Ecosystems are often made up of interactions between large numbers of species. They are considered complex systems because the behaviour of the system as a whole is not always obvious from the properties of the individual parts. A complex system can be represented by a network: a set of interconnected objects. In the case of ecological networks and food webs, the objects are species and the connections are interactions between species. Many complex systems are dynamic and exhibit intricate time series. Time series analysis has been developed to understand a wide range of natural phenomena. This thesis deals with the structure, dynamics, and robustness of ecological networks, the spatial dynamics of fluctuations in a social system, and the analysis of cardiac time series. Biodiversity on Earth is decreasing largely due to human-induced causes. My work looks at the effect of anthropogenic change on ecological networks. In Chapter Two, I investigate predator adaptation on food-web robustness following species extinctions. I identify a new theoretical category of species that may buffer ecosystems against environmental change. In Chapter Three, I study changes in parasitoid-host (consumer-resource) interaction frequencies between complex and simple environments. I show that the feeding preferences of parasitoid species actively change in response to habitat modification. Ecological networks are embedded in spatially-heterogeneous landscapes. In Chapter Four, I assess the role of geography on population fluctuations in an analogous social system. I demonstrate that fluctuations in the number of venture capital firms registered in cities in the United States of America are consistent with spatial and temporal contagion. Understanding how physiological signals vary through time is of interest to medical practitioners. In Chapter Five, I present a technique for quickly quantifying disorder in high frequency event series. Applying the algorithm to patient cardiac time series provides a rapid way to detect the onset of heart arrhythmia. Increasingly, answers to scientific questions lie at the intersection of traditional disciplines. This thesis applies techniques developed in physics and mathematics to problems in ecology and medicine.

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, λ_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 λ_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, λ₂, 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.

<p>Transport properties within the Boltzmann transport equation for metallic multi-layer structures as well as bulk materials, were the prime topic of this work. <i>Ab initio</i> total energy calculations for Hydrogen loaded metallic multi-layers were performed in order to shed some light onto problem of H depleted layers at the interfaces that have been experimentally observed. It was explained in connection with structural relaxation of the interface layers. </p><p>Further on conductivity behavior of Fe/V vs. Mo/V during Hydrogen load was discussed. The difference in, on first sight, rather similar multi-layer structures was explained by the magnitude of Hydrogen induced Vanadium expansion. Problem of variation of conductivity with changed c/a ratio of metals and semiconductors in general was addressed as well. The variations due to change of the Fermi surface of the corresponding materials were observed as well as some intriguing general patterns. The phenomenon could be regarded as piezoresistivity on electronic structure level. For the 3d transition metals variation of conductivity/resistivity through the period was studied.</p><p>A possible explanation for anomalous behavior of Manganese resistivity due to its much greater lattice constant in comparison to its neighbors in the period is presented. Field of disordered alloys and low dimensional magnetism was touched by discussing Mo/Ru formation energy as well as magnetic nano-wires grown on surfaces.</p><p>All total energy calculations as well as band structure calculations were performed by using Density Functional Theory based numerical computations. A short but comprehensive review of most common linear-response electron transport techniques is given.</p>

Transport properties within the Boltzmann transport equation for metallic multi-layer structures as well as bulk materials, were the prime topic of this work. Ab initio total energy calculations for Hydrogen loaded metallic multi-layers were performed in order to shed some light onto problem of H depleted layers at the interfaces that have been experimentally observed. It was explained in connection with structural relaxation of the interface layers. Further on conductivity behavior of Fe/V vs. Mo/V during Hydrogen load was discussed. The difference in, on first sight, rather similar multi-layer structures was explained by the magnitude of Hydrogen induced Vanadium expansion. Problem of variation of conductivity with changed c/a ratio of metals and semiconductors in general was addressed as well. The variations due to change of the Fermi surface of the corresponding materials were observed as well as some intriguing general patterns. The phenomenon could be regarded as piezoresistivity on electronic structure level. For the 3d transition metals variation of conductivity/resistivity through the period was studied. A possible explanation for anomalous behavior of Manganese resistivity due to its much greater lattice constant in comparison to its neighbors in the period is presented. Field of disordered alloys and low dimensional magnetism was touched by discussing Mo/Ru formation energy as well as magnetic nano-wires grown on surfaces. All total energy calculations as well as band structure calculations were performed by using Density Functional Theory based numerical computations. A short but comprehensive review of most common linear-response electron transport techniques is given.

This thesis discusses the mesoscopic physics of two examples for soft condensed matter: (i) aeolian sand transport and the ensuing structure formation and (ii) solutions of stiff biopolymers. It emphasizes the impact of a heterogeneous mesoscale structure on the macroscopic phenomenology. For the aeolian sand transport, we start with a coarse-grained description of the collisions between mobile grains and the sand bed. Combining the collision geometry with basic physical principles, like momentum and energy conservation, we derive the full splash statistics as a function of impact velocity and impactor--bed grain-size ratio. This serves as a starting point for attacking the complicated transport statistics of wind-blown sand. Two approaches are proposed: first, a two-species approximation that distinguishes between high-energy rebounding grains and low-energy bed ejecta, second, a statistical description that resolves the full distribution of grain trajectories. While the former provides an ideal framework to accurately predict macroscopic averages, the latter resolves the heterogeneous mesoscale structure of the transport layer. Both approaches are shown to be in excellent agreement with various laboratory and field data. We moreover establish a new perspective on the transport's saturation transients that illustrates the crucial influence of the intermittent turbulent wind fluctuations in the field, thereby resolving a long-standing debate. Eventually, we address the formation of megaripples, an aeolian bedform that is made from strongly polydisperse sand. Combining our proposed theory with long-term field measurements, we clarify the importance of wind-driven sand sorting and, again, intermittent turbulent fluctuations. Our approach suggests to describe the megaripples as down-scaled dunes, as indeed support by various field data for their morphology and migration. In the second part of the thesis, we consider the mesoscale structure and its influence on the viscoelastic response of entangled biopolymer solutions. Their mechanics is determined by the topological entanglements of the filamentous polymers that cannot pass through each other. The tube model for semiflexible polymers represents this effect on a mean-field level, where test filament is confined to a tube-like cage formed by surrounding polymers. We employ it to investigate the solution's mesoscale packing structure and its change under finite shear deformations. Comparing our predictions with systematic computer simulations and experiments, we find the tube deformations to relax quickly after the deformation, while tube alignment and hairpin conformations are found to be long lived. In a second step, we propose a new perspective on the entangled solution's dynamics. Accounting for the nonaffine response at the level of the test filament, and assuming sticky or frictional polymer contacts, we argue that soft bending deformations of the filaments can couple to stiff axial stretching modes. This allows us to explain various experimentally observed similarities of the entangled solutions to crosslinked networks, like the increasing elastic modulus with increasing length and bending rigidity of the filaments or the softening--stiffening transition as a function of polymer concentration, polymer length, deformation rate, and various solvent properties.:I Aeolian sand transport and megaripple formation 1 Introduction 2 The splash process 3 Aeolian sand transport 4 Structure formation 5 Outlook Bibliography II Solutions of stiff biopolymers 6 Introduction 7 Entangled solutions 8 Viscoelastic response Appendix Bibliography Acknowledgments

Recent resonant inelastic x-ray scattering (RIXS) experiments have detected a significant high-energy spin-excitation anisotropy in the nematic phase of the enigmatic iron-based superconductor FeSe, whose origin remains controversial. We apply an itinerant model previously used to describe the spin-excitation anisotropy as measured by neutron scattering measurements, with magnetic fluctuations included within the RPA approximation. The calculated RIXS cross section exhibits overall agreement with the RIXS data, including the high energy spin-excitation anisotropy

We study the low-temperature physics arising in models of a strongly correlated, tunnel-coupled double quantum dot (DQD), particularly the two-impurity Anderson model (2AIM) and the two-impurity Kondo model (2IKM), employing a combination of physical arguments and the Numerical Renormalisation Group. These models exhibit a rich range of Kondo physics. In the regime with essentially one electron on each dot, there is a competition between the Kondo effect and the interdot exchange interaction. This competition gives rise to a quantum phase transition (QPT) between local singlet and Kondo singlet phases in the 2IKM, which becomes a continuous crossover in the 2AIM as a result of the interlead charge transfer present. The 2IKM is known to exhibit two-channel Kondo (2CK) physics at the QPT, and we investigate whether this is also the case for the 2AIM at the crossover. We find that while in principle 2CK physics can be observed in the 2AIM, extremely low temperatures are required, such that it is unlikely that 2CK physics will be observed in an experimental DQD system in the near future. We have studied the effect of a magnetic field on the 2AIM and the 2IKM, finding that both the zero-field QPT in the 2IKM and the zero-field crossover in the 2AIM, persist to finite field. This presents the possibility of observing 2CK physics in an experimental DQD at finite field, but we find that the temperatures required to do so are extremely low. We show that longer even-numbered chains of spins also exhibit QPTs at finite field, and argue that a 2N-spin chain should undergo N QPTs as field is increased (starting deep in the local singlet phase at zero field). We have also carried out a joint theoretical-experimental study of a carbon nanotube based DQD, in collaboration with Dr. Mark Buitelaar et al. The agreement between experimental and theoretical results is good, and the experiments are able to access the crossover present in the 2AIM at finite field. Furthermore, the experiments show the wide range of physics exhibited by DQD systems, and illustrate the utility of such systems in probing correlated electron physics.

Molecular dynamics (MD) simulations are used to compute the equilibrium dynamics of a single component fluid with Yukawa interaction potential v(r) = (Ze)^2 exp(−r/λs )/4π eps_0 r. This system, which is known as the Yukawa one-component plasma (YOCP), represents a simplified description of a non-ideal plasma consisting of ions, charge Ze, and electrons. For finite screening lengths λs, the MD results are used to investigate the domain of validity of the hydrodynamic description, i.e., the description given by the Navier-Stokes equations. The way in which this domain depends on the thermodynamic conditions of the YOCP, as well as the strength and range of the interactions, is determined. Remarkably, it is found that the domain of validity is completely determined by the range of the interactions (i.e., λs); this alone determines the maximum wave number k_max at which the hydrodynamic description is applicable. The dynamics of the YOCP at wavevectors beyond k_max are then investigated; these are shown to be in striking agreement with a simple and well known generalisation of the Navier-Stokes equations. In the extreme case of the Coulomb interaction potential (λs = ∞), the very existence of a hydrodynamic description is a known but unsolved problem [Baus & Hansen, 1980]. For this important special case, known as the one-component plasma (OCP), it is shown that the ordinary hydrodynamic description is never valid. Since the OCP is the prototypical system representing a non-ideal plasma, a number of different approaches for modelling its dynamics have been formulated previously. By computing the relevant quantities with MD, the applicability of a number of models proposed in the literature is examined for the first time.

In this work, we wish to determine the free energy landscape and the nucleation rate associated with the process of homogeneous ice nucleation. To do this, we simulate the homogeneous nucleation of ice with the mW monatomic model of water and with all-atom models of water using primarily the umbrella sampling rare event method. We find that the use of the mW model of water, which has simpler dynamics compared to all-atom models of water, but is nevertheless surprisingly good at reproducing experimental data, results in very reasonable agreement with classical nucleation theory, in contrast to some previous simulations of homogeneous ice nucleation. We suggest that previous simulations did not observe the lowest free energy pathway in order parameter space because of their use of global order parameters, leading to a deviation from classical nucleation theory predictions. Whilst monatomic water can nucleate reasonably quickly, all-atom models of water are considerably more difficult to simulate, primarily because of their slow dynamics of ice growth and the fact that standard order parameters do not work well in driving nucleation when such models are being used. In this thesis, we describe a local, rotationally invariant order parameter that is capable of growing ice homogeneously in a biassed simulation without the unnatural effects introduced by global order parameters, and without leading to non-physical chain-like growth of 'ice' clusters that results from a naïve implementation of the standard Steinhardt-Ten Wolde order parameter. We have successfully used this order parameter to force the growth of ice clusters in simulations of all-atom models of water. However, although ice growth can be achieved, equilibrating simulations with all-atom models of water is extremely difficult. We describe several approaches to speeding up the equilibration in all-atom models of water to enable the computation of free energy profiles for homogeneous ice nucleation.

This thesis considers two areas of research in non-equilibrium soft matter at the mesoscale. In the first part we introduce active colloids in the context of active matter and focus on the particular case of phoretic colloids. The general theory of phoresis is presented along with an expression for the phoretic velocity of a colloid and its rotational diffusion in two and three dimensions. We introduce a model for thermally active colloids that absorb light and emit heat and propel through thermophoresis. Using this model we develop the equations of motion for their collective dynamics and consider excluded volume through a lattice gas formalism. Solutions to the thermoattractive collective dynamics are studied in one dimension analytically and numerically. A few numerical results are presented for the collective dynamics in two dimensions. We simulate an unconfined system of thermally active colloids under directed illumination with simple projection based geometric optics. This system self-organises into a comet-like swarm and exhibits a wide range of non- equilibrium phenomena. In the second part we review the background of polymer translocation, including key experiments, theoretical progress and simulation studies. We present, discuss and use a common model to investigate the potential of patterned nanopores for stochastic sensing and identification of polynucleotides and other heteropolymers. Three pore patterns are characterised in terms of the response of a homopolymer with varying attractive affinity. This is extended to simple periodic block co-polymer heterostructures and a model device is proposed and demonstrated with two stochastic sensing algorithms. We find that mul- tiple sequential measurements of the translocation time is sufficient for identification with high accuracy. Motivated by fluctuating biological channels and the prospect of frequency based selectivity we investigate the response of a homopolymer through a pore that has a time dependent geometry. We show that a time dependent mobility can capture many features of the frequency response.