University of California, Santa Barbara

About: University of California, Santa Barbara is a education organization based out in Santa Barbara, California, United States. It is known for research contribution in the topics: Population & Galaxy. The organization has 30281 authors who have published 80852 publications receiving 4626827 citations. The organization is also known as: UC Santa Barbara & UCSB.

The finite state projection algorithm for the solution of the chemical master equation.

Abstract: This article introduces the finite state projection (FSP) method for use in the stochastic analysis of chemically reacting systems. One can describe the chemical populations of such systems with probability density vectors that evolve according to a set of linear ordinary differential equations known as the chemical master equation (CME). Unlike Monte Carlo methods such as the stochastic simulation algorithm (SSA) or tau leaping, the FSP directly solves or approximates the solution of the CME. If the CME describes a system that has a finite number of distinct population vectors, the FSP method provides an exact analytical solution. When an infinite or extremely large number of population variations is possible, the state space can be truncated, and the FSP method provides a certificate of accuracy for how closely the truncated space approximation matches the true solution. The proposed FSP algorithm systematically increases the projection space in order to meet prespecified tolerance in the total probability density error. For any system in which a sufficiently accurate FSP exists, the FSP algorithm is shown to converge in a finite number of steps. The FSP is utilized to solve two examples taken from the field of systems biology, and comparisons are made between the FSP, the SSA, and tau leaping algorithms. In both examples, the FSP outperforms the SSA in terms of accuracy as well as computational efficiency. Furthermore, due to very small molecular counts in these particular examples, the FSP also performs far more effectively than tau leaping methods.

The Low-luminosity End of the Radius-Luminosity Relationship for Active Galactic Nuclei

Abstract: We present an updated and revised analysis of the relationship between the H{beta} broad-line region (BLR) radius and the luminosity of the active galactic nucleus (AGN). Specifically, we have carried out two-dimensional surface brightness decompositions of the host galaxies of nine new AGNs imaged with the Hubble Space Telescope Wide Field Camera 3. The surface brightness decompositions allow us to create ''AGN-free'' images of the galaxies, from which we measure the starlight contribution to the optical luminosity measured through the ground-based spectroscopic aperture. We also incorporate 20 new reverberation-mapping measurements of the H{beta} time lag, which is assumed to yield the average H{beta} BLR radius. The final sample includes 41 AGNs covering four orders of magnitude in luminosity. The additions and updates incorporated here primarily affect the low-luminosity end of the R{sub BLR}-L relationship. The best fit to the relationship using a Bayesian analysis finds a slope of {alpha}= 0.533{sup +0.035}{sub -0.033}, consistent with previous work and with simple photoionization arguments. Only two AGNs appear to be outliers from the relationship, but both of them have monitoring light curves that raise doubt regarding the accuracy of their reported time lags. The scatter around the relationship is found to be 0.19more » {+-} 0.02 dex, but would be decreased to 0.13 dex by the removal of these two suspect measurements. A large fraction of the remaining scatter in the relationship is likely due to the inaccurate distances to the AGN host galaxies. Our results help support the possibility that the R{sub BLR}-L relationship could potentially be used to turn the BLRs of AGNs into standardizable candles. This would allow the cosmological expansion of the universe to be probed by a separate population of objects, and over a larger range of redshifts.« less

Baselines and Degradation of Coral Reefs in the Northern Line Islands

Abstract: Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.

Consequences of dominance: a review of evenness effects on local and regional ecosystem processes

Abstract: The composition of communities is strongly altered by anthropogenic manipulations of biogeochemical cycles, abiotic conditions, and trophic structure in all major ecosystems. Whereas the effects of species loss on ecosystem processes have received broad attention, the consequences of altered species dominance for emergent properties of communities and ecosystems are poorly investigated. Here we propose a framework guiding our understanding of how dominance affects species interactions within communities, processes within ecosystems, and dynamics on regional scales. Dominance (or the complementary term, evenness) reflects the distribution of traits in a community, which in turn affects the strength and sign of both intraspecifc and interspecific interactions. Consequently, dominance also mediates the effect of such interactions on species coexistence. We review the evidence for the fact that dominance directly affects ecosystem functions such as process rates via species identity (the dominant trait) and evenness (the frequency distribution of traits), and indirectly alters the relationship between process rates and species richness. Dominance also influences the temporal and spatial variability of aggregate community properties and compositional stability (invasibility). Finally, we propose that dominance affects regional species coexistence by altering metacommunity dynamics. Local dominance leads to high beta diversity, and rare species can persist because of source-sink dynamics, but anthropogenically induced environmental changes result in regional dominance and low beta diversity, reducing regional coexistence. Given the rapid anthropogenic alterations of dominance in many ecosystems and the strong implications of these changes, dominance should be considered explicitly in the analysis of consequences of altered biodiversity.