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The usefulness of large-scale structure as a probe of cosmology and structure formation is increasing as large deep surveys in multi-wavelength bands are becoming possible. The observational analysis of large-scale structure guided by large volume numerical simulations are beginning to offer us complementary information and crosschecks of cosmological parameters estimated from the anisotropies in Cosmic Microwave Background (CMB) radiation. Understanding structure formation and evolution and even galaxy formation history is also being aided by observations of different redshift snapshots of the Universe, using various tracers of large-scale structure.This dissertation work covers aspects of large-scale structure from the baryon acoustic oscillation scale, to that of large scale filaments and galaxy clusters. First, I discuss a large- scale structure use for high precision cosmology. I investigate the reconstruction of Baryon Acoustic Oscillation (BAO) peak within the context of Lagrangian perturbation theory, testing its validity in a large suite of cosmological volume N-body simulations. Then I consider galaxy clusters and the large scale filaments surrounding them in a high resolution N-body simulation. I investigate the geometrical properties of galaxy cluster neighborhoods, focusing on the filaments connected to clusters. Using mock observations of galaxy clusters, I explore the the correlations of scatter in galaxy cluster mass estimates from multi-wavelength observations and different measurement techniques. I also examine the sources of the correlated scatter by considering the intrinsic and environmental properties of clusters.

The usefulness of large-scale structure as a probe of cosmology and structure formation is increasing as large deep surveys in multi-wavelength bands are becoming possible. The observational analysis of large-scale structure guided by large volume numerical simulations are beginning to offer us complementary information and crosschecks of cosmological parameters estimated from the anisotropies in Cosmic Microwave Background (CMB) radiation. Understanding structure formation and evolution and even galaxy formation history is also being aided by observations of different redshift snapshots of the Universe, using various tracers of large-scale structure.This dissertation work covers aspects of large-scale structure from the baryon acoustic oscillation scale, to that of large scale filaments and galaxy clusters. First, I discuss a large- scale structure use for high precision cosmology. I investigate the reconstruction of Baryon Acoustic Oscillation (BAO) peak within the context of Lagrangian perturbation theory, testing its validity in a large suite of cosmological volume N-body simulations. Then I consider galaxy clusters and the large scale filaments surrounding them in a high resolution N-body simulation. I investigate the geometrical properties of galaxy cluster neighborhoods, focusing on the filaments connected to clusters. Using mock observations of galaxy clusters, I explore the the correlations of scatter in galaxy cluster mass estimates from multi-wavelength observations and different measurement techniques. I also examine the sources of the correlated scatter by considering the intrinsic and environmental properties of clusters.

We develop and test with cosmological simulations a physically motivated theory for how the interplay between gravity, pressure, cooling, and self-shielding set the redshift--dependent mass scale at which halos can accrete intergalactic gas. This theory provides a physical explanation for the halo mass scale that can accrete unshocked intergalactic gas, which has been explained with ad hoc criteria tuned to reproduce the results of a few simulations. Furthermore, it provides an intuitive explanation for how this mass scale depends on the reionization redshift, the amplitude of the ionizing background, and the redshift. We show that accretion is inhibited onto more massive halos than had been thought because previous studies had focused on the gas fraction of halos rather than the instantaneous mass that can accrete gas. A halo as massive as 10^11 Msun cannot accrete intergalactic gas at z=0, even though typically its progenitors were able to accrete gas at higher redshifts. We describe a simple algorithm that can be implemented in semi-analytic models, and we compare the predictions of this algorithm to numerical simulations., Comment: 13 pages, 8 figures; submitted to MNRAS

We develop and test with cosmological simulations a physically motivated theory for how the interplay between gravity, pressure, cooling, and self-shielding set the redshift--dependent mass scale at which halos can accrete intergalactic gas. This theory provides a physical explanation for the halo mass scale that can accrete unshocked intergalactic gas, which has been explained with ad hoc criteria tuned to reproduce the results of a few simulations. Furthermore, it provides an intuitive explanation for how this mass scale depends on the reionization redshift, the amplitude of the ionizing background, and the redshift. We show that accretion is inhibited onto more massive halos than had been thought because previous studies had focused on the gas fraction of halos rather than the instantaneous mass that can accrete gas. A halo as massive as 10^11 Msun cannot accrete intergalactic gas at z=0, even though typically its progenitors were able to accrete gas at higher redshifts. We describe a simple algorithm that can be implemented in semi-analytic models, and we compare the predictions of this algorithm to numerical simulations., Comment: 13 pages, 8 figures; submitted to MNRAS

The challenge of obtaining galaxy cluster masses is increasingly being addressed by multiwavelength measurements. As scatters in measured cluster masses are often sourced by properties of or around the clusters themselves, correlations between mass scatters are frequent and can be significant, with consequences for errors on mass estimates obtained both directly and via stacking. Using a high resolution 250 Mpc/h side N-body simulation, combined with proxies for observational cluster mass measurements, we obtain mass scatter correlations and covariances for 243 individual clusters along ~96 lines of sight each, both separately and together. Many of these scatters are quite large and highly correlated. We use principal component analysis (PCA) to characterize scatter trends and variations between clusters. PCA identifies combinations of scatters, or variations more generally, which are uncorrelated or non-covariant. The PCA combination of mass measurement techniques which dominates the mass scatter is similar for many clusters, and this combination is often present in a large amount when viewing the cluster along its long axis. We also correlate cluster mass scatter, environmental and intrinsic properties, and use PCA to find shared trends between these. For example, if the average measured richness, velocity dispersion and Compton decrement mass for a cluster along many lines of sight are high relative to its true mass, in our simulation the cluster's mass measurement scatters around this average are also high, its sphericity is high, and its triaxiality is low. Our analysis is based upon estimated mass distributions for fixed true mass. Extensions to observational data would require further calibration from numerical simulations, tuned to specific observational survey selection functions and systematics., Comment: 18 pages, 12 figures, final version to appear in MNRAS, helpful changes from referee and others incorporated

The challenge of obtaining galaxy cluster masses is increasingly being addressed by multiwavelength measurements. As scatters in measured cluster masses are often sourced by properties of or around the clusters themselves, correlations between mass scatters are frequent and can be significant, with consequences for errors on mass estimates obtained both directly and via stacking. Using a high resolution 250 Mpc/h side N-body simulation, combined with proxies for observational cluster mass measurements, we obtain mass scatter correlations and covariances for 243 individual clusters along ~96 lines of sight each, both separately and together. Many of these scatters are quite large and highly correlated. We use principal component analysis (PCA) to characterize scatter trends and variations between clusters. PCA identifies combinations of scatters, or variations more generally, which are uncorrelated or non-covariant. The PCA combination of mass measurement techniques which dominates the mass scatter is similar for many clusters, and this combination is often present in a large amount when viewing the cluster along its long axis. We also correlate cluster mass scatter, environmental and intrinsic properties, and use PCA to find shared trends between these. For example, if the average measured richness, velocity dispersion and Compton decrement mass for a cluster along many lines of sight are high relative to its true mass, in our simulation the cluster's mass measurement scatters around this average are also high, its sphericity is high, and its triaxiality is low. Our analysis is based upon estimated mass distributions for fixed true mass. Extensions to observational data would require further calibration from numerical simulations, tuned to specific observational survey selection functions and systematics., Comment: 18 pages, 12 figures, final version to appear in MNRAS, helpful changes from referee and others incorporated

We construct a filament catalogue using an extension of the halo based filament finder of Zhang et al.(2009), in a 250 Mpc/h side N-body simulation, and study the properties of filaments ending upon or surrounding galaxy clusters (within 10 Mpc/h). In this region, the majority of filamentary mass, halo mass, and galaxy richness centered upon the cluster tends to lie in sheets, which are not always coincident. Fixing a sheet width of 3 Mpc/h for definiteness, we find the sheet orientations and (connected) filamentary mass, halo mass and richness fractions relative to the surrounding sphere. Filaments usually have one or more endpoints outside the sheet determined by filament or halo mass or richness, with at least one having a large probability to be aligned with the perpendicular of the plane. Scatter in mock cluster mass measurements, for several observables, is often correlated with the observational direction relative to these local sheets, most often for richness and weak lensing, somewhat less for Compton decrement, and least often for velocity dispersions. The long axis of the cluster also tends to lie in the sheet andits orientiation relative to line of sight also correlates with mass scatter., Comment: References and explanations added as suggested, revised results for cluster inertia tensor (some correlations stronger than reported previously)

We construct a filament catalogue using an extension of the halo based filament finder of Zhang et al.(2009), in a 250 Mpc/h side N-body simulation, and study the properties of filaments ending upon or surrounding galaxy clusters (within 10 Mpc/h). In this region, the majority of filamentary mass, halo mass, and galaxy richness centered upon the cluster tends to lie in sheets, which are not always coincident. Fixing a sheet width of 3 Mpc/h for definiteness, we find the sheet orientations and (connected) filamentary mass, halo mass and richness fractions relative to the surrounding sphere. Filaments usually have one or more endpoints outside the sheet determined by filament or halo mass or richness, with at least one having a large probability to be aligned with the perpendicular of the plane. Scatter in mock cluster mass measurements, for several observables, is often correlated with the observational direction relative to these local sheets, most often for richness and weak lensing, somewhat less for Compton decrement, and least often for velocity dispersions. The long axis of the cluster also tends to lie in the sheet andits orientiation relative to line of sight also correlates with mass scatter., Comment: References and explanations added as suggested, revised results for cluster inertia tensor (some correlations stronger than reported previously)

The baryon acoustic oscillation (BAO) method for constraining the expansion history is adversely affected by non-linear structure formation, which washes out the correlation function peak created at decoupling. To increase the constraining power of low z BAO experiments, it has been proposed that one use the observed distribution of galaxies to "reconstruct'' the acoustic peak. Recently Padmanabhan, White and Cohn provided an analytic formalism for understanding how reconstruction works within the context of Lagrangian perturbation theory. We extend that formalism to include the case of biased tracers of the mass and, because the quantitative validity of LPT is questionable, we investigate reconstruction in N-body simulations. We find that LPT does a good job of explaining the trends seen in simulations for both the mass and for biased tracers and comment upon the implications this has for reconstruction., Comment: 9 pages, 8 figures

The baryon acoustic oscillation (BAO) method for constraining the expansion history is adversely affected by non-linear structure formation, which washes out the correlation function peak created at decoupling. To increase the constraining power of low z BAO experiments, it has been proposed that one use the observed distribution of galaxies to "reconstruct'' the acoustic peak. Recently Padmanabhan, White and Cohn provided an analytic formalism for understanding how reconstruction works within the context of Lagrangian perturbation theory. We extend that formalism to include the case of biased tracers of the mass and, because the quantitative validity of LPT is questionable, we investigate reconstruction in N-body simulations. We find that LPT does a good job of explaining the trends seen in simulations for both the mass and for biased tracers and comment upon the implications this has for reconstruction., Comment: 9 pages, 8 figures

We explore the evolution of the large-scale anisotropy in the velocity field caused by the gravitational pancaking effect assuming a LCDM universe. The Millennium Run halo catalogs at four different redshifts, z=0, 0.5, 1 and z=2 are analyzed to find that the pancaking effect starts to intervene the hierarchical structure formation at redshift z=2 when a characteristic pancake scale is around 3 Mpc/h. It is also clearly shown how the degree and scale of the pancaking effect changes with time. An analytic model based on the Zel'dovich approximation is presented to explain quantitatively the evolution of the velocity-pancake alignment. A cosmological implication of our finding and a possibility of detecting a signal in real universe are discussed., Comment: accepted by ApJ, 21 pages, 6 figures, discussion and error analysis improved

We explore the evolution of the large-scale anisotropy in the velocity field caused by the gravitational pancaking effect assuming a LCDM universe. The Millennium Run halo catalogs at four different redshifts, z=0, 0.5, 1 and z=2 are analyzed to find that the pancaking effect starts to intervene the hierarchical structure formation at redshift z=2 when a characteristic pancake scale is around 3 Mpc/h. It is also clearly shown how the degree and scale of the pancaking effect changes with time. An analytic model based on the Zel'dovich approximation is presented to explain quantitatively the evolution of the velocity-pancake alignment. A cosmological implication of our finding and a possibility of detecting a signal in real universe are discussed., Comment: accepted by ApJ, 21 pages, 6 figures, discussion and error analysis improved

We analyze the Millennium run semi-analytic galaxy catalog to explore quantitatively the gravitational pancaking effect on the orientation of galaxy velocity field. We first calculate the probability density distribution of the cosine of the angle between the velocity of a field galaxy and the direction normal to a local pancake plane which is determined using two nearest neighbor field galaxies. A clear signal of alignment is detected for the case that the pancake scale is in the range of $5-8h^{-1}$ Mpc. The tendency of the velocity-pancake alignment is found to still exist when the pancakes are determined using three neighbor galaxies, indicating that it has a spatial coherence. The degree of the velocity-pancake alignment is shown to increase with the velocity magnitude and the local density, while it decreases with the separation distance from the galaxy to the pancake and disappears when the pancake has a filamentary shape. A final conclusion is that our work may provide another clue to understanding the large-scale structure in the universe., Comment: accepted by ApJL, new analyses included, discussions improved

We analyze the Tully catalog of nearby galaxies to investigate the local pancaking effect on the orientation of disk galaxies. We first select only those edge-on disk galaxies in the catalog whose axis-ratios are less than 0.1 to measure their spin axes unambiguously. A local pancake at the location of each selected galaxy is found as a plane encompassing the two nearest neighbor disks. Then, we examine statistically the inclinations of the galaxy spin axes relative to the local pancake planes. It is detected that the Tully disk galaxies tend to be inclined onto the local pancake planes, and the average inclination angles decrease with the pancake scale. We also construct a theoretical model for the inclination of disk galaxies relative to the local pancakes in the frame of the linear tidal torque theory. The comparison of the theoretical prediction with the observational result demonstrates a good agreement. Finally, we conclude that it is a first detection of the local pancaking effect on the orientation of disk galaxies, which is consistent with the scenario that the gravitational tidal field promotes the formation of pancakes on small mass scale., Comment: submitted to the ApJL, 12 pages, 2 ps figures

We analyze the Millennium run semi-analytic galaxy catalog to explore quantitatively the gravitational pancaking effect on the orientation of galaxy velocity field. We first calculate the probability density distribution of the cosine of the angle between the velocity of a field galaxy and the direction normal to a local pancake plane which is determined using two nearest neighbor field galaxies. A clear signal of alignment is detected for the case that the pancake scale is in the range of $5-8h^{-1}$ Mpc. The tendency of the velocity-pancake alignment is found to still exist when the pancakes are determined using three neighbor galaxies, indicating that it has a spatial coherence. The degree of the velocity-pancake alignment is shown to increase with the velocity magnitude and the local density, while it decreases with the separation distance from the galaxy to the pancake and disappears when the pancake has a filamentary shape. A final conclusion is that our work may provide another clue to understanding the large-scale structure in the universe., Comment: accepted by ApJL, new analyses included, discussions improved

We analyze the Tully catalog of nearby galaxies to investigate the local pancaking effect on the orientation of disk galaxies. We first select only those edge-on disk galaxies in the catalog whose axis-ratios are less than 0.1 to measure their spin axes unambiguously. A local pancake at the location of each selected galaxy is found as a plane encompassing the two nearest neighbor disks. Then, we examine statistically the inclinations of the galaxy spin axes relative to the local pancake planes. It is detected that the Tully disk galaxies tend to be inclined onto the local pancake planes, and the average inclination angles decrease with the pancake scale. We also construct a theoretical model for the inclination of disk galaxies relative to the local pancakes in the frame of the linear tidal torque theory. The comparison of the theoretical prediction with the observational result demonstrates a good agreement. Finally, we conclude that it is a first detection of the local pancaking effect on the orientation of disk galaxies, which is consistent with the scenario that the gravitational tidal field promotes the formation of pancakes on small mass scale., Comment: submitted to the ApJL, 12 pages, 2 ps figures