Integral finite surgeries on knots in S^3

Using the correction terms in Heegaard Floer homology, we prove that if a knot in S³ admits a positive integral T-, O-, or I-type surgery, it must have the same knot Floer homology as one of the knots given in our complete list, and the resulting manifold is orientation-preservingly homeomorphic to the p-surgery on the corresponding knot.

Advanced density functional theory methods for materials science

In this work we chiefly deal with two broad classes of problems in computational materials science, determining the doping mechanism in a semiconductor and developing an extreme condition equation of state. While solving certain aspects of these questions is well-trodden ground, both require extending the reach of existing methods to fully answer them. Here we choose to build upon the framework of density functional theory (DFT) which provides an efficient means to investigate a system from a quantum mechanics description.

Zinc Phosphide (Zn₃P₂) could be the basis for cheap and highly efficient solar cells. Its use in this regard is limited by the difficulty in n-type doping the material. In an effort to understand the mechanism behind this, the energetics and electronic structure of intrinsic point defects in zinc phosphide are studied using generalized Kohn-Sham theory and utilizing the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional for exchange and correlation. Novel 'perturbation extrapolation' is utilized to extend the use of the computationally expensive HSE functional to this large-scale defect system. According to calculations, the formation energy of charged phosphorus interstitial defects are very low in n-type Zn₃P₂ and act as 'electron sinks', nullifying the desired doping and lowering the fermi-level back towards the p-type regime. Going forward, this insight provides clues to fabricating useful zinc phosphide based devices. In addition, the methodology developed for this work can be applied to further doping studies in other systems.

Accurate determination of high pressure and temperature equations of state is fundamental in a variety of fields. However, it is often very difficult to cover a wide range of temperatures and pressures in an laboratory setting. Here we develop methods to determine a multi-phase equation of state for Ta through computation. The typical means of investigating thermodynamic properties is via ’classical’ molecular dynamics where the atomic motion is calculated from Newtonian mechanics with the electronic effects abstracted away into an interatomic potential function. For our purposes, a ’first principles’ approach such as DFT is useful as a classical potential is typically valid for only a portion of the phase diagram (i.e. whatever part it has been fit to). Furthermore, for extremes of temperature and pressure quantum effects become critical to accurately capture an equation of state and are very hard to capture in even complex model potentials. This requires extending the inherently zero temperature DFT to predict the finite temperature response of the system. Statistical modelling and thermodynamic integration is used to extend our results over all phases, as well as phase-coexistence regions which are at the limits of typical DFT validity. We deliver the most comprehensive and accurate equation of state that has been done for Ta. This work also lends insights that can be applied to further equation of state work in many other materials.

Optical properties of excited silicon and germanium at low temperatures

Part I of this thesis deals with 3 topics concerning the luminescence from bound multi-exciton complexes in Si. Part II presents a model for the decay of electron-hole droplets in pure and doped Ge.

Part I.

We present high resolution photoluminescence data for Si doped With Al, Ga, and In. We observe emission lines due to recombination of electron-hole pairs in bound excitons and satellite lines which have been interpreted in terms of complexes of several excitons bound to an impurity. The bound exciton luminescence in Si:Ga and Si:Al consists of three emission lines due to transitions from the ground state and two low lying excited states. In Si:Ga, we observe a second triplet of emission lines which precisely mirror the triplet due to the bound exciton. This second triplet is interpreted as due to decay of a two exciton complex into the bound exciton. The observation of the second complete triplet in Si:Ga conclusively demonstrates that more than one exciton will bind to an impurity. Similar results are found for Si:Al. The energy of the lines show that the second exciton is less tightly bound than the first in Si:Ga. Other lines are observed at lower energies. The assumption of ground state to ground-state transitions for the lower energy lines is shown to produce a complicated dependence of binding energy of the last exciton on the number of excitons in a complex. No line attributable to the decay of a two exciton complex is observed in Si:In.

We present measurements of the bound exciton lifetimes for the four common acceptors in Si and for the first two bound multi-exciton complexes in Si:Ga and Si:Al. These results are shown to be in agreement with a calculation by Osbourn and Smith of Auger transition rates for acceptor bound excitons in Si. Kinetics determine the relative populations of complexes of various sizes and work functions, at temperatures which do not allow them to thermalize with respect to one another. It is shown that kinetic limitations may make it impossible to form two-exciton complexes in Si:In from a gas of free excitons.

We present direct thermodynamic measurements of the work functions of bound multi-exciton complexes in Al, B, P and Li doped Si. We find that in general the work functions are smaller than previously believed. These data remove one obstacle to the bound multi-exciton complex picture which has been the need to explain the very large apparent work functions for the larger complexes obtained by assuming that some of the observed lines are ground-state to ground-state transitions. None of the measured work functions exceed that of the electron-hole liquid.

Part II.

A new model for the decay of electron-hole-droplets in Ge is presented. The model is based on the existence of a cloud of droplets within the crystal and incorporates exciton flow among the drops in the cloud and the diffusion of excitons away from the cloud. It is able to fit the experimental luminescence decays for pure Ge at different temperatures and pump powers while retaining physically reasonable parameters for the drops. It predicts the shrinkage of the cloud at higher temperatures which has been verified by spatially and temporally resolved infrared absorption experiments. The model also accounts for the nearly exponential decay of electron-hole-droplets in lightly doped Ge at higher temperatures.

Methods for melting temperature calculation

Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly.

We propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments.

We propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which the melting temperature is a design criterion.

We present in detail two examples of refractory materials. First, we demonstrate how key material properties that provide guidance in the design of refractory materials can be accurately determined via ab initio thermodynamic calculations in conjunction with experimental techniques based on synchrotron X-ray diffraction and thermal analysis under laser-heated aerodynamic levitation. The properties considered include melting point, heat of fusion, heat capacity, thermal expansion coefficients, thermal stability, and sublattice disordering, as illustrated in a motivating example of lanthanum zirconate (La₂Zr₂O₇). The close agreement with experiment in the known but structurally complex compound La₂Zr₂O₇ provides good indication that the computation methods described can be used within a computational screening framework to identify novel refractory materials. Second, we report an extensive investigation into the melting temperatures of the Hf-C and Hf-Ta-C systems using ab initio calculations. With melting points above 4000 K, hafnium carbide (HfC) and tantalum carbide (TaC) are among the most refractory binary compounds known to date. Their mixture, with a general formula Ta_xHf_1-xC_y, is known to have a melting point of 4215 K at the composition Ta₄HfC₅, which has long been considered as the highest melting temperature for any solid. Very few measurements of melting point in tantalum and hafnium carbides have been documented, because of the obvious experimental difficulties at extreme temperatures. The investigation lets us identify three major chemical factors that contribute to the high melting temperatures. Based on these three factors, we propose and explore a new class of materials, which, according to our ab initio calculations, may possess even higher melting temperatures than Ta-Hf-C. This example also demonstrates the feasibility of materials screening and discovery via ab initio calculations for the optimization of "higher-level" properties whose determination requires extensive sampling of atomic configuration space.

Cavity Optomechanics at Millikelvin Temperatures

The field of cavity optomechanics, which concerns the coupling of a mechanical object's motion to the electromagnetic field of a high finesse cavity, allows for exquisitely sensitive measurements of mechanical motion, from large-scale gravitational wave detection to microscale accelerometers. Moreover, it provides a potential means to control and engineer the state of a macroscopic mechanical object at the quantum level, provided one can realize sufficiently strong interaction strengths relative to the ambient thermal noise. Recent experiments utilizing the optomechanical interaction to cool mechanical resonators to their motional quantum ground state allow for a variety of quantum engineering applications, including preparation of non-classical mechanical states and coherent optical to microwave conversion. Optomechanical crystals (OMCs), in which bandgaps for both optical and mechanical waves can be introduced through patterning of a material, provide one particularly attractive means for realizing strong interactions between high-frequency mechanical resonators and near-infrared light. Beyond the usual paradigm of cavity optomechanics involving isolated single mechanical elements, OMCs can also be fashioned into planar circuits for photons and phonons, and arrays of optomechanical elements can be interconnected via optical and acoustic waveguides. Such coupled OMC arrays have been proposed as a way to realize quantum optomechanical memories, nanomechanical circuits for continuous variable quantum information processing and phononic quantum networks, and as a platform for engineering and studying quantum many-body physics of optomechanical meta-materials.

However, while ground state occupancies (that is, average phonon occupancies less than one) have been achieved in OMC cavities utilizing laser cooling techniques, parasitic absorption and the concomitant degradation of the mechanical quality factor fundamentally limit this approach. On the other hand, the high mechanical frequency of these systems allows for the possibility of using a dilution refrigerator to simultaneously achieve low thermal occupancy and long mechanical coherence time by passively cooling the device to the millikelvin regime. This thesis describes efforts to realize the measurement of OMC cavities inside a dilution refrigerator, including the development of fridge-compatible optical coupling schemes and the characterization of the heating dynamics of the mechanical resonator at sub-kelvin temperatures.

We will begin by summarizing the theoretical framework used to describe cavity optomechanical systems, as well as a handful of the quantum applications envisioned for such devices. Then, we will present background on the design of the nanobeam OMC cavities used for this work, along with details of the design and characterization of tapered fiber couplers for optical coupling inside the fridge. Finally, we will present measurements of the devices at fridge base temperatures of T_f = 10 mK, using both heterodyne spectroscopy and time-resolved sideband photon counting, as well as detailed analysis of the prospects for future quantum applications based on the observed optically-induced heating.

Finite differences and a coupled analytic technique with applications to explosions and earthquakes

An analytic technique is developed that couples to finite difference calculations to extend the results to arbitrary distance. Finite differences and the analytic result, a boundary integral called two-dimensional Kirchhoff, are applied to simple models and three seismological problems dealing with data. The simple models include a thorough investigation of the seismologic effects of a deep continental basin. The first problem is explosions at Yucca Flat, in the Nevada test site. By modeling both near-field strong-motion records and teleseismic P-waves simultaneously, it is shown that scattered surface waves are responsible for teleseismic complexity. The second problem deals with explosions at Amchitka Island, Alaska. The near-field seismograms are investigated using a variety of complex structures and sources. The third problem involves regional seismograms of Imperial Valley, California earthquakes recorded at Pasadena, California. The data are shown to contain evidence of deterministic structure, but lack of more direct measurements of the structure and possible three-dimensional effects make two-dimensional modeling of these data difficult.

Part I: The abortive infection of bacteriophage øx174 at low temperatures. Part II: The early stages in the process of infection by bacteriophage øx174

Part I

The infection of E. coli by ΦX174 at 15°C is abortive; the cells are killed by the infection but neither mature phage nor SS (single-stranded) DNA are synthesized. Parental RF (replicative form) is formed and subsequently replicated at 15°C. The RF made at 15°C shows normal infectivity and full competence to act as precursor to progeny SS DNA after an increase in temperature to 37°C. The investigations suggest that all of the proteins required for SS DNA synthesis and phage maturation are present in the abortive infection at 15°C.

Three possible causes are suggested for the abortive infection at 15°C: (a) A virus-coded protein whose role is essential to the infection is made at 15°C and assumes its native conformation, but its rate of activity is too low at this temperature to sustain the infection process. (b) Virus maturation may involve the formation of a DNA-protein complex and conformational changes which have an energy threshold infrequently reached at 15°C. (c) A host-coded protein present in uninfected cells, and whose activity is essential to the infection at all temperatures, but not to the host at 15°C, is inactive at 15°C. An hypothesis of this type is offered which proposes that the temperature-limiting factor in SS DNA synthesis in vivo may reflect a temperature-dependent property of the host DNA polymerase.

Part II

Three distinct stages are demonstrated in the process whereby ΦX174 invades its host: (1) Attachment: The phage attach to the cell in a manner that does not irreversibly alter the phage particle and which exhibits "single-hit" kinetics. The total charge on the phage particle is demonstrated to be important in determining the rate at which stable attachment is effected. The proteins specified by ΦX cistrons II, III and VII play roles, which may be indirect, in the attachment reaction. (2) Eclipse: 'The attached phage undergo a conformational change. Some of the altered phage particles spontaneously detach from the cell (in a non-infective form) while the remainder are more tightly bound to the cell. The altered phage particles detached (spontaneously or chemically) from such complexes have at least 40% of their DNA extruded from the phage coat. It is proposed that this particle is, or derives from, a direct intermediate in the penetration of the viral DNA.

The kinetics for the eclipse of attached phage particles are first-order with respect to phage concentration and biphasic; about 85% of the phage eclipse at one rate (k = 0.86 min^-1) and the remainder do so at a distinctly lesser rate (k = 0.21 min^-1).

The eclipse event is very temperature-dependent and has the relatively high Arrhenius activation energy of 36.6 kcal/mole, indicating the cooperative nature of the process. The temperature threshold for eclipse is 17 to 18°C.

At present no specific ΦX cistron is identified as affecting the eclipse process. (3) DNA penetration: A fraction of the attached, eclipsed phage particles corresponding in number to the plaque-forming units complete DNA penetration. The penetrated DNA is found in the cell as RF, and the empty phage protein coat remains firmly attached to the exterior of the cell. This step is inhibited by prior irradiation of the phage with relatively high doses of UV light and is insensitive to the presence of KCN and NaN₃. Temporally excluded superinfecting phages do not achieve DNA penetration.

Both eclipsed phage particles and empty phage protein coats may be dissociated from infected cells; some of their properties are described.

Avoided temperatures by young fish [Translation from: Informatsionnyi Byulleten Biologiya Vnutrennikh Vod No.50, 45-47, 1981]

Directed local changes of water temperature for the purpose of controlling the behaviour of fish are based on the knowledge of the characteristics of seasonal-age dynamics of their thermoadaptation possibilities. These possibilities are still inadequately studied especially in relation to avoided temperatures. By the authors the attempt was made to determine zones of avoided temperatures for the young of five species of fish (bream, roach, blue bream, perch, peled) in the summer period of the year, and also to assess the influence on them of additional factors, in particular mechanical driving. In parallel in two-fold repetition were conducted experiments on the determination of selected, shock and lethal temperatures of these fish. Experiments were conducted with fish, caught in the littoral of the Rybinsk reservoir.

Influence of starvation on selected temperatures in the young of bream, roach and perch [Translation from: Informatsionnyi Byulleten Biologiya Vnutrennikh Vod No.50, 45-47, 1981]

Works devoted to the influence of starvation on temperature selection by fishes are few and their conclusions are contradictory. This study determined the influence of brief, up to 14 days, starvation on temperature selection by young fishes. The experiments were carried out in August-September 1976 on fingerling bream (Abramis brama L.), roach (Rutilus rutilus L.) and perch (Perca fluviatilis L.) with body lengths of 3-5 cm and weight 0.5-1.2 g. The young fish were caught in the littoral by seine-nets or small drag-nets. Immediately after catching the fish they were put in acclimatization boxes. The period of acclimatization did not exceed 2 days for bream and roach at a temperature of 20 °C and 6 days for perch at 17 °C. Before the start of the experiment and for the first 10 days of the experiment the fish were fed with oligochaetes, earthworms and daphnia, after that feeding discontinued. At the end of a 10-14 day period the giving of food was resumed. The study concludes that the experiments have shown that in the summer season the factor of starvation significantly changes the reaction to the gradient of temperature in young cyprihids - roach and bream.