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The Cosmic Stories: Beginning, Evolution and Present Days of the Universe
Get PDFThis work presents three studies of independent astrophysical phenomena which cover a full timeline of the universe from the epoch of inflation to the present day. Along with our results we provide concise overviews of the considered phenomena and outline major open questions.
The first part of this work is focused on the epoch of inflation. We analyze the evolution of early density fluctuations which originate during inflation and connect physical fields driving inflation with observable parameters. We study several inflationary scenarios, specifically one field inflation, in which the only field present during that epoch is the inflaton field and two field inflation, in which along with the inflaton field the epoch of inflation is effected by the second scalar field - curvaton field. Single field inflationary models predict nearly Gaussian initial conditions and hence a detection of non-Gaussianity would be a signature of more complex inflationary scenarios. In this work we study the effect of primordial non-Gaussianity on the cosmic microwave background (CMB) and on large-scale structure in a two-field inflationary model in which both the inflaton and curvaton fields contribute to the primordial density fluctuations. We show that in addition to the previously described enhancement of the galaxy bias on large scales, this setup results in large-scale stochasticity. We provide joint constraints on the local non-Gaussianity parameter f nl and the ratio of the amplitude of primordial perturbations due to the inflaton and curvaton using WMAP and Sloan Digital Sky Survey (SDSS) data.
The second and largest part of this study is focused on the formation of the first cosmic structures and the effect of relative velocity between dark matter and baryonic fluids. In that part we discuss a very important and previously unnoticed effect which significantly changes the process of structure formation in the early universe. At the time of recombination, baryons and photons decoupled and the sound speed in the baryonic fluid dropped from relativistic, to the thermal velocity of the hydrogen atoms. This is less than the relative velocity of baryons and dark matter computed via linear perturbation theory, so we infer that there are supersonic coherent flows of the baryons relative to the underlying potential wells created by the dark matter. As a result, the advection of small-scale perturbations (near the baryonic Jeans scale) by large-scale velocity flows is important for the formation of the first structures. This effect involves a quadratic term in the cosmological perturbation theory equations and hence has not been included in studies based on linear perturbation theory. We show that the relative motion suppresses the abundance of the first bound objects, even if one only investigates dark matter halos, and leads to qualitative changes in their spatial distribution, such as introducing scale-dependent bias and stochasticity. We further discuss possible observable implications of this effect for high-redshift galaxy clustering and reionization. Specifically we discuss in detail the effect of the relative velocity on the gas content in the early galaxies, minihaloes and the first stars. This part of the thesis also includes a concise overview of the recent studies that investigated various aspects of the relative velocity effect and showed its importance for topics ranging from star formation to precision cosmology.
The third and final part of the thesis covers interaction between expanding shocks of the supernovae explosions with the interstellar medium. The shocks of supernovae remnants represent a unique cosmic environment which allows detailed studies of plasma physics and high-energy astrophysics phenomena in conditions unreachable in the Earth-based laboratories. Specifically, shocks of supernovae remnants are associated with production of cosmic rays - the most energetic particles that we can observe. In our study we are specifically focused on the science of Balmer-dominated shocks (BDS) - a subset of collisionless, fast shocks dominated by hydrogen line emission with both broad and narrow components. The unique feature of BDS is that they are directly observable and their observations provide an opportunity for direct testing of the phase space structure and ion velocity distribution inside of shocks.
Understanding of physical phenomena occurring inside of astrophysical shocks requires precise knowledge of cross sections for high-nl proton-hydrogen collisions. Until now scientists have been using approximations for these cross sections which fall short of the precision needed for robust analysis of the observed data and can no longer satisfy needs of the astrophysical community. Guided by the demand in high-precision calculations of the cross sections we developed and implemented a robust method for direct solution of the Schroedinger partial differential equation on a grid. In this work we provide a detailed description of our computational algorithm for calculating cross sections in high-nl proton-hydrogen collisions and show results for n ≤ 4. We describe the code we developed, show the results of consistency tests and describe possible extensions. Finally, we show how our results are applied to the studies of Balmer-dominated shocks and specifically how the precise cross sections for n ≤ 4 can be used in computing Balmer decrement - the ratio of Halpha and Hbeta line intensities. </p
Structural Insights into Tail-Anchored Protein Targeting by Get3
Get PDFTranslocation of membrane proteins from the point of synthesis to their integration in the membrane is critical to the function of the cell. Tail-anchored (TA) proteins are an important class of membrane proteins with a single transmembrane domain (TMD) close to the carboxyl-terminus. They are defined topologically by having their amino-terminus in the cytosol and their carboxyl-terminus on the exterior side of the membrane. Since the TMD is sequestered by the ribosome during translation, co-translational translocation of TA proteins by the SRP-dependent pathway is not possible. The Guided Entry of Tail-anchored proteins (GET) pathway post-translationally targets TA proteins to the endoplasmic reticulum (ER) membrane. The conserved nucleotide hydrolase Get3 is the central protein in the pathway that specifically binds the TMD of TA proteins to chaperone them from a sorting complex of Get4, Get5, Sgt2 and other chaperones to an ER membrane receptor formed by Get1 and Get2. We have created a model for the mechanism of Get3 TA protein binding coupled to nucleotide state using X-ray crystallography, structural modeling and mutagenesis experiments. We then demonstrate expression, purification and crystallization of complexes of Get3 with TA proteins for structural studies. Finally, we present a crystal structure of a tetrameric archaeal Get3 homologue that forms a central hydrophobic chamber and is capable of binding TA proteins. Using small-angle X-ray scattering, the structure is comparable to a tetrameric fungal Get3 complex with TA protein, which is capable of TA protein membrane integration in vitro. This suggests a model in which a tetramer of Get3 binds TA proteins for delivery to the membrane
Phonon Anharmonicity of Ionic Compounds and Metals
Get PDFVibrational studies of materials at elevated temperatures are relatively rare, and most phonon work also has emphasized harmonic behavior. Non-harmonic effects are often unexplored. These non-harmonic effects can be important for many properties of the material, such as thermal transport and phase stability.
Phonon theory and computational methods are briefly reviewed, and the experimental techniques for phonon study, such as Raman spectroscopy and inelastic neutron scattering, are discussed. Several experiments on phonon anharmonicity were performed, and interpreted with these computational methods.
In Raman spectroscopy studies on the phonon dynamics of hafnia and zirconia, Raman line positions, and shapes of temperatures to 1000 K were measured and the types of modes that exhibit the most anharmonicity were characterized and correlated to the vibrational displacements of individual atoms in the unit cell. It was found that anharmonicity in these systems is rich in information and strongly mode dependent.
Using time-of-flight inelastic neutron scattering, we found purely quartic transverse modes with an anomalous mode stiffening with temperature, and related these modes to the enormous negative thermal expansion of the DO9 structure of scandium fluoride.
Using second-order perturbation theory, phonon linewidths from the third-order anharmonicity were calculated from first-principles density functional theory with the supercell finite-displacement method. For face-centered cubic aluminum, the good agreement between calculations and the phonon density of states up to 750 K indicates that the third-order phonon-phonon interactions calculated can account for the lifetime broadenings of phonons in aluminum to at least 80% of its melting temperature.</p
The Design, Synthesis, and Application of Ruthenium Metathesis Catalysts for the Preparation of Small Molecules and Polymers
Get PDFOlefin metathesis is a widely used method for constructing carbon–carbon double bonds. This methodology has broad applications in organic and polymer chemistry, and the continued design of highly efficient catalysts has been critical to the success of this reaction. The main goal of this thesis was to design and synthesize new catalysts for better selectivity and for improved properties for targeted applications, as well as to explore different ligand structures for optimal catalyst performance in olefin metathesis.
The application of ruthenium catalysts for the ring-opening metathesis polymerization of challenging monomer 1,5-dimethyl-1,5-cyclooctadiene in the presence of a chain transfer agent is discussed in chapter 2. A variety of complexes were explored to find the ideal catalyst for this transformation, enabling the synthesis of telechelic polyisoprene, which has extensive applications in block copolymerization.
Chiral N-alkyl, N-aryl NHC ruthenium catalysts were designed and synthesized to improve the enantioselectivity during asymmetric ring-opening cross-metathesis. Mechanistic studies of these catalysts revealed a preference for methylidene propagation compared to previous NHC catalysts. Chapter 3 describes these studies, in addition to the screening of a variety of chiral ligands for optimal enantioselectivity. Some of these catalysts gave very high enantioselectivity, comparable to the best reported ruthenium catalysts. Insights into the stability of these complexes as a propagating methylidene led to investigating them in applications where propagation as a methylidene is desirable.
N-aryl, N-alkyl NHC ruthenium catalysts were designed and synthesized for improved selectivity during ethenolysis reactions, which require a ruthenium methylidene species to react with an internal olefin to yield a terminal olefin and a ruthenium alkylidene species. Subsequent reaction of this ruthenium alkylidene species with ethylene gives the other terminal olefin. This reaction can be applied to the internal olefin of seed oils to generate valuable products that are typically derived from petroleum sources, thus providing an environmentally friendly route to the same products. An important component of ethenolysis catalysts is stability to existing as a methylidene, a property of the N-aryl, N-alkyl NHC ruthenium catalysts described in chapter 4.
Chapter 5 describes the design and synthesis of sterically hindered N-aryl, N-alkyl NHC ruthenium catalysts for application in latent metathesis. These complexes also show excellent stability at elevated temperatures for extended periods of time.
Appendix A contains NMR spectra for catalysts described in chapter 4, as well as X-ray crystal structures for two of the catalysts.
Appendix B contains NMR spectra for catalysts described in chapter 5, as well as X-ray crystal structures for two of those catalysts.</p
Three Paths to Particle Dark Matter
Get PDFIn this thesis, we explore examples of each of the three primary strategies for the detection of particle dark matter: indirect detection, direct detection, and collider production.
We first examine the indirect detection of weakly interacting massive particle (WIMP) dark matter via the gamma-ray photons produced by astrophysical WIMP annihilation. Such photons may be observed by the Fermi Gamma-ray Space Telescope. We propose the gamma-ray-flux probability distribution function (PDF) as a probe of the Galactic halo substructure predicted to exist by N-body simulations. The PDF is calculated for a phenomenological model of halo substructure; it is shown that the PDF may allow a statistical detection of substructure.
Next, we consider the direct detection of WIMPs. We explore the ability of directional nuclear-recoil detectors to constrain the local velocity distribution of WIMP dark matter by performing Bayesian parameter estimation on simulated recoil-event data sets. We discuss in detail how directional information, when combined with measurements of the recoil-energy spectrum, helps break degeneracies in the velocity-distribution parameters. Considering the possibility that velocity structures such as cold tidal streams or a dark disk may also be present in addition to the Galactic halo, we discuss the potential of upcoming experiments to probe such structures.
We then study the collider production of light gravitino dark matter. Light gravitino production results in spectacular signals, including di-photons, delayed photons, kinked charged tracks, and heavy metastable charged particles. We find that observable numbers of light-gravitino events may be found in future collider data sets. Remarkably, this data is also well suited to distinguish between scenarios with light gravitino dark matter, with striking implications for early-Universe cosmology.
Finally, we investigate the related matter of radiative corrections to the decay rate of charged fermions caused by the presence of a thermal bath of photons. The cancellation of finite-temperature infrared divergences in the decay rate is described in detail. Temperature-dependent radiative corrections to the two-body decay of a hypothetical charged fermion and to electroweak decays of a muon are given. We touch upon possible implications of these results for charged particles in the early Universe.</p
Targeting Tumors and the Kidney with siRNA Nanoparticles and Evaluation of Extracellular MicroRNA-based Methodologies to Track Their Activity
Get PDFThe goal of my thesis work is to discover new ways to enable the use of nanoparticle therapeutics to treat human disease. The work presented here touches on several areas in medicine and is united by a common theme: engineering ways to make, use, and evaluate therapeutics that maximize the benefit to the patient and minimize the harm. I have explored three interrelated strategies to achieve my objectives: (1) the use of targeted-nanoparticle-based therapeutics to deliver therapeutic entities to specific sites in the body, (2) the use of a highly specific type of therapeutic, siRNA, and (3) the evaluation of strategies for using extracellular microRNAs to non invasively monitor therapeutic activity and disease response to that activity.
In Chapter 2, I present the first evidence of targeted-nanoparticle delivery of siRNA to solid tumors following systemic administration to patients. My coworkers and I demonstrate both dose-dependent accumulation of the siRNA nanoparticles and evidence of gene knockdown via the canonical RNAi mechanism.
Chapters 3 – 5 describe the therapeutic potential of targeted nanoparticles (one version used in the clinic and described in Chapter 2) for: (i) targeting ribonucleotide reductase subunit M2 in human melanoma cell lines (Chapter 3), (ii) Herceptin-targeted nanoparticles containing siRNA against Her2 in Her2(+) breast cancer (Chapter 4), and (iii) siRNA targeting the “undruggable” protein N-Ras for N-Ras mutant melanomas (Chapter 5).
Chapters 6 – 8 focus on the interaction of nanoparticles with the kidney. Chapter 6 explores a previously unknown phenomenon of size-dependent glomerular accumulation of nanoparticles. In Chapter 7, a new mechanism of clearance for polycation-polymer-based nucleic acid delivery systems is demonstrated, based on interactions between polymer components in the nanoparticle and the anionic surface of the renal filtration barrier, explaining the rapid clearance of these siRNA nanoparticle systems. Chapter 8 illustrates targeted-nanoparticle delivery of siRNA to the kidney.
In Chapter 9, I test the hypothesis that analysis of tumor-secreted microRNAs within patient blood samples can be used as real-time markers of drug pharmacodynamics. Specifically, I focus on efforts to characterize microRNA expression patterns following pharmacologic inhibition of the oncogene BRAF in melanoma cells and their secreted exosomes.</p
Surface Maps into Free Groups
Get PDFWe exploit the combinatorial properties of surface maps into free groups to prove several new results in the field of stable commutator length and bounded cohomology. We show that random homomorphisms between free groups are isometries of scl; we prove interesting properties of the scl unit ball; we describe a transfer construction for quasimorphisms and give an infinite family of chains whose scl it certifies; we linearize the dynamics of endomorphisms on free groups and use this to prove that random endomorphisms can be realized by surface immersions, which provides many examples of surface subgroups of HNN extensions of free groups; and finally, we give an algorithm to compute scl in free products of finite or infinite cyclic groups that generalizes and improves previous work
Peer Effects in Social Networks: Search, Matching Markets, and Epidemics
Get PDFSocial network analysis emerged as an important area in sociology in the early 1930s, marking a shift from looking at individual attribute data to examining the relationships between people and groups. Surveying many different types of real-world networks, researchers quickly found that different types of social networks tend to share a common set of structural characteristics, including small diameter, high clustering, and heavy-tailed degree distributions. Moving beyond real networks, in the 1990s researchers began to propose random network models to explain these commonly observed social network structures. These models laid the foundation for investigation into problems where the underlying network plays a key role, from the spread of information and disease, to the design of distributed communication and search algorithms, to mechanism design and public policy. Here we focus on the role of peer effects in social networks. Through this lens, we develop a mathematically tractable random network model incorporating searchability, propose a novel way to model and analyze two-sided matching markets with externalities, model and calculate the cost of an epidemic spreading on a complex network, and examine the impact of conforming and non-conforming peer effects in vaccination decisions on public health policy.
Throughout this work, the goal is to bring together knowledge and techniques from diverse fields like sociology, engineering, and economics, exploiting our understanding of social network structure and generative models to understand deeper problems that — without this knowledge — could be intractable. Instead of crippling our analysis, social network characteristics allow us to reach deeper insights about the interaction between a particular problem and the network underlying it.</p
Quantum Nonequilibrium Physics with Rydberg Atoms
Get PDFA Rydberg atom is an atom excited to a high energy level, and there is a strong dipole-dipole interaction between nearby Rydberg atoms. While there has been much interest in closed systems of Rydberg atoms, less is known about open systems of Rydberg atoms with spontaneous emission. This thesis explores the latter.
We consider a lattice of atoms, laser-excited from the ground state to a Rydberg state and spontaneously decaying back to the ground state. Using mean-field theory, we study the how the steady-state Rydberg population varies across the lattice. There are three phases: uniform, antiferromagnetic, and oscillatory.
Then we consider the dynamics of the quantum model when mean-field theory predicts bistability. Over time, the system occasionally jumps between a state of low Rydberg population and a state of high Rydberg population. We explain how entanglement and quantum measurement enable the jumps, which are otherwise classically forbidden.
Finally, we let each atom be laser-excited to a short-lived excited state in addition to a Rydberg state. This three-level configuration leads to rich spatiotemporal dynamics that are visible in the fluorescence from the short-lived excited state. The atoms develop strong spatial correlations that change on a long time scale.</p
Multiscale Modeling and Computation of 3D Incompressible Turbulent Flows
Get PDFIn the first part, we present a mathematical derivation of a closure relating the Reynolds stress to the mean strain rate for incompressible turbulent flows. This derivation is based on a systematic multiscale analysis that expresses the Reynolds stress in terms of the solutions of local periodic cell problems. We reveal an asymptotic structure of the Reynolds stress by invoking the frame invariant property of the cell problems and an iterative dynamic homogenization of large- and small-scale solutions. The Smagorinsky model for homogeneous turbulence is recovered as an example to illustrate our mathematical derivation. Another example is turbulent channel flow, where we derive a simplified turbulence model based on the asymptotic flow structure near the wall. Additionally, we obtain a nonlinear model by using a second order approximation of the inverse flow map function. This nonlinear model captures the effects of the backscatter of kinetic energy and dispersion and is consistent with other models, such as a mixed model that combines the Smagorinsky and gradient models, and the generic nonlinear model of Lund and Novikov.
Numerical simulation results at two Reynolds numbers using our simplified turbulence model are in good agreement with both experiments and direct numerical simulations in turbulent channel flow. However, due to experimental and modeling errors, we do observe some noticeable differences, e.g. , root mean square velocity fluctuations at Reτ = 180.
In the second part, we present a new perspective on calculating fully developed turbulent flows using a data-driven stochastic method. General polynomial chaos (gPC) bases are obtained based on the mean velocity profile of turbulent channel flow in the offline part. The velocity fields are projected onto the subspace spanned by these gPC bases and a coupled system of equations is solved to compute the velocity components in the Karhunen-Loeve expansion in the online part. Our numerical results have shown that the data-driven stochastic method for fully developed turbulence offers decent approximations of statistical quantities with a coarse grid and a relatively small number of gPC base elements.</p