Obtaining a complete census of cosmic star formation requires an understanding of the faint star-forming galaxies that are beyond the detection limits of our current surveys. To find these faint galaxies, we use the power of gravitational lensing from foreground massive galaxy clusters to push the detection limits of the Hubble Space Telescope (HST) to much fainter luminosities. Combining very deep ultraviolet, optical and near-IR imaging from HST, with magnification of strong gravitational lensing from three foreground galaxy clusters, we discover a sample of 780 ultra-faint star-forming galaxies at 1 < z < 3. The UV absolute magnitude of these galaxies are extended down to very faint magnitudes of MUV < −12.5 AB mag. Using this unprecedented sample, we study the evolution of the UV luminosity function (LF) between 1 < z < 3. We find that the UV LFs are steep with an estimate of faint-end slopes of α = −1.56±0.04, α = −1.72±0.04 and α = −1.94±0.06 at 1.0 < z < 1.6, 1.6 < z < 2.2 and 2.2 < z < 3.0, respectively. We demonstrate that there is no sign of turnover in these UV LFs at least down to Muv = −14. As an important consequence of steep LFs, we show that the faint star-forming galaxies covered in this study with −18 < Muv < −12.5, produce a majority (55% − 60%) of the unobscured UV luminosity density at 1 < z < 3. Furthermore, we examine two techniques, fitting a power law to broad-band photometry as well as best-fit SED for each object, to study the evolution of rest-frame UV spectral slopes β for these ultra-faint galaxies. We demonstrate that our UV spectral slopes β change with UV luminosity, such that galaxies become bluer at fainter luminosities. However, we show that the UV spectral slope β−Muv correlation is not tight and there is a large intrinsic scatter in the UV slope distribution at a given Muv. Using hydro-dynamical simulations of dwarf galaxies, we demonstrate that the bursty star formation histories alone can explain the intrinsic scatter in β.

Biological macromolecules such as proteins are remarkable machines at the nano scale. The mechanical motion of proteins that is present in every living system allows those molecules to perform theie specific tasks. Most proteins are enzymes. Enzymes bind to their substrates, speed up the chemical reaction and release the products. Upon this binding and unbinding they undergo a large conformational motion. In case of Guanylate Kinase, the protein under study in my thesis, this deformation is about 1 nm, relatively large compared to the enzyme’s size (~4nm). This conformational motion is essential to the protein’s activity. Proteins are not rigid solids, but rather deformable, wiggling and jiggling inside a medium. This deformability is a general materials property of a folded protein. Enzymes can be deformed and their activity can be modulated by perturbations other than ligand binding.

Fluctuations of enzymes have been studied for a long time and although some progress has been made, still much is unknown about proteins dynamics. In my thesis I try to reveal a little more about proteins dynamics by studying the effect of different kinds of perturbations. For this purpose, a nano-rheology technique is used which allows us to detect deformations as small as half an Angstrom. In this technique we look at the molecule as a whole: the interior polymer chain wrapped by the surface hydration layer. An oscillatory force is applied to the protein, and the amplitude of the resulting oscillation is measured. It has been shown previously, that enzymes are viscoelastic: dissipative at low frequencies and elastic at higher frequencies. I have looked, more closely, for the origin of this atomic scale dissipation.

First, I study the contribution of the hydration layer, which is an integral part of the molecule, by modifying it using an order-inducing compound: Dimethyl Sulfoxide (DMSO), which, at small concentrations is harmless to a protein’s native forms. This compound was added to the molecule’s surface, i.e. the hydration shell, and formed strong hydrogen bonds with water molecules. Even at small DMSO concentrations a significant change in the dynamics was observed: the enzyme became stiffer. The effect is bigger at lower frequencies where enzyme shows dissipative behavior. In that sense, DMSO makes the enzyme more dissipative.

For the first time with this experimental setup, I measured the phase of the response (i.e. the phase difference between the applied force and the resulting deformation, which is basically the imaginary part of the amplitude). Having the ability to measure the phase, we have direct access to dissipation measurements. Phase measurements also revealed that DMSO makes the enzyme more dissipative, which suggest that the hydration layer partially controls the viscoelastic behavior.

Then I investigated at the contribution of the interior, i.e. the polymer chain bulk. To do so I induced point mutations in specific residues of the amino-acid sequence. The mutation points are in a region that goes under a huge strain as the enzyme goes from an open to a closed configuration. Surprisingly, one of the mutated proteins is 10 times more active than the wild type, meaning that the rate of the enzymatic reaction is 10 times faster with the mutated enzyme.

Mechanics of the mutated proteins were studied using the same nano-rheology technique, and some changes were observed, suggesting that both the interior and the surface contribute to dissipation.

I then looked at the deformation caused by ligand binding, in order to see if there is any difference in how different mutants deform upon binding the substrates or unbinding the products. Since the effect of ligand binding is small, our detection method was improved to increase the sensitivity and therefore be able to detect these small deformations. It was seen that some ligands make the enzyme softer while others make the enzyme stiffer. In some cases ligand binding’s signature was only detectable in phase measurements. Overall the conformational change caused by ligand binding was very similar among different mutants, with one exception. For one of the ligands (Guanylate monophosphate-GMP, which makes the enzyme stiffer) the fast mutant seems to have two binding events: one at low concentrations of the ligand and one at higher concentrations, whereas in the wild type only the low-concentration binding event is observed. It seems like the hyperactive mutant might have two binding sites for GMP: at higher concentrations, GMP might bind to ATP binding site. This is a case where specificity is traded off with speed: the mutant is faster but less specific.

Overall, some of my main results are:

- Hydration layer is an integral part of the molecule which is partially responsible for dissipation.

- Both interior and the surface contribute to the viscoelastic behavior. A dissipative contribution in the elastic regime is observed which can be associated with a second dissipation term, namely the one of the bulk.

- Phase measurements provide direct access to dissipation measurements at the atomic scale.

Vibrio cholerae causes the diarrheal disease cholera that affects millions of people across the globe and causes over 100,000 deaths yearly. V. cholerae must out-compete the commensal gut microbial community (the gut microbiome) to establish itself in the gut and cause disease. The major functions of normal gut microbiota include nutrient metabolism, nutrient absorption, drug metabolism, and contribute to gut immunomodulation. V. cholerae is a gram-negative bacteria and a major human GI pathogen, despite improvements in treatment and understanding of the mechanisms of pathogenesis, cholera remains a significant global health burden.We describe here that during infection with V. cholerae, individuals with different gut microbiome response differently. We used suckling and adult germfree mice models to introduce different gut communities and examine gut microbiome structure during V. cholerae infection. Next, we showed that the community which includes strains from healthy human is able to decrease cholera infection. Then we identified Vibrio-antagonistic microbes across many different microbiome contexts by setting up combinatorial experiment. Second, we explored how healthy community causes colonization resistance. We showed that this is mediated through the bile salt hydrolase enzyme activity which degrades the bile salt taurocholate that activates the expression of virulence genes. In this dissertation, we used the transplantation of complete human fecal microbiomes and defined communities in both germfree adult mice and suckling antibiotic treated mice models to demonstrate that the variation in gut microbiome can result in different V. cholerae colonization outcomes.

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Modern Persian literary histories generally characterize the decades leading up to the Iranian Revolution of 1979 as a single episode of accumulating political anxieties in Persian poetics, as in other areas of cultural production. According to the dominant literary-historical narrative, calls for "committed poetry" (she`r-e mota`ahhed) grew louder over the course of the radical 1970s, crescendoed with the monarch's ouster, and then faded shortly thereafter as the consolidation of the Islamic Republic shattered any hopes among the once-influential Iranian Left for a secular, socio-economically equitable political order. Such a narrative has proven useful for locating general trends in poetic discourses of the last five decades, but it does not account for the complex and often divergent ways in which poets and critics have reconciled their political and aesthetic commitments. This dissertation begins with the historical assumption that in Iran a question of how poetry must serve society and vice versa did in fact acquire a heightened sense of urgency sometime during the ideologically-charged years surrounding the revolution. But the dissertation departs from episodic approaches to modern Persian literature by demonstrating how the various discursive responses to the question--both in theory and in poetic practice--do not fit neatly into one concept of "political" poetry. Simply put, the term "commitment" (ta`ahhod) refers to an on-going, unresolved debate in Persian poetics, not a discrete literary-historical phenomenon. Thus, even among ideologically aligned and/or self-identifying "committed" poets and critics, one encounters significant variations in the ways that each individual has understood poetics and politics to intersect.

This dissertation investigates the ways that three modern Iranian poets work through the intersection of poetry and politics in both their theoretical writings and their verse. In each of the three cases, the poets agree that poetry serves as a locus of political resistance and in this sense all three poets might fall under the general rubric of commitment that supposedly marked the period in which they wrote. However, as I demonstrate, each case study also produces a distinct poetics of commitment. In Sa`id Soltanpur (chapter one) the dissertation locates a militant poetics, arguing that poetry can participate directly in armed liberation struggles. In M.R. Shafi`i Kadkani (chapter two) the dissertation encounters a poetics of moral outrage, arguing that the canonical traditions of Persian classical and Islamic mystical poetry provide the discursive means through which to intervene in contemporary socio-political conditions. In Ahmad Shamlu (chapter three) the dissertation locates a humanist poetics that treats poetry's invitation for critical reflective judgement as itself a form of resistance to repressive state and economic structures, but does not put forth any particular alternative structure in their place. Finally, the dissertation concludes by considering the the poetry and criticism of Mohammad Mokhtari (chapter four) as articulations of a post-revolutionary poetics of commitment.

Methodologically, the dissertation takes special care to distinguish between the theories as they are articulated in discursive prose and the particular way that the poems themselves respond to, expand upon, or challenge the theories' claims. For its theoretical framework, the dissertation attempts to place modern Persian poetics in dialogue with Sartre's writings on commitment, Adorno's response to Sartre, Frankfurt School aesthetics, and European and American poetries. Ultimately, the dissertation aims to demonstrate how the question of poetry's service to society historically produced fruitful and variegated debates in Persian poetics and that the question remains relevant and unresolved today.

The dissertation also includes an appendix with original, parallel translations of the Persian poems considered at length throughout the main body of the text.

Engineering of the membrane-like tissue structures to be utilized in highly dynamic loading environments such as the cardiovascular system has been a challenge in the past decade. Scaffolds are critical components of the engineered tissue membranes and allow them being formed in vitro and remain secure in vivo when implanted in the body. Several approaches have been taken to develop scaffolds for tissue membranes. However, all methods entail limitations due to structural vulnerability, short-term functionality, and mechanical properties of the resulted membrane constructs. To overcome these issues, we have developed a novel hybrid scaffold made of an extra thin layer of metal mesh tightly enclosed by biological matrix components. This approach retains all the advantages of using biological scaffolds while developing a strong extracellular matrix that can stand various types of loads after implantation inside the body.

With the increasing complexity of application software there is an acute need for software analysis approaches that are capable of identifying bugs, failures, and most importantly vulnerabilities on a large scale. In this dissertation, first we stress the necessity of having automated software analysis approaches and then propose analysis approaches for detecting vulnerabilities in software via analysis and testing in general, and security assessment in particular. We show the efficiency and effectiveness of these analysis techniques in detecting vulnerabilities.

First, we study security issues in smartphone applications by studying the security discrepancies between Android apps and their website counterparts, depicting the essential need of efficient software analysis techniques to fully automate the mobile app analysis process. By a comprehensive study on 100 popular app-web pairs, we find that, with respect to various security policies, the mobile apps often have weaker or non-existent security measures compared to their website counterparts.

Second, as a consequence of the former, we develop AndroidSlicer, the first novel, efficient, and effective dynamic program slicing tool for Android apps that is useful for a variety of tasks, from testing to debugging to security assessment. Our work in this domain focuses on making large scale applications of slicing practical in order to detect bugs and vulnerabilities in real-world apps. We present two new applications of the dynamic slicing technique in mobile apps: (1) detecting the "stuck'' states (missing progress indicators) in mobile apps. We present, implement, and evaluate ProgressDroid, a tool for discovering missing progress indicator bugs based on program dependencies; and (2) detecting security vulnerabilities in unique device ID generators.

Finally, in the same vein of deploying analysis tools for detecting vulnerabilities, we present GAGA, an efficient genetic algorithm for graph anonymization that simultaneously delivers high anonymization and utility preservation. Experiments show that GAGA improves the defense against DA techniques by reducing the rate of successfully de-anonymized users by at least a factor of 2.7 in comparison to the baseline and at the same time, under 16 graph and application utility metrics, GAGA is overall the best at preserving utilities.