In this thesis we discuss various aspects of topological string theories. In particular we provide a derivation of the holomorphic anomaly equation for open strings and study aspects of the Ooguri, Strominger, and Vafa conjecture. Topological string theory is a computable theory. The amplitudes of the closed topological string satisfy a holomorphic anomaly equation, which is a recursive differential equation. Recently this equation has been extended to the open topological string. We discuss the derivation...

The structure and synthesis of DNA is important. Traditionally,high-resolution structures are solved with X-ray crystallography, and kinetic measurements are taken with consumption of large amount of reagents. In this thesis, I developed new optical methods to probe the DNA structure and to measure kinetics of DNA synthesis. I measured the helical rise of A-form DNA at the single molecule level using a near-field optical microscope that has sub-10 nm resolution. The microscope is a combination...

Disks are ubiquitous around young stars. Over time, disks dissipate, revealing planets that formed hidden by their natal dust. Since direct detection of young planets at small orbital radii is currently impossible, other tracers of planet formation must be found. One sign of disk evolution, potentially linked to planet formation, is the opening of a gap or inner hole in the disk. In this thesis, I have identified and characterized several cold disks with large...

1. A Model of Fermi Acceleration at Shock Fronts A model of first order Fermi acceleration at shock fronts is developed. A "fast" hydromagnetic shock is assumed to be propogating toward an isolated magnetic mirror in an otherwise uniform magnetic field which is not parallel to the shock front. The behavior of an ensemble of particles trapped between the mirror and the shock is studied and a differential equation describing the balance of particle injection...

The behavior of a permanent gas bubble in liquids under oscillating pressure fields is studied by a linearized theory. The derived thermodynamic relation tends to indicate average isothermality for high frequency limit, contrary to the usual intuitive reasonings. The growth of the gas bubble under the oscillating pressure fields due to the effect of rectification of mass is also investigated. The effect is small, being of second order, but accumulating. The absence of resulting large...

Three topics concerned with heterogeneous diffusion flames are considered in Part I. Experiments have been conducted to determine the interference effects during burning for droplet arrays. The burning rate law applicable for single droplets has been found to be valid also for two-, five-, and nine-droplet arrays. A heterogeneous diffusion flame formed between liquid sodium and gaseous titanium tetrachloride was found to deposit small particles of titanium on the combustion chamber wall. The burning rate...

According to General Relativity a perturbed black hole will return to a stable configuration by the emission of gravitational radiation in a superposition of quasi-normal modes. Such a perturbation will occur due to the coalescence of a black hole binary, following their inspiral and subsequent merger. At late times the waveform, which we refer to as a ringdown, is expected to be dominated by a single mode. As the waveform is well-known the method of...

As gravitational wave astronomy prepares for the first detections of gravitational waves from compact-object binary inspirals, theoretical work is required on the study of (i) gravitational-wave sources, (ii) the signals emitted by those sources, and (iii) the searches for those signals in detector data. This thesis describes work on all three fronts. (i) We discuss intermediate-mass-ratio inspirals (IMRIs) of black holes or neutron stars into intermediate-mass black holes (IMBHs) that could be detected with Advanced...

The uncertainty in biospheric carbon dioxide (CO2) flux estimates drives divergent projections of future climate and uncertainty in prescriptions for climate mitigation. The terrestrial carbon sink can be inferred from atmospheric CO2 observations with transport models via inversion methods. Regional CO2 flux estimates remain uncertain due to the mixture of uncertainties caused by transport models, prior estimates of biospheric fluxes, large-scale CO2 boundary inflow, the assumptions in the inversion process, and the limited density of...

In this thesis, we analyze high-permittivity dielectric waveguides for use as guiding structures of millimeter waves. Two basic geometries are considered: the circular and rectangular guides. In Part I, we describe the theory of round fibers surrounded by an infinite cladding. Millimeter wavelengths are comparable to the physical dimensions of the guide. Therefore, a large difference in permittivity between the core and the cladding is required in order to provide for a tight confinement of...

Advances in nanoscience and nanotechnology hold enormous promises to benefit humankind in basic research, industry, and everyday life. One particular class of the vast field of nanodevices is resonant nanoelectromechanical systems (NEMS), which have recently attracted considerable research interest. While many of obstacles have been overcome in fundamental physics and engineering research of NEMS, intriguing questions and technological challenges remain unmet. This thesis is primarily focused on the studies of parametric, nonlinear, and coupled NEMS...

Spectra have been obtained in the 2μ atmospheric window with a resolution of 32 and 65Å of late-type dwarfs, giants, supergiants, and long period variables. In the non-variable stars, the first overtone band of C0 at 2.29μ shows a systematic increase with both increasing luminosity and decreasing temperature. This increasing strength is interpreted as arising from an increase in turbulence and a decrease in atmospheric opacity. The 1.87μ band of H2O appears only in stars...

In multi-armed bandit problems, agents must repeatedly choose among uncertain alternatives whose true values they can learn about only through experimentation. Information acquired from experimentation is valuable because it tells the agent whether to select a particular option again in the future. Economically significant applications include brand choice, natural resource exploration, research and development and, as special cases, job and price search. Despite the importance of these applications, little is known about whether firms and...

NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Experiments are described in which velocities were measured ahead of a semi-infinite Rankine body moving parallel to a uniform magnetic field in a conducting fluid. The flow disturbance in front of the body is found to increase in length as [...], where N is the interaction parameter. In most of the experiments this parameter was varied...

The problems of the two-dimensional unsteady cavity in internal flow are treated and linear theories are developed. In Part I, the two- dimensional supercavitating flow past a flat plate heaving and pitching with small amplitudes in a choked tunnel is investigated and a linearized solution is obtained using the acceleration potential. The flat plate is inclined at a small angle of attack to the oncoming flow and the cavity pressure is assumed to be constant....

When coherent illumination is reflected from or transmitted through a medium which causes random phase changes in the illumination, a random interference pattern termed speckle results. We have studied speckle in an imaging system and have described and measured the effect of polarization of the illumination, the first order statistics of speckle intensity, and the autocorrelation of speckle intensity as a function of space and wavelength variables. We have measured the relationship between the amount...

A convergent series representation for the internal partition function of polyelectronic atoms is obtained by assuming a covolume equation of state for the gas as previously applied by Fermi and Urey to the hydrogen atom. The present investigation is limited to those cases wherein only extranuclear electronic excitation occurs. The contribution of these electronic states to the thermodynamic functions is obtained from an acceptable approximation to the sum of the convergent series for the partition...

NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Let [...] be a set of finite groups and define [...] to be the intersection of all sets of groups which contain [...] and are closed under the operations of subgroup, factor group and direct product. The equivalence relation defined by [...] if [...] = [...] is studied and it is shown that if Qn and...

This package includes the MATLAB app GUI, source code, and search algorithm for the preprint "Stochastic simulation platform for visualization and estimation of transcriptional kinetics." The GUI simulates and visualizes RNA transcription; the source code allows implementation of more complex reaction schema; the search algorithm performs parameter estimation. The code is based on the Gillespie algorithm and implemented in MATLAB.

In situ hybridization methods enable the mapping of mRNA expression within intact biological samples. With current approaches, it is challenging to simultaneously detect multiple target mRNAs in vertebrate embryos and tissue sections – a significant limitation in attempting to study interacting regulatory elements in systems most relevant to human development and disease. This thesis presents a multiplexed fluorescent in situ hybridization method based on orthogonal amplification with hybridization chain reaction (HCR). Using this approach, RNA...

This thesis describes the essential roles of Dna2 and the Tim/Tipin complex in the maintenance of genomic stability. Dna2 participates in DNA replication and double-strand break repair by homologous recombination. Meanwhile, the Tim/Tipin complex is required for efficient checkpoint activation upon replication stress, which can be caused by stalled DNA replication forks. While yeast genetics and experiments with purified proteins have revealed much about yeast Dna2, we chose to pursue characterization of metazoan Dna2 using...

(1) The presence of small amounts of water dissolved within nominally-anhydrous minerals in the earth has significant effects on the chemistry of melting in the Earth’s mantle. Upwelling rock containing water will melt at greater depths than the same rock would if it were volatile-free, and the chemistry of these hydrous melts is expected to be quite different from that of anhydrous melts. We have developed new experimental techniques and applied them to melting under...

The π-stack of DNA is competent for mediating charge transport (CT), both by single-step and multi-step mechanisms. The yield of long-range single-step CT from photoexcited 2-aminopurine to guanine across adenine tracts has a shallow, periodic distance dependence, with increasing amplitude and decreasing slope with temperature. To measure total CT yield, herein we employ the fast radical traps N2-cyclopropylguanine (CPG), and N6-cyclopropyladenine (CPA), which are similar to the unmodified bases, but undergo rapid decomposition upon oxidation....

Metabolic networks in the cell break down food and resources to create useful energy and components. At the same time they use those same components and energy in the process, thus making autocatalysis an unavoidable part of core metabolism. The simplest and most widely studied autocatalytic network is the glycolytic pathway. It is common to every cell of living organisms, from bacteria to humans. Its special autocatalytic structure, like the structure of many similar autocatalytic...

During synaptic transmission in the central nervous system, neuroreceptors transduce a chemical signal into an electrical signal, a process that is mediated by both ligand-gated ion channels (LGICs) and G-protein coupled receptors (GPCRs). The work in this thesis examines structure-function relationships within these receptors, with a focus on elucidating the mechanism of molecular recognition during ligand binding. We utilize conventional and unnatural amino acid mutagenesis, structural derivatives of agonists, and homology models to identify specific...