In various astrophysical and high-energy density plasma flows, the evolution and behavior of the magnetic field can greatly influence flow morphology and result in transient phenomena. Many existing magnetohydrodynamic codes used in astrophysics and high energy density physics often ignore plasma self-magnetization and treat other physics related to magnetic field such as viscosity, thermal conduction, and resistivity as isotropic. This work is focused on constructing a computational model based on the Braginskii plasma transport theory, specifically the effects due to the Biermann battery process, and anisotropic resistive, viscous, and thermal transport processes. This model reflects on the ability of the magnetic field to modify the transport processes throughout the plasma, as well as enables the generation of spontaneous magnetic fields. For certain plasma configurations, the magnetic field dynamics brought on through these processes can come to dominate the evolution of the system at very small scales, leading to a stiff system of equations and necessitating an implicit solution to the magnetic induction equation. To relax this stiffness constraint, we implement a multigrid-based Crank-Nicolson implicit solver. We present implementation details of the corresponding computational model and its related verification results. We apply the verified model to the Kelvin-Helmholtz instability problem under high-energy density conditions. We carry out a series of numerical experiments and compare the obtained instability growth rates to benchmark results. We design a high-energy density shock tube experiment for conditions on the OMEGA laser and compare the obtained magnetic field growth to theoretically predicted results. / A Dissertation submitted to the Department Scientific Computing in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2018. / July 16, 2018. / Biermann Battery, High-energy density, Instabilities, Kelvin-Helmholtz, Resistivity / Includes bibliographical references. / Tomasz Plewa, Professor Directing Dissertation; Mark Sussman, University Representative; Gordon Erlebacher, Committee Member; Chen Huang, Committee Member; Ming Ye, Committee Member.

Chemical evolution of stellar plasma is one of the most critical components of computational models in stellar astrophysics. Nuclear abundance distributions resulting from chains of nuclear reactions serve as a key comparison tool against observations, used to further constrain models. To that end, we focus on improving the accuracy of model abundances. In most cases, abundances are obtained in the course of hydrodynamic simulations performed on Eulerian meshes. Unfortunately, those models are subject to the unphysical mixing of nuclear species due to numerical diffusion effects. For more reliable nucleosynthesis calculations, mass motions are described using passively advected Lagrangian tracer particles. These particles represent fluid elements, recording their thermodynamic histories which are subsequently used to drive detailed nucleosynthesis calculations in a post-processing procedure performed with large number of relevant isotopes. Accuracy of nucleosynthesis calculations strongly depends on the accurate coupling between fluid represented on the Eulerian mesh and tracer particles. The coupling involves both interpolation of Eulerian data to particles as well as integrating equations of motion of particles. Both steps contribute numerical errors resulting in divergence of particle tracks from fluid streamlines. Here we propose a new particle advection scheme driven by only the hydrodynamics, replacing the interpolation step of particle motion and show preliminary results. We also introduce an interpolation method for mapping our post-processed nucleosynthesis results back onto our Eulerian mesh. Spatial convergence studies are performed for the Eulerian hydrodynamic nucleosynthesis results and the remapped, post-processed Lagrangian results using a reactive Hawley-Zabusky flow. / A Dissertation submitted to the Department of Scientific Computing in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2018. / July 16, 2018. / Astrophysics, Nucleosynthesis, Particle Meshes, Supernovae / Includes bibliographical references. / Tomasz Plewa, Professor Directing Dissertation; Mark Sussman, University Representative; Gordon Erlebacher, Committee Member; Sachin Shanbhag, Committee Member; Ming Ye, Committee Member.

Includes abstract. Includes bibliographical references (leaves 76-77).

This dissertation presents spectroscopic studies of gas in galaxy halos and large-scale structures through high-resolution quasar absorption lines. The broad goal of this effort is to learn how galaxies acquire their gas and how they return it to the intergalactic medium, or more generally, how galaxies interact with their environment. The study of the absorption lines due to the extraplanar 21cm “Outer Arm” (OA) of the Milky Way toward two quasars, H1821+643 and HS0624+6907, provides valuable insight into the gas accretion processes. It yields the following results. (1) The OA is a multiphase cloud and high ions show small but significant offsets in velocity and are unlikely to be cospatial with the low ions. (2) The overall metallicity of the OA is Z=0.3–0.5[special characters omitted], but nitrogen is underabundant. (3) The abundance of N, O, and S derived are roughly consistent with outer-galaxy emission-line abundances and the metallicity gradient derived from H II regions. The similarity of the OA kinematics to several nearby high velocity clouds (HVCs, e.g. Complexes C, G, and H) suggests that these clouds could be detritus from a merging satellite galaxy. To test this hypothesis, we build up a simple model including tidal tripping, ram-pressure stripping, and dynamical friction to consider whether the OA could be debris affiliated with the Monoceros Ring. Our model can roughly reproduce the spatial and velocity characteristics of the OA. Moreover, the metallicity of the OA is similar to the higher metallicities measured in the younger stellar components of the Monoceros Ring and the progenitor candidate, the CMa overdensity. However, both our model and the Galactic warp scenario can not explain other HVCs that are likely to be related to the OA. Instead of acquiring gas, some galaxies have their gas removed through various physical processes. Ram-pressure stripping and tidal interaction are important mechanisms for galaxies to loose their gas. The high-resolution spectrum of Mrk205 combined with H I 21 cm, CO emission, and infrared observations is utilized to study a unique transforming galaxy NGC4319. We find: (1) the object has lost most of its diffuse interstellar H I. (2) molecular hydrogen remains in the disk of the galaxy. The H2 column density is low, but the molecular gas fraction is extraordinarily high. CO emission is also clearly detected, but only from the barred central region. (3) There is very little evidence of recent star formation in the galaxy. The results appears to match many of the predictions of Quilis et al. (2000), suggesting NGC4319 is undergoing a transformation from a spiral into an S0 due to ram-pressure stripping, possibly in tandem with tidal stripping. To understand the characteristics of gas (especially warm-hot intergalactic medium) in large scale structures, similar high resolution spectra of 31 quasars were selected based on the galaxy density showing in the 2MASS map. They provide an unbiased sample for the study of the correlation between O VI/H I absorbers and galaxies and 2MASS galaxy groups at low redshift (z < 0.04). We totally discover 52 Lyα absorbers and 7 O VI absorbers, and O VI is clearly detected using the stacking and “pixel optical depth” techniques for nearby galaxies along the sightlines. It seems that the locations of the O VI absorbers do not correlated with the spacial distribution of large-scale structures manifested by galaxy groups, but more closely associated with individual galaxies. It indicates that the galactic winds and “feedback” plays important role in polluting the IGM with O VI. Finally, we perform an extra investigation on the variable O VI and N V emission from the black hole binary LMC X-3 in our original absorption line study of the hot Galactic halo and the ISM of the LMC using LMC X-3 as a background source. We observe significant velocity and intensity variation in both O VI and N V emission. Their trends suggest that illumination of the B-star atmosphere by the intense X-ray emission from the accreting black hole creates a hot spot on one side of the B star, and this hot spot is the origin of the O VI and N V emission.

We investigate three aspects in the determinations of molecular gas masses from $\sp{12}$CO, $\sp{13}$CO, and dust emission. Using the $\sp{12}$CO, $\sp{13}$CO J = 2 $-$ 1 and 1 $-$ 0 as well as CS J = 2 $-$ 1 data obtained with the 14m FCRAO telescope, in conjunction with radiative transfer calculations, we estimate the average temperature and density of the molecular gas at the centers of two actively star-forming galaxies, NGC 2146 and IC 342. The physical conditions of the gas in the nuclei of these two galaxies differ from those in the disk of our own Galaxy. However, the CO luminosity to molecular gas mass ratios are found to be similar in these two galaxies. The ratios are within a factor of 2 of the value in the Milky Way if the Galactic CO abundance is assumed. We present a simple model to estimate the dust temperature distributions in galaxies based on the FIR/submm observations. The uncertainties in the dust mass owing to inexact modelling of the temperature distribution, uncertainty in the emissivity law, imprecision in the observed data, and the presence of a correlation between grain size and temperature are examined. The dust masses are estimated from the derived dust temperature distributions in 12 galaxies making use of the available data at 60, 100, 345, and 761 $\mu$m. The comparison between the dust masses obtained from our model calculations and the gas masses deduced from $\sp{12}$CO J = 1 $-$ 0 observations yields an average H$\sb2$-to-dust mass ratio of $181 \pm \sbsp{91}{119}$. In the determination of H$\sb2$ column density from $\sp{13}$CO emission the clumpiness of material in molecular clouds has not been considered in the evaluation of the uncertainties. We take this effect into account to examine the uncertainties owing to the use of the LTE approximation. The clumpy cloud model proposed by Kwan and Sanders (1986) is used over a wide range of parameters. Our calculations indicate that the largest uncertainty arises from the assumption that all levels possess a common excitation temperature in estimating the partition function. The partition function can be either overestimated, owing to subthermal excitations in high J levels, or underestimated, probably owing to an underestimate of the mean excitation temperature when the volumn filling factor is so small that the surface coverage factor of antenna beam is less than one. The uncertainties in N(H$\sb2$) can be reduced by using an alternative formula to estimate the partition function.

Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because (a) molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and (b) molecular clouds have not been mapped to sufficiently high spatial resolution to resolve the interaction. This work addresses the interaction between molecular outflows and the L1641 molecular cloud by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point $\sp{12}$CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H sc II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation. The energetics derived for the molecular outflows indicate that there is sufficient momentum available to the molecular cloud from the currently present molecular outflows to support the cloud against gravitational collapse. Remnant holes and adjacent multicomponent lines at some locations in the cloud suggest that past molecular outflows may have disrupted the cloud and are evacuating the region around the source.

We present observations of rotational transitions for several interstellar molecules whose formation may be related to grain processes and discuss their implications for interstellar chemistry. Interstellar hydrogen sulfide has been observed at fractional abundances f(H$\sb2$S) $\sim$ 10$\sp{-9}$ relative to H$\sb2$ towards cold, dark clouds, while its abundance is enhanced by a factor of 1000 in the Orion hot core and the plateau. H$\sb2$S may be evaporating from the grain mantles in the hot core, and even in the cold, dark clouds, grain surface reactions may be responsible for the gas-phase H$\sb2$S abundances. We also derive an upper limit for the HDS abundance (HDS) / (H$\sb2$S) $\leq$ 6 $\times$ 10$\sp{-4}$ in the Orion hot core. H$\sb2$CS ortho-to-para ratios have been observed to be $\sim$1.8 towards TMC-1, which may suggest that H$\sb2$CS is in equilibrium with the expected grain temperature (10 K) and gas-grain exchanges are taking place effectively in cold, dark clouds. We derive a ratio of $\sim$3, the statistical value, for Orion(3N1E) and NGC7538, and $\sim$2 for Orion(KL). We derive upper limits of the ethyl cyanide column densities of $\sim$3 $\times$ 10$\sp{12}$ cm$\sp{-2}$ towards TMC-1 and L134N. Together with the detection for vinyl cyanide, there may be no necessity of invoking grain surface synthesis for these highly saturated species in cold clouds, but the desorption processes seem to be quite inefficient for these heavy molecules. Finally, we have surveyed HOCO$\sp+$ as a tracer of interstellar CO$\sb2$ towards many galactic sources, and derive f(HOCO$\sp+$) $\sim$ 10$\sp{-8} - 10\sp{-9}$ in the Galactic center and $\leq$10$\sp{-10}$ for cold dark clouds. The observed abundance of HOCO$\sp+$ in the Galactic center is $\sim$3 and $\sim$1 orders of magnitude larger than that predicted by ion-molecule chemistry and shock chemistry, respectively. UV photolysis of grain mantles may produce CO$\sb2$ efficiently, resulting in a large abundance of HOCO$\sp+$ in the Galactic center. Interstellar grains are thought to play crucial roles in the chemistry of interstellar molecular clouds, and our results give some constraints on the highly uncertain grain processes, as well as on the gas phase processes.

The ionizing starbirth activity in M101, M82, and NGC 1569 has been investigated via CCD imagery at H$\alpha$, R, I, and (SIII) bands. The three galaxies are compared with one another and with M51, M83, and the Milky Way in terms of their starbirth intensities, starbirth efficiencies, and possible starbirth histories. The globally-averaged starbirth intensities that are inferred from the extinction-corrected H$\alpha$ surface brightnesses vary by $\sim$3 orders of magnitude, with M101 and the Milky Way defining the low end and with M82 defining the high-intensity regime. The annular-averaged starbirth intensities correlate strongly with the H$\sb2$ surface densities and with the total gas surface densities, where near-linear relationships are obtained. Unusually high starbirth efficiencies and eruptive gaseous morphologies are evident in M82, NGC 1569, and NGC 5461--one of the supergiant HII region complexes in M101. Crude indices of the galaxies' starbirth histories indicate temporally declining starbirth intensities in M101 and the Milky Way but currently "bursting" starbirth intensities in M82 and NGC 1569. In M101, annular-averaged photometry of the H$\alpha$ emission yields a much flatter galactocentric profile of surface brightness than that of the red-continuum starlight. The corresponding e-folding scale lengths are 9 and 3.3 kpc. respectively, thus implying significant differences between the galactocentric distributions of current-epoch massive star formation and past-averaged star formation. Moreover, the giant HII regions in M101 show significant variations in H$\alpha$ equivalent width as a function of both galactocentric radius and H$\alpha$ luminosity. These variations can be attributed to changes in the upper stellar mass limits of the ionizing clusters--M(upper) increasing in the outer galaxy, where the brighter HII regions are more numerous. The galactocentric variation in H$\alpha$ equivalent widths appears more closely related to the galaxy's radial profile of differential rotation than to its monotonic gradient in O/H abundances. The ionizing stellar populations in early-type, late-type, and starburst galaxies are discussed in terms of these results.

We review current indirect evidence that supports the hypothesis that disks of gas and dust surround young stars in their formation stages. Current theoretical models explain this evidence, in particular the observed spectral energy distributions $\lambda$F$\sb{\lambda}\propto\lambda\sp{-\eta}$ and luminosities. We argue that a consequence of these models is a flared disk structure H(r) $\propto$ r$\sp{\rm z}$ that should be observable, yielding a relation between the flaring constant z and the spectral index $\eta$ that can be used to propose an evolutionary sequence for the geometry of such disks. We performed high resolution observations in the infrared, aimed imaging scattered radiation from dust embedded in circumstellar disks in solar type pre-main sequence stars. We used an infrared array recently developed by the Kitt Peak National Observatory, in combination with the 4 meter telescope. These observations were analyzed using different super-resolution techniques such as image motion suppression, speckle shift-and-add, contrast-ratio analysis, maximum entropy restorations, and speckle interferometry. We present the results of these studies for the star SCrA, as a case study. However, we discovered that the response function of the telescope has three peaks, with typical separations of half to one arc second, and variations in intensity and position of 30% in times as short as one minute. This unstable response sets a limit of only 2 mag/$\prime\prime\sp2$ fainter than the central star for any extended structure that can be resolved, which is brighter than the 3.75 mag/$\prime\prime\sp2$ expected for a flared disk, and thus hampers the possibility of recovering disks structures. In addition, we find that the noise in long exposure images in the infrared is proportional to the signal, possibly due to the low number of speckles at these wavelengths. On the other hand, the noise in the speckles themselves appears to be of Poisson type, but the events that make those statistics are not individual photons, but bunches of many, such that the number of photons in each event is proportional to the intensity of the source.

We have studied the gas and dust properties and the star forming activity in G216-2.5 (also called Maddalena's cloud), a cold, massive GMC that has no evidence for star formation. We have mapped 11 square degrees in the J = 1-0 transitions of $\sp{12}$CO and $\sp{13}$CO using the QUARRY fifteen-beam array receiver on the 14 m telescope at FCRAO. We have confirmed the results of Maddalena and Thaddeus (1985) that the cloud is unusually cold and has very broad linewidths $(\Delta V\sim8$ km s$\sp{-1}).$ The visual extinction to $\sp{13}$CO column density ratio is found to be similar to that in local molecular clouds, suggesting that if the gas to dust ratio is normal, the $\sp{13}$CO abundance relative to molecular hydrogen in this cloud is similar to that found for clouds near the sun. The low gas and dust temperatures found for this cloud are largely due to the absence of heating by massive stars. The exceptionally low gas temperature can be explained if the cosmic-ray heating rate is reduced by a factor of two in the outer Galaxy. Low luminosity, and presumably low mass, young stars have been identified in this cloud. These young stars are found preferentially on the edge of the cloud. Clusters of T Tauri stars are found in two locations within G216-2.5. The mass of the cloud has been established by several techniques, and masses between 1 $\times$ 10$\sp5$ and 6 $\times$ 10$\sp5$ $M\sb\odot$ were obtained. It is suggested that G216-2.5 is a remnant cloud from a past episode of massive star formation for the following reasons. First, the cloud has a relatively large velocity dispersion for a non-star-forming GMC. Second, there is clear evidence for shells and rings within the cloud, which may be the fossil remains of its earlier star formation activity. Third, the kinematics of the cloud is dominated by a global velocity gradient suggesting that the cloud is part of a very large expanding shell. Lastly, the discrepancy between the LTE and virial masses may be explained if the cloud has been severely perturbed and is currently expanding. G216-2.5 may be part of a larger star forming complex that includes the adjacent H scII region S287 and its molecular cloud.