Sub-millimeter galaxies (SMGs) are a population of dusty, obscured sources that represent some of the most extreme sites of star-formation in the Universe. These galaxies have total far–infrared (FIR) luminosities of 10E12–10E13Lsol and colossal star formation rates (SFRs) of ∼100–1000 Msol/yr, with the FIR–emission arising due to the reprocessing of ultraviolet radiation from massive, young stars by dust. Despite their discovery nearly 20 years ago, our understanding of the SMG population has been hampered by the coarse resolution (FWHM = 15–30′′) of single-dish sub-millimeter surveys. In this thesis I present observations of FIR–bright (S870>∼1mJy) galaxies that have precise identifications from high-resolution imaging taken with sub–mm/mm interferometers. I present a multi-wavelength study of 96 SMGs that have unambiguous identifications from observations with Atacama Large Millimeter sub–millimeter Array (ALMA) and determine that the photometric redshift distribution for the SMG population has a median of zphot=2.5±0.2. I show that if the star formation activity in SMGs has a timescale of ~100Myr then their descendants at z~0 would have a space density and absolute H –band magnitude distribution that are in good agreement with a volume limited sample of local ellipticals. The low resolution of single-dish surveys has led to concerns about the blending of multiple individual galaxies into a single sub–millimeter source. I present ALMA observations of a sample of 30 bright, single–dish–identified sub-mm sources and show that 61(+19 -15)% are comprised of a blend of multiple SMGs brighter than >∼1mJy. Furthermore, I show that source blending boosts the apparent single-dish number counts by 20% at S870>7.5 mJy. A morphological analysis of the far-infrared emission from a subset of 23 of the brightest sources detected in the ALMA maps shows that the intense starburst in SMGs occurs in a compact region with a median physical half–light diameter of 2.4±0.2kpc. Finally, I present observations of two far–infrared–bright quasars, a potential transition stage in the evolution of SMGs. By considering the gas and black hole properties of these sources I show that they are consistent with the evolutionary scenario where far-infrared bright quasars represent a short phase in the transformation of a starburst dominated SMGs into an unobscured quasar.

Simulations including solely dark matter performed over the last three decades have delivered an accurate and robust description of the cosmic web and dark matter structures. With the advent of more precise cosmological probes, planned and ongoing, and dark matter detection experiments, this numerical modelling has to be improved to incorporate the complex non-linear and energetic processes taking place during galaxy formation. We use the ``Evolution and Assembly of GaLaxies and their Environment'' (EAGLE) suite of cosmological simulations to investigate the effects of baryons and astrophysical processes on the underlying dark matter distribution. Many effects are expected and we investigate (i): the modification of the profile of halos from the Navarro-Frenk-White profile shape found in collisionless simulations, including the changes in the dark matter profiles themselves, (ii) the changes of the inner density profiles of rich clusters, where observations have suggested a deviation from the standard cold dark matter paradigm, (iii) the offset created by astrophysical process between the centre of galaxies and the centre of the dark matter halo in which they reside and, (iv) the changes in the shape of the dark matter profile due to baryons in the centre of Milky Way halos and the impact these changes have on the morphology of the annihilation signal that could be observed as an indirect proof of the existence of dark matter. In all cases we find that the baryons play a significant role and change the results found in collisionless simulations dramatically. This highlights the need for more simulations like EAGLE to better understand and analyse future cosmology surveys. We also conduct a thorough study of the hydrodynamics solver parameters used in these simulations, assess their impact on the simulated galaxy population and show how robust some of the EAGLE results are against such variations.

This research project is multidisciplinary in nature. It involves the use of biomolecular design –peptide design – and the synthesis of small organic compounds to generate conformational switching in peptide structures. In this thesis, we demonstrate that we can design and synthesize de novo peptide sequences with the necessary information to assemble as α-helical coiled-coil structures when associated with their corresponding peptide partners. In addition, some of the peptide structures are designed to form both α-helical coiled-coils and fibrous systems. Since we aim to promote conformational changes in the initial folding states of our peptide assemblies, the design of these individual sequences that we refer to as chassis peptides includes tuneable positions which after being modified will help these changes to happen. We make use of the Negishi reaction to synthesize unnatural amino acids – pyridyl-alanine analogues – for metal-binding investigations. The insertion of these novel amino acids into our self-assembling peptide systems provides different conformational changes depending on the positions in which these amino acids are inserted. These experiments are an attempt to form novel metal-based chiral biocatalysts. They also allow us to investigate to what extent peptide self-assembly can control metal binding and to what extent the metal binding can control peptide self-assembly. This research project also includes the synthesis of an azobenzene derivative for trans-to-cis and cis-to-trans photoisomerization. We successfully attached an azobenzene linker to three different coiled-coil forming peptide structures, exhibiting different switching efficiency in each. By using these photoswitches we induce conformational changes in the secondary structure of the peptide structures by the use of light. Some of these are reversible structural changes which makes it a potential power source for protein motors.

In this thesis we investigate the influence that environment has on the formation and evolution of galaxies in the Galaxy And Mass Assembly (GAMA) survey. The highly complete equatorial regions of GAMA cover 180 square degrees of the sky, providing spectroscopic redshifts for 180,000 galaxies brighter than m_r = 19.8. GAMA is the largest multi-wavelength spectroscopic survey of its kind to date, designed to study aspects of galaxy formation on scales of <1 Mpc. The dependence of the galaxy luminosity function (LF) on local environment is well described by linear relations with overdensity. The faint end slope of the LF is largely independent of environment but steepens in void regions. The environmental dependence shows little evolution over the last 3 Gyrs, and can again be parameterised by a linear relation when split by colour. The dependence of the LF on the cosmic web classification can be predicted from its dependence on overdensity and the distribution of overdensities within each cosmic web structure. Observations from the GAMA survey can be theoretically interpreted by comparing to predictions made by the semi-analytic galaxy formation model of GALFORM through lightcone mock catalogues, which exhibit the same selection criteria as GAMA. Galaxy groups trace the underlying distribution of dark matter haloes in the Universe, and the use of galaxy group properties to infer the properties of dark matter, such as halo mass, is explored. Measurements of the galaxy density profile in galaxy groups in the GAMA survey and in the lightcone mocks suggest that the GALFORM model predicts the galaxy density profile to be too centrally concentrated. Comparisons to galaxy surveys such as GAMA lead to a bright future for the studies of galaxy formation.

This thesis concerns the use of dimeric coiled-coil peptides as components for synthetic protein motors. Studies of the hub structures of two motor designs are described. Firstly, I discuss experiments on the interactions between peptides designed for use in the Tumbleweed hub, a three-legged motor design containing three dimeric coiled-coil domains. Biophysical characterisation is carried out, including experiments to test the specificity of the interactions, which enable the peptides to be successful potential components for a stable hub structure. Secondly, I discuss the design of another motor hub, with two coiled-coil domains, using similar peptides to those used in the Tumbleweed system. The requirements for this design to produce a progressive motor are discussed. The design requires one peptide spanning the length of the motor hub, which has residues involved in both coiled-coil domains. These two coiled coil-contributing regions are linked by a central span of residues. Inducing a conformational change in this central region, in order to change the dimensions of the hub, is investigated, with the introduction of an azobenzene moiety in its cis and trans isomeric forms, using MD simulations. The ability of various residues to affect the range of conformational states this central region occupies is also investigated. Experimental studies of one of the possible systems are outlined and analysed.

Star formation is detected in any galaxy with an appreciable amount of gas and the vast majority of stars form in embedded clusters. However, very few bound star clusters are detected in the Milky Way, which has led to the hypothesis that as many as 90% of these clusters are disrupted during the early stages of their evolution. Many of those that do survive are likely to be progenitors of globular clusters that are observed in elliptical galaxies, and in the bulge and halo regions of spiral galaxies. In order to understand how star clusters form and evolve, and the disruption mechanisms they encounter, it is necessary to observe star clusters during their earliest evolutionary stages. This is difficult to observe in quiescent galaxies like the Milky Way where only a few newly formed star clusters have currently been detected. Gas-rich interacting and merging galaxies however, host thousands of newly formed star clusters and are ideal targets to observe the evolution of star clusters. In this thesis star clusters are observed in galaxy mergers for a range of evolutionary states using both photometric and spectroscopic data. We find evidence that tidal interactions have produced new cluster populations in two separate galaxy mergers. Analysis of the cluster populations in these mergers also suggest that tidal interactions do not destroy more clusters than they produce, in disagreement with simulations in the literature. Furthermore, we observe several star clusters that may be the product of merging between multiple clusters. These star clusters show spectral features consistent with multiple episodes of star formation. If these clusters remain bound for the next few Gyrs, they could explain the multiple stellar population feature observed in globular clusters in the Galaxy. We also explore the possibility of star clusters evolving to form the halo cluster population of their host merger before the progenitor disks coalesce. Star clusters are generally found in the halo population of a galaxy merger once the progenitor nuclei coalesce. However, some galaxy mergers like the Antennae harbour star clusters that may be forming their halo cluster population before their progenitor nuclei merge. This suggests that star clusters begin to form the halo cluster population of a galaxy merger before the progenitor nuclei coalesce. We recommend future surveys of gas-rich major galaxy mergers to study young ( ∼ few hundred Myr) star clusters in dense and quiescent regions to further support our findings.

In this thesis, the effect of scintillation arising from atmospheric optical turbulence on exoplanet transit and secondary eclipse photometry is examined. Atmospheric scintillation arises from the propagation of phase aberrations resulting from wavefront perturbations due to optical turbulence high in the atmosphere. Scintillation causes intensity variations of astronomical targets, which is a problem in exoplanet transit photometry, where the measurement of a decrease in brightness of 1% or less is required. For this reason, ground-based telescopes have inferior photometric precision compared to their space-based counterparts, despite having the advantage of a reduced cost. In contrast with previous work on the detection limits of fast photometry, which is obtained for an atmosphere averaged over time, the actual scintillation noise can vary considerably from night to night depending on the magnitude of the high-altitude turbulence. From simulation of turbulent layers, the regimes where scintillation is the dominant source of noise on photometry are presented. These are shown to be in good agreement with the analytical, layer based, equations for scintillation. Through Bayesian analysis, the relationship between the errors on the light and the uncertainties on the astrophysical parameters are examined. The errors on the light curve arising from scintillation linearly increase the scatter on the astrophysical parameters with a gradient in the range of 0.68 -0.80. The noise due to the photometry aperture is investigated. It is found that for short exposure in times in good seeing, speckle noise contributes to noise in photometry for aperture sizes of up to approximately 2.3xFWHM. The results from simultaneous turbulence profiling and time-series photometry are presented. It is found that turbulence profiling can be used to accurately predict the amount of scintillation noise present in photometric observations. An investigation of the secondary eclipse of WASP-12b on the William Herschel Telescope (WHT) is performed, resulting in a high quality z’-band light curve for WASP-12b consistent with a carbon-rich model and with no evidence for strong thermal inversion.

Energetic feedback from the Active Galactic Nucleus (AGN) of the Brightest Cluster Galaxy (BCG) is required to prevent catastrophic cooling of the intra-cluster medium (ICM) in galaxy clusters. Evidence for this is seen through the inflation of cavities in the ICM by AGN-launched, radio-emitting jets, and understanding this process is an active area of research. Radio observations play an integral role in this, as they trace the active stages of the feedback cycle. Understanding the radio properties of BCGs is therefore paramount for understanding both galaxy clusters and AGN feedback processes globally. Within this thesis, the BCGs in a large ($>$700) sample of X-ray selected clusters are studied. We observe these BCGs with a wide variety of facilities, building a census of their radio properties across a range of frequencies, timescales and angular resolutions. Radio spectral energy distributions (SEDs) are built for over 200 BCGs, and then decomposed into two components; a core, attributable to ongoing nuclear activity, and a non-core, attributable to historical accretion. Both components are not only more common, but also significantly more powerful in cool-core (CC) clusters than non-cool core (NCC) clusters. However, it is the presence of an {\em active} core that shows BCGs in CC clusters are constantly `on' - explaining how they regulate their environments over gigayear timescales. We observe 35 currently active BCGs at high (15~--~353~GHz) radio frequencies, and monitor their variability. Self-absorbed, active components are found to be common at high frequency. Little variability is seen on $<$year timescales, although longer term variation of $\approx$10\% annually over few-decade timescales is observed. Evidence is presented for a hitherto unseen component in BCG spectra that may be attributable to a naked Advection Dominated Accretion Flow (ADAF). The milli-arcsecond scale radio properties of 59 sources are studied, with a large range of morphologies recovered although no evidence is found for dual AGN being common in BCGs. Finally, we present a study that has more than doubled the number of HI absorption systems known in BCGs. We show that both the detection rate and column densities observed are strongly affected by the multi-scale properties of the radio continuum. All our clear detections are redshifted or at the systemic velocity. Most HI appears to be located in a clumpy torus that is replenished by residual material cooling from the ICM, linking the environment to the central engine and completing the feedback cycle.

In this thesis, we examine the relationship between the metal-enriched intergalactic medium (IGM) and galaxies at z < 1. In particular, we investigate the nature and consequence of feedback from active galactic nuclei (AGN) and supernovae, which shape the evolution of galaxies and are responsible for enriching the IGM with metals. The IGM is surveyed in ultraviolet (UV) absorption lines against background quasars (QSOs), whilst galaxies are surveyed in emission by means of optical photometry and spectroscopy. Simulated samples of IGM absorption systems and galaxies are also extracted from the Evolution and Assembly of GaLaxies and their Environments (EAGLE) cosmological hydrodynamical simulation for critical comparison with the data. We present the results of two primary studies that are designed to address key questions on the nature and consequence of feedback: 1. We examine complex absorption profiles in the spectrum of a QSO at z ~ 1, that trace a metal-rich outflow originating from the host galaxy. We show that these absorption profiles originate from dense, sub-pc scale gas clumps at distances of a few kpc from the central AGN. The gas is likely to be dynamically unstable, and is potentially far from ionization equilibrium. We favour a scenario in which the clumps are formed in-situ, and are entrained in a hot (T > 10^6 K) outflowing wind that may trace the majority of the mass, but is undetected in the UV. These observations provide a detailed set of constraints on the nature of feedback in QSO host galaxies. 2. We investigate the distribution and dynamics of metal-enriched gas around galaxies at z < 1 through the two-point cross- and auto-correlation functions of OVI absorbers and galaxies.

In this thesis, we will investigate the collider phenomenology and cosmological consequences of extensions of the Standard Model (SM) with hidden sectors coupled to the SM via a Higgs portal coupling. We will explore how models with classical scale invariance, where all mass scales are dynamically generated, can address the shortcomings of the SM without destabilising the Higgs mass. The matter-antimatter asymmetry in the Universe and the tiny masses of active neutrinos are addressed in a U(1)$_{B-L}$ extension of the SM with GeV scale right-handed neutrinos. We then investigate a range of models with both Abelian and non-Abelian gauge groups in the hidden sector to show how we can stabilise the Higgs potential and at the same time provide phenomenologically viable dark matter candidates where all scales in the theory have a common origin. For non-Abelian gauge groups in the hidden sector, we also show that hidden magnetic monopoles can make up a significant fraction of dark matter. The dark matter in this model, which consists of both magnetic monopoles and gauge bosons, has long-range self-interactions which could explain the too-big-to-fail-problem at small scales in the standard cold dark matter scenario. We then study the collider phenomenology of hidden sector models with dark matter candidates through a simplified model framework both at the LHC and at a future 100 TeV collider. Hidden sector extensions of the SM with a Higgs portal coupling give a rich and predictive model building framework for BSM physics without introducing a large hierarchy of scales.