University of California, Santa Cruz

About: University of California, Santa Cruz is a education organization based out in Santa Cruz, California, United States. It is known for research contribution in the topics: Galaxy & Population. The organization has 15541 authors who have published 44120 publications receiving 2759983 citations. The organization is also known as: UCSC & UC, Santa Cruz.

Ribosomes and translation

Abstract: The ribosome is a large multifunctional complex composed of both RNA and proteins. Biophysical methods are yielding low-resolution structures of the overall architecture of ribosomes, and high-resolution structures of individual proteins and segments of rRNA. Accumulating evidence suggests that the ribosomal RNAs play central roles in the critical ribosomal functions of tRNA selection and binding, translocation, and peptidyl transferase. Biochemical and genetic approaches have identified specific functional interactions involving conserved nucleotides in 16S and 23S rRNA. The results obtained by these quite different approaches have begun to converge and promise to yield an unprecedented view of the mechanism of translation in the coming years.

A discriminative framework for detecting remote protein homologies.

Abstract: A new method for detecting remote protein homologies is introduced and shown to perform well in classifying protein domains by SCOP superfamily. The method is a variant of support vector machines using a new kernel function. The kernel function is derived from a generative statistical model for a protein family, in this case a hidden Markov model. This general approach of combining generative models like HMMs with discriminative methods such as support vector machines may have applications in other areas of biosequence analysis as well.

Resolving the Structure of Cold Dark Matter Halos

Abstract: We present results of a convergence study in which we compare the density profiles of cold dark matter halos simulated with varying mass and force resolutions. We show that although increasing the mass and force resolution allows one to probe deeper into the inner halo regions, the halo profiles converge on scales larger than the "effective" spatial resolution of the simulation. This resolution is defined by both the force softening and the mass resolution. On radii larger than the "effective" spatial resolution, density profiles do not experience any systematical trends when the number of particles or the force resolution increases further. In the simulations presented in this paper, we are able to probe the density profile of a relaxed isolated galaxy-size halo on scales r = (0.005-1)rvir. We find that the density distribution at resolved scales can be well approximated by the profile suggested by Moore and coworkers: ρ ∝ x-1.5(1 + x1.5)-1, where x = r/rs and rs is the characteristic radius. The analytical profile proposed by Navarro and coworkers, ρ ∝ x-1(1 + x)-2, also provides a good fit, with the same relative errors of about 10% for radii larger than 1% of the virial radius. For this limit, both analytical profiles fit well because for high-concentration galaxy-size halos, the differences between these profiles become significant only on scales well below 0.01rvir. We also find that halos of similar mass may have density profiles with somewhat different parameters (characteristic radius, maximum rotation velocity, etc.) and shapes. We associate this scatter in properties with differences in halo merger histories and with the amount of substructure present in the analyzed halos.

The Dependence of Halo Clustering on Halo Formation History, Concentration, and Occupation

Abstract: We investigate the dependence of dark matter halo clustering on halo formation time, density profile concentration, and subhalo occupation number, using high-resolution numerical simulations of a ?CDM cosmology. We confirm results that halo clustering is a function of halo formation time at fixed mass and that this trend depends on halo mass. For the first time, we show unequivocally that halo clustering is a function of halo concentration and show that the dependence of halo bias on concentration, mass, and redshift can be accurately parameterized in a simple way: b(M,c|z) = b(M|z)b(c|M/M). Interestingly, the scaling between bias and concentration changes sign with the value of M/M: high-concentration (early forming) objects cluster more strongly for M M, while low-concentration (late forming) objects cluster more strongly for rare high-mass halos, M M. We show the first explicit demonstration that host dark halo clustering depends on the halo occupation number (of dark matter subhalos) at fixed mass and discuss implications for halo model calculations of dark matter power spectra and galaxy clustering statistics. The effect of these halo properties on clustering is strongest for early-forming dwarf-mass halos, which are significantly more clustered than typical halos of their mass. Our results suggest that isolated low-mass galaxies (e.g., low surface brightness dwarfs) should have more slowly rising rotation curves than their more clustered counterparts and may have consequences for the dearth of dwarf galaxies in voids. They also imply that self-calibrating richness-selected cluster samples with their clustering properties might overestimate cluster masses and bias cosmological parameter estimation.

On the Luminosity of Young Jupiters

Abstract: Traditional thermal evolution models of giant planets employ arbitrary initial conditions selected more for computational expediency than physical accuracy. Since the initial conditions are eventually forgotten by the evolving planet, this approach is valid for mature planets, if not young ones. To explore the evolution at young ages of jovian mass planets, we have employed model planets created by one implementation of the core-accretion mechanism as initial conditions for evolutionary calculations. The luminosities and early cooling rates of young planets are highly sensitive to their internal entropies, which depend on the formation mechanism and are highly model dependent. As a result of the accretion shock through which most of the planetary mass is processed, we find lower initial internal entropies than commonly assumed in published evolution tracks. Consequently, young Jovian planets are smaller, cooler, and several to 100 times less luminous than predicted by earlier models. Furthermore, the time interval during which the young Jupiters are fainter than expected depends on the mass of planet. Jupiter mass planets (1MJ) align with the conventional model luminosity in as little at 20 million years, but 10MJ planets can take up to 1 billion years to match commonly cited luminosities, given our implementation of the core-accretion mechanism. If our assumptions, especially including our treatment of the accretion shock, are correct and if extrasolar Jovian planets indeed form with low entropy, then young Jovian planets are substantially fainter at young ages than currently believed. Furthermore, early evolution tracks should be regarded as uncertain for much longer than the commonly quoted 106 yr. These results have important consequences both for detection strategies and for assigning masses to young Jovian planets based on observed luminosities.