierarchy, we show that the spin-3/2 Regge excitation of the right-handed top quark is the lightest of such resonances in a significant region of parameter space, possibly lying below the TeV scale, and discuss its potential signatures at the Tevatron and at the LHC. Finally, we study the emission of sub-eV scalar particles by maximally rotating Kerr black holes, motivated by the recent string axiverse proposal. We focus on the spectrum of unstable scalar bound states in the superradiant regime, leading to an exponentially large axion cloud around astrophysical black holes, and analyze two semi-analytical methods for computing the growth rate of this instability, comparing the obtained results with previous analytical and numerical analyses.

This Thesis studies some aspects of string compactifications with particular em- phasis on moduli stabilisation and cosmology. In Chapter 1 I motivate the study of string compactifications as a way to build on the successes of the Standard Model of Particle Physics and of the theory of General Relativity. Chapter 2 constitutes an overview of the technical background necessary for the study of flux compactifications. I sketch how the desire to obtain a supersymmet- ric theory in four dimensions constrains us to consider compactifications of the ten dimensional theory in six dimensional Calabi-Yau orientifolds. I argue that it is strictly necessary to stabilise the geometry of this compact space in order to have a phenomenologically viable four dimensional theory. I introduce the large volume scenario of type IIB compactifications that successfully incorporates fluxes and sub- leading corrections to yield a four dimensional theory with broken supersymmetry and all geometrical moduli stabilised. The next four Chapters are devoted to the study of some phenomenological aspects of moduli stabilisation and constitute the original work developed for this Thesis. In Chapter 3 I investigate the consequences of field redefinitions in the stabilisation of moduli and supersymmetry breaking, finding that redefinitions of the small blow- up moduli do not significantly alter the standard picture of moduli stabilisation in the large volume scenario and that the soft supersymmetry breaking terms are generated at the scale of the gravitino mass. Chapter 4 deals with the putative destabilisation of the volume modulus by very dense objects. The analysis of the moduli potential shows that even the densest astrophysical objects cannot destabilise the moduli, and that destabilisation is only achievable in the context of black hole formation and cosmological singularities. In Chapter 5 I present a model of inflation within the large volume scenario. The inflaton is identified with a geometric modulus, the fibre modulus, and its potential generated by poly-instanton effects. The model is shown to be robust and consistent with current observational constraints. In Chapter 6 I introduce a model of quintessence, where the quintessence field and its potential share the same origin with the inflationary model of the previous Chapter. This model constitutes a stringy realisation of supersymmetric large extra dimensions, where supersymmetry, the low gravity scale and the scale of dark energy are intrinsically connected. I conclude in Chapter 7 outlining the direction of future research.

Hydrodynamics is an effective theory that is extremely successful in describing a wide range of physical phenomena in liquids, gases and plasmas. However, our understanding of the structure of the theory, its microscopic origins and its behaviour at strong coupling is far from complete. To understand how an effective theory of dissipative hydrodynamics could emerge from a closed microscopic system, we analyse the structure of effective Schwinger-Keldysh Closed-Time-Path theories. We use this structure and the action principle for open systems to derive the energy-momentum balance equation for a dissipative fluid from an effective CTP Goldstone action. Near hydrodynamical equilibrium, we construct the first-order dissipative stress-energy tensor and derive the Navier-Stokes equations. Shear viscosity is shown to vanish, while bulk viscosity and thermodynamical quantities are determined by the form of the effective action. The exploration of strongly interacting states of matter, particularly in the hydrodynamic regime, has been a major recent application of gauge/string duality. The strongly coupled theories involved are typically deformations of large-$N$ SUSY gauge theories with exotic matter that are unusual from a low-energy point of view. In order to better interpret holographic results, an understanding of the weak-coupling behaviour of such gauge theories is essential. We study the exact and SUSY-broken N=1 and N=2 super-QED with finite densities of electron number and R-charge, respectively. Despite the fact that fermionic fields couple to the chemical potentials, the strength of scalar-fermion interactions, fixed by SUSY, prevents a Fermi surface from forming. This is important for hydrodynamical excitations such as zero sound. Intriguingly, in the absence of a Fermi surface, the total charge need not be stored in the scalar condensates alone and fermions may contribute. Gauss-Bonnet gravity is a useful laboratory for non-perturbative studies of the higher derivative curvature effects on transport coefficients of conformal fluids with holographic duals. It was previously known that shear viscosity can be tuned to zero by adjusting the Gauss-Bonnet coupling, &lambda;_GB, to its maximal critical value. To understand the behaviour of the fluid in this limit, we compute the second-order transport coefficients non-perturbatively in &lambda;_GB and show that the fluid still produces entropy, while diffusion and sound attenuation are suppressed at all order in the hydrodynamic expansion. We also show that the theory violates a previously proposed universal relation between three of the second order transport coefficients. We further compute the only second-order coefficient thus far unknown, &lambda;₂, in the N=4 super Yang-Mills theory with the leading-order 't Hooft coupling correction. Intriguingly, the universal relation is not violated by these leading-order perturbative corrections. Finally, by adding higher-derivative photon field terms to the action, we study charge diffusion and non-perturbative parameter regimes in which the charge diffusion constant vanishes.

Many industrial processes use biological agents as catalysts. In this context, the study of the cellular metabolism becomes relevant for planning the best strategies (environmental and/or genetic modifications) to manipulate the cell in order to maximise the production of a metabolite of interest and minimise the by-products one. This increases the yield of the fermentation and reduces the cost of product recovery; thereby the profitability of the process is improved. The intracellular reactions are carried out in a complex, crowded and heterogeneous medium composed by solid components (macromolecules, ions, enzymes, small solutes, etc.) in a fluid phase called cytoplasm, all of them enclosed within the cellular membrane. The interactions among the intracellular components (as well as with the extracellular environment) determine the behaviour of the organism. The modelling and simulations of these interactions help the understanding of the metabolism. The aim of this thesis is to provide generic tools for the analysis and simulation of metabolic systems under the intracellular environmental conditions. In particular, this research focuses on the estimation of metabolic fluxes and the simulation of the diffusion process. The stoichiometric models have been widely used for the calculation of unmeasured fluxes in a metabolic network, assuming the system is at steady state. The addition of thermodynamic constraints allows only the prediction of fluxes that go in the direction of the Gibbs free energy drop. The Gibbs free energy change ( ) depends on the (intracellular) environmental conditions and determine the direction, feasibility and reversibility of the reactions involved in the pathways. The thermodynamically constrained stoichiometric model proposed here allows the estimation of the range of fluxes of a metabolic network, where the information about the presence of the enzymes that catalyse the reactions can be incorporated (if available). The effect of considering a zero flux reaction as blocked or at equilibrium on the flux predictions was investigated, as well as the environmental conditions ionic strength, temperature and pH. Additionally, since the solid components within the cell occupy about 40% of its total volume, these crowding conditions could alter the thermodynamic feasibility of the pathways. For this reason, the thermodynamically constrained stoichiometric model is extended to incorporate the crowding effect. The case study used in this work is the central carbon metabolic network of Actinobacillus succinogenes for the production of succinic acid from glycerol, a by-product in the biodiesel manufacture. Moreover, the crowding conditions also affect the diffusion of the molecules. The prokaryotic cells have been widely used in fermentation processes for the production of metabolites of interest. In this type of cells the diffusion is the primary mean of the particles’ motion, so that the diffusion reduction due to the crowding conditions could affect the possibility of encounter among the reactants, decreasing the reactions’ rate and therefore the yield of the process. A methodology based on the Lattice Boltzmann Method (LBM) and the Scaled Particle Theory (SPT) is presented in this thesis for fast simulations of the diffusion of hard-disk molecules in 2D crowded systems, which also allows evaluating the effect of the molecules’ size on their diffusion.

A growing body of evidence suggests that some Science teachers use drama-based strategies in order to promote understanding of abstract scientific concepts. These strategies employ action and imagination to simulate systems and processes that are too fast, too slow, too big, too small, too expensive or too dangerous to observe in the classroom. A small group of quantitative and qualitative studies over the past thirty years has suggested that these physical simulations enable learning in secondary students, by promoting discourse and by conveying concept features through a range of sensations. The field is as yet under-theorised, consisting of single case designs and unreplicated methodologies. This multiple case study focused upon an intervention design based on a pedagogical model developed in my Masters research. This study aimed to explore the characteristics of students' interaction and the nature of their resultant conceptions over four months. Each case focussed upon one of eight Key Stage 3 and Key Stage 4 classes across a variety of UK schools. In each, a curriculum-based particle theory topic was taught in a double-period lesson. Data included video, participant observations, and interviews with three students from each class collected at pre, post and delayed intervals. Findings suggested that the pedagogy engendered engagement and self-regulation in group model-making tasks, and supported thought experiment-type visualisations of dynamic processes. Conceptual development was found to continue up to four months after the lessons. A model of learning was developed in which social interaction and multimodal discourse promoted the association of conceptual features with affective, visual and embodied images, which supported recall, discussion and further conceptual development in the longer term.