Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this diversity, there are numerous models of $1/f$ noise. In this dissertation, I summarize my research into models based on linking the characteristic times of fluctuations of a quantity to its multiplicity of states. With this condition satisfied, I show that a quantity will undergo $1/f$ fluctuations and exhibit associated properties, such as slow dynamics, divergence of time scales, and ergodicity breaking. I propose that multiplicity-dependent characteristic times come about when a system shares a constant, maximized amount of entropy with a finite bath. This may be the case when systems are imperfectly coupled to their thermal environment and the exchange of conserved quantities is mediated through their local environment. To demonstrate the effects of multiplicity-dependent characteristic times, I present numerical simulations of two models. The first consists of non-interacting spins in $0$-field coupled to an explicit finite bath. This model has the advantage of being degenerate, so that its multiplicity alone determines the dynamics. Fluctuations of the alignment of this model will be compared to voltage fluctuations across a mesoscopic metal-insulator-metal junction. The second model consists of classical, interacting Heisenberg spins with a dynamic constraint that slows fluctuations according to the multiplicity of the system's alignment. Fluctuations in one component of the alignment will be compared to the flux noise in superconducting quantum interference devices (SQUIDs). Finally, I will compare both of these models to each other and some of the most popular models of $1/f$ noise, including those based on a superposition of exponential relaxation processes and those based on power law renewal processes.

The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life.

Doping and alloying agents are commonly used to engineer the properties of magnetic materials. This study investigates the effects of doping manganese in thin films of Ni80Fe20 (permalloy) and Ni65Fe15Co20 magnetic systems for low power memory technologies, including those that operate at low temperature.

Elemental manganese is anti-ferromagnetic with a Neel temperature of 100 K. When used as a dopant in a magnetic material, it is found to often align its moment in an antiferromagnetic direction. Thus, the addition of manganese might be expected to reduce the overall saturation magnetization (MS) of the magnetic system. In this study, we show that the use of manganese dopants in Ni80Fe20 (permalloy) and Ni65Fe15Co20 thin films can reduce their saturation magnetization and still retain excellent switching properties.

Magnetic properties and transport properties were determined using Vibrating Sample Magnetometer. A 19% decrease in the MS of (Ni80Fe20)1-xMnx thin films and a 36% decrease for (Ni65Fe15Co20)1-xMnx thin films for dopant levels of x = 30%. The impact of depositing a ruthenium (Ru) under-layer for (Ni65Fe15Co20)1-xMnx system was also studied.

The structural (lattice parameters and phases), surface (roughness and topography) and electrical properties (resistivity and mean free path) of the Mn-doped Ni65Fe15Co20 films were determined with X-Ray Diffraction, Atomic Force Microscopy and Four-Point probe technique respectively.

The properties were analyzed and Ni65Fe15Co20 system with Ru- under-layer with 20 at. % Mn content was found to exhibit the following low-field switching properties at 10 K; MS~700 emu.cm-3, easy axis coercivity ~10 Oe and hard axis coercivity ~5 Oe, easy axis squareness ~0.9 and anisotropy field ~12 Oe, that are deemed useful for low-power memory applications that could be used at cryogenic temperatures.

To determine the transport properties thought these magnetic layers for use in superconductor/ferromagnetic memory structures, a study of the oxidation conditions of Al films was performed in order to produce a reliable aluminum oxide tunnel barrier on top of these films. The production of N-I-F-S (Normal metal-Insulator-Ferromagnet-Superconductor) tunnel junctions will allow for the investigation of the tunneling density of states as a function of ferromagnetic layer thickness, allowing for the determination of important transport parameters relevant to magnetic barrier Josephson junction devices.

What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory ought to be broad enough as to not be constrained to an Earth-based biochemistry. In this dissertation, the philosophy of studying living systems from the perspective of traditional physics is first explored as a motivating discussion for subsequent research. Traditionally, we have often thought of the physical world from a bottom-up approach: things happening on a smaller scale aggregate into things happening on a larger scale. In addition, the laws of physics are generally considered static over time. Research suggests that biological evolution may follow dynamic laws that (at least in part) change as a function of the state of the system. Of the three featured research projects, cellular automata (CA) are used as a model to study certain aspects of living systems in two of them. These aspects include self-reference, open-ended evolution, local physical universality, subjectivity, and information processing. Open-ended evolution and local physical universality are attributed to the vast amount of innovation observed throughout biological evolution. Biological systems may distinguish themselves in terms of information processing and storage, not outside the theory of computation. The final research project concretely explores real-world phenomenon by means of mapping dominance hierarchies in the evolution of video game strategies. Though the main question of how life differs from non-life remains unanswered, the mechanisms behind open-ended evolution and physical universality are revealed.

This dissertation research has involved microscopic characterization of magnetic nanostructures using off-axis electron holography and Lorentz microscopy. The nanostructures investigated have included Co nanoparticles (NPs), Au/Fe/GaAs shell/core nanowires (NWs), carbon spirals with magnetic cores, magnetic nanopillars, Ni-Zn-Co spinel ferrite and CoFe/Pd multilayers. The studies have confirmed the capability of holography to describe the behavior of magnetic structures at the nanoscale.

The phase changes caused by the fringing fields of chains consisting of Co NPs were measured and calculated. The difference between chains with different numbers of Co NPs followed the trend indicated by calculations. Holography studies of Au/Fe/GaAs NWs grown on (110) GaAs substrates with rotationally non-uniform coating confirmed that Fe was present in the shell and that the shell behaved as a bar magnet. No fringing field was observed from NWs with cylindrical coating grown on (111)B GaAs substrates. The most likely explanation is that magnetic fields are confined within the shells and form closed loops. The multiple-magnetic-domain structure of iron carbide cores in carbon spirals was imaged using phase maps of the fringing fields. The strength and range of this fringing field was insufficient for manipulating the carbon spirals with an external applied magnetic field. No magnetism was revealed for CoPd/Fe/CoPd magnetic nanopillars. Degaussing and MFM scans ruled out the possibility that saturated magnetization and sample preparation had degraded the anisotropy, and the magnetism, respectively. The results suggested that these nanopillars were not suitable as candidates for prototypical bit information storage devices.

Observations of Ni-Zn-Co spinel ferrite thin films in plan-view geometry indicated a multigrain magnetic domain structure and the magnetic fields were oriented in-plane only with no preferred magnetization distribution. This domain structure helps explain this ferrite's high permeability at high resonance frequency, which is an unusual character.

Perpendicular magnetic anisotropy (PMA) of CoFe/Pd multilayers was revealed using holography. Detailed microscopic characterization showed structural factors such as layer waviness and interdiffusion that could contribute to degradation of the PMA. However, these factors are overwhelmed by the dominant effect of the CoFe layer thickness, and can be ignored when considering magnetic domain structure.

In this work, a new method, "Nanobonding" [1,2] is conceived and researched to bond Si-based surfaces, via nucleation and growth of a 2 D silicon oxide SiOxHx interphase connecting the surfaces at the nanoscale across macroscopic domains. Nanobonding cross-bridges two smooth surfaces put into mechanical contact in an O2/H2O mixed ambient below T <200 °C via arrays of SiOxHx molecules connecting into a continuous macroscopic bonding interphase. Nano-scale surface planarization via wet chemical processing and new spin technology are compared via Tapping Mode Atomic Force Microscopy (TMAFM) , before and after nano-bonding. Nanobonding uses precursor phases, 2D nano-films of beta-cristobalite (beta-c) SiO2, nucleated on Si(100) via the Herbots-Atluri (H-A) method [1]. beta-c SiO2 on Si(100) is ordered and flat with atomic terraces over 20 nm wide, well above 2 nm found in native oxides. When contacted with SiO2 this ultra-smooth nanophase can nucleate and grow domains with cross-bridging molecular strands of hydroxylated SiOx, instead of point contacts. The high density of molecular bonds across extended terraces forms a strong bond between Si-based substrates, nano- bonding [2] the Si and silica. A new model of beta-cristobalite SiO2 with its <110> axis aligned along Si[100] direction is simulated via ab-initio methods in a nano-bonded stack with beta-c SiO2 in contact with amorphous SiO2 (a-SiO2), modelling cross-bridging molecular bonds between beta-c SiO2 on Si(100) and a-SiO2 as during nanobonding. Computed total energies are compared with those found for Si(100) and a-SiO2 and show that the presence of two lattice cells of !-c SiO2 on Si(100) and a-SiO2 lowers energy when compared to Si(100)/ a-SiO2 Shadow cone calculations on three models of beta-c SiO2 on Si(100) are compared with Ion Beam Analysis of H-A processed Si(100). Total surface energy measurements via 3 liquid contact angle analysis of Si(100) after H-A method processing are also compared. By combining nanobonding experiments, TMAFM results, surface energy data, and ab-initio calculations, an atomistic model is derived and nanobonding is optimized. [1] US Patent 6,613,677 (9/2/03), 7,851,365 (12/14/10), [2] Patent Filed: 4/30/09, 10/1/2011

III-nitride alloys are wide band gap semiconductors with a broad range of applications in optoelectronic devices such as light emitting diodes and laser diodes. Indium gallium nitride light emitting diodes have been successfully produced over the past decade. But the progress of green emission light emitting devices has been limited by the incorporation of indium in the alloy, mainly due to phase separation. This difficulty could be addressed by studying the growth and thermodynamics of these alloys. Knowledge of thermodynamic phase stabilities and of pressure - temperature - composition phase diagrams is important for an understanding of the boundary conditions of a variety of growth techniques. In this dissertation a study of the phase separation of indium gallium nitride is conducted using a regular solution model of the ternary alloy system. Graphs of Gibbs free energy of mixing were produced for a range of temperatures. Binodal and spinodal decomposition curves show the stable and unstable regions of the alloy in equilibrium. The growth of gallium nitride and indium gallium nitride was attempted by the reaction of molten gallium - indium alloy with ammonia at atmospheric pressure. Characterization by X-ray diffraction, photoluminescence, and secondary electron microscopy show that the samples produced by this method contain only gallium nitride in the hexagonal phase. The instability of indium nitride at the temperatures required for activation of ammonia accounts for these results. The photoluminescence spectra show a correlation between the intensity of a broad green emission, related to native defects, and indium composition used in the molten alloy. A different growth method was used to grow two columnar-structured gallium nitride films using ammonium chloride and gallium as reactants and nitrogen and ammonia as carrier gasses. Investigation by X-ray diffraction and spatially-resolved cathodoluminescence shows the film grown at higher temperature to be primarily hexagonal with small quantities of cubic crystallites, while the one grown at lower temperature to be pure hexagonal. This was also confirmed by low temperature photoluminescence measurements. The results presented here show that cubic and hexagonal crystallites can coexist, with the cubic phase having a much sharper and stronger luminescence. Controlled growth of the cubic phase GaN crystallites can be of use for high efficiency light detecting and emitting devices. The ammonolysis of a precursor was used to grow InGaN powders with different indium composition. High purity hexagonal GaN and InN were obtained. XRD spectra showed complete phase separation for samples with x < 30%, with ~ 9% indium incorporation in the 30% sample. The presence of InGaN in this sample was confirmed by PL measurements, where luminescence from both GaN and InGaN band edge are observed. The growth of higher indium compositions samples proved to be difficult, with only the presence of InN in the sample. Nonetheless, by controlling parameters like temperature and time may lead to successful growth of this III-nitride alloy by this method.