Understanding planet formation through high precision photometry and spectroscopy

From studies of protoplanetary disks to extrasolar planets and planetary debris, we aim to understand the full evolution of a planetary system. Observational constraints from ground- and space-based instrumentation allows us to measure the properties of objects near and far and are central to developing this understanding. We present here three observational campaigns that, when combined with theoretical models, reveal characteristics of different stages and remnants of planet formation. The Kuiper Belt provides evidence of chemical and dynamical activity that reveals clues to its primordial environment and subsequent evolution. Large samples of this population can only be assembled at optical wavelengths, with thermal measurements at infrared and sub-mm wavelengths currently available for only the largest and closest bodies. We measure the size and shape of one particular object precisely here, in hopes of better understanding its unique dynamical history and layered composition.

Molecular organic chemistry is one of the most fundamental and widespread facets of the universe, and plays a key role in planet formation. A host of carbon-containing molecules vibrationally emit in the near-infrared when excited by warm gas, T~1000 K. The NIRSPEC instrument at the W.M. Keck Observatory is uniquely configured to study large ranges of this wavelength region at high spectral resolution. Using this facility we present studies of warm CO gas in protoplanetary disks, with a new code for precise excitation modeling. A parameterized suite of models demonstrates the abilities of the code and matches observational constraints such as line strength and shape. We use the models to probe various disk parameters as well, which are easily extensible to others with known disk emission spectra such as water, carbon dioxide, acetylene, and hydrogen cyanide.

Lastly, the existence of molecules in extrasolar planets can also be studied with NIRSPEC and reveals a great deal about the evolution of the protoplanetary gas. The species we observe in protoplanetary disks are also often present in exoplanet atmospheres, and are abundant in Earth's atmosphere as well. Thus, a sophisticated telluric removal code is necessary to analyze these high dynamic range, high-resolution spectra. We present observations of a hot Jupiter, revealing water in its atmosphere and demonstrating a new technique for exoplanet mass determination and atmospheric characterization. We will also be applying this atmospheric removal code to the aforementioned disk observations, to improve our data analysis and probe less abundant species. Guiding models using observations is the only way to develop an accurate understanding of the timescales and processes involved. The futures of the modeling and of the observations are bright, and the end goal of realizing a unified model of planet formation will require both theory and data, from a diverse collection of sources.

Towards conditional RNAi : shape and sequence transduction with small conditional RNAs

RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement “conditional RNAi.” Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.

To implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.

We demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.

Wave induced oscillations in harbors of arbitrary shape

Theoretical and experimental studies were conducted to investigate the wave induced oscillations in an arbitrary shaped harbor with constant depth which is connected to the open-sea.

A theory termed the “arbitrary shaped harbor” theory is developed. The solution of the Helmholtz equation, ∇²f + k²f = 0, is formulated as an integral equation; an approximate method is employed to solve the integral equation by converting it to a matrix equation. The final solution is obtained by equating, at the harbor entrance, the wave amplitude and its normal derivative obtained from the solutions for the regions outside and inside the harbor.

Two special theories called the circular harbor theory and the rectangular harbor theory are also developed. The coordinates inside a circular and a rectangular harbor are separable; therefore, the solution for the region inside these harbors is obtained by the method of separation of variables. For the solution in the open-sea region, the same method is used as that employed for the arbitrary shaped harbor theory. The final solution is also obtained by a matching procedure similar to that used for the arbitrary shaped harbor theory. These two special theories provide a useful analytical check on the arbitrary shaped harbor theory.

Experiments were conducted to verify the theories in a wave basin 15 ft wide by 31 ft long with an effective system of wave energy dissipators mounted along the boundary to simulate the open-sea condition.

Four harbors were investigated theoretically and experimentally: circular harbors with a 10° opening and a 60° opening, a rectangular harbor, and a model of the East and West Basins of Long Beach Harbor located in Long Beach, California.

Theoretical solutions for these four harbors using the arbitrary shaped harbor theory were obtained. In addition, the theoretical solutions for the circular harbors and the rectangular harbor using the two special theories were also obtained. In each case, the theories have proven to agree well with the experimental data.

It is found that: (1) the resonant frequencies for a specific harbor are predicted correctly by the theory, although the amplification factors at resonance are somewhat larger than those found experimentally,(2) for the circular harbors, as the width of the harbor entrance increases, the amplification at resonance decreases, but the wave number bandwidth at resonance increases, (3) each peak in the curve of entrance velocity vs incident wave period corresponds to a distinct mode of resonant oscillation inside the harbor, thus the velocity at the harbor entrance appears to be a good indicator for resonance in harbors of complicated shape, (4) the results show that the present theory can be applied with confidence to prototype harbors with relatively uniform depth and reflective interior boundaries.