Vector-borne diseases have a profound impact on world health. The two most well-known and costly diseases are dengue fever and malaria, both spread by mosquito vectors. In the last decade, many new solutions to halting the spread of these diseases have been sought, including vector-mediated disease suppression. The work presented here seeks to generate alleles to effect this suppression, and engineer a drive system to replace the native population. Additional work on systems to keep...

The focus of this thesis is a collection of problems of timely interest in orbital dynamics and interior structure of planetary bodies. The first three chapters are dedicated to understanding the interior structure of close-in, gaseous extrasolar planets (hot Jupiters). In order to resolve a long-standing problem of anomalously large hot Jupiter radii, we proposed a novel magnetohydrodynamic mechanism responsible for inflation. The mechanism relies on the electro-magnetic interactions between fast atmospheric flows and the...

This thesis contains work on four topics which fit into two broad areas of research: the quest to understand structure formation and through it the properties of the dark matter, and the search for primordial gravitational radiation. The first project details the effect of an accretion shock on the colors of satellites in galaxy clusters. A new model of ram pressure stripping including an accretion shock with variable radius is developed and implemented in the...

Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. A molecular wire, DNA conducts charge with shallow distance dependence, yet mismatches and lesions attenuate this process. We have proposed a model where repair proteins, containing redox-active [4Fe4S] clusters, utilize DNA charge transport (CT) to scan the genome for lesions. Based on this model, proteins are predicted to redistribute onto strands where DNA CT is...

The discovery and use of fluorescent proteins has been of extreme importance in biological imaging of cells, tissues, and organs. In order to address some of the limitations of fluorescent tags, second harmonic generation can be used. Second harmonic generating nanoprobes allow nontoxic, long-term imaging that, with proper functionalization, can be utilized for biological imaging applications. As a proof of principle, commercial tetragonal barium titanate nanoparticles were functionalized to expose surface amine groups, which could...

Seismic tomography and waveform modeling reveal several prominent structures in the Earth's lower mantle: (1) the D" discontinuity, defined by a seismic velocity increase of 1-3% about 250 km above the core-mantle boundary (CMB), (2) Ultralow-velocity zones (ULVZs), which are thin, isolated patches with anomalously low seismic wavespeed at the CMB, and (3) two large, low-shear velocity provinces (LLSVPs) beneath Africa and the Pacific Ocean. The geodynamics of these structures are investigated using numerical convection...

Substantial evidence from galaxies, galaxy clusters, and cosmological scales suggests that ~85% of the matter of our universe is invisible. The missing matter, or "dark matter" is likely composed of non-relativistic, non-baryonic particles, which have very rare interactions with baryonic matter and with one another. Among dark matter candidates, Weakly Interacting Massive Particles (WIMPs) are particularly well motivated. In the early universe, thermally produced particles with weak-scale mass and interactions would `freeze out’ at the...

MicroRNAs are a class of ~22 nucleotide RNA molecules with roles in diverse biological processes. Here I focus on two microRNAs, miR-155 and miR-125b, and reveal pathways by which their dysregulation leads to myeloproliferative disorder (MPD) and leukemia, respectively. I begin by searching for miR-155 target genes relevant to MPD. By writing an algorithm to search microarray data for predicted microRNA target genes, I identified 89 candidate target genes for miR-155 in myeloid cells. Literature...

This thesis is a report of the transport properties of bilayer two-dimensional electron systems found in GaAs/AlGaAs double quantum well semiconductor heterostructures. When a strong perpendicular magnetic field is applied so that the total Landau filling factor is equal to one and if the two layers are close enough together, a novel quantum Hall (QH) state with strong interlayer correlations can form. This QH state is often described as an excitonic condensate, in which electrons...

This thesis presents an effort to miniaturize conventional optical microscopy to a chip level using microfluidic technology. Modern compound microscopes use a set of bulk glass lenses to form magnified images from biological objects. This limits the possibility of shrinking the size of a microscope system. The invention of micro/nanofabrication technology gives hope to engineers who want to rethink the way we build optical microscopes. This advancement can fundamentally reform the way clinicians and biologists...

The Coupled Cluster Green’s function method is expanded to periodic systems and preliminary results of the spectral function for diamond and graphene are shown. Future improvements and potential applications are discussed.

Methane is an ideal alternative to petroleum refining as a chemical feedstock source since it is highly abundant an inexpensive. However, the lack of selective methane oxidation catalysts has limited such utilization. Starting from cytochrome P450 CYP102A1 (BM3) from Bacillus megaterium, which prefers C12-C20 fatty acids as its substrates, I investigated several protein engineering approaches to shift the enzyme’s substrate specificity toward small gaseous alkanes, with the ultimate goal of methane. By continuing previous directed...

To better understand and improve the cathode process for Proton exchange membrane fuel cell, we studied systematically the mechanism of oxygen reduction reaction (ORR) on group 8–11 metals and their alloys using density functional theory calculations. To address the contribution of solvent effect, we developed a practical implicit solvation model based on Poisson-Boltzmann equation. We discovered that solvation changed greatly the reaction barriers and hence the pathways preferences. The two well known mechanisms O2-diss and...

Achieving agile autonomous flight by an insect-sized micro aerial vehicle (MAV) will require improved technology that is radically smaller, lighter, and more power-efficient. One animal that has solved the problem is the fly, a virtuoso among insect flyers whose nervous system can perform sophisticated aerial maneuvers under severe computational constraints. This thesis is concerned with understanding and emulating the dynamics of the fly's feedback control system. Because vision is noisy and information rich, processing time...

This dissertation takes a step toward a general framework for solving network information theory problems by studying the capacity region of networks through the entropy region. We first show that the capacity of a large class of acyclic memoryless multiuser information theory problems can be formulated as convex optimization over the region of entropy vectors of the network random variables. This capacity characterization is universal, and is advantageous over previous formulations in that it is...

The proclivity of silica for ferric hydroxide sorption sites allows for an Archean iron cycle involving iron-silica co-precipitation and deposition of banded iron formations (BIF). Considering the tendency of viruses to also sorb iron, here we investigate the possibility that viruses were involved in the iron cycle and potentially deposited in BIFs. A known concentration of Syn33a cyanophages was introduced into each media and the viral particles remaining in solution after a short centrifugation were...

This dissertation is motivated by the lack of scalable methods for the analysis and synthesis of different large-scale complex systems appearing in electrical and computer engineering. The systems of interest in this work are power networks, analog circuits, antenna systems, communication networks and distributed control systems. By combining theories from control and optimization, the high-level objective is to develop new design tools and algorithms that explicitly exploit the physical properties of these practical systems (e.g.,...

A natural goal in designing mechanisms for auctions and public projects is to maximize the social welfare while incentivizing players to bid truthfully. If these are the only concerns, the problem is easily solved by use of the VCG mechanism. Unfortunately, this mechanism is not computationally efficient in general and there are currently no other general methods for designing truthful mechanisms. However, it is possible to design computationally efficient VCG-based mechanisms which approximately maximize the...

Shock compression experiments provide access to high pressures in a laboratory setting. Matter at extreme pressures is often studied by utilizing a well controlled planar impact between two flat plates to generate a one dimensional shock wave. While these experiments are a powerful tool in equation of state (EOS) development, they are inherently limited by the velocity of the impacting plate. In an effort to dramatically increase the range of pressures which can be studied...

Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit structured as a phosphorelay embedded in multiple transcriptional feedback loops, and which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are 'bandpass'-like, in the sense that activation occurs within a limited band of Spo0A~P concentrations, and have recently been shown to pulse in a cell-cycle-dependent...

Interactions between microorganisms and minerals significantly impact microbial diversity and geochemical cycles in diverse settings. However, methodological difficulty has inhibited past study of microbe–mineral interactions in fine-grained subsurface environments. Conventional sampling poorly resolves microbial diversity at the fine scale necessary to perceive overall community differences between mineral substrates that are thoroughly mixed. In particular, the importance of microbial attachment to minerals in unconsolidated marine sediments remains poorly constrained despite extensive geobiological research in these settings....

Which one comes first: segmentation or recognition? We propose a unified framework for carrying out the two simultaneously and without supervision. The framework combines a flexible probabilistic model for representing the shape and appearance of each segment, with the popular "bag of visual words" model for recognition. If applied to a collection of images, our framework can simultaneously discover the segments of each image, and the correspondence between such segments, without supervision. Such recurring segments...

Aging is characterized by the declining ability of an organism to maintain homeostasis, which eventually leads to death. Dietary restriction (DR), the reduction of nutrients without malnutrition, extends lifespan in various organisms, yet its molecular underpinnings are poorly understood. We show that in Drosophila, DR upregulates the translational repressor 4EBP, the eukaryotic translation initiation factor 4E binding protein, and that this upregulation is necessary for the full lifespan extension upon DR and sufficient to extend...

While massive star clusters have been detected in almost every galaxy with appreciable star formation, they are most prevalent in interacting and merging galaxies. As many as 95% of these clusters will ultimately be disrupted, often in the first 10 Myr, but those clusters that do survive may be the progenitors of globular clusters. Many questions exist regarding these massive clusters and the processes that lead to their formation and disruption, including the uniformity of...

We show that the Lawrence-Krammer representation of the BMW algebra of type An-1 over the field Q(l,r) is generically irreducible, but that for some values of the parameters l and r, when these are specialized in the field of complex numbers, it becomes reducible. When the representation is reducible, we describe the invariant subspaces by giving their dimension and some spanning vectors.