The heavy fermion superconductor CeCoIn5 demonstrates remarkable similarities to the high-Tc cuprates in many of its properties including proximity to antiferromagnetism, quasi-two-dimensionality, d-wave superconductivity, and departures from Fermi liquid behaviour in the normal state. It is also a “high-Tc” superconductor in the context of the heavy fermions. The experimental technique of microwave cavity perturbation has been used to measure the electrodynamics of a single crystal of CeCoIn5 over a range of temperatures, from 80 mK to 35 K, in a dilution refrigerator. Measurements at multiple frequencies required the development of an in-situ technique for the bolometric detection of the surface resistance. This has allowed conductivity spectra to be acquired, resulting in several important results. First, the resolution of an unexplained fractional power law in the penetration depth has been achieved by properly isolating the nodal quasiparticle contribution, revealing a previously unseen linear temperature dependence in CeCoIn5, as expected for a d-wave superconductor. Second, the temperature evolution of the microwave conductivity spectra implies that the effective mass of the quasiparticles continues to change below Tc, hinting that quantum criticality remains important even in the superconducting state. Third, conductivity spectra that are strikingly similar to those from YBa2Cu3O6+y suggest a strong connection in the underlying charge dynamics, as both CeCoIn5 and YBa2Cu3O6+y show a collapse in the quasiparticle scattering rate below Tc. Finally, the spectra indicate the presence of multiband effects.
Collagen is a key component of the extracellular matrix and is the most abundant protein in vertebrates. Collagen is found in almost every connective tissue of the body including skin, bone, tendon, cartilage, arteries and cornea, where it plays a crucial role in providing structural support. Collagen molecules self-assemble to form hierarchical structures, from single molecules to fibrils to fibers and tissues. Structural and mechanical changes at the molecular level may affect self-assembly of the molecules and the resulting tissue. Despite its significance, the mechanics of collagen and its flexibility at the molecular level remain contentious, and collagen has been variously described as a flexible polymer to a semi-rigid rod. In this thesis, I present my work developing and utilizing experimental and analytical tools to study the mechanical proprieties of molecular collagen. I carefully designed and controlled a wide variety of experimental conditions, such as different collagen types and sources, solution pH and salt concentrations, and analysed the results in search of potential reasons for inconsistency in reported results of collagen flexibility at the basic molecular level. Atomic force microscopy (AFM) imaging is used to study effect of environmental factors such as ionic strength and pH on molecular conformations and flexibility of single collagen molecules. In addition, molecular conformations of different types of collagen from different sources are compared using AFM imaging. I measure persistence length of collagen molecules, a measure of flexibility, arising due to the conformational sampling of collagen. My results link the bending energy of collagen molecules to how tightly the helix is wound. In order to analyse AFM images of collagen, I developed an image and statistical analysis algorithm, SmarTrace, optimized for my images of collagen. The program was validated using images of DNA with known persistence length, then applied to collagen molecules. Analysis of different types of collagen in two different solutions and type I collagen in solutions of different ionic strength and pH show that collagen's flexibility depends strongly on ionic strength and pH. In addition, it shows that different types of collagen show similar average conformational characteristics in a given solution environment. In addition, mechanical properties and force-response of single collagen and procollagen molecules are studied using optical tweezers. I discuss the challenges of stretching single collagen proteins, whose length is much less than the size of the microspheres used as manipulation handles, and show how instrumental design and biochemistry can be used to overcome these challenges. The result of this work is an improved understanding of the sensitivity of molecular flexibility, stability and response of collagen to environmental factors. This can shed light on identifying underlying mechanisms of collagen-related diseases as well as designing and producing improved engineered biomaterials with tunable properties.
Scanning Hall probe microscopy is a quantitative magnetic imaging technique with high magnetic flux sensitivity and high spatial resolution. Hall sensors have untapped potential to match the sensitivity of superconducting quantum interference devices (SQUIDs), which are well-known in magnetic microscopy for their flux sensitivity. Furthermore, Hall probes can do so with better spatial resolution. My thesis supports this conclusion with a theoretical calculation while comparing the Hall probe technique to other kinds of magnetic imaging. I have explored further improvements in the overall design and materials of Hall probes. I have obtained and analyzed magnetotransport data for various concentrations of lead in bismuth films and Hall probes. Bismuth, a compensated metal, is a good alternative to semiconductor Hall probes. The presence of electron and hole carriers, though, reduces the Hall effect, and bismuth would be even better for Hall sensors if one kind of carrier were compensated. A doping between 0 and 0.1% lead in bismuth appears to be best for lead-doped bismuth Hall probe operation. I have also made significant progress in the design and fabrication of a more durable Hall probe shape, inspired by hard drive read heads. The novel design should enable operation closer to the sample surface, improving spatial resolution and making it easier to detect flux.
Prompted by current experiments on mechanically driven F1 ATP synthase, we investigate optimal (minimum-dissipation) driving protocols of rotary mechanochemical motors. We propose a simple model system coupling chemical reactions to mechanical motion under periodic boundary conditions, driven by a periodic time-dependent force. Under linear response approximations near equilibrium and near nonequilibrium steady states, optimal driving protocols are determined by a generalized friction coefficient. Such a model has a periodic generalized friction coefficient that peaks near system energy barriers, implying optimal protocols that proceed rapidly when the system is overwhelmingly in a single macrostate, but slow significantly near energy barriers, harnessing thermal fluctuations to kick the system over the energy barriers for free.
Semiconductor nanowires are promising candidates for the emerging nano-scale optoelectronics. They provide opportunities for novel axial and lateral designs with the possibility of improvement in the device performance and reduction in the size. An essential requirement for this research and development is the fundamental understanding of the electronic, electrical and optical properties of semiconductor nanowires. This thesis aims to address several critical factors that limit commercial integration of GaAs nanowire devices. The latter includes investigation of novel nanowire growth methods and understanding the charge transport properties in axial and radial structures. I grew gold-catalyzed GaAs nanowires via the vapour-liquid-solid mechanism using the metalorganic chemical vapor deposition technique. A thin GaP shell was used to passivate the sidewall surface states in GaAs nanowires. Electrical and optical measurements were carried out on the core/shell GaAs/GaP nanowires to demonstrate unpinning of the Fermi level by improvement in the nanowire resistivity and photoluminescence, respectively. Control of the surface recombination velocity in GaAs nanowires was also achieved using a thin lattice-matched InGaP passivating shell. This was determined through an enhancement of the minority carrier diffusion lengths in GaAs/InGaP nanowires measured using electron beam induced current technique. In addition, axial GaAs nanowire p-n junctions were fabricated to demonstrate a free-standing single nanowire photodetector. The degree of the p-n junction abruptness and the impact of the Au reservoir effect was studied by a numerical modeling of the corresponding electrostatic potential. This model was further verified using electron holography measurements. Radial GaAs nanowire p-n junctions combined with a novel growth technique lead to development of GaAs homostructure radial tunnel diodes. A lithography-free growth method took advantage of an array of Ga2O3 coated GaAs pedestals to electrically isolate nanowire devices from the substrate. Nano-probe measurements of radial GaAs nanowire p-n junctions indicated clear tunneling current-voltage properties.
Jets, collimated sprays of particles, are the most commonly produced objects in high energy subatomic collisions. Jets are the final state of colliding quarks and gluons. The fraction of a jet's energy that is measured by a calorimeter is called the response. Quark jets (jets initiated by quarks) and gluon jets (jets initiated by gluons) have a different response in the calorimeter. In this thesis the response of quark and gluon jets is reconstructed using jets in dijet and photon + jet events. To measure jet response in dijet events a method is developed to correct the energy of one jet in a dijet event so that it may be used as a reference object in the calibration procedure. The reconstructed dijet, quark and gluon responses are shown to agree with Monte Carlo simulation predictions within their uncertainties.
Information is often considered as an abstract entity, but it is always stored and processed by a physical medium. As such, it obeys all the restrictions and possibilities related to the laws of physics. In 1961, Rolf Landauer proposed the existence of a fundamental energetic cost associated with information processing: each time information is processed in a logically irreversible way, at least kTln2 of heat is released, on average, into the surrounding bath. This principle also resolves the long-standing threat to the second law of thermodynamics posed by Maxwell's demon. Although the Landauer principle has been widely accepted, it remained untested and controversial for more than half a century. The small amount of heat released as a result of logically irreversible operations was hard to detect in any conventional information-processing device. With recent technical and theoretical advances in micromanipulations, this became possible. In my graduate study, I used and calibrated a feedback trap to execute logical operations and measure the tiny energetic cost associated with them. I start this thesis with a brief review of stochastic thermodynamics and information theory, followed by my experimental approach. I present two feedback traps: one that I inherited and the other that I developed later in my studies. Both traps use the same real-time calibration method based on a recursive maximum likelihood algorithm. The calibrated trap was initially used to test the Landauer principle and show that erasing a symmetric one-bit memory requires kTln2 work on average, while no work is required for similar protocols with no net erasure. This experiment confirmed Landauer's hypothesis that information is physical. In my later work, I explored information in more complex environments. I experimentally studied erasure for a memory encoded in an asymmetric double-well potential. I found that the average work to erase can be below kTln2, as predicted by a recent theory. Surprisingly, erasure protocols that differ subtly give measurably different values for the asymptotic work, a result I explain by showing that one protocol is symmetric with respect to time reversal, while the other is not. The differences between the protocols help clarify the distinctions between thermodynamic and logical reversibility. I further explored the same phenomena divorced from Landauer's principle, where a system starts and ends in the same equilibrium state, and I show that arbitrarily slow transformations, produced by smooth deformations of a double-well potential, need not be reversible. Finally, I present my work towards a direct test of the form of the Shannon entropy function.
Compared to systems with only a steric interaction, a colloidal system with an attractive interaction, caused by addition of a polymer, exhibits a richer set of phases. Richer because more phases are possible; for example, one can actually see the coexistence of liquid, gas and crystal phases in equilibrium. In this thesis, we studied the crystallization of colloid particles in a colloid-polymer system. To understand how crystals nucleate within different phases, the samples investigated were in the three-phase region of the colloid-polymer phase diagram. Experiments were carried out in a microgravity environment on board the International Space Station (ISS). The samples were photographed as they crystallized and captured images were sent to Earth. Python scripts were developed to analyze data from the images. One key observation similar to that observed in a hard-sphere system was the formation of dendrites in one of the samples suggesting diffusion-limited growth.
Silicon-based qubits are one of the most promising technologies for the construction of a quantum computer. The nuclear spins of phosphorus donors in enriched silicon have among the longest coherence times of any solid-state system. In this thesis, I examine the phosphorus in silicon system in the regime of "zero" magnetic field. Laser spectroscopy and magnetic resonance are used to characterize the phosphorus in silicon system in this environment. I show the system can be hyperpolarized and has ~10 s coherence times. Additionally, the methods and apparatus developed for this study prove useful for the study of other similar but more exotic systems.
This thesis narrates the analysis of a novel series of polybenzimidazole-based ionenes via X-ray scattering, neutron scattering, and molecular dynamics simulation. The ionenes have been reported as stable hydroxide-conducting solid polymer electrolytes. Robust anionexchange membranes with strong conductivity are necessary for the wide application of anion-exchange membrane fuel cells, which are a compelling alternative to the internal combustion engine. Three length scales were observed: ion-polymer, polymer-polymer (and ion-ion), and the monomer length. No structure was visible above the monomer length, which is rare in high-performance ion-conducting membranes. In a preliminary molecular dynamics simulation, water molcules were observed forming bridges between anions, even at a low level of hydration.