How are galaxies assigned to halos? Searching for assembly bias in the SDSS galaxy clustering

Clustering of dark matter halos has been shown to depend on halo properties beyond mass such as halo concentration, a phenomenon referred to as halo assembly bias. Standard halo occupation models (HOD) in large scale structure studies assume that halo mass alone is sufficient in characterizing the connection between galaxies and halos. Modeling of galaxy clustering can face systematic effects if the number of galaxies within a halo is correlated with other halo properties. Using the Small MultiDark-Planck high resolution $N$-body simulation and the clustering measurements of the Sloan Digital Sky Survey (SDSS) DR7 main galaxy sample, we investigate the extent to which the concentration-dependence of halo occupation can be constrained. Furthermore, we study how allowing for the concentration dependence can improve our modeling of galaxy clustering. Our constraints on HOD with assembly bias suggest that satellite population is not correlated with halo concentration at fixed halo mass. At fixed halo mass, our constraints favor lack of correlation between the occupation of centrals and halo concentration in the most luminous samples ($M_{\rm r}<-21.5,-21$), and modest correlation in the $M_{\rm r}<-20.5,-20, -19.5$ samples. We show that in comparison with abundance-matching mock catalogs, our findings suggest qualitatively similar but modest levels of the impact of halo assembly bias on galaxy clustering. The effect is only present in the central occupation and becomes less significant in brighter galaxy samples. Furthermore, by performing model comparison based on information criteria, we find that in most cases, the standard mass-only HOD model is still favored by the observations.Comment: Accepted for publication in Ap

RnaseIII and T4 Polynucleotide Kinase Sequence Biases and Solutions During RNA-Seq Library Construction

Background: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. Results: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5' and 3' end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. Conclusions: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data.National Institute on Alcohol Abuse and Alcoholism (NIAAA) AA12404, AA019382, AA020926, AA016648National Institutes of Health (NIH) R01 GM088344Waggoner Center for Alcohol and Addiction Researc

Star Formation Quenching Timescale of Central Galaxies in a Hierarchical Universe

Central galaxies make up the majority of the galaxy population, including the majority of the quiescent population at $\mathcal{M}_* > 10^{10}\mathrm{M}_\odot$. Thus, the mechanism(s) responsible for quenching central galaxies plays a crucial role in galaxy evolution as whole. We combine a high resolution cosmological $N$-body simulation with observed evolutionary trends of the "star formation main sequence," quiescent fraction, and stellar mass function at $z < 1$ to construct a model that statistically tracks the star formation histories and quenching of central galaxies. Comparing this model to the distribution of central galaxy star formation rates in a group catalog of the SDSS Data Release 7, we constrain the timescales over which physical processes cease star formation in central galaxies. Over the stellar mass range $10^{9.5}$ to $10^{11} \mathrm{M}_\odot$ we infer quenching e-folding times that span $1.5$ to $0.5\; \mathrm{Gyr}$ with more massive central galaxies quenching faster. For $\mathcal{M}_* = 10^{10.5}\mathrm{M}_\odot$, this implies a total migration time of $\sim 4~\mathrm{Gyrs}$ from the star formation main sequence to quiescence. Compared to satellites, central galaxies take $\sim 2~\mathrm{Gyrs}$ longer to quench their star formation, suggesting that different mechanisms are responsible for quenching centrals versus satellites. Finally, the central galaxy quenching timescale we infer provides key constraints for proposed star formation quenching mechanisms. Our timescale is generally consistent with gas depletion timescales predicted by quenching through strangulation. However, the exact physical mechanism(s) responsible for this still remain unclear.Comment: 16 pages, 11 figure

Kinetic study of copper chemistry in chemical mechanical polishing (CMP) by an in-situ real time measurement technique

This work describes a systematic approach to study chemical reactions of copper in contact with various chemical agents and to construct a coherent etching rate model based on the fundamental chemistry. Reactions of copper with chemical agents were investigated by in-situ real time technique, quartz crystal microgravimetry (QCM). Kinetic processes were followed by QCM measurement and analyzed. A coherent etching rate formula was built based on the kinetic analysis of fundamental reactions. The requirement of repeated experiments for studying copper chemistry motivated us to develop a high throughput measurement system. We utilized surface plasmon resonance (SPR) imaging combined with multi flow channel or multi electrode for high throughput design. Fundamental physics of SPR technique and instrumental design will be provided in detail. We expect this study has an impact on relatively advanced area that utilizes copper, such as chemical mechanical polishing (CMP) in semiconductor process