<p> A 2014 study by the US Department of Energy conducted at Lawrence Berkeley National Laboratory estimated that U.S. data centers consumed 70 billion kWh of electricity. This represents about 1.8% of the total U.S. electricity consumption. Putting this in perspective 70 billion kWh of electricity is the equivalent of roughly 8 big nuclear reactors, or around double the nation's solar panel output. Developing new memory technologies capable of reducing this power consumption would be greatly beneficial as our demand for connectivity increases in the future. One newly emerging candidate for an information carrier in low power memory devices is the magnetic skyrmion. This magnetic texture is characterized by its specific non-trivial topology, giving it particle-like characteristics. Recent experimental work has shown that these skyrmions can be stabilized at room temperature and moved with extremely low electrical current densities. This rapidly developing field requires new measurement techniques capable of determining the topology of these textures at greater speed than previous approaches. In this dissertation, I give a brief introduction to the magnetic structures found in Fe/Gd multilayered systems. I then present newly developed techniques that streamline the analysis of Lorentz Transmission Electron Microscopy (LTEM) data. These techniques are then applied to further the understanding of the magnetic properties of these Fe/Gd based multilayered systems. </p><p> This dissertation includes previously published and unpublished co-authored material.</p><p>

<p> <i>Ruthenium chloride</i> (RuCl₃) is a 4d halide and relativistic Mott insulator where <i>Ruthenium</i> atoms form a honeycomb lattice. Electronic interactions and spin-orbit coupling work together to give RuCl₃ its insulating behavior. This brings forth exciting physics predicted in the frame of the Kitaev model including exotic ground states like zigzag ordering and quantum spin liquids. We prepared samples for experiments that aim to test for these exotic states. Nanofabrication techniques such as mechanical exfoliation, electron beam lithography, and thin film deposition, were used to obtain crystals of about 20 <i>nm </i> in thickness to make devices for testing. Preliminary electronic transport measurements were performed. In the low bias regime, all samples presented a thermal activation energy of ~80 <i>meV</i>. In the high bias regime, electronic transport was ruled by Frenkel-Poole emission. When large vertical electric fields were applied via a back-gate voltage, a higher bias voltage was needed to thermally activate charge carriers. The presence of a vertical electric field seemed to impede Frenkel-Poole emission. Larger fields will be needed to reach either the valence band or the conduction band of RuCl₃ which has an energy band gap of at least 1.7 <i> eV</i>, probed by angle resolved photoemission spectroscopy (ARPES). More powerful gating techniques should be tested such as electrostatic ionic liquid gating, which will allow probing magnetic ordered ground states, predicted in the frame of the Kitaev model. </p><p>

<p> While the electrical transport characteristics of organic electronic devices are generally inferior to their inorganic counterparts, organic materials offer many advantages over inorganics. The materials used in organic devices can often be deposited using cheap and simple processing techniques such as spincoating, inkjet printing, or roll-to-roll processing; allow for large-scale, flexible devices; and can have the added benefits of being transparent or biodegradable.</p><p> In this manuscript, we examine the role of solvents in the performance of pentacene-based devices using the ferroelectric copolymer polyvinylidene fluoride-trifluoroethylene (PVDF-TrFe) as a gate insulating layer. High dipole moment solvents, such as dimethyl sulfoxide, used to dissolve the copolymer for spincoating increase the charge carrier mobility in field-effect transistors (FETs) by nearly an order of magnitude as compared to lower dipole moment solvents. The polarization in Al/PVDF-TrFe/Au metal-ferroelectric-metal devices also shows an increase in remnant polarization of ~20% in the sample using dimethyl sulfoxide as the solvent for the ferroelectric. Interestingly, at low applied electric fields of ~100 MV/m a remnant polarization is seen in the high dipole moment device that is nearly 3.5 times larger than the value observed in the lower dipole moment samples, suggesting that the degree of dipolar order is higher at low operating voltages for the high dipole moment device.</p><p> We will also discuss the use of peptide-based nanostructures derived from natural amino acids as building blocks for biocompatible devices. These peptides can be used in a bottom-up process without the need for expensive lithography. Thin films of L,L-diphenylalanine micro/nanostructures (FF-MNSs) were used as the dielectric layer in pentacene-based FETs and metal-insulator-semiconductor diodes both in bottom-gate and top-gate structures. It is demonstrated that the FFMNSs can be functionalized for detection of enzyme-analyte interactions. This work opens up a novel and facile route towards scalable organic electronics using peptide nanostructures as scaffolding and as a platform for biosensing. </p><p>

<p> Active nematics are a class of nonequilibrium systems which have received much attention in the form of continuum models in recent years. For the dense, highly ordered case which is of particular interest, these models focus almost exclusively on suspensions of active particles in which the flow of the medium plays a key role in the dynamical equations. Many active nematics, however, reside at an interface or on a surface where friction excludes the effects of long-range flow. In the following pages we shall construct a general model which describes these systems with overdamped dynamical equations. Through numerical and analytical investigation we detail how many of the striking nonequilibrium behaviors of active nematics arise in such systems. </p><p> We shall first discuss how the activity in these systems gives rise to an instability in the nematic ordered state. This instability leads to phase-separation in which bands of ordered active nematic are interspersed with bands of the disordered phase. We expose the factors which control the density contrast and the stability of these bands through numerical investigation. </p><p> We then turn to the highly ordered phase of active nematic materials, in which striking nonequilibrium behaviors such as the spontaneous formation, self-propulsion, and ordering of charge-half defects occurs. We extend the overdamped model of an active nematic to describe these behaviors by including the advection of the director by the active forces in the dynamical equations. We find a new instability in the ordered state which gives rise to defect formation, as well as an analog of the instability which is seen in models of active nematic suspensions. Through numerical investigations we expose a rich phenomenology in the neighborhood of this new instability. The phenomenology includes a state in which the orientations of motile, transient defects form long-range order. This is the first continuum model to contain such a state, and we compare the behavior seen here with similar states seen in the experiments and simulations of Stephen DeCamp and Gabriel Redner et. al. [1] </p><p> Finally, we propose the measurement of defect shape as a mechanism for the comparison between continuum theories of active nematics and the experimental and simulated realiza- tions of these systems. We present a method for making these measurements which allows for averaging and statistical analysis, and use this method to determine how the shapes of defects depend on the parameters of our continuum theory. We then compare these with the shapes of defects which we measure in the experiments and simulations mentioned above in order to place these systems in the parameter space of our model. It is our hope that this mechanism for comparison between models and realizations of active nematics will provide a key to pairing the two more closely.</p><p>

<p> A two-dimensional electron system exposed to a strong perpendicular magnetic field at low temperatures (usually below one Kelvin) forms a new state of matter that exhibits the fractional quantum Hall effect. This phenomenon has been observed in graphene, a naturally occurring two-dimensional electron system. The theoretical understanding of the FQHE in graphene is complicated by the fact the electrons have valley and spin degrees of freedom. As a result, the different single-particle energy levels (Landau levels) of the electrons can mix with each other. This Landau level mixing is intrinsic to graphene and must be considered in any realistic theoretical treatment. Recently, an effective model Hamiltonian which includes Landau level mixing has been formulated in terms of Haldane pseudopotentials: this model includes emergent three-body interactions in addition to renormalizing the two-body interactions. We construct an effective real-space two-body interaction potential using a closed form expression found in the literature that can model various realistic effects including Landau level mixing. Our method will allow us to fully tackle the physics of the fractional quantum Hall effect in graphene and provide a method for extending our studies to realistic models of semiconductor heterostructure systems as well.</p><p>

In this thesis, we studied the self-assembly of nanoparticles at liquid metal-water interfaces and oil-water interfaces. We demonstrated a simple approach to form nanostructured electronic devices by self-assembly of nanoparticles at liquid metal surfaces. In this approach, two liquid-metal droplets, which were coated with a monolayer of ligand-stabilized nanoparticles, were brought into contact. They did not coalesce but instead remained separated by the nanoparticles assembled at the interface. Devices formed by this method showed electron transport between droplets that was characteristic of the Coulomb blockade, where current was suppressed below a tunable threshold voltage because of the energy of charging individual nanoparticles. Further studies of this approach demonstrated the potential of interfacial assembly in fabricating microscopic electronic devices over a large area in a cost-effective and time-efficient fashion. Micrometer-scale Ga droplets coated with nanoparticles were fabricated using ultrasonication and then deposited on patterned substrates to form microscopic devices. I-V measurements showed Coulomb blockade effect in the devices containing more than one nanoparticle junction. The measured threshold voltages increased with number of junctions as expected for devices arranged in series. We also studied experimentally the energy of adsorption, Δ E, of nanoparticles and microparticles at the oil-water and Ga-water interfaces by monitoring the decrease of interfacial tension as the particles bind. For citrate-stabilized gold nanoparticles assembling on a droplet of octafluoropentyl acrylate, we found ΔE=−5.1 kBT for particle radius R=2.5 nm, and Δ E ∝ R2 for larger sizes. Gold nanoparticles with (1-mercaptoundec-11-yl) tetra(ethylene glycol) ligand had a much larger binding energy (ΔE=−60.4 kBT) and an energy barrier against adsorption. For polystyrene spheres with R=1.05 µm, we found ΔE=−0.9×10 6 kBT. We also found that the binding energy depended on the composition of the oil phase and could be tuned by the salt concentration of the nanoparticle suspension. At Ga-water interfaces, we found that ΔE of Au-cit and Au-TEG nanoparticles were much larger. We have also studied desorption of polystyrene microparticles from oil-water interfaces by changing experimental conditions, including addition of nanoparticles, cross-linking ligand molecules or in response to chemical interactions between the particles and the oil. We found that microparticles can desorb even though the adsorption energy is large. We also found that the desorbed particle formed a surprising 'tail'-like structure.

Surface Plasmon Polaritons (SPPs) are considered to be attractive components for plasmonics and nanophotonic devices due to their sensitivity to interface changes, and their ability to guide and confine light beyond the diffraction limit. They have been utilized in SPP resonance sensors and near field imaging techniques and, more recently, SPP experiments to monitor and control ultrafast charge carrier and energy relaxation dynamics in thin films. In this thesis, we discuss excitation and propagation properties of ultrafast SPPs on thin extended metal films and SPP waveguide structures. In addition, localized and propagating surface plasmon interactions in functional plasmonic nanostructures will also be addressed. For the excitation studies of ultrafast SPPs, we have done detailed analysis of femtosecond surface plasmon pulse generation under resonant excitation condition using prism coupling technique. Our results show that photon-SPP coupling is a resonant process with a finite spectral bandwidth that causes spectral phase shift and narrowing of the SPP pulse spectrum. Both effects result in temporal pulse broadening and, therefore, set a lower limit on the duration of ultrafast SPP pulses. These findings are necessary for the successful integration of plasmonic components into high-speed SPP circuits and time-resolved SPP sensors. To demonstrate interactions between localized and propagating surface plasmons, we used block-copolymer based self assembly techniques to deposit long range ordered gold nanoparticle arrays onto silver thin films to fabricate composite nanoparticle thin film structures. We demonstrate that these gold nanoparticle arrays interact with SPPs that propagate at the film/nanoparticle interface and therefore, modify the dispersion relation of SPPs and lead to strong field localizations. These results are important and advantageous for plasmonic device applications. For the propagation studies of ultrafast SPPs, we have designed and constructed a home-built femtosecond photon scanning tunneling microscope (fsPSTM) to visualize ultrafast SPPs in photonic devices based on metal nanostructures. Temporal and phase information have been obtained by incorporating the fsPSTM into one arm of a Mach-Zehnder interferometer, allowing heterodyne detection. Understanding plasmon propagation in metal nanostructures is a requirement for implementing such structures into optoelectronic and telecommunication technologies.

Biophysics is the study of the complex physical processes occurring in biological systems that are responsible for life. This dissertation addresses three important topics in biophysics: ionic transport, biomineralization, and force spectroscopy. Ionic transport involves the passage of ions through a special class of hollow, transmembrane proteins called ion channels which regulate the movement of charged species across nearly all biological membranes with varying degrees of specificity. Despite the fundamental importance of these channels to many physiological processes little is known about how channel structure and composition couple to determine its function. Deriving inspiration from these systems, a simple computational platform is developed to study the salient features of these channels in order to better understand the fundamental physics of these systems. The results of this work indicate that a converging-diverging region formed within the pore to create a single constriction is the most effective method to regulate the passage of ions through the pore. By controlling the geometry of the constriction the local potential and chemical gradients can be manipulated to tailor the channel for specific applications. The process of selective extraction and incorporation of local elements from the surrounding environment into functional structures under strict biological control is known as biomineralization. As an initial step to gain a more fundamental understanding of directed crystallization of zinc oxide molecular dynamics simulations were performed to study the conformational behavior of two experimentally derived biomimetic peptides in a precursor solution. Substantial differences in the conformational properties and affinity for zinc and hydroxide ions in solution were observed. These findings are in qualitative agreement with experimental observations. The mechanical response of biopolymers such as RNA and DNA to externally applied forces is a topic that has received wide interest both experimentally and theoretically. In the first of two separate force spectroscopy studies, the mechanical response of linear uncharged polymer chains of variable molecular weight subjected to repeated pulling-retraction cycles in poor solvent was investigated. It was found that the observed hysteresis in this system is highly dependent on the speed at which the chain is perturbed. In the second study, the force-induced globule-coil transition of a linear polyelectrolyte chain in poor solvent was examined. It was observed that the magnitude of the change in the degree of ionization of the chain at the transition is a strong function of counterion size and Coulombic strength.

We investigated four different problems using coarse grained computational models : self-assembly of single stranded (ss) DNA virus, ejection dynamics of double stranded(ds) DNA from phages, translocation of ssDNA through MspA protein pore, and segmental dynamics of a polymer translocating through a synthetic nanopore. In the first part of the project, we investigated the self-assembly of a virus with and without its genome. A coarse-grained model was proposed for the viral subunit proteins and its genome (ssDNA). Langevin dynamics simulation, and replica exchange method were used to determine the kinetics and energetics of the self-assembly process, respectively. The self-assembly follows a nucleation-growth kind of mechanism. The ssDNA plays a crucial role in the self-assembly by acting as a template and enhancing the local concentration of the subunits. The presence of the genome does not changes the mechanism of the self-assembly but it reduces the nucleation time and enhances the growth rate by almost an order of magnitude. The second part of the project involves the investigation of the dynamics of the ejection of dsDNA from phages. A coarse-grained model was used for the phage and dsDNA. Langevin dynamics simulation was used to investigate the kinetics of the ejection. The ejection is a stochastic process and a slow intermediate rate kinetics was observed for most ejection trajectories. We discovered that the jamming of the DNA at the pore mouth at high packing fraction and for a disordered system is the reason for the intermediate slow kinetics. The third part of the project involves translocation of ssDNA through MspA protein pore. MspA protein pore has the potential for genome sequencing because of its ability to clearly distinguish the four different nucleotides based on their blockade current, but it is a challenge to use this pore for any practical application because of the very fast traslocation time. We resolved the state of DNA translocation reported in the recent experimental work . We also investigated two methods for slowing down the translocation process: pore mutation and use of alternating voltage. Langevin dynamics simulation and Poisson Nernst Planck solver were used for the investigation. We demonstrated that mutation of the protein pore or applying alternating voltage is not a perfect solution for increasing translocation time deterministically. Both strategies resulted in enhanced average translocation time as well as the width of the translocation time distribution. The increase in the width of the translocation time distribution is undesired. In the last part of the project, we investigated the applicability of the polyelectrolyte theory in the computer simulation of polyelectrolyte translocation through nanopores. We determined that the Debye Hückel approximation is acceptable for most translocation simulations as long as the coarse grained polymer bead size is comparable or larger than the Debye length. We also determined that the equilibrium translocation theory is applicable to the polyelectrolyte translocation through a nanopore under biasing condition. The unbiased translocation behavior of a polyelectrolyte chain is qualitatively different from the Rouse model predictions, except for the case where the polyelectrolyte is very small compared to the nanopore.

Spin glasses have been the subject of intense study and considerable controversy for decades, and the low-temperature phase of short-range spin glasses is still poorly understood. Our main goal is to improve our understanding in this area and find an answer to the following question: Are there only a single pair or a countable infinity of pure states in the low temperature phase of the EA spin glass? To that aim we first start by introducing spin glasses and provide a brief history of their research, then proceed to describe our method of simulation, the parallel tempering Monte Carlo algorithm. Next, we present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. In order to understand how the parallel tempering algorithm works, we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the parallel tempering Monte Carlo method. We examine the correlation between static and dynamic observables for ∼ 5000 disorder realizations and up to 1000 spins down to temperatures at 20% of the critical temperature, and our results show that autocorrelation times are directly correlated with the roughness of the free-energy landscape. In the following chapters, the three- and four-dimensional Edwards-Anderson and mean-field Sherrington-Kirkpatrick Ising spin glasses are studied again via large scale Monte Carlo simulations at low temperatures, deep within the spin glass phase. Performing a careful statistical analysis of several thousand independent disorder realizations and using an observable that detects peaks in the overlap distribution, we show that the Sherrington-Kirkpatrick and Edwards-Anderson models have a distinctly different low-temperature behavior. We arrive to the following conclusion: The structure of the spin-glass overlap distribution for the Edwards-Anderson model suggests that its low-temperature phase has only a single pair of pure states. Finally we present results for several new observables, along with a few preliminary studies and suggestions for future research.