Optical detection of galaxy clusters

This thesis first presents a relatively straight forward approach for detecting galaxy clusters using spectroscopic data. A friend-of-friends algorithm based on that of Huchra & Geller (1982) is implemented with linking parameters that take into account selection effects on the the 2dF-SDSS and QSO (2SLAQ) Luminous Red Galaxy Survey (Cannon et al. 2006). The linking parameters are constrained using a mock halo catalogue. The galaxy groups and clusters found with this method have an average velocity dispersion of \sigma v = 467:97 kms-1 and an average size of R clt = 0:78 h-1Mpc. Cluster masses are estimated using the cluster velocity dispersions and appear consistent with values expected for genuine structures. The spectroscopic cluster catalogue is then used to calibrate and compare with a more complex method for detecting clusters using photometric redshifts based on the method of Botzler et al. (2004). The spectroscopic cluster catalogue can be reproduced by around 38% and up to 80% if matching is made only to groups and clusters with six or more members. This code is also applied to the Megaz-LRG DR7 catalogue (Collister & Lahav 2004) producing two catalogues. One that appears to have a good level of completeness relative to the 2SLAQ spectroscopic catalogue. A spectroscopic follow up of some preliminary results from the photometric cluster finder was made using the Anglo-Australian Telescope, which show that the majority of the clusters analysed are genuine and approximate masses can be estimated from the cluster velocity dispersions. Finally, some initials results from on going work in the Dark Energy Survey collaboration are presented, which cover simulated galaxy photometric redshift and colour analysis as well as cluster detection

Infrared spectroscopy of phytochrome and model pigments

Fourier-transform infrared difference spectra between the red-absorbing and far-red-absorbing forms of oat phytochrome have been measured in H2O and 2H2O. The difference spectra are compared with infrared spectra of model compounds, i.e. the (5Z,10Z,15Z)- and (5Z,10Z,15E)-isomers of 2,3,7,8,12,13,17,18-octaethyl-bilindion (Et8-bilindion), 2,3-dihydro-2,3,7,8,12,13,17,18-octaethyl-bilindion (H2Et8-bilindion), and protonated H2Et8-bilindion in various solvents. The spectra of the model compounds show that only for the protonated forms can clear differences between the two isomers be detected. Since considerable differences are present between the spectra of Et8-bilindion and H2Et8-bilindion, it is concluded that only the latter compound can serve as a model system of phytochrome. The 2H2O effect on the difference spectrum of phytochrome supports the view that the chromophore in red-absorbing phytochrome is protonated and suggests, in addition, that it is also protonated in far-red-absorbing phytochrome. The spectra show that protonated carboxyl groups are influenced. The small amplitudes in the difference spectra exclude major changes of protein secondary structure

Entropic Tension in Crowded Membranes

Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape controlling the conformational transitions suffered by such proteins. For membrane channels, this effect can alter the critical membrane tension at which they undergo a transition from a closed to an open state, and therefore influence protein function \emph{in vivo}. Despite their obvious importance, crowding phenomena in membranes are much less well studied than in the cytoplasm. Using statistical mechanics results for hard disk liquids, we show that crowding induces an entropic tension in the membrane, which influences transitions that alter the projected area and circumference of a membrane protein. As a specific case study in this effect, we consider the impact of crowding on the gating properties of bacterial mechanosensitive membrane channels, which are thought to confer osmoprotection when these cells are subjected to osmotic shock. We find that crowding can alter the gating energies by more than $2\;k_BT$ in physiological conditions, a substantial fraction of the total gating energies in some cases. Given the ubiquity of membrane crowding, the nonspecific nature of excluded volume interactions, and the fact that the function of many membrane proteins involve significant conformational changes, this specific case study highlights a general aspect in the function of membrane proteins.Comment: 20 pages (inclduing supporting information), 4 figures, to appear in PLoS Comp. Bio

Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes

Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β2-adrenergic receptor (β2AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β2AR. We show that the select ligands bind preferentially to different predicted conformers of β2AR, and identify a role of β2AR extracellular region as an allosteric binding site for larger drugs such as salmeterol. Thus, drugs and ligands can be used as "computational probes" to systematically identify protein conformers with likely biological significance. © 2012 Isin et al

The Roles of Transmembrane Domain Helix-III during Rhodopsin Photoactivation

Background: Rhodopsin, the prototypic member of G protein-coupled receptors (GPCRs), undergoes isomerization of 11- cis-retinal to all-trans-retinal upon photoactivation. Although the basic mechanism by which rhodopsin is activated is well understood, the roles of whole transmembrane (TM) helix-III during rhodopsin photoactivation in detail are not completely clear. Principal Findings: We herein use single-cysteine mutagenesis technique to investigate conformational changes in TM helices of rhodopsin upon photoactivation. Specifically, we study changes in accessibility and reactivity of cysteine residues introduced into the TM helix-III of rhodopsin. Twenty-eight single-cysteine mutants of rhodopsin (P107C-R135C) were prepared after substitution of all natural cysteine residues (C140/C167/C185/C222/C264/C316) by alanine. The cysteine mutants were expressed in COS-1 cells and rhodopsin was purified after regeneration with 11-cis-retinal. Cysteine accessibility in these mutants was monitored by reaction with 4, 49-dithiodipyridine (4-PDS) in the dark and after illumination. Most of the mutants except for T108C, G109C, E113C, I133C, and R135C showed no reaction in the dark. Wide variation in reactivity was observed among cysteines at different positions in the sequence 108–135 after photoactivation. In particular, cysteines at position 115, 119, 121, 129, 131, 132, and 135, facing 11-cis-retinal, reacted with 4-PDS faster than neighboring amino acids. The different reaction rates of mutants with 4-PDS after photoactivation suggest that the amino acids in different positions in helix-III are exposed to aqueous environment to varying degrees. Significance: Accessibility data indicate that an aqueous/hydrophobic boundary in helix-III is near G109 and I133. The lack of reactivity in the dark and the accessibility of cysteine after photoactivation indicate an increase of water/4-PDS accessibility for certain cysteine-mutants at Helix-III during formation of Meta II. We conclude that photoactivation resulted in water-accessible at the chromophore-facing residues of Helix-III.National Institutes of Health (U.S.) (grant GM28289)National Eye Institute (Grant Grant EY11716)National Science Foundation (U.S.) (grant EIA-0225609

Friends-of-Friends Groups and Clusters in the 2SLAQ Catalogue

We present a catalogue of galaxy groups and clusters selected using a friends-of-friends algorithm with a dynamic linking length from the 2dF-SDSS and QSO (2SLAQ) luminous red galaxy survey. The linking parameters for the code are chosen through an analysis of simulated 2SLAQ haloes. The resulting catalogue includes 313 clusters containing 1,152 galaxies. The galaxy groups and clusters have an average velocity dispersion of sigma_v = 467.97 km/s and an average size of R_clt = 0.78 Mpc/h. Galaxies from regions of one square degree and centred on the galaxy clusters were downloaded from the Sloan Digital Sky Survey Data Release 6 (SDSS DR6). Investigating the photometric redshifts and cluster red-sequence of these galaxies shows that the galaxy clusters detected with the FoF algorithm are reliable out to z~0.6. We estimate masses for the clusters using their velocity dispersions. These mass estimates are shown to be consistent with 2SLAQ mock halo masses. Further analysis of the simulation haloes shows that clipping out low richness groups with large radii improves the purity of catalogue from 52% to 88%, while retaining a completeness of 94%. Finally, we test the two-point correlation function of our cluster catalogue. We find a best-fitting power law model with parameters r0 = 24\pm4 Mpc/h and gamma = -2.1\pm 0.2, which are in agreement with other low redshift cluster samples and consistent with a {\Lambda}CDM universe.Comment: 17 pages, 14 figure

Euclid preparation. III. Galaxy cluster detection in the wide photometric survey, performance and algorithm selection

Galaxy cluster counts in bins of mass and redshift have been shown to be a competitive probe to test cosmological models. This method requires an efficient blind detection of clusters from surveys with a well-known selection function and robust mass estimates, which is particularly challenging at high redshift. The Euclid wide survey will cover 15 000 deg2 of the sky, avoiding contamination by light from our Galaxy and our solar system in the optical and near-infrared bands, down to magnitude 24 in the H-band. The resulting data will make it possible to detect a large number of galaxy clusters spanning a wide-range of masses up to redshift ∼2 and possibly higher. This paper presents the final results of the Euclid Cluster Finder Challenge (CFC), fourth in a series of similar challenges. The objective of these challenges was to select the cluster detection algorithms that best meet the requirements of the Euclid mission. The final CFC included six independent detection algorithms, based on different techniques, such as photometric redshift tomography, optimal filtering, hierarchical approach, wavelet and friend-of-friends algorithms. These algorithms were blindly applied to a mock galaxy catalog with representative Euclid-like properties. The relative performance of the algorithms was assessed by matching the resulting detections to known clusters in the simulations down to masses of M₂₀₀ ∼ 10^(13.25) M⊙. Several matching procedures were tested, thus making it possible to estimate the associated systematic effects on completeness to 80% completeness for a mean purity of 80% down to masses of 10¹⁴ M⊙ and up to redshift z = 2. Based on these results, two algorithms were selected to be implemented in the Euclid pipeline, the Adaptive Matched Identifier of Clustered Objects (AMICO) code, based on matched filtering, and the PZWav code, based on an adaptive wavelet approach

Euclid: Fast two-point correlation function covariance through linear construction

We present a method for fast evaluation of the covariance matrix for a two-point galaxy correlation function (2PCF) measured with the Landy- Szalay estimator. The standard way of evaluating the covariance matrix consists in running the estimator on a large number of mock catalogs, and evaluating their sample covariance. With large random catalog sizes (random-to-data objects'ratio M≫ 1) the computational cost of the standard method is dominated by that of counting the data-random and random-random pairs, while the uncertainty of the estimate is dominated by that of data-data pairs. We present a method called Linear Construction (LC), where the covariance is estimated for small random catalogs with a size of M = 1 and M = 2, and the covariance for arbitrary M is constructed as a linear combination of the two. We show that the LC covariance estimate is unbiased. We validated the method with PINOCCHIO simulations in the range r = 20-200 h-1 Mpc. With M = 50 and with 2 h-1 Mpc bins, the theoretical speedup of the method is a factor of 14. We discuss the impact on the precision matrix and parameter estimation, and present a formula for the covariance of covariance.</p